pose¶
Bindings for core::pose namespace
- class pyrosetta.rosetta.core.pose.MiniPose¶
Bases:
pybind11_object
not quite (silent_structs don’t necessarily have xyz). Kind of like a Conformation but without the overtree of an atom_tree.
Should save memory compared to keeping the full pose (which includes atom_tree, energies etc.) This is a bit like the SilentStruct – although that class has gotten a bit complicated – easier to start from scratch.
- assign(self: pyrosetta.rosetta.core.pose.MiniPose, : pyrosetta.rosetta.core.pose.MiniPose) pyrosetta.rosetta.core.pose.MiniPose ¶
C++: core::pose::MiniPose::operator=(const class core::pose::MiniPose &) –> class core::pose::MiniPose &
- atom_name(self: pyrosetta.rosetta.core.pose.MiniPose, atom_id: pyrosetta.rosetta.core.id.AtomID) str ¶
C++: core::pose::MiniPose::atom_name(class core::id::AtomID) const –> const std::string &
- atom_names_list(self: pyrosetta.rosetta.core.pose.MiniPose) pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t ¶
C++: core::pose::MiniPose::atom_names_list() const –> const class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > > &
- coords(self: pyrosetta.rosetta.core.pose.MiniPose) pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t ¶
C++: core::pose::MiniPose::coords() const –> const class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &
- fold_tree(self: pyrosetta.rosetta.core.pose.MiniPose) pyrosetta.rosetta.core.kinematics.FoldTree ¶
C++: core::pose::MiniPose::fold_tree() const –> const class core::kinematics::FoldTree &
- sequence(self: pyrosetta.rosetta.core.pose.MiniPose) str ¶
C++: core::pose::MiniPose::sequence() const –> const std::string &
- size(self: pyrosetta.rosetta.core.pose.MiniPose) int ¶
C++: core::pose::MiniPose::size() const –> unsigned long
- variant_types(self: pyrosetta.rosetta.core.pose.MiniPose, seq_num: int) pyrosetta.rosetta.utility.vector1_std_string ¶
C++: core::pose::MiniPose::variant_types(const unsigned long) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &
- variant_types_list(self: pyrosetta.rosetta.core.pose.MiniPose) pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t ¶
C++: core::pose::MiniPose::variant_types_list() const –> const class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > > &
- xyz(self: pyrosetta.rosetta.core.pose.MiniPose, atom_id: pyrosetta.rosetta.core.id.AtomID) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: core::pose::MiniPose::xyz(class core::id::AtomID) const –> const class numeric::xyzVector<double> &
- class pyrosetta.rosetta.core.pose.PDBInfo¶
Bases:
pybind11_object
maintains pdb residue & atom information inside a Pose
- Upon creation of new residue records, e.g. when calling the
constructors without ‘init’ or appending/prepending residues, the chain letter for the new records will be set to a character, currently ‘^’, denoting “empty record”. This character may be looked up by calling the static method PDBInfo::empty_record().
- Class implementation is biased towards simplicity and fast lookup.
Residue/atom information are kept in vectors. An internally maintained PDBPoseMap provides mapping from pdb -> pose residue numbering. This causes residue mutators to be a bit more expensive due to map updates, but this is ok because they are typically called sparingly. Accessors and mutators have overloaded method convention, while special mutators use .set_* convention.
- class AtomRecord¶
Bases:
pybind11_object
internal struct for storing PDB atom related information
- property altLoc¶
- property isHet¶
- property occupancy¶
- property temperature¶
- class ResidueRecord¶
Bases:
pybind11_object
internal struct for storing PDB residue related information
- assign(self: pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord, : pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord) pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord ¶
C++: core::pose::PDBInfo::ResidueRecord::operator=(const struct core::pose::PDBInfo::ResidueRecord &) –> struct core::pose::PDBInfo::ResidueRecord &
- property atomRec¶
- property chainID¶
- property iCode¶
- property label¶
- property resSeq¶
- property segmentID¶
- add_reslabel(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, label: str) None ¶
adds a label associated to a pose resid.
residue in pose numbering
string that is the “label”
C++: core::pose::PDBInfo::add_reslabel(unsigned long, const std::string &) –> void
- add_unrecognized_atoms(self: pyrosetta.rosetta.core.pose.PDBInfo, UAs: pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord) None ¶
remembers info about atoms not read into the pose
C++: core::pose::PDBInfo::add_unrecognized_atoms(class utility::vector1<class core::pose::UnrecognizedAtomRecord, class std::allocator<class core::pose::UnrecognizedAtomRecord> >) –> void
- alt_loc(*args, **kwargs)¶
Overloaded function.
alt_loc(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int) -> str
- Returns the alternate location for the <atom_index> atom of pose
residue <res>
- example(s):
pose.pdb_info().alt_loc(1,1)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::alt_loc(const unsigned long, const unsigned long) const –> const char &
alt_loc(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int, loc: str) -> None
- Sets the alternate location of the <atom_index> atom of pose
residue <res> to <loc>
: <loc> is an alternate location character
C++: core::pose::PDBInfo::alt_loc(const unsigned long, const unsigned long, const char) –> void
- append_res(*args, **kwargs)¶
Overloaded function.
append_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, natoms: int) -> None
append_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, natoms: int, n: int) -> None
Appends residue records given a pose residue number <res>
residue to append after (in internal/pose numbering)
number of atoms in type of appended residue
number of residue records to append
C++: core::pose::PDBInfo::append_res(const unsigned long, const unsigned long, const unsigned long) –> void
- assign(self: pyrosetta.rosetta.core.pose.PDBInfo, info: pyrosetta.rosetta.core.pose.PDBInfo) pyrosetta.rosetta.core.pose.PDBInfo ¶
copy assignment
C++: core::pose::PDBInfo::operator=(const class core::pose::PDBInfo &) –> class core::pose::PDBInfo &
- attach_to(self: pyrosetta.rosetta.core.pose.PDBInfo, conf: pyrosetta.rosetta.core.conformation.Conformation) None ¶
Attaches the Conformation <conf> and begins observation
example(s):
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::attach_to(class core::conformation::Conformation &) –> void
- bfactor(*args, **kwargs)¶
Overloaded function.
bfactor(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int) -> float
Returns the temperature for the <atom_index> atom of pose residue <res>
- example(s):
pose.pdb_info().temperature(1,1)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::bfactor(const unsigned long, const unsigned long) const –> const double &
bfactor(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int, t: float) -> None
- Sets the temperature of the <atom_index> atom of pose residue
<res> to <t>
C++: core::pose::PDBInfo::bfactor(const unsigned long, const unsigned long, const double) –> void
- chain(*args, **kwargs)¶
Overloaded function.
chain(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> str
Returns the chain letter for pose residue <res>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.pdb_info().chain(3)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::chain(const unsigned long) const –> const char &
chain(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, chain_id: str) -> None
Sets the chain letter of pose residue <res> to <chain_id>
chain_id should not be the empty record character, currently ‘^’
Returns the pdb insertion code of residue <res>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.pdb_info().chain(3,”R”)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::chain(const unsigned long, const char) –> void
- chain_sequences(*args, **kwargs)¶
Overloaded function.
chain_sequences(self: pyrosetta.rosetta.core.pose.PDBInfo, chain_sequences: pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t) -> None
- Note: The chain sequences information is only initialized if it is needed.
Generally this requires using the -run:preserve_header options flag.
C++: core::pose::PDBInfo::chain_sequences(class std::map<char, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<char>, class std::allocator<struct std::pair<const char, class utility::vector1<std::string, class std::allocator<std::string > > > > >) –> void
chain_sequences(self: pyrosetta.rosetta.core.pose.PDBInfo, chain: str) -> pyrosetta.rosetta.utility.vector1_std_string
C++: core::pose::PDBInfo::chain_sequences(char) –> class utility::vector1<std::string, class std::allocator<std::string > >
chain_sequences(self: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t
C++: core::pose::PDBInfo::chain_sequences() –> class std::map<char, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<char>, class std::allocator<struct std::pair<const char, class utility::vector1<std::string, class std::allocator<std::string > > > > >
- clear_reslabel(*args, **kwargs)¶
Overloaded function.
clear_reslabel(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> None
clean all the label(s) associated to a pose resid.
residue in pose numbering
C++: core::pose::PDBInfo::clear_reslabel(const unsigned long) –> void
clear_reslabel(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, match_label: str) -> None
- Clean a specific label of a specific residue if that label contains
the string.
C++: core::pose::PDBInfo::clear_reslabel(const unsigned long, const std::string &) –> void
- copy(self: pyrosetta.rosetta.core.pose.PDBInfo, input_info: pyrosetta.rosetta.core.pose.PDBInfo, copy_from: int, copy_to: int, start_from: int) None ¶
Copyies a section from PDBInfo <input_info>
the PDBInfo to copy from
the first residue position in input_info to copy
the final residue position in input_info to copy
- the first residue position in this PDBInfo to
copy into
C++: core::pose::PDBInfo::copy(const class core::pose::PDBInfo &, const unsigned long, const unsigned long, const unsigned long) –> void
- crystinfo(self: pyrosetta.rosetta.core.pose.PDBInfo) pyrosetta.rosetta.core.io.CrystInfo ¶
Returns the pdb crystinfo
C++: core::pose::PDBInfo::crystinfo() const –> class core::io::CrystInfo
- delete_res(*args, **kwargs)¶
Overloaded function.
delete_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> None
delete_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, n: int) -> None
Deletes <n> residue records starting from pose residue <res>
residue to start deleting from (in internal/pose numbering)
number of residue records to delete
C++: core::pose::PDBInfo::delete_res(const unsigned long, const unsigned long) –> void
- detach_from(self: pyrosetta.rosetta.core.pose.PDBInfo) None ¶
Detaches the Conformation and stops observation
takes no arguments because PDBInfo can only observe one Conformation at a time
- example(s):
pose.pdb_info().detach_from()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::detach_from() –> void
- static empty_record() str ¶
- Returns the chain letter character specifying “empty record”,
currently ‘^’
C++: core::pose::PDBInfo::empty_record() –> char
- get_num_unrecognized_atoms(self: pyrosetta.rosetta.core.pose.PDBInfo) int ¶
C++: core::pose::PDBInfo::get_num_unrecognized_atoms() const –> const unsigned long &
- get_num_unrecognized_res(self: pyrosetta.rosetta.core.pose.PDBInfo) int ¶
C++: core::pose::PDBInfo::get_num_unrecognized_res() const –> const unsigned long &
- get_reslabels(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) pyrosetta.rosetta.utility.vector1_std_string ¶
returns the pose(number) labels associated to the residue
residue in pose numbering
C++: core::pose::PDBInfo::get_reslabels(const unsigned long) const –> class utility::vector1<std::string, class std::allocator<std::string > >
- get_unrecognized_atoms(self: pyrosetta.rosetta.core.pose.PDBInfo) pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord ¶
remembers info about atoms not read into the pose
C++: core::pose::PDBInfo::get_unrecognized_atoms() const –> const class utility::vector1<class core::pose::UnrecognizedAtomRecord, class std::allocator<class core::pose::UnrecognizedAtomRecord> > &
- get_unrecognized_res_name(self: pyrosetta.rosetta.core.pose.PDBInfo, i: int) str ¶
C++: core::pose::PDBInfo::get_unrecognized_res_name(const unsigned long &) const –> const std::string &
- get_unrecognized_res_size(self: pyrosetta.rosetta.core.pose.PDBInfo, i: int) int ¶
C++: core::pose::PDBInfo::get_unrecognized_res_size(const unsigned long &) const –> const unsigned long &
- header_information(*args, **kwargs)¶
Overloaded function.
header_information(self: pyrosetta.rosetta.core.pose.PDBInfo, header_information: pyrosetta.rosetta.core.io.HeaderInformation) -> None
- Note: The header information is only initialized if it is needed.
Generally this requires using the -run:preserve_header options flag.
C++: core::pose::PDBInfo::header_information(class std::shared_ptr<class core::io::HeaderInformation>) –> void
header_information(self: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.core.io.HeaderInformation
C++: core::pose::PDBInfo::header_information() –> class std::shared_ptr<class core::io::HeaderInformation>
- icode(*args, **kwargs)¶
Overloaded function.
icode(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> str
Returns the pdb insertion code of residue <res>
- example(s):
pose.pdb_info().icode(3)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::icode(const unsigned long) const –> const char &
icode(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, ins_code: str) -> None
Sets the insertion code of pose residue <res> to _code>
Returns the pdb insertion code of residue <res>
example(s):
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::icode(const unsigned long, const char) –> void
- is_het(*args, **kwargs)¶
Overloaded function.
is_het(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int) -> bool
- Returns true if the <atom_index> atom of pose residue <res>
is a heteratom
- : atom index within instance of core::conformation::Residue,
currently Rosetta’s pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)
C++: core::pose::PDBInfo::is_het(const unsigned long, const unsigned long) const –> const bool &
is_het(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int, flag: bool) -> None
- Sets the heteroatom flag of the <atom_index> atom of pose
residue <res> to <flag>
currently Rosetta’s pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)
C++: core::pose::PDBInfo::is_het(const unsigned long, const unsigned long, const bool) –> void
- is_observing(self: pyrosetta.rosetta.core.pose.PDBInfo) pyrosetta.rosetta.std.weak_ptr_const_core_conformation_Conformation_t ¶
- Returns the Conformation if this PDBInfo is currently observing
a conformation, otherwise return NULL
- example(s):
pose.pdb_info().is_observing()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::is_observing() –> class std::weak_ptr<const class core::conformation::Conformation>
- modeltag(*args, **kwargs)¶
Overloaded function.
modeltag(self: pyrosetta.rosetta.core.pose.PDBInfo) -> str
Returns the model tag for a multi-model pdb
- example(s):
pose.pdb_info().modeltag()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::modeltag() const –> const std::string &
modeltag(self: pyrosetta.rosetta.core.pose.PDBInfo, tag: str) -> None
Sets the model tag for a multi-model pdb to <tag>
- example(s):
pose.pdb_info().modeltag(‘Number1’)
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::modeltag(const std::string &) –> void
- name(*args, **kwargs)¶
Overloaded function.
name(self: pyrosetta.rosetta.core.pose.PDBInfo) -> str
Returns the pdb name
- example(s):
pose.pdb_info().name()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::name() const –> const std::string &
name(self: pyrosetta.rosetta.core.pose.PDBInfo, s: str) -> None
Sets the pdb name
- example(s):
pose.pdb_info().name(‘MyPDB’)
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::name(const std::string &) –> void
- natoms(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) int ¶
Returns the number of atoms represented for the residue <res>
: residue <res> must be in pose numbering
- example(s):
pose.pdb_info().natoms(3)
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::natoms(const unsigned long) const –> unsigned long
- nres(self: pyrosetta.rosetta.core.pose.PDBInfo) int ¶
Returns the number of residues represented in PDBInfo
- example(s):
pose.pdb_info().nres()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::nres() const –> unsigned long
- num_chains(self: pyrosetta.rosetta.core.pose.PDBInfo) int ¶
Returns the total number of (chain letter) chains in the pose
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.pdb_info().num_chains()
- see also:
pose pose.annotated_sequence pose.fold_tree pose.num_jump
pose.pdb_info().chain pose.pdb_info().pdb2pose
C++: core::pose::PDBInfo::num_chains() const –> int
- number(*args, **kwargs)¶
Overloaded function.
number(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> int
Returns the pdb sequence number of pose residue <res>
- example(s):
pose.pdb_info().number(3)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::number(const unsigned long) const –> const int &
number(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, pdb_res: int) -> None
Sets the pdb sequence residue number of pose residue <res> to <pdb_res>
Returns the pdb insertion code of residue <res>
- example(s):
pose.pdb_info().number(3,81)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::number(const unsigned long, const int) –> void
- obsolete(*args, **kwargs)¶
Overloaded function.
obsolete(self: pyrosetta.rosetta.core.pose.PDBInfo) -> bool
Returns true if PDBInfo is obsolete and needs updating
This flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.
- example(s):
pose.pdb_info().obsolete()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::obsolete() const –> bool
obsolete(self: pyrosetta.rosetta.core.pose.PDBInfo, flag: bool) -> None
Sets the obsolete state to <flag>
this flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.
C++: core::pose::PDBInfo::obsolete(bool) –> void
- occupancy(*args, **kwargs)¶
Overloaded function.
occupancy(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int) -> float
Returns the occupancy for the <atom_index> atom of pose residue <res>
- example(s):
pose.pdb_info().occupancy(1,1)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::occupancy(const unsigned long, const unsigned long) const –> const double &
occupancy(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int, occ: float) -> None
- Sets the occupancy of the <atom_index> atom of pose residue
<res> to <occ>
C++: core::pose::PDBInfo::occupancy(const unsigned long, const unsigned long, const double) –> void
- on_connection_change(self: pyrosetta.rosetta.core.pose.PDBInfo, event: pyrosetta.rosetta.core.conformation.signals.ConnectionEvent) None ¶
Updates when connection to Conformation is changed
C++: core::pose::PDBInfo::on_connection_change(const struct core::conformation::signals::ConnectionEvent &) –> void
- on_identity_change(self: pyrosetta.rosetta.core.pose.PDBInfo, event: pyrosetta.rosetta.core.conformation.signals.IdentityEvent) None ¶
Updates atom records when residue identity changes in Conformation
C++: core::pose::PDBInfo::on_identity_change(const struct core::conformation::signals::IdentityEvent &) –> void
- on_length_change(self: pyrosetta.rosetta.core.pose.PDBInfo, event: pyrosetta.rosetta.core.conformation.signals.LengthEvent) None ¶
- Updates residue and atom records when length changes in Conformation,
obsoletes PDBInfo
C++: core::pose::PDBInfo::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void
- parse_pdbinfo_labels(self: pyrosetta.rosetta.core.pose.PDBInfo, lines: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
parse PDBInfo-LABEL: lines from a collection of lines
Lines not containing PDBInfo-LABEL are ignored
the lines to parse
C++: core::pose::PDBInfo::parse_pdbinfo_labels(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &) –> void
- pdb2pose(*args, **kwargs)¶
Overloaded function.
pdb2pose(self: pyrosetta.rosetta.core.pose.PDBInfo, chain: str, res: int) -> int
pdb2pose(self: pyrosetta.rosetta.core.pose.PDBInfo, chain: str, res: int, icode: str) -> int
pdb2pose(self: pyrosetta.rosetta.core.pose.PDBInfo, chain: str, res: int, icode: str, segmentID: str) -> int
- Returns the pose numbering of the pdb residue with chain letter <chain>,
pdb residue <res>, and insertion code <icode>
- : <icode> is not required, returns 0 if not found,
pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything
- example(s):
pose.pdb_info().pdb2pose(“B”,5)
- See also:
Pose PDBInfo PDBInfo.pose2pdb
C++: core::pose::PDBInfo::pdb2pose(const char, const int, const char, const std::string &) const –> unsigned long
pdb2pose(self: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.core.pose.PDBPoseMap
Returns the internally maintained PDBPoseMap
example(s):
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::pdb2pose() const –> const class core::pose::PDBPoseMap &
- pose2pdb(*args, **kwargs)¶
Overloaded function.
pose2pdb(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> str
pose2pdb(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, conn: str) -> str
Returns the pdb numbering string of pose residue <res>
- : pdb string contains the chain letter and number
pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything
- example(s):
pose.pdb_info().pose2pdb(25)
- See also:
Pose PDBInfo PDBInfo.pdb2pose
C++: core::pose::PDBInfo::pose2pdb(const unsigned long, const std::string &) const –> std::string
- prepend_res(*args, **kwargs)¶
Overloaded function.
prepend_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, natoms: int) -> None
prepend_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, natoms: int, n: int) -> None
Prepends residue records before given pose residue number <res>
residue to prepend before (in internal/pose numbering)
number of atoms in type of appended residue
number of residue records to prepend
C++: core::pose::PDBInfo::prepend_res(const unsigned long, const unsigned long, const unsigned long) –> void
- rebuild_pdb2pose(self: pyrosetta.rosetta.core.pose.PDBInfo) None ¶
rebuilds PDBPoseMap from scratch
C++: core::pose::PDBInfo::rebuild_pdb2pose() –> void
- remarks(*args, **kwargs)¶
Overloaded function.
remarks(self: pyrosetta.rosetta.core.pose.PDBInfo) -> pyrosetta.rosetta.core.io.Remarks
Returns the pdb remarks (mutable)
we allow direct access to the remarks vector because its state is independent of the rest of PDBInfo and it’s much more convenient for the user
- example(s):
pose.pdb_info().remarks()
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::remarks() –> class core::io::Remarks &
remarks(self: pyrosetta.rosetta.core.pose.PDBInfo, in: pyrosetta.rosetta.core.io.Remarks) -> None
Sets the pdb remarks to <in>
example(s):
- See also:
Pose PDBInfo
C++: core::pose::PDBInfo::remarks(const class core::io::Remarks &) –> void
- replace_res(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, natoms: int) None ¶
“Replaces” residue record for pose residue <res>
Leaves information in residue record untouched, but resizes and zeroes atom records for the residue.
residue to replace
number of atoms in type of residue
C++: core::pose::PDBInfo::replace_res(const unsigned long, const unsigned long) –> void
- replace_res_remap_bfactors(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, tgt: pyrosetta.rosetta.core.conformation.Residue) None ¶
same as replace_res BUT remaps B factors from src to tgt
C++: core::pose::PDBInfo::replace_res_remap_bfactors(const unsigned long, const class core::conformation::Residue &) –> void
- res_haslabel(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, target_label: str) bool ¶
uses std iterators to check if a residue has a label associated to it
residue in pose numbering
string to look for inside the labes associated to the residue
C++: core::pose::PDBInfo::res_haslabel(unsigned long, const std::string &) const –> bool
- resize_atom_records(*args, **kwargs)¶
Overloaded function.
resize_atom_records(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, n: int) -> None
resize_atom_records(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, n: int, zero: bool) -> None
Ensures <n> atom records for residue <res> are available
: if <zero> is true, zero the atom records for this residue
C++: core::pose::PDBInfo::resize_atom_records(const unsigned long, const unsigned long, const bool) –> void
resize_atom_records(self: pyrosetta.rosetta.core.pose.PDBInfo, n: int) -> None
resize_atom_records(self: pyrosetta.rosetta.core.pose.PDBInfo, n: int, zero: bool) -> None
Ensures <n> atom records for residue <res> are available
: if <zero> is true, zero the atom records for this residue
C++: core::pose::PDBInfo::resize_atom_records(const unsigned long, const bool) –> void
resize_atom_records(self: pyrosetta.rosetta.core.pose.PDBInfo, pose: pyrosetta.rosetta.core.pose.Pose) -> None
Updates the number of atom records with respect to atoms in <pose>
Number of internally available atom records will be adjusted to match number of atoms within each residue in Pose. Only newly created records will be zeroed, any existing records are untouched.
C++: core::pose::PDBInfo::resize_atom_records(const class core::pose::Pose &) –> void
- resize_residue_records(self: pyrosetta.rosetta.core.pose.PDBInfo, n: int) None ¶
Resizes for <n> residue records
Leaves atom record state inconsistent. Atom records for remaining residues are untouched while new residues have no atom records, so make sure and call one of resize_atom_records() afterwards if necessary.
Do not use this method for ins/del of residues, as it leaves the data state inconsistent. See append_res/prepend_res/delete_res for that type of functionality.
C++: core::pose::PDBInfo::resize_residue_records(const unsigned long) –> void
- segmentID(*args, **kwargs)¶
Overloaded function.
segmentID(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) -> str
Returns the segment ID code of residue <res>
- example(s):
pose.pdb_info().icode(3)
C++: core::pose::PDBInfo::segmentID(const unsigned long) const –> const std::string &
segmentID(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, segmentID: str) -> None
Sets the insertion code of pose residue <res> to _code>
Returns the pdb insertion code of residue <res>
example(s):
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::segmentID(const unsigned long, const std::string &) –> void
- set_chains(self: pyrosetta.rosetta.core.pose.PDBInfo, id: str) None ¶
Sets all residue chain ids to the character <id>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::PDBInfo::set_chains(const char) –> void
- set_crystinfo(self: pyrosetta.rosetta.core.pose.PDBInfo, crystinfoin: pyrosetta.rosetta.core.io.CrystInfo) None ¶
Sets the pdb crystinfo
C++: core::pose::PDBInfo::set_crystinfo(class core::io::CrystInfo) –> void
- set_resinfo(*args, **kwargs)¶
Overloaded function.
set_resinfo(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, chain_id: str, pdb_res: int) -> None
set_resinfo(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, chain_id: str, pdb_res: int, ins_code: str) -> None
set_resinfo(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, chain_id: str, pdb_res: int, ins_code: str, segmentID: str) -> None
set_resinfo(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, chain_id: str, pdb_res: int, ins_code: str, segmentID: str, clear_labels: bool) -> None
- Sets the chain letter, pdb sequence residue numbering, and insertion
code for pose residue <res> to <chain_id> , <pdb_res> , and _code> respectfully
- : convenience method; more efficient than doing each individually
due to map updates
Returns the pdb insertion code of residue <res>
- example(s):
pose.pdb_info().icode(3)
- See also:
Pose PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.number PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::set_resinfo(const unsigned long, const char, const int, const char, const std::string &, bool) –> void
- short_desc(self: pyrosetta.rosetta.core.pose.PDBInfo) str ¶
- Returns a short description of the contents of the PDBInfo.
The current format of this is something like “A:1-3 B:9-11”
- example(s);
pose.pdb_info().short_desc()
- See Also:
PDBInfo PDBInfo.show Pose.pdb_info
C++: core::pose::PDBInfo::short_desc() const –> std::string
- show(self: pyrosetta.rosetta.core.pose.PDBInfo, out: pyrosetta.rosetta.std.ostream) None ¶
- Displays segments of PDB information, segments may or may not
be entire chains
- example(s);
pose.pdb_info().show()
- See Also:
PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.nres PDBInfo.number Pose Pose.pdb_info
C++: core::pose::PDBInfo::show(std::ostream &) const –> void
- tag(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int) str ¶
Returns a tag for residue <res> like C:1235 (or C:QA:1235 if segment ID is present)
- example(s):
pose.pdb_info().icode(3)
C++: core::pose::PDBInfo::tag(const unsigned long) const –> std::string
- temperature(*args, **kwargs)¶
Overloaded function.
temperature(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int) -> float
Returns the temperature for the <atom_index> atom of pose residue <res>
- example(s):
pose.pdb_info().temperature(1,1)
- See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
C++: core::pose::PDBInfo::temperature(const unsigned long, const unsigned long) const –> const double &
temperature(self: pyrosetta.rosetta.core.pose.PDBInfo, res: int, atom_index: int, t: float) -> None
- Sets the temperature of the <atom_index> atom of pose residue
<res> to <t>
C++: core::pose::PDBInfo::temperature(const unsigned long, const unsigned long, const double) –> void
- tighten_memory(self: pyrosetta.rosetta.core.pose.PDBInfo) None ¶
Tightens memory usage
C++: core::pose::PDBInfo::tighten_memory() –> void
- write_pdbinfo_labels(self: pyrosetta.rosetta.core.pose.PDBInfo, remark_lines: pyrosetta.rosetta.utility.vector1_std_string) None ¶
write REMARK PDBInfo-LABEL: lines for output to pose
the output container
C++: core::pose::PDBInfo::write_pdbinfo_labels(class utility::vector1<std::string, class std::allocator<std::string > > &) const –> void
- class pyrosetta.rosetta.core.pose.PDBPoseMap¶
Bases:
pybind11_object
- PDBPoseMap can be queried with PDB information (chain, sequence position)
and returns a pose’s resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map.
- danpf.edu – In order to avoid breaking workflows I added a secondary map
that tracks the map<ResidueKey, Size> without the segmentID field being checked. This is sort of a strange if you use segmentIDs, but if you don’t you won’t notice any differences.
- assign(self: pyrosetta.rosetta.core.pose.PDBPoseMap, m: pyrosetta.rosetta.core.pose.PDBPoseMap) pyrosetta.rosetta.core.pose.PDBPoseMap ¶
copy assignment
C++: core::pose::PDBPoseMap::operator=(const class core::pose::PDBPoseMap &) –> class core::pose::PDBPoseMap &
- clear(self: pyrosetta.rosetta.core.pose.PDBPoseMap) None ¶
clear the current mapping data
C++: core::pose::PDBPoseMap::clear() –> void
- conditional_erase(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str, segmentID: str, pose_res: int) bool ¶
remove mapping for pdb residue key only if Pose residue matches
chain id
pdb residue numbering
insertion code, use ‘ ‘ if no insertion code
the mapped Pose residue
true if key-value pair erase, false otherwise
C++: core::pose::PDBPoseMap::conditional_erase(const char, const int, const char, const std::string &, const unsigned long) –> bool
- erase(*args, **kwargs)¶
Overloaded function.
erase(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str) -> None
erase(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str, segmentID: str) -> None
forcibly remove mapping for pdb residue key
chain id
pdb residue numbering
insertion code, use ‘ ‘ if no insertion code
C++: core::pose::PDBPoseMap::erase(const char, const int, const char, const std::string &) –> void
- fill(self: pyrosetta.rosetta.core.pose.PDBPoseMap, info: core::pose::PDBInfo) None ¶
fill with corresponding pdb -> pose residue mapping
does not clear any currently existing mapping data
C++: core::pose::PDBPoseMap::fill(const class core::pose::PDBInfo &) –> void
- find(*args, **kwargs)¶
Overloaded function.
find(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int) -> int
find(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str) -> int
find(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str, segmentID: str) -> int
lookup pose numbering
chain id
pdb residue numbering
insertion code
pose numbering for residue, returns 0 if not found
this will default to return the no-segmentID version if we can’t find it!
C++: core::pose::PDBPoseMap::find(const char, const int, const char, const std::string &) const –> unsigned long
- insert(self: pyrosetta.rosetta.core.pose.PDBPoseMap, chain: str, pdb_res: int, ins_code: str, segmentID: str, pose_res: int) None ¶
insert pdb -> pose number mapping
chain id
pdb residue numbering
insertion code, use ‘ ‘ if no insertion code
pose numbering for residue
- if the chain is equal to the PDBInfo’s empty record character,
the insertion will be skipped
C++: core::pose::PDBPoseMap::insert(const char, const int, const char, const std::string &, const unsigned long) –> void
- size(self: pyrosetta.rosetta.core.pose.PDBPoseMap) int ¶
number of mappings
C++: core::pose::PDBPoseMap::size() const –> unsigned long
- class pyrosetta.rosetta.core.pose.Pose¶
Bases:
pybind11_object
The Pose class represents a molecular system (protein-dna-ligand…) as a container of Rosetta Residue objects together with a Conformation object that defines how internal coordinate changes propagate through the system and an Energies object that stores information from the last energy evaluation.
The main responsibilities of the pose are:
Kinematic:
(a) to update the xyz coordinates in response to changes to internal degrees of freedom, and (b) to update internal coordinates when the user modifes the xyz (Cartesian) coords,
Scoring:
(a) to keep track of what parts of the structure have changed since the last score evaluation, and (b) to cache residue and residue-pair energies for efficient re-use
As a container:
The pose provides a single object for passing a molecular system and for copying of entire molecules or stretches of molecules from one Pose object into another.
Output Methods: Common Methods: Pose.assign Pose.atom_tree Pose.conformation Pose.dump_pdb Pose.dump_cif Pose.dump_mmtf Pose.dump_file Pose.energies Pose.fold_tree Pose.pdb_info Pose.residue Pose.sequence Pose.size
- aa(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) pyrosetta.rosetta.core.chemical.AA ¶
Returns the chemical::AA of the residue at <seqpos>
- example(s):
pose.aa(17)
- See also:
Pose
- Pose.Residue
Pose.sequence Residue
C++: core::pose::Pose::aa(const unsigned long) const –> enum core::chemical::AA
- add_constraint(self: pyrosetta.rosetta.core.pose.Pose, cst: core::scoring::constraints::Constraint) core::scoring::constraints::Constraint ¶
adding a constraint is done by cloning the input constraint. A const copy is then returned
C++: core::pose::Pose::add_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>) –> class std::shared_ptr<const class core::scoring::constraints::Constraint>
- add_constraints(self: pyrosetta.rosetta.core.pose.Pose, csts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t ¶
Add a list of constraints to a pose.
C++: core::pose::Pose::add_constraints(const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &) –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >
- alpha(self: pyrosetta.rosetta.core.pose.Pose, pos: int) float ¶
Returns the alpha torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.alpha(1)
- See also:
Pose Pose.residue Pose.set_alpha Residue
C++: core::pose::Pose::alpha(const unsigned long) const –> double
- annotated_sequence(*args, **kwargs)¶
Overloaded function.
annotated_sequence(self: pyrosetta.rosetta.core.pose.Pose) -> str
annotated_sequence(self: pyrosetta.rosetta.core.pose.Pose, show_all_variants: bool) -> str
- Returns the variant-tagged string representing the
residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]
- example(s):
pose.annotated_sequence()
- See also:
Pose Pose.sequence Pose.size
Residue
C++: core::pose::Pose::annotated_sequence(bool) const –> std::string
- append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) None ¶
glues to seqpos and perhaps also seqpos+1
C++: core::pose::Pose::append_polymer_residue_after_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void
- append_pose_by_jump(*args, **kwargs)¶
Overloaded function.
append_pose_by_jump(self: pyrosetta.rosetta.core.pose.Pose, src: pyrosetta.rosetta.core.pose.Pose, jump_anchor_residue: int) -> None
append_pose_by_jump(self: pyrosetta.rosetta.core.pose.Pose, src: pyrosetta.rosetta.core.pose.Pose, jump_anchor_residue: int, jump_anchor_atom: str) -> None
append_pose_by_jump(self: pyrosetta.rosetta.core.pose.Pose, src: pyrosetta.rosetta.core.pose.Pose, jump_anchor_residue: int, jump_anchor_atom: str, jump_root_atom: str) -> None
Appends source pose conformation to pose by a new jump
C++: core::pose::Pose::append_pose_by_jump(const class core::pose::Pose &, const unsigned long, const std::string &, const std::string &) –> void
- append_residue_by_atoms(*args, **kwargs)¶
Overloaded function.
append_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str) -> None
append_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str, start_new_chain: bool) -> None
append_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str, start_new_chain: bool, lookup_bond_length: bool) -> None
Appends <new_rsd> (a residue) to pose by a new bond to a given atom
This function effectively wraps append_residue_by_bond for an easier syntax. Instead of having to know what the connection, anchor residue, and anchor connection are, we give the atoms and query the ResidueType for the remaining information.
If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.
Otherwise the incoming coordinates of new_rsd are preserved.
C++: core::pose::Pose::append_residue_by_atoms(const class core::conformation::Residue &, const bool, const std::string &, const unsigned long, const std::string &, const bool, const bool) –> void
- append_residue_by_bond(*args, **kwargs)¶
Overloaded function.
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection: int, anchor_residue: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection: int, anchor_residue: int, anchor_connection: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection: int, anchor_residue: int, anchor_connection: int, start_new_chain: bool) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection: int, anchor_residue: int, anchor_connection: int, start_new_chain: bool, lookup_bond_length: bool) -> None
Appends <new_rsd> (a residue) to pose by a new bond
The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType
If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.
Otherwise the incoming coordinates of new_rsd are preserved.
C++: core::pose::Pose::append_residue_by_bond(const class core::conformation::Residue &, const bool, const int, const unsigned long, const int, const bool, const bool) –> void
- append_residue_by_jump(*args, **kwargs)¶
Overloaded function.
append_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, jump_anchor_residue: int) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, jump_anchor_residue: int, jump_anchor_atom: str) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, jump_anchor_residue: int, jump_anchor_atom: str, jump_root_atom: str) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, jump_anchor_residue: int, jump_anchor_atom: str, jump_root_atom: str, start_new_chain: bool) -> None
Appends <new_rsd> (a residue) to pose by a new jump
C++: core::pose::Pose::append_residue_by_jump(const class core::conformation::Residue &, const unsigned long, const std::string &, const std::string &, const bool) –> void
- append_residues(self: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, jump_connection: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
- Convenience function to add a bunch of residues at once to the end of the pose
jump_connection lists the residue (in the new pose) to which to attach the residue by jump a value of 0 for jump_connection means that the residue will be attached polymerically to the previous residue.
C++: core::pose::Pose::append_residues(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- apply_transform(xform)¶
Apply a homogeneous transform to the current pose.
- Args:
xform (np.ndarray): A homogeneous transform.
- apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.pose.Pose, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) None ¶
- Apply a transform of the Rx + v form, where R is a
rotation matrix and v is a translation vector.
C++: core::pose::Pose::apply_transform_Rx_plus_v(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void
- assign(self: pyrosetta.rosetta.core.pose.Pose, src: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pose.Pose ¶
- Copies <src> into the pose where it remains possible that two
Poses may point to each other in non-const ways or share non-bitwise constant data between them (E.g. the AtomTree observer system).
- example(s):
test_pose.assign(pose)
- See also:
Pose
C++: core::pose::Pose::operator=(const class core::pose::Pose &) –> class core::pose::Pose &
- atom_tree(self: pyrosetta.rosetta.core.pose.Pose) core::kinematics::AtomTree ¶
Returns the pose AtomTree
C++: core::pose::Pose::atom_tree() const –> const class core::kinematics::AtomTree &
- batch_get_xyz(self: pyrosetta.rosetta.core.pose.Pose, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID, points: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
Gets the locations (xyz) of pose AtomIDs in <ids>
C++: core::pose::Pose::batch_get_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> void
- batch_set_xyz(self: pyrosetta.rosetta.core.pose.Pose, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID, points: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None ¶
- Sets the locations (xyz) of pose AtomIDs in <ids>
to mathcing PointPositions in <points>
C++: core::pose::Pose::batch_set_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void
- beta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the beta torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.beta(2)
- See also:
Pose Pose.residue Pose.set_beta Residue
C++: core::pose::Pose::beta(const unsigned long) const –> double
- center(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Sets pose coordinates such that the pose center is at the Euclidean origin
C++: core::pose::Pose::center() –> void
- chain(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) int ¶
Returns the chain number of residue <seqpos>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.chain(3)
- see also:
pose pose.num_chains pose.annotated_sequence
- pose.chain_sequence
pose.fold_tree pose.sequence foldtree
C++: core::pose::Pose::chain(const unsigned long) const –> unsigned long
- chain_begin(self: pyrosetta.rosetta.core.pose.Pose, chain_num: int) int ¶
Returns the sequence position of the beginning of chain <chain_num>.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. This is a pass-through function which returns conformation_->chain_begin( chain_num )
- example(s):
pose.chain_begin(1)
- see also:
pose pose.num_chains pose.annotated_sequence
- pose.chain_sequence
pose.fold_tree pose.sequence foldtree
C++: core::pose::Pose::chain_begin(const unsigned long) const –> unsigned long
- chain_end(self: pyrosetta.rosetta.core.pose.Pose, chain_num: int) int ¶
Returns the sequence position of the end of chain <chain_num>.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. This is a pass-through function which returns conformation_->chain_end( chain_num )
- example(s):
pose.chain_end(1)
- see also:
pose pose.num_chains pose.annotated_sequence
- pose.chain_sequence
pose.fold_tree pose.sequence foldtree
C++: core::pose::Pose::chain_end(const unsigned long) const –> unsigned long
- chain_sequence(self: pyrosetta.rosetta.core.pose.Pose, chain_in: int) str ¶
Returns the sequence for the chain number <chain_in>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- Example(s):
pose.chain_sequence(1)
- See also:
Pose Pose.chain Pose.residue Pose.sequence
C++: core::pose::Pose::chain_sequence(const unsigned long) const –> std::string
- chi(*args, **kwargs)¶
Overloaded function.
chi(self: pyrosetta.rosetta.core.pose.Pose, chino: int, seqpos: int) -> float
Returns the <chino> chi torsion angle of residue <seqpos>
assumes the residue is an amino acid or monosaccharide
- example(s):
pose.chi(1,7)
- See also:
Pose Pose.set_chi Pose.residue Residue
C++: core::pose::Pose::chi(const int, const unsigned long) const –> double
chi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) -> float
Returns the chi torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.chi(7)
- See also:
Pose Pose.residue Pose.set_chi Residue
C++: core::pose::Pose::chi(const unsigned long) const –> double
- clear(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Empty the pose contents
- example(s):
pose.clear()
- See also:
Pose Pose.assign Pose.empty
C++: core::pose::Pose::clear() –> void
- clear_sequence_constraints(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Remove all sequence constraints from this pose.
C++: core::pose::Pose::clear_sequence_constraints() –> void
- clone(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pose.Pose ¶
clone the conformation
C++: core::pose::Pose::clone() const –> class std::shared_ptr<class core::pose::Pose>
- conformation(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.Conformation ¶
Returns the pose Conformation (non-const access)
C++: core::pose::Pose::conformation() –> class core::conformation::Conformation &
- conformation_ptr(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.Conformation ¶
Returns the pose Conformation pointer (nonconst access)
WHOA: This is not cool. The Pose cannot hand out access to the OP directly. Do not use.
C++: core::pose::Pose::conformation_ptr() –> class std::shared_ptr<class core::conformation::Conformation> &
- const_data_cache(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.basic.datacache.ConstDataMap ¶
Read access to the const data cache
C++: core::pose::Pose::const_data_cache() const –> const class basic::datacache::ConstDataMap &
- constraint_set(*args, **kwargs)¶
Overloaded function.
constraint_set(self: pyrosetta.rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
C++: core::pose::Pose::constraint_set() const –> class std::shared_ptr<const class core::scoring::constraints::ConstraintSet>
constraint_set(self: pyrosetta.rosetta.core.pose.Pose, : core::scoring::constraints::ConstraintSet) -> None
C++: core::pose::Pose::constraint_set(class std::shared_ptr<class core::scoring::constraints::ConstraintSet>) –> void
- copy_segment(self: pyrosetta.rosetta.core.pose.Pose, size: int, src: pyrosetta.rosetta.core.pose.Pose, begin: int, src_begin: int) None ¶
- Copy a stretch of coordinates/torsions from <src>
to pose
C++: core::pose::Pose::copy_segment(const unsigned long, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void
- corresponding_residue_in_current(self: pyrosetta.rosetta.core.pose.Pose, ref_residue_index: int, ref_pose_name: str) int ¶
Returns the index of a residue in this pose corresponding to a residue in a reference pose.
Throws an error if the reference pose with the given name doesn’t exist, or the residue number doesn’t exist in that reference pose. Returns zero if no corresponding residue exists in this pose (e.g. if the residue in question has been deleted.
C++: core::pose::Pose::corresponding_residue_in_current(const unsigned long, const std::string &) const –> unsigned long
- data(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.basic.datacache.BasicDataCache ¶
BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh
C++: core::pose::Pose::data() –> class basic::datacache::BasicDataCache &
- decrement_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
Find all mappings in the new pose after seqpos in all ReferencePose objects, and decrement them by 1.
If there is no ReferencePose object, do nothing.
C++: core::pose::Pose::decrement_reference_pose_mapping_after_seqpos(const unsigned long) –> void
- delete_polymer_residue(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
- Delete a residue in the pose.
Update Observers. Update any Reference Poses
C++: core::pose::Pose::delete_polymer_residue(const unsigned long) –> void
- delete_residue_range_slow(self: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) None ¶
Delete a range of residues in the pose.
- Calls confromation::delete_residue_range_slow().
Update Observers. Update any Reference Poses
C++: core::pose::Pose::delete_residue_range_slow(const unsigned long, const unsigned long) –> void
- delete_residue_slow(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
- Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.
Update Observers. Update any Reference Poses
C++: core::pose::Pose::delete_residue_slow(const unsigned long) –> void
- delta(self: pyrosetta.rosetta.core.pose.Pose, pos: int) float ¶
Returns the delta torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.delta(4)
- See also:
Pose Pose.residue Pose.set_delta Residue
C++: core::pose::Pose::delta(const unsigned long) const –> double
- detached_copy(self: pyrosetta.rosetta.core.pose.Pose, src: pyrosetta.rosetta.core.pose.Pose) None ¶
- Performs a deep copy of the src Pose into this Pose in a way
that guarantees that no non-bitwise-constant data is shared between them (such as the AtomTree’s observer system) – this Pose will be effectively detached from any data that lives in other objects.
C++: core::pose::Pose::detached_copy(const class core::pose::Pose &) –> void
- display_secstruct(space=8, page=80)¶
Use DSSP to assign secondary structure codes to each residue in a Pose, store the result in the Pose, and display the result.
- Args:
- space (int): Spacing of residue number labels in display.
Defaults to 8.
- page (int): Number of characters per line in dispaly.
Defaults to 80.
- dof(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.DOF_ID) float ¶
Returns the value of the AtomTree DOF <id>
- See also:
Pose DOF_ID
C++: core::pose::Pose::dof(const class core::id::DOF_ID &) const –> double
- dump_cif(self: pyrosetta.rosetta.core.pose.Pose, file_name: str) None ¶
Export pose data to the mmCIF file <file_name>
- example(s):
pose.dump_cif(‘new_01.cif’)
- See also:
Pose pose_from_cif dump_file
C++: core::pose::Pose::dump_cif(const std::string &) const –> void
- dump_file(self: pyrosetta.rosetta.core.pose.Pose, file_name: str) None ¶
Export pose data to a file, <file_name>, determining which type of file format to write based on the file extension
- example(s):
pose.dump_file(‘new_01.pdb’) pose.dump_file(‘new_01.cif’)
- See also:
Pose dump_cif dump_mmtf dump_file
C++: core::pose::Pose::dump_file(const std::string &) const –> void
- dump_mmtf(self: pyrosetta.rosetta.core.pose.Pose, file_name: str) None ¶
Export pose data to the mmtf file <file_name>
- example(s):
pose.dump_mmtf(‘new_01.mmtf’)
- See also:
Pose pose_from_mmtf dump_file
C++: core::pose::Pose::dump_mmtf(const std::string &) const –> void
- dump_pdb(*args, **kwargs)¶
Overloaded function.
dump_pdb(self: pyrosetta.rosetta.core.pose.Pose, file_name: str) -> bool
Export pose data to the PDB file <file_name>
- example(s):
pose.dump_pdb(‘new_01.pdb’)
- See also:
Pose pose_from_pdb dump_cif dump_file
C++: core::pose::Pose::dump_pdb(const std::string &) const –> bool
dump_pdb(self: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None
C++: core::pose::Pose::dump_pdb(std::ostream &) const –> void
dump_pdb(self: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
for writing a specified subset of residues in pdb format
C++: core::pose::Pose::dump_pdb(std::ostream &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void
- dump_scored_pdb(self: pyrosetta.rosetta.core.pose.Pose, file_name: str, scorefxn: core::scoring::ScoreFunction) None ¶
- Export pose data to the PDB file <file_name>,
add some score output
C++: core::pose::Pose::dump_scored_pdb(const std::string &, const class core::scoring::ScoreFunction &) –> void
- empty(self: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if there are no residues in the conformation
- example(s):
pose.empty()
- See also:
Pose Pose.clear
- Pose.sequence
Pose.size
C++: core::pose::Pose::empty() const –> bool
- energies(self: pyrosetta.rosetta.core.pose.Pose) core::scoring::Energies ¶
Returns the pose Energies (non-const access)
C++: core::pose::Pose::energies() –> class core::scoring::Energies &
- epsilon(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the epsilon torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.epsilon(5)
- See also:
Pose Pose.residue Pose.set_epsilon Residue
C++: core::pose::Pose::epsilon(const unsigned long) const –> double
- fold_tree(*args, **kwargs)¶
Overloaded function.
fold_tree(self: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.FoldTree
Returns the pose FoldTree
- example(s):
pose.fold_tree()
- See also:
Pose FoldTree
C++: core::pose::Pose::fold_tree() const –> const class core::kinematics::FoldTree &
fold_tree(self: pyrosetta.rosetta.core.pose.Pose, fold_tree_in: pyrosetta.rosetta.core.kinematics.FoldTree) -> None
Sets the pose FoldTree to <fold_tree_in>
- example(s):
pose.fold_tree( foldtree )
- See also:
Pose pose.fold_tree FoldTree
C++: core::pose::Pose::fold_tree(const class core::kinematics::FoldTree &) –> void
- gamma(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the gamma torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.gamma(3)
- See also:
Pose Pose.residue Pose.set_gamma Residue
C++: core::pose::Pose::gamma(const unsigned long) const –> double
- get_hbonds(calculate_derivative=False, exclude_bb=False, exclude_bsc=False, exclude_scb=False, exclude_sc=False)¶
Return the HBondSet for all hydrogen bonds in the Pose.
- Args:
caclulate_derivative (bool): Defaults to False. exclube_bb (bool): Exclude backbone hydrogen bonds from the returned HBondSet.
Defaults to False.
- exclube_bsc (bool): Exclude backbone–side-chain hydrogen bonds from the returned HBondSet.
Defaults to False.
- exclube_scb (bool): Exclude side-chain–backbone hydrogen bonds from the returned HBondSet.
Defaults to False.
- exclube_sc (bool): Exclude side-chain hydrogen bonds from the returned HBondSet.
Defaults to False.
- Returns:
pyrosetta.rosetta.core.scoring.hbonds.HBondSet: THe selected hydrogen bonds in the Pose.
- get_self_ptr(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pose.Pose ¶
C++: core::pose::Pose::get_self_ptr() –> class std::shared_ptr<class core::pose::Pose>
- get_self_weak_ptr(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.weak_ptr_core_pose_Pose_t ¶
C++: core::pose::Pose::get_self_weak_ptr() –> class std::weak_ptr<class core::pose::Pose>
- glycan_tree_branch_sequence(self: pyrosetta.rosetta.core.pose.Pose, start_residue: int) str ¶
- Return the IUPAC sequence of a single branch of a glycan tree,
Beginning with residue number <start_residue>.
C++: core::pose::Pose::glycan_tree_branch_sequence(const unsigned long) const –> std::string
- glycan_tree_sequence(self: pyrosetta.rosetta.core.pose.Pose, residue_in_tree: int) str ¶
Return the IUPAC sequence of the entire glycan tree encompassing residue number <residue_in_tree>.
C++: core::pose::Pose::glycan_tree_sequence(const unsigned long) const –> std::string
- glycan_tree_set(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet ¶
- Get information on any glycan trees within this pose.
If this is not setup, will return a nullptr due to the const nature of the function.
- The GlycanTreeSet holds information on the connectivity of the glycan residues and if
they are free or attached to a pose.
- example(s):
pose.glycan_tree_set() conformation.glycan_tree_set()
- See also:
pose.residue(3).is_carbohydrate() pose.residue(3).carbohydrate_info()
C++: core::pose::Pose::glycan_tree_set() const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTreeSet>
- has_dof(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.DOF_ID) bool ¶
Returns true if pose has DOF <id>
- See also:
Pose DOF_ID
C++: core::pose::Pose::has_dof(const class core::id::DOF_ID &) const –> bool
- has_reference_pose(self: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if a pose has at least one reference pose, false otherwise.
C++: core::pose::Pose::has_reference_pose() const –> bool
- increment_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
Find all mappings in the new pose after seqpos in all ReferencePose objects, and increment them by 1.
If there is no ReferencePose object, do nothing.
C++: core::pose::Pose::increment_reference_pose_mapping_after_seqpos(const unsigned long) –> void
- insert_residue_by_atoms(*args, **kwargs)¶
Overloaded function.
insert_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int) -> None
insert_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str) -> None
insert_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str, start_new_chain: bool) -> None
insert_residue_by_atoms(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool, connect_atom: str, anchor_rsd_seqpos: int, anchor_connect_atom: str, start_new_chain: bool, lookup_bond_length: bool) -> None
C++: core::pose::Pose::insert_residue_by_atoms(const class core::conformation::Residue &, const unsigned long, const bool, const std::string &, const unsigned long, const std::string &, const bool, const bool) –> void
- insert_residue_by_bond(*args, **kwargs)¶
Overloaded function.
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool, lookup_bond_length: bool) -> None
This code sorely belongs in Pose.cc
Adds <new_rsd_in> to pose at <seqpos>
C++: core::pose::Pose::insert_residue_by_bond(const class core::conformation::Residue &, const unsigned long, unsigned long, const bool, const std::string &, const std::string &, bool, const bool) –> void
- insert_residue_by_jump(*args, **kwargs)¶
Overloaded function.
insert_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None
insert_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atomno: str) -> None
insert_residue_by_jump(self: pyrosetta.rosetta.core.pose.Pose, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atomno: str, root_atomno: str) -> None
This code sorely belongs in Pose.cc
Adds <new_rsd_in> to pose at <seqpos>
C++: core::pose::Pose::insert_residue_by_jump(const class core::conformation::Residue &, const unsigned long, unsigned long, const std::string &, const std::string &) –> void
- is_centroid(self: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if pose is ResidueType centroid
convenience test for residue_type_set
- example(s):
pose.is_centroid()
- See also:
Pose Pose.is_fullatom Residue ResidueType
C++: core::pose::Pose::is_centroid() const –> bool
- is_fullatom(self: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if pose is ResidueType fullatom
convenience test for residue_type_set
- example(s):
pose.is_fullatom()
- See also:
Pose Pose.is_centroid Residue ResidueType
C++: core::pose::Pose::is_fullatom() const –> bool
- jump(*args, **kwargs)¶
Overloaded function.
jump(self: pyrosetta.rosetta.core.pose.Pose, jump_number: int) -> core::kinematics::Jump
Returns the pose FoldTree Jump <jump_number>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.jump(1)
- See also:
Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge Jump
C++: core::pose::Pose::jump(const int) const –> const class core::kinematics::Jump &
jump(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.AtomID) -> core::kinematics::Jump
Returns the pose FoldTree Jump <id>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.set_jump(R5N)
- See also:
Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge AtomID
C++: core::pose::Pose::jump(const class core::id::AtomID &) const –> const class core::kinematics::Jump &
- membrane_info(self: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.membrane.MembraneInfo ¶
- Get information about the membrane orientaiton, geometry, and
lipid composition within this pose
MembraneInfo contains all information pertaining to the conformation and composition of a membrane enviornment
- example(s):
pose.membrane_info() conformation.membrane_info()
C++: core::pose::Pose::membrane_info() –> class std::shared_ptr<class core::conformation::membrane::MembraneInfo>
- metric(self: pyrosetta.rosetta.core.pose.Pose, calculator_name: str, key: str, val: pyrosetta.rosetta.basic.MetricValueBase) None ¶
C++: core::pose::Pose::metric(const std::string &, const std::string &, class basic::MetricValueBase &) const –> void
- mu(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the mu torsion angle of oligourea residue <seqpos>.
Mu is defined as CM(n)-NU(n)-C(n)-N(n+1) for an oligourea.
Assumes residue is an oligourea.
- example(s):
pose.mu(21)
- See also:
Pose Pose.set_mu Pose.residue Residue
Vikram K. Mulligan (vmullig.edu)
C++: core::pose::Pose::mu(const unsigned long) const –> double
- num_chains(self: pyrosetta.rosetta.core.pose.Pose) int ¶
- example(s):
pose.num_chains()
- see also:
pose pose.chain pose.annotated_sequence
- pose.chain_sequence
pose.fold_tree pose.sequence foldtree
C++: core::pose::Pose::num_chains() const –> unsigned long
- num_jump(self: pyrosetta.rosetta.core.pose.Pose) int ¶
Returns the number of jumps in the pose FoldTree
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- example(s):
pose.num_jump()
- See also:
Pose Pose.jump Pose.set_jump FoldTree Jump
C++: core::pose::Pose::num_jump() const –> unsigned long
- observer_cache(self: pyrosetta.rosetta.core.pose.Pose) core::pose::datacache::ObserverCache ¶
ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh
C++: core::pose::Pose::observer_cache() –> class core::pose::datacache::ObserverCache &
- omega(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the omega torsion angle of residue <seqpos> in degrees
assumes the residue is an amino acid or monosaccharide
- example(s):
pose.omega(3)
- See also:
Pose Pose.residue Pose.set_omega Residue
C++: core::pose::Pose::omega(const unsigned long) const –> double
- pdb_info(*args, **kwargs)¶
Overloaded function.
pdb_info(self: pyrosetta.rosetta.core.pose.Pose) -> core::pose::PDBInfo
Returns the pose PDBInfo
NULL if no PDBInfo instance exists, the PDBInfo instance otherwise
C++: core::pose::Pose::pdb_info() –> class std::shared_ptr<class core::pose::PDBInfo>
pdb_info(self: pyrosetta.rosetta.core.pose.Pose, new_info: core::pose::PDBInfo) -> core::pose::PDBInfo
Sets pose PDBInfo to <new_info>
the new PDBInfo to copy, pass NULL
if you want to zero the existence of PDBInfo inside this Pose
the prior PDBInfo instance
C++: core::pose::Pose::pdb_info(class std::shared_ptr<class core::pose::PDBInfo>) –> class std::shared_ptr<class core::pose::PDBInfo>
- pdb_rsd(chain_and_resNo)¶
Look up a specific PDB-numbered residue and return it.
- Args:
- chain_and_resNo (tuple): a tuple representing the PDB description of the residue
in the format (chainID, resNo). For example, residue 1 on chain A would be (“A”, 1).
- Returns:
pyrosetta.core.conformation.Residue or None: the Residue instance in the Pose. returns None if the PDB residue identifier is invalid.
- phi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the phi torsion angle of residue <seqpos> in degrees
assumes the residue is an amino acid or monosaccharide
- example(s):
pose.phi(1)
- See also:
Pose Pose.residue Pose.set_phi Residue
C++: core::pose::Pose::phi(const unsigned long) const –> double
- prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.pose.Pose, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) None ¶
glues to seqpos and perhaps also seqpos-1
C++: core::pose::Pose::prepend_polymer_residue_before_seqpos(const class core::conformation::Residue &, const unsigned long, const bool) –> void
- print_metric(self: pyrosetta.rosetta.core.pose.Pose, calculator_name: str, key: str) str ¶
C++: core::pose::Pose::print_metric(const std::string &, const std::string &) const –> std::string
- psi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
- Returns the psi torsion angle of residue <seqpos> in degrees
Note: assumes the residue is an amino acid or monosaccharide
- example(s):
pose.psi(2)
- See also:
Pose Pose.residue Pose.set_psi Residue
C++: core::pose::Pose::psi(const unsigned long) const –> double
- real_to_virtual(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
Switch residues to VIRTUAL
VIRTUAL residues are the same except not SCORED or DUMPED.
- example(s):
pose.real_to_virtual(3)
- See also:
Pose ResidueType
C++: core::pose::Pose::real_to_virtual(unsigned long) –> void
- reference_pose_from_current(*args, **kwargs)¶
Overloaded function.
reference_pose_from_current(self: pyrosetta.rosetta.core.pose.Pose, ref_pose_name: str) -> None
reference_pose_from_current(self: pyrosetta.rosetta.core.pose.Pose, ref_pose_name: str, override_current: bool) -> None
Create a new reference pose from the current state of the pose.
- If a ReferencePoseSet object does not exist, this function will create it.
If override_current is set to true, will override any currently set reference pose with the ref_pose_name.
C++: core::pose::Pose::reference_pose_from_current(const std::string &, bool) –> void
- reference_pose_set(self: pyrosetta.rosetta.core.pose.Pose) core::pose::reference_pose::ReferencePoseSet ¶
Access the ReferencePoseSet object (non-const).
If a ReferencePoseSet object does not exist, this function will create it.
C++: core::pose::Pose::reference_pose_set() –> class std::shared_ptr<class core::pose::reference_pose::ReferencePoseSet>
- reference_pose_set_cop(self: pyrosetta.rosetta.core.pose.Pose) core::pose::reference_pose::ReferencePoseSet ¶
Const-access the ReferencePoseSet object.
If a ReferencePoseSet object does not exist, this function will throw an error.
C++: core::pose::Pose::reference_pose_set_cop() const –> class std::shared_ptr<const class core::pose::reference_pose::ReferencePoseSet>
- remove_constraint(*args, **kwargs)¶
Overloaded function.
remove_constraint(self: pyrosetta.rosetta.core.pose.Pose, cst: core::scoring::constraints::Constraint) -> bool
remove_constraint(self: pyrosetta.rosetta.core.pose.Pose, cst: core::scoring::constraints::Constraint, object_comparison: bool) -> bool
re object_comparison see comment for ConstraintSet::remove_constraint function
C++: core::pose::Pose::remove_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>, bool) –> bool
- remove_constraints(*args, **kwargs)¶
Overloaded function.
remove_constraints(self: pyrosetta.rosetta.core.pose.Pose, csts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> bool
remove_constraints(self: pyrosetta.rosetta.core.pose.Pose, csts: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison: bool) -> bool
re object_comparison see comment for ConstraintSet::remove_constraint function
C++: core::pose::Pose::remove_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >, bool) –> bool
remove_constraints(self: pyrosetta.rosetta.core.pose.Pose) -> bool
C++: core::pose::Pose::remove_constraints() –> bool
- replace_residue(*args, **kwargs)¶
Overloaded function.
replace_residue(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, orient_backbone: bool) -> None
Replaces the residue at <seqpos> with <new_rsd_in>
C++: core::pose::Pose::replace_residue(const unsigned long, const class core::conformation::Residue &, const bool) –> void
replace_residue(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, atom_pairs: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t) -> None
- Replaces the residue at <seqpos> with <new_rsd>
based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works This code sorely belongs in Pose.cc
C++: core::pose::Pose::replace_residue(const int, const class core::conformation::Residue &, const class utility::vector1<struct std::pair<std::string, std::string >, class std::allocator<struct std::pair<std::string, std::string > > > &) –> void
- residue(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) pyrosetta.rosetta.core.conformation.Residue ¶
- Returns the Residue at position <seqpos> (read access)
Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date
- example(s):
pose.residue(4)
- See also:
Pose Pose.sequence Pose.size Residue ResidueType
C++: core::pose::Pose::residue(const unsigned long) const –> const class core::conformation::Residue &
- residue_data(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) pyrosetta.rosetta.basic.datacache.BasicDataCache ¶
- Returns the DataCache held by Residue at position <seqpos> (read/write access)
Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date
- example(s):
pose.residue_data(4)
- See also:
Pose Pose.residue Pose.sequence Pose.size Residue ResidueType
C++: core::pose::Pose::residue_data(const unsigned long) –> class basic::datacache::BasicDataCache &
- residue_pairs(primary_residue_selector=<pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector object>, secondary_residue_selector=<pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector object>, neighborhood_distance_maximum=None, sequence_distance_minimum=None)¶
Iterate the permutations of residue pairs from two selections which are within a cartesian and/or outside a sequence distance cutoff.
The method uses the PrimarySequenceNeighborhoodSelector and NeighborhoodResidueSelector under the hood. Note that all _permutations_ of residues are yielded, not _combinations_. If you prefer combinations simply check if residue_pair[0].sequence_position() > residue_pair[1].sequence_position():.
primary_residue_selector - ResidueSelector secondary_residue_selector - ResidueSelector neighborhood_distance - float sequence_distance - int
return - iterator(tuple(Residue, Residue))
- residue_type(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Returns the ResidueType at position <seqpos> (read access)
Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date
- example(s):
pose.residue_type(5)
- See also:
Pose Pose.residue Pose.residue_type_ptr Pose.sequence Pose.size Residue ResidueType
C++: core::pose::Pose::residue_type(const unsigned long) const –> const class core::chemical::ResidueType &
- residue_type_ptr(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Returns the ResidueTypeCOP for position <seqpos> (read access)
Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date
- example(s):
pose.residue_type_ptr(5)
- See also:
Pose Pose.residue Pose.residue_type Pose.sequence Pose.size Residue ResidueType
C++: core::pose::Pose::residue_type_ptr(const unsigned long) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- residue_type_set_for_pose(*args, **kwargs)¶
Overloaded function.
residue_type_set_for_pose(self: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet
residue_type_set_for_pose(self: pyrosetta.rosetta.core.pose.Pose, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet
- Return the custom ResidueTypeSet for the Pose, if any.
Otherwise will return the appropriate global ResidueTypeSet
If mode is INVALID_t (the default), the returned ResidueTypeSet is the one corresponding to the majority of the residues in the Pose. i.e. FULL_ATOM if pose.is_fullatom(); CENTROID if pose.is_centriod()
- examples(s):
pose.residue_type_set_for_pose() pose.residue_type_set_for_pose( core::chemical::CENTROID_t )
- See also:
Pose Pose.is_fullatom Pose.is_centroid ResidueTypeSet
C++: core::pose::Pose::residue_type_set_for_pose(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>
- property residues¶
- property reslabels¶
- rotate(R)¶
Apply a rotation matrix to all of the coordinates in a Pose.
- Args:
p (Pose): The Pose instance to manipulate R (np.mat): A rotation matrix to apply to the Pose coordinates
- property scores¶
- scoring_begin(self: pyrosetta.rosetta.core.pose.Pose, info: core::scoring::ScoreFunction) None ¶
Called by ScoreFunction at the beginning of scoring
C++: core::pose::Pose::scoring_begin(const class core::scoring::ScoreFunction &) –> void
- scoring_end(self: pyrosetta.rosetta.core.pose.Pose, scorefxn: core::scoring::ScoreFunction) None ¶
Called by ScoreFunction at the end of scoring
C++: core::pose::Pose::scoring_end(const class core::scoring::ScoreFunction &) –> void
- secstruct(*args, **kwargs)¶
Overloaded function.
secstruct(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) -> str
- Returns the secondary structure of residue <seqpos>
this usually comes from fragments. The conformation object will not invoke DSSP to determine the secondary structure if e.g. it has not been made from fragments. ‘H’ = helical ‘E’ = strand or sheet ‘L’ = loop
- example(s):
pose.secstruct(3)
- See also:
Pose Pose.residue Pose.set_secstruct Residue
C++: core::pose::Pose::secstruct(const unsigned long) const –> char
secstruct(self: pyrosetta.rosetta.core.pose.Pose) -> str
Returns a string representing pose secondary structure
- example(s):
pose.secstruct()
- See also:
Pose Pose.residue Pose.set_secstruct Residue
C++: core::pose::Pose::secstruct() const –> std::string
- sequence(*args, **kwargs)¶
Overloaded function.
sequence(self: pyrosetta.rosetta.core.pose.Pose) -> str
Returns a string representing the 1-letter-coded sequence of the pose conformation.
- example(s):
pose.sequence()
- See also:
Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.size
C++: core::pose::Pose::sequence() const –> std::string
sequence(self: pyrosetta.rosetta.core.pose.Pose, resnum_start: int, resnum_end: int) -> str
Returns a string representing the 1-letter-coded sequence of the pose conformation. From start to end.
- example(s):
pose.sequence()
- See also:
Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.size
C++: core::pose::Pose::sequence(unsigned long, unsigned long) const –> std::string
- set_alpha(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the alpha torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_alpha(1)
- See also:
Pose Pose.alpha Pose.residue Residue
C++: core::pose::Pose::set_alpha(const unsigned long, const double) –> void
- set_beta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the beta torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_beta(2)
- See also:
Pose Pose.beta Pose.residue Residue
C++: core::pose::Pose::set_beta(const unsigned long, const double) –> void
- set_chi(*args, **kwargs)¶
Overloaded function.
set_chi(self: pyrosetta.rosetta.core.pose.Pose, chino: int, seqpos: int, setting: float) -> None
Sets the <chino> chi torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an amino acid or monosaccharide
- example(s):
pose.set_chi(1,7,120)
- See also:
Pose Pose.chi Pose.residue Residue
C++: core::pose::Pose::set_chi(const int, const unsigned long, const double) –> void
set_chi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) -> None
Sets the chi torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_chi(7)
- See also:
Pose Pose.chi Pose.residue Residue
C++: core::pose::Pose::set_chi(const unsigned long, const double) –> void
- set_const_data(self: pyrosetta.rosetta.core.pose.Pose, category: str, name: str, original: pyrosetta.rosetta.core.pose.Pose) None ¶
- template specialization for when storing a Pose inside a Pose. For the sake of
thread safety, the Pose that should be stored must represent a deep copy – one that does not contain pointers to any outside objects through which it might “communicate” behind the scenes or which might try to communicate with the starting pose. Therefore, a “detached_copy” of the original pose is created.
C++: core::pose::Pose::set_const_data(const std::string &, const std::string &, const class core::pose::Pose &) –> void
- set_delta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the delta torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_delta(4)
- See also:
Pose Pose.delta Pose.residue Residue
C++: core::pose::Pose::set_delta(const unsigned long, const double) –> void
- set_dof(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.DOF_ID, setting: float) None ¶
Sets the value of the AtomTree DOF <id>
- See also:
Pose DOF_ID
C++: core::pose::Pose::set_dof(const class core::id::DOF_ID &, const double) –> void
- set_epsilon(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the epsilon torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_epsilon(5)
- See also:
Pose Pose.epsilon Pose.residue Residue
C++: core::pose::Pose::set_epsilon(const unsigned long, const double) –> void
- set_gamma(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the gamma torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_gamma(3)
- See also:
Pose Pose.gamma Pose.residue Residue
C++: core::pose::Pose::set_gamma(const unsigned long, const double) –> void
- set_jump(*args, **kwargs)¶
Overloaded function.
set_jump(self: pyrosetta.rosetta.core.pose.Pose, jump_number: int, new_jump: core::kinematics::Jump) -> None
Sets the pose FoldTree Jump <jump_number> to <new_jump>
- example(s):
pose.set_jump(1,jump1)
- See also:
Pose Pose.fold_tree Pose.jump FoldTree FoldTree.jump_edge Jump
C++: core::pose::Pose::set_jump(const int, const class core::kinematics::Jump &) –> void
set_jump(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.AtomID, new_jump: core::kinematics::Jump) -> None
Sets the pose FoldTree Jump <id> to <new_jump>
- example(s):
pose.set_jump(1,jump1)
- See also:
Pose Pose.fold_tree Pose.jump FoldTree FoldTree.jump_edge AtomID
C++: core::pose::Pose::set_jump(const class core::id::AtomID &, const class core::kinematics::Jump &) –> void
- set_mu(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the mu torsion angle of oligourea residue <seqpos> to <setting>.
Mu is defined as CM(n)-NU(n)-C(n)-N(n+1) for an oligourea.
<setting> must be in degrees. Assumes residue is an oligourea.
- example(s):
pose.set_mu(21, 58.9)
- See also:
Pose Pose.mu Pose.residue Residue
Vikram K. Mulligan (vmullig.edu)
C++: core::pose::Pose::set_mu(const unsigned long, const double) –> void
- set_new_conformation(self: pyrosetta.rosetta.core.pose.Pose, new_conformation: pyrosetta.rosetta.core.conformation.Conformation) None ¶
- Now that the conformation_ member data is an owning pointer,
and we have derived classes of Conformation.
C++: core::pose::Pose::set_new_conformation(class std::shared_ptr<const class core::conformation::Conformation>) –> void
- set_new_energies_object(self: pyrosetta.rosetta.core.pose.Pose, energies: core::scoring::Energies) None ¶
- Now that the energies_ member data is an owning pointer,
and we have derived classes of Energies.
C++: core::pose::Pose::set_new_energies_object(class std::shared_ptr<class core::scoring::Energies>) –> void
- set_omega(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the omega torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an amino acid or monosaccharide
- example(s):
pose.set_omega(3, 180.0)
- See also:
Pose Pose.omega Pose.residue Residue
C++: core::pose::Pose::set_omega(const unsigned long, const double) –> void
- set_phi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the phi torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an amino acid or monosaccharide
- example(s):
pose.set_phi(1, -23.7)
- See also:
Pose Pose.phi Pose.residue Residue
C++: core::pose::Pose::set_phi(const unsigned long, const double) –> void
- set_psi(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the psi torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an amino acid or monosaccharide
- example(s):
pose.set_psi(2, 45.3)
- See also:
Pose Pose.psi Pose.residue Residue
C++: core::pose::Pose::set_psi(const unsigned long, const double) –> void
- set_ring_conformation(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, ring_num: int, conformer: pyrosetta.rosetta.core.chemical.rings.RingConformer) None ¶
Set the given residue and ring’s ring conformation, if appropriate.
C++: core::pose::Pose::set_ring_conformation(const unsigned long, const unsigned long, const struct core::chemical::rings::RingConformer &) –> void
- set_secstruct(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: str) None ¶
Assign the secondary structure of residue <seqpos> to <setting>
- example(s):
pose.set_secstruct(3,’H’)
- See also:
Pose Pose.residue Pose.secstruct Residue
C++: core::pose::Pose::set_secstruct(const unsigned long, const char) –> void
- set_theta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos> to <setting>.
Theta is defined as N(n)-CA(n)-CM(n)-C(n) for a beta-amino acid, and N(n)-CA(n)-CM(n)-NU(n) for an oligourea.
<setting> must be in degrees. Assumes residue is a beta-amino acid or oligourea.
- example(s):
pose.set_theta(21, 58.9)
- See also:
Pose Pose.theta Pose.residue Residue
Vikram K. Mulligan (vmullig.edu)
C++: core::pose::Pose::set_theta(const unsigned long, const double) –> void
- set_torsion(self: pyrosetta.rosetta.core.pose.Pose, id: core::id::TorsionID, setting: float) None ¶
- Sets the Conformation torsion angle identified
by <id> to <setting>
- See also:
Pose TorsionID
C++: core::pose::Pose::set_torsion(const class core::id::TorsionID &, const double) –> void
- set_xyz(*args, **kwargs)¶
Overloaded function.
set_xyz(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.AtomID, point: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
- Sets the location (xyz) of pose AtomID <id> to
the PointPosition <point>
- See also:
Pose Pose.residue Pose.xyz Residue
C++: core::pose::Pose::set_xyz(const class core::id::AtomID &, const class numeric::xyzVector<double> &) –> void
set_xyz(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.NamedAtomID, point: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None
- Sets the location (xyz) of pose NamedAtomID <id>
to the PointPosition <point>
- See also:
Pose Pose.residue Pose.xyz Residue
C++: core::pose::Pose::set_xyz(const class core::id::NamedAtomID &, const class numeric::xyzVector<double> &) –> void
- set_zeta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int, setting: float) None ¶
Sets the zeta torsion angle of residue <seqpos> to <setting>
<setting> must be in degrees, assumes residue is an nucleic acid
- example(s):
pose.set_zeta(6)
- See also:
Pose Pose.zeta Pose.residue Residue
C++: core::pose::Pose::set_zeta(const unsigned long, const double) –> void
- size(self: pyrosetta.rosetta.core.pose.Pose) int ¶
Returns the number of residues in the pose conformation.
- example(s):
pose.size()
- See also:
Pose Pose.size Pose.sequence
C++: core::pose::Pose::size() const –> unsigned long
- split_by_chain(*args, **kwargs)¶
Overloaded function.
split_by_chain(self: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
Returns a vector of poses with one element per (chain number) chain of the original pose
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::Pose::split_by_chain() const –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >
split_by_chain(self: pyrosetta.rosetta.core.pose.Pose, chain_id: int) -> pyrosetta.rosetta.core.pose.Pose
Return a new pose with just the residues from the specified (chain number) chain.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::Pose::split_by_chain(unsigned long) const –> class std::shared_ptr<class core::pose::Pose>
- stub_from_id(self: pyrosetta.rosetta.core.pose.Pose, id: core::id::NamedStubID) core::kinematics::Stub ¶
C++: core::pose::Pose::stub_from_id(const class core::id::NamedStubID &) –> class core::kinematics::Stub
- theta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos>.
Theta is defined as N(n)-CA(n)-CM(n)-C(n) for a beta-amino acid, and N(n)-CA(n)-CM(n)-NU(n) for an oligourea.
Assumes residue is a beta-amino acid or oligourea.
- example(s):
pose.theta(21)
- See also:
Pose Pose.set_theta Pose.residue Residue
Vikram K. Mulligan (vmullig.edu)
C++: core::pose::Pose::theta(const unsigned long) const –> double
- torsion(self: pyrosetta.rosetta.core.pose.Pose, id: core::id::TorsionID) float ¶
Returns the Conformation torsion angle identified by <id>
- See also:
Pose TorsionID
C++: core::pose::Pose::torsion(const class core::id::TorsionID &) const –> double
- total_atoms(self: pyrosetta.rosetta.core.pose.Pose) int ¶
- Returns the total number of atoms in the pose conformation
- example:
pose.total_atoms()
C++: core::pose::Pose::total_atoms() const –> unsigned long
- total_residue(self: pyrosetta.rosetta.core.pose.Pose) int ¶
Returns the number of residues in the pose conformation
This wrapper for size() is provided for mostly historical reasons.
- example(s):
pose.total_residue()
- See also:
Pose Pose.size Pose.sequence
C++: core::pose::Pose::total_residue() const –> unsigned long
- transfer_constraint_set(self: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: core::pose::Pose::transfer_constraint_set(const class core::pose::Pose &) –> void
- translate(t)¶
Apply a translation to all of the coordinates in a Pose.
- Args:
p (Pose): The Pose instance to manipulate t (np.array): A vector to add to the Pose coordinates
- update_actcoord(self: pyrosetta.rosetta.core.pose.Pose, resid: int) None ¶
Updates the action coordinates for pose residue <resid>
C++: core::pose::Pose::update_actcoord(unsigned long) –> void
- update_actcoords(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Called by PairEPotential to update the action coordinates for all residues
C++: core::pose::Pose::update_actcoords() –> void
- update_orbital_coords(self: pyrosetta.rosetta.core.pose.Pose, resid: int) None ¶
C++: core::pose::Pose::update_orbital_coords(unsigned long) –> void
- update_pose_chains_from_pdb_chains(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Updates the pose chain IDs to match the pdb chain letters.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
This does not reorder the pose, it just starts a new (chain number) chain each time the chain letters change.
C++: core::pose::Pose::update_pose_chains_from_pdb_chains() –> void
- update_residue_neighbors(self: pyrosetta.rosetta.core.pose.Pose) None ¶
Updates neighbor links in the pose Energies object
C++: core::pose::Pose::update_residue_neighbors() –> void
- virtual_to_real(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
Switch residues from VIRTUAL to a REAL residue
- example(s):
pose.virtual_to_real(3)
- See also:
Pose ResidueType
C++: core::pose::Pose::virtual_to_real(unsigned long) –> void
- xyz(*args, **kwargs)¶
Overloaded function.
xyz(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.numeric.xyzVector_double_t
Returns the location (xyz) of pose AtomID <id>
- example(s):
atom = AtomID(1,1) pose.xyz(atom)
- See also:
Pose Pose.residue AtomID Residue Residue.xyz
C++: core::pose::Pose::xyz(const class core::id::AtomID &) const –> const class numeric::xyzVector<double> &
xyz(self: pyrosetta.rosetta.core.pose.Pose, id: pyrosetta.rosetta.core.id.NamedAtomID) -> pyrosetta.rosetta.numeric.xyzVector_double_t
Returns the location (xyz) of pose NamedAtomID <id>
Tutorial soon… See also:
Pose Pose.residue NamedAtomID Residue Residue.xyz
C++: core::pose::Pose::xyz(const class core::id::NamedAtomID &) const –> const class numeric::xyzVector<double> &
- zero_reference_pose_mapping_at_seqpos(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
Find all mappings in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal).
If there is no ReferencePose object, do nothing.
C++: core::pose::Pose::zero_reference_pose_mapping_at_seqpos(const unsigned long) –> void
- zeta(self: pyrosetta.rosetta.core.pose.Pose, seqpos: int) float ¶
Returns the zeta torsion angle of residue <seqpos>
assumes the residue is an nucleic acid
- example(s):
pose.zeta(6)
- See also:
Pose Pose.residue Pose.set_zeta Residue
C++: core::pose::Pose::zeta(const unsigned long) const –> double
- class pyrosetta.rosetta.core.pose.PoseCoordPickMode¶
Bases:
pybind11_object
Members:
PoseCoordPickMode_NBR
PoseCoordPickMode_CA
PoseCoordPickMode_CB
PoseCoordPickMode_CB_else_CA
PoseCoordPickMode_BB
PoseCoordPickMode_N_CA_C
PoseCoordPickMode_N_CA_C_CB
PoseCoordPickMode_N_C_O
PoseCoordPickMode_BNP
PoseCoordPickMode_HVY
PoseCoordPickMode_HVY_IF_NP
PoseCoordPickMode_ALL
PoseCoordPickMode_CBorCA
PoseCoordPickMode_NUL
- PoseCoordPickMode_ALL = <PoseCoordPickMode.PoseCoordPickMode_ALL: 11>¶
- PoseCoordPickMode_BB = <PoseCoordPickMode.PoseCoordPickMode_BB: 4>¶
- PoseCoordPickMode_BNP = <PoseCoordPickMode.PoseCoordPickMode_BNP: 8>¶
- PoseCoordPickMode_CA = <PoseCoordPickMode.PoseCoordPickMode_CA: 1>¶
- PoseCoordPickMode_CB = <PoseCoordPickMode.PoseCoordPickMode_CB: 2>¶
- PoseCoordPickMode_CB_else_CA = <PoseCoordPickMode.PoseCoordPickMode_CB_else_CA: 3>¶
- PoseCoordPickMode_CBorCA = <PoseCoordPickMode.PoseCoordPickMode_CBorCA: 12>¶
- PoseCoordPickMode_HVY = <PoseCoordPickMode.PoseCoordPickMode_HVY: 9>¶
- PoseCoordPickMode_HVY_IF_NP = <PoseCoordPickMode.PoseCoordPickMode_HVY_IF_NP: 10>¶
- PoseCoordPickMode_NBR = <PoseCoordPickMode.PoseCoordPickMode_NBR: 0>¶
- PoseCoordPickMode_NUL = <PoseCoordPickMode.PoseCoordPickMode_NUL: 13>¶
- PoseCoordPickMode_N_CA_C = <PoseCoordPickMode.PoseCoordPickMode_N_CA_C: 5>¶
- PoseCoordPickMode_N_CA_C_CB = <PoseCoordPickMode.PoseCoordPickMode_N_CA_C_CB: 6>¶
- PoseCoordPickMode_N_C_O = <PoseCoordPickMode.PoseCoordPickMode_N_C_O: 7>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.pose.RID_FileSource¶
Bases:
RID_Source
Representation of a file input support A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages
- assign(self: pyrosetta.rosetta.core.pose.RID_FileSource, : pyrosetta.rosetta.core.pose.RID_FileSource) pyrosetta.rosetta.core.pose.RID_FileSource ¶
C++: core::pose::RID_FileSource::operator=(const class core::pose::RID_FileSource &) –> class core::pose::RID_FileSource &
- fname(self: pyrosetta.rosetta.core.pose.RID_FileSource) str ¶
C++: core::pose::RID_FileSource::fname() const –> const std::string &
- linenum(self: pyrosetta.rosetta.core.pose.RID_FileSource) int ¶
C++: core::pose::RID_FileSource::linenum() const –> unsigned long
- source_string(self: pyrosetta.rosetta.core.pose.RID_FileSource) str ¶
C++: core::pose::RID_FileSource::source_string() const –> std::string
- class pyrosetta.rosetta.core.pose.RID_Source¶
Bases:
pybind11_object
A class to hold information about where a ResidueIndexDescriptor comes from, to allow for better error messages
- assign(self: pyrosetta.rosetta.core.pose.RID_Source, : pyrosetta.rosetta.core.pose.RID_Source) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::RID_Source::operator=(const class core::pose::RID_Source &) –> class core::pose::RID_Source &
- source_string(self: pyrosetta.rosetta.core.pose.RID_Source) str ¶
C++: core::pose::RID_Source::source_string() const –> std::string
- class pyrosetta.rosetta.core.pose.ResidueIndexDescription¶
Bases:
pybind11_object
a class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another.
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription, : pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.ResidueIndexDescription ¶
C++: core::pose::ResidueIndexDescription::operator=(const class core::pose::ResidueIndexDescription &) –> class core::pose::ResidueIndexDescription &
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
- Turn the internal data into a pose index (in the range from 1 to total residue)
If it can’t be converted, throw an exception, unless no_error is true. If no_error is true, return 0 or a residue number outside the pose range.
C++: core::pose::ResidueIndexDescription::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd¶
Bases:
ResidueIndexDescription
a class which represents the last residue in the Pose
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd, : pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd) pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd ¶
C++: core::pose::ResidueIndexDescriptionChainEnd::operator=(const class core::pose::ResidueIndexDescriptionChainEnd &) –> class core::pose::ResidueIndexDescriptionChainEnd &
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionChainEnd, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
C++: core::pose::ResidueIndexDescriptionChainEnd::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue¶
Bases:
ResidueIndexDescription
a class which represents the last residue in the Pose
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue, : pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue) pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue ¶
C++: core::pose::ResidueIndexDescriptionLastResidue::operator=(const class core::pose::ResidueIndexDescriptionLastResidue &) –> class core::pose::ResidueIndexDescriptionLastResidue &
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionLastResidue, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
C++: core::pose::ResidueIndexDescriptionLastResidue::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB¶
Bases:
ResidueIndexDescription
a class which represents a residue index as a PDB information (chain, resindex, insertion code)
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB, : pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB) pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB ¶
C++: core::pose::ResidueIndexDescriptionPDB::operator=(const class core::pose::ResidueIndexDescriptionPDB &) –> class core::pose::ResidueIndexDescriptionPDB &
- chain(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB) str ¶
C++: core::pose::ResidueIndexDescriptionPDB::chain() const –> char
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- insertion_code(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB) str ¶
C++: core::pose::ResidueIndexDescriptionPDB::insertion_code() const –> char
- resindex(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB) int ¶
C++: core::pose::ResidueIndexDescriptionPDB::resindex() const –> int
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
C++: core::pose::ResidueIndexDescriptionPDB::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum¶
Bases:
ResidueIndexDescription
a class which represents a residue index as a literal, Rosetta/Pose numbered integer
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum, : pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum) pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum ¶
C++: core::pose::ResidueIndexDescriptionPoseNum::operator=(const class core::pose::ResidueIndexDescriptionPoseNum &) –> class core::pose::ResidueIndexDescriptionPoseNum &
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- pose_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum) int ¶
C++: core::pose::ResidueIndexDescriptionPoseNum::pose_index() const –> unsigned long
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
C++: core::pose::ResidueIndexDescriptionPoseNum::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose¶
Bases:
ResidueIndexDescription
a class which represents a residue index as a reference-pose enabled information.
- assign(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose, : pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose) pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose ¶
C++: core::pose::ResidueIndexDescriptionRefPose::operator=(const class core::pose::ResidueIndexDescriptionRefPose &) –> class core::pose::ResidueIndexDescriptionRefPose &
- get_source(self: pyrosetta.rosetta.core.pose.ResidueIndexDescription) pyrosetta.rosetta.core.pose.RID_Source ¶
C++: core::pose::ResidueIndexDescription::get_source() const –> class std::shared_ptr<const class core::pose::RID_Source>
- refpose_name(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose) str ¶
C++: core::pose::ResidueIndexDescriptionRefPose::refpose_name() const –> const std::string &
- refpose_number(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose) int ¶
C++: core::pose::ResidueIndexDescriptionRefPose::refpose_number() const –> unsigned long
- refpose_offset(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose) int ¶
C++: core::pose::ResidueIndexDescriptionRefPose::refpose_offset() const –> long
- resolve_index(*args, **kwargs)¶
Overloaded function.
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose, p: pyrosetta.rosetta.core.pose.Pose) -> int
resolve_index(self: pyrosetta.rosetta.core.pose.ResidueIndexDescriptionRefPose, p: pyrosetta.rosetta.core.pose.Pose, no_error: bool) -> int
C++: core::pose::ResidueIndexDescriptionRefPose::resolve_index(const class core::pose::Pose &, bool) const –> unsigned long
- class pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord¶
Bases:
pybind11_object
info about an atom in a unrecognized res (not in pose, but we want to remember it)
- assign(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord, : pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord ¶
C++: core::pose::UnrecognizedAtomRecord::operator=(const class core::pose::UnrecognizedAtomRecord &) –> class core::pose::UnrecognizedAtomRecord &
- atom_name(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) str ¶
C++: core::pose::UnrecognizedAtomRecord::atom_name() const –> const std::string &
- coords(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: core::pose::UnrecognizedAtomRecord::coords() const –> const class numeric::xyzVector<double> &
- res_name(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) str ¶
C++: core::pose::UnrecognizedAtomRecord::res_name() const –> const std::string &
- res_num(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) int ¶
C++: core::pose::UnrecognizedAtomRecord::res_num() const –> const unsigned long &
- temp(self: pyrosetta.rosetta.core.pose.UnrecognizedAtomRecord) float ¶
C++: core::pose::UnrecognizedAtomRecord::temp() const –> const double &
- pyrosetta.rosetta.core.pose.addVirtualResAsRoot(*args, **kwargs)¶
Overloaded function.
addVirtualResAsRoot(pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Adds a VRT res to the end of the pose at the center of mass.
Reroots the structure on this res.
C++: core::pose::addVirtualResAsRoot(class core::pose::Pose &) –> void
addVirtualResAsRoot(xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None
- Adds a virtual residue to the end of the pose at the specified location.
Roots the structure on this residue.
C++: core::pose::addVirtualResAsRoot(const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.add_comment(pose: pyrosetta.rosetta.core.pose.Pose, key: str, val: str) None ¶
- Adds a key-value pair to the STRING_MAP in the Pose DataCache. If
there is no STRING_MAP in the DataCache, one is created.
C++: core::pose::add_comment(class core::pose::Pose &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.add_custom_variant_type_to_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, variant_type: str, seqpos: int) None ¶
C++: core::pose::add_custom_variant_type_to_pose_residue(class core::pose::Pose &, const std::string &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.add_lower_terminus_type_to_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
C++: core::pose::add_lower_terminus_type_to_pose_residue(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.add_score_line_string(pose: pyrosetta.rosetta.core.pose.Pose, key: str, val: str) None ¶
Sets a PDB-style REMARK entry in the Pose.
This is different from a comment in its interpretation by the silent-file output machinery. A REMARK is written on its own separate line in the output silent-file, while a comment is written as part of the Pose SCORE: lines.
C++: core::pose::add_score_line_string(class core::pose::Pose &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.add_upper_terminus_type_to_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
C++: core::pose::add_upper_terminus_type_to_pose_residue(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.add_variant_type_to_pose_residue(*args, **kwargs)¶
Overloaded function.
add_variant_type_to_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, variant_type: pyrosetta.rosetta.core.chemical.VariantType, seqpos: int) -> None
Construct a variant of an existing pose residue.
C++: core::pose::add_variant_type_to_pose_residue(class core::pose::Pose &, const enum core::chemical::VariantType, const unsigned long) –> void
add_variant_type_to_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, variant_type: str, seqpos: int) -> None
C++: core::pose::add_variant_type_to_pose_residue(class core::pose::Pose &, const std::string &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.add_variant_type_to_residue(old_rsd: pyrosetta.rosetta.core.conformation.Residue, variant_type: pyrosetta.rosetta.core.chemical.VariantType, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.Residue ¶
Construct a variant of an existing residue.
C++: core::pose::add_variant_type_to_residue(const class core::conformation::Residue &, const enum core::chemical::VariantType, const class core::pose::Pose &) –> class std::shared_ptr<class core::conformation::Residue>
- pyrosetta.rosetta.core.pose.all_atom_center(pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Get the center of the indicated residues
This computes an equally-weighted, all-atom (including virtuals and hydrogens) center
C++: core::pose::all_atom_center(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class numeric::xyzVector<double>
- pyrosetta.rosetta.core.pose.annotated_to_oneletter_sequence(annotated_seq: str) str ¶
- Returns the oneletter_sequence that corresponds to the given
annotated sequence.
C++: core::pose::annotated_to_oneletter_sequence(const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.append_pose_to_pose(*args, **kwargs)¶
Overloaded function.
append_pose_to_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) -> None
append_pose_to_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, new_chain: bool) -> None
Append residues of pose2 to pose1.
C++: core::pose::append_pose_to_pose(class core::pose::Pose &, const class core::pose::Pose &, bool) –> void
- pyrosetta.rosetta.core.pose.append_pose_with_glycan_residues(*args, **kwargs)¶
Overloaded function.
append_pose_with_glycan_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) -> None
append_pose_with_glycan_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, resnum_to_be_appended: int) -> None
Append an empty or current Pose with saccharide residues, building branches as necessary.
C++: core::pose::append_pose_with_glycan_residues(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >, unsigned long) –> void
- pyrosetta.rosetta.core.pose.append_subpose_to_pose(*args, **kwargs)¶
Overloaded function.
append_subpose_to_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int) -> None
append_subpose_to_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int, new_chain: bool) -> None
Append specified residues of pose2 to pose1.
C++: core::pose::append_subpose_to_pose(class core::pose::Pose &, const class core::pose::Pose &, unsigned long, unsigned long, bool) –> void
- pyrosetta.rosetta.core.pose.atom_id_to_named_atom_id(atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.NamedAtomID ¶
C++: core::pose::atom_id_to_named_atom_id(const class core::id::AtomID &, const class core::pose::Pose &) –> class core::id::NamedAtomID
- pyrosetta.rosetta.core.pose.attributes_for_get_resnum_selector(*args, **kwargs)¶
Overloaded function.
attributes_for_get_resnum_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, xsd: utility::tag::XMLSchemaDefinition) -> None
attributes_for_get_resnum_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, xsd: utility::tag::XMLSchemaDefinition, tag: str) -> None
attributes_for_get_resnum_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, xsd: utility::tag::XMLSchemaDefinition, tag: str, description: str) -> None
Companion function for get_resnum_selector
Appends relevant XMLSchemaAttributes to the AttributeList; needs the xsd because it adds restricted types
C++: core::pose::attributes_for_get_resnum_selector(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.attributes_for_get_resnum_string(*args, **kwargs)¶
Overloaded function.
attributes_for_get_resnum_string(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_get_resnum_string(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, prefix: str) -> None
Companion function for get_resnum_string
Appends relevant XMLSchemaAttributes to the AttributeList
C++: core::pose::attributes_for_get_resnum_string(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.attributes_for_parse_resnum(*args, **kwargs)¶
Overloaded function.
attributes_for_parse_resnum(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, att_name: str) -> None
attributes_for_parse_resnum(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, att_name: str, description: str) -> None
Companion function for parse_resnum
Appends relevant XMLSchemaAttributes to the AttributeList
C++: core::pose::attributes_for_parse_resnum(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.attributes_for_saved_reference_pose(*args, **kwargs)¶
Overloaded function.
attributes_for_saved_reference_pose(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_saved_reference_pose(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, attribute_name: str) -> None
- convenience function to access pointers to poses that will be stored
in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable
C++: core::pose::attributes_for_saved_reference_pose(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.attributes_for_saved_reference_pose_w_description(*args, **kwargs)¶
Overloaded function.
attributes_for_saved_reference_pose_w_description(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str) -> None
attributes_for_saved_reference_pose_w_description(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, description: str, attribute_name: str) -> None
- convenience function to access pointers to poses that will be stored
in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable
C++: core::pose::attributes_for_saved_reference_pose_w_description(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.canonical_atom_count(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
count the number of canonical amino acid atoms in the pose
C++: core::pose::canonical_atom_count(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.canonical_residue_count(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
count the number of canonical residues in the pose
C++: core::pose::canonical_residue_count(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.center_of_mass(*args, **kwargs)¶
Overloaded function.
center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t
Get the center of the indicated residues
WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)
C++: core::pose::center_of_mass(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class numeric::xyzVector<double>
center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose, start: int, stop: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t
Get the center of the indicated residues
WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)
C++: core::pose::center_of_mass(const class core::pose::Pose &, const int, const int) –> class numeric::xyzVector<double>
- pyrosetta.rosetta.core.pose.chain_end_res(*args, **kwargs)¶
Overloaded function.
chain_end_res(pose: pyrosetta.rosetta.core.pose.Pose, chain: int) -> int
compute last residue number of a chain
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- /
This is mostly indirection to Conformation::chain_end(), but with better error checking
C++: core::pose::chain_end_res(const class core::pose::Pose &, const unsigned long) –> unsigned long
chain_end_res(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
compute last residue numbers of all chains
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
- /
This is mostly an indirection to Conformation::chain_endings(), though with better handling of the last residue
C++: core::pose::chain_end_res(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.clearPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str) None ¶
Clear a specific data type from the arbitrary data cache in the pose.
C++: core::pose::clearPoseExtraScore(class core::pose::Pose &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.clearPoseExtraScores(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Clear ALL PoseExtraScores
C++: core::pose::clearPoseExtraScores(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.compare_atom_coordinates(*args, **kwargs)¶
Overloaded function.
compare_atom_coordinates(lhs: pyrosetta.rosetta.core.pose.Pose, rhs: pyrosetta.rosetta.core.pose.Pose) -> bool
compare_atom_coordinates(lhs: pyrosetta.rosetta.core.pose.Pose, rhs: pyrosetta.rosetta.core.pose.Pose, n_dec_places: int) -> bool
this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.
Steven Lewis smlewi.com
one pose to compare
one pose to compare
number of decimal places to compare for the coordinates (remember == doesn’t work for float); defaults to 3 which is PDB accuracy
C++: core::pose::compare_atom_coordinates(const class core::pose::Pose &, const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.compare_binary_protein_silent_struct(lhs: pyrosetta.rosetta.core.pose.Pose, rhs: pyrosetta.rosetta.core.pose.Pose) bool ¶
this function compares poses for equality up to the information stored in the binary protein silent struct format.
C++: core::pose::compare_binary_protein_silent_struct(const class core::pose::Pose &, const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.core.pose.compute_unique_chains(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool ¶
Compute uniq chains in a complex, based on sequence identity
- Returns a vector of pose length with true/false of uniq chain
true is unique, false is not
C++: core::pose::compute_unique_chains(class core::pose::Pose &) –> class utility::vector1<bool, class std::allocator<bool> >
- pyrosetta.rosetta.core.pose.conf2pdb_chain(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_char ¶
get Conformation chain number -> PDBInfo chain mapping
- Any chains whose PDBInfo chain records are marked entirely as
PDBInfo::empty_record() will be mapped to that character.
- the mapping if PDBInfo available and chains appear consistent,
otherwise prints a warning and returns a default mapping (1=A, 2=B_
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::conf2pdb_chain(const class core::pose::Pose &) –> class std::map<unsigned long, char, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, char> > >
- pyrosetta.rosetta.core.pose.convert_from_std_map(atom_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t ¶
C++: core::pose::convert_from_std_map(const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, const class core::pose::Pose &) –> class core::id::AtomID_Map<class core::id::AtomID>
- pyrosetta.rosetta.core.pose.correctly_add_2prime_connection_variants(pose: pyrosetta.rosetta.core.pose.Pose, twoprime_res: int, next_res: int) None ¶
C++: core::pose::correctly_add_2prime_connection_variants(class core::pose::Pose &, const unsigned long, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.correctly_add_cutpoint_variants(*args, **kwargs)¶
Overloaded function.
correctly_add_cutpoint_variants(pose: pyrosetta.rosetta.core.pose.Pose) -> None
Add cutpoint variants to all residues annotated as cutpoints in the FoldTree in the Pose.
C++: core::pose::correctly_add_cutpoint_variants(class core::pose::Pose &) –> void
correctly_add_cutpoint_variants(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int) -> None
correctly_add_cutpoint_variants(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int, check_fold_tree: bool) -> None
correctly_add_cutpoint_variants(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int, check_fold_tree: bool, next_res_in: int) -> None
- Add CUTPOINT_LOWER and CUTPOINT_UPPER types to two residues, remove incompatible types, and declare
a chemical bond between them.
The pose to modify.
The index of the CUTPOINT_LOWER residue.
If true, a check is performed to confirm that the residues in question represent a cutpoint in the foldtree in the pose.
The index of the CUTPOINT_UPPER residue. If not provided, or if set to 0, this defaults to the cutpoint_res + 1 residue. Must be specified for cyclic geometry.
C++: core::pose::correctly_add_cutpoint_variants(class core::pose::Pose &, const unsigned long, const bool, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.correctly_remove_variants_incompatible_with_lower_cutpoint_variant(pose: pyrosetta.rosetta.core.pose.Pose, res_index: int) None ¶
Remove variant types incompatible with CUTPOINT_LOWER from a position in a pose.
Vikram K. Mulligan (vmullig.edu).
The pose on which to operate.
The index of the residue on which to operate.
C++: core::pose::correctly_remove_variants_incompatible_with_lower_cutpoint_variant(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.correctly_remove_variants_incompatible_with_upper_cutpoint_variant(pose: pyrosetta.rosetta.core.pose.Pose, res_index: int) None ¶
Remove variant types incompatible with CUTPOINT_UPPER from a position in a pose.
Vikram K. Mulligan (vmullig.edu).
The pose on which to operate.
The index of the residue on which to operate.
C++: core::pose::correctly_remove_variants_incompatible_with_upper_cutpoint_variant(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.create_subpose(src: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, f: pyrosetta.rosetta.core.kinematics.FoldTree, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Create a subpose of the src pose. PDBInfo is set as NULL.
C++: core::pose::create_subpose(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::kinematics::FoldTree &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.declare_cutpoint_chemical_bond(*args, **kwargs)¶
Overloaded function.
declare_cutpoint_chemical_bond(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int) -> None
declare_cutpoint_chemical_bond(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int, next_res_in: int) -> None
Create a chemical bond from lower to upper residue across CUTPOINT_LOWER/CUTPOINT_UPPER.
This will prevent steric repulsion.
The pose to modify.
The index of the CUTPOINT_LOWER residue.
The index of the CUTPOINT_UPPER residue. If not provided, or if set to 0, this defaults to the cutpoint_res + 1 residue. Must be specified for cyclic geometry.
C++: core::pose::declare_cutpoint_chemical_bond(class core::pose::Pose &, const unsigned long, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.deep_copy(source: core::pose::Pose) core::pose::Pose ¶
- Note that this does a clone(), which isn’t actually a full deep copy (which would be detached_copy())
This may or may not have implications for multithreaded use.
C++: core::pose::deep_copy(const class core::pose::Pose &) –> class std::shared_ptr<class core::pose::Pose>
- pyrosetta.rosetta.core.pose.definite_terminal_root(*args, **kwargs)¶
Overloaded function.
definite_terminal_root(cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, nres: int, i: int) -> bool
C++: core::pose::definite_terminal_root(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const unsigned long) –> bool
definite_terminal_root(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> bool
C++: core::pose::definite_terminal_root(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.delete_comment(pose: pyrosetta.rosetta.core.pose.Pose, key: str) None ¶
- Deletes the entry in the STRING_MAP associated with the
given key.
C++: core::pose::delete_comment(class core::pose::Pose &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.disulfide_pairs_from_sfr(pose: pyrosetta.rosetta.core.pose.Pose, fd: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t ¶
extract disulfide pairing from SFR
C++: core::pose::disulfide_pairs_from_sfr(const class core::pose::Pose &, const class core::io::StructFileRep &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >
- pyrosetta.rosetta.core.pose.dump_comment_pdb(file_name: str, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
dumps pose+ comments to pdb file
C++: core::pose::dump_comment_pdb(const std::string &, const class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.effective_lower_terminus_based_on_working_res(i: int, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long) bool ¶
C++: core::pose::effective_lower_terminus_based_on_working_res(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool
- pyrosetta.rosetta.core.pose.effective_upper_terminus_based_on_working_res(i: int, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, nres_full: int) bool ¶
C++: core::pose::effective_upper_terminus_based_on_working_res(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.energy_from_pose(*args, **kwargs)¶
Overloaded function.
energy_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, sc_type: pyrosetta.rosetta.core.scoring.ScoreType) -> float
C++: core::pose::energy_from_pose(const class core::pose::Pose &, const enum core::scoring::ScoreType &) –> double
energy_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, sc_type: str) -> float
C++: core::pose::energy_from_pose(const class core::pose::Pose &, const std::string &) –> double
- pyrosetta.rosetta.core.pose.extract_tag_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) str ¶
Returns a string giving the pose’s tag if there is such a thing or “UnknownTag” otherwise.
C++: core::pose::extract_tag_from_pose(class core::pose::Pose &) –> std::string
- pyrosetta.rosetta.core.pose.fix_pdbinfo_damaged_by_insertion(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Repair pdbinfo of inserted residues that may have blank chain and zero
seqpos. Assumes insertions only occur _after_ a residue.
C++: core::pose::fix_pdbinfo_damaged_by_insertion(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.fix_up_residue_type_variants(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: core::pose::fix_up_residue_type_variants(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.fix_up_residue_type_variants_at_strand_beginning(pose: pyrosetta.rosetta.core.pose.Pose, res: int) None ¶
C++: core::pose::fix_up_residue_type_variants_at_strand_beginning(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.fix_up_residue_type_variants_at_strand_end(pose: pyrosetta.rosetta.core.pose.Pose, res: int) None ¶
C++: core::pose::fix_up_residue_type_variants_at_strand_end(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.getPoseExtraFloatScores(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_float ¶
C++: core::pose::getPoseExtraFloatScores(const class core::pose::Pose &) –> class std::map<std::string, float, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, float> > >
- pyrosetta.rosetta.core.pose.getPoseExtraScore(*args, **kwargs)¶
Overloaded function.
getPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str) -> float
return value is ExtraScore if exist, runtime_assert if it doesn’t exist
C++: core::pose::getPoseExtraScore(const class core::pose::Pose &, const std::string &) –> double
getPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: float) -> bool
return bool is T/F for whether the requested datum exists. “value” is the data, pass-by-ref.
C++: core::pose::getPoseExtraScore(const class core::pose::Pose &, const std::string &, double &) –> bool
getPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: str) -> bool
return bool is T/F for whether the requested datum exists. “value” is the data, pass-by-ref.
C++: core::pose::getPoseExtraScore(const class core::pose::Pose &, const std::string &, std::string &) –> bool
- pyrosetta.rosetta.core.pose.getPoseExtraStringScores(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_std_string ¶
C++: core::pose::getPoseExtraStringScores(const class core::pose::Pose &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >
- pyrosetta.rosetta.core.pose.get_all_comments(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_std_string ¶
- Gets a map< string, string > representing comments about the Pose in
the form of key-value pairs.
C++: core::pose::get_all_comments(const class core::pose::Pose &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >
- pyrosetta.rosetta.core.pose.get_all_score_line_strings(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_std_string ¶
- Gets a map< string, string > representing score_line_strings about the Pose in
the form of key-value pairs.
C++: core::pose::get_all_score_line_strings(const class core::pose::Pose &) –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >
- pyrosetta.rosetta.core.pose.get_bb_torsion(torsion_id: int, pose: pyrosetta.rosetta.core.pose.Pose, sequence_position: int) float ¶
- Get a particular backbone torsion, phi, psi, omega (see core::types)
Works with carbohydrates. Think about moving this to pose itself.
C++: core::pose::get_bb_torsion(unsigned long, const class core::pose::Pose &, unsigned long) –> double
- pyrosetta.rosetta.core.pose.get_center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
Get center of mass of a pose.
This computes an equally-weighted, all-(non-virtual)-heavy atom center.
C++: core::pose::get_center_of_mass(const class core::pose::Pose &) –> class numeric::xyzVector<double>
- pyrosetta.rosetta.core.pose.get_chain_from_chain_id(chain_id: int, pose: pyrosetta.rosetta.core.pose.Pose) str ¶
Get the chain letter for the first residue in a given chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
Keep in mind that not all residues with the given chain number will necessarily have the returned chain letter
C++: core::pose::get_chain_from_chain_id(const unsigned long &, const class core::pose::Pose &) –> char
- pyrosetta.rosetta.core.pose.get_chain_from_jump_id(jump_id: int, pose: pyrosetta.rosetta.core.pose.Pose) str ¶
Get the chain letter of the chain built by the given jump.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
Keep in mind that not every residue with the returned chain ID will be downstream of this jump.
C++: core::pose::get_chain_from_jump_id(const unsigned long &, const class core::pose::Pose &) –> char
- pyrosetta.rosetta.core.pose.get_chain_id_from_chain(*args, **kwargs)¶
Overloaded function.
get_chain_id_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
Attempt to get the chain number which correspond to the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
If the chain letter corresponds to more than one chain letter, raise an error
C++: core::pose::get_chain_id_from_chain(const std::string &, const class core::pose::Pose &) –> unsigned long
get_chain_id_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
Attempt to get the chain number which correspond to the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
If the chain letter corresponds to more than one chain letter, raise an error
C++: core::pose::get_chain_id_from_chain(const char &, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_chain_id_from_jump_id(jump_id: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
Get the chain ID of the residue directly built by the given jump.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
Keep in mind that not every residue with the returned chain ID will be downstream of this jump.
C++: core::pose::get_chain_id_from_jump_id(const unsigned long &, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_chain_ids_from_chain(*args, **kwargs)¶
Overloaded function.
get_chain_ids_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all chain numbers for the residues with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned chain numbers are in sorted order
C++: core::pose::get_chain_ids_from_chain(const std::string &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
get_chain_ids_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all chain numbers for the residues with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned chain numbers are in sorted order
C++: core::pose::get_chain_ids_from_chain(const char &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_chain_ids_from_chains(*args, **kwargs)¶
Overloaded function.
get_chain_ids_from_chains(chains: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all chain numbers for the residues with the given chain letters
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned chain numbers are in sorted order
C++: core::pose::get_chain_ids_from_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
get_chain_ids_from_chains(chains: pyrosetta.rosetta.utility.vector1_char, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all chain numbers for the residues with the given chain letters
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned chain numbers are in sorted order
C++: core::pose::get_chain_ids_from_chains(const class utility::vector1<char, class std::allocator<char> > &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_chain_residues(pose: pyrosetta.rosetta.core.pose.Pose, chain_id: int) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t ¶
Get all residues which correspond to the given chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_chain_residues(const class core::pose::Pose &, unsigned long) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >
- pyrosetta.rosetta.core.pose.get_chains(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Get all the chain numbers from conformation
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
This is a rather silly function, as it will just return a vector with entries from 1 to pose->num_chains() (as chains numbers are sequential starting from 1
C++: core::pose::get_chains(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_comment(pose: pyrosetta.rosetta.core.pose.Pose, key: str, val: str) bool ¶
- Attempts to access the entry in the STRING_MAP associated with the
given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified.
C++: core::pose::get_comment(const class core::pose::Pose &, const std::string &, std::string &) –> bool
- pyrosetta.rosetta.core.pose.get_constraints_from_link_records(pose: pyrosetta.rosetta.core.pose.Pose, sfr: pyrosetta.rosetta.core.io.StructFileRep) None ¶
C++: core::pose::get_constraints_from_link_records(class core::pose::Pose &, const class core::io::StructFileRep &) –> void
- pyrosetta.rosetta.core.pose.get_definite_terminal_root(*args, **kwargs)¶
Overloaded function.
get_definite_terminal_root(pose: pyrosetta.rosetta.core.pose.Pose, partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, fixed_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int
get_definite_terminal_root(pose: pyrosetta.rosetta.core.pose.Pose, partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, fixed_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, disallow_cutpoint_closed_upper: bool) -> int
C++: core::pose::get_definite_terminal_root(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> unsigned long
get_definite_terminal_root(pose: pyrosetta.rosetta.core.pose.Pose, partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int
get_definite_terminal_root(pose: pyrosetta.rosetta.core.pose.Pose, partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, disallow_cutpoint_closed_upper: bool) -> int
C++: core::pose::get_definite_terminal_root(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> unsigned long
- pyrosetta.rosetta.core.pose.get_hash_excluding_chain(*args, **kwargs)¶
Overloaded function.
get_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
get_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> int
Get a value representing the position of all the atoms for residues which don’t have the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_hash_excluding_chain(const char &, const class core::pose::Pose &, const std::string &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_hash_from_chain(*args, **kwargs)¶
Overloaded function.
get_hash_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
get_hash_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> int
Get a value representing the position of all the atoms for residues with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_hash_from_chain(const char &, const class core::pose::Pose &, const std::string &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_hash_from_pos(pos: pyrosetta.rosetta.numeric.xyzVector_double_t) int ¶
Utility function for get_hash_from_chain() - get hash for an isolated position.
C++: core::pose::get_hash_from_pos(const class numeric::xyzVector<double> &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_jump_id_from_chain(*args, **kwargs)¶
Overloaded function.
get_jump_id_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
Get the jump number for the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jump here is the jumps which is directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. If there’s more than one jump which builds residues with the given chain letter, return the smallest numbered jump (even if it’s not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain, hard exit.
C++: core::pose::get_jump_id_from_chain(const std::string &, const class core::pose::Pose &) –> unsigned long
get_jump_id_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
Get the jump number for the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jump here is the jumps which is directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. If there’s more than one jump which builds residues with the given chain letter, return the smallest numbered jump (even if it’s not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain, hard exit.
C++: core::pose::get_jump_id_from_chain(const char &, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_jump_id_from_chain_id(chain_id: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
Attempt to get the jump number which correspond to the given chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jump here is the jump which is directly upstream of a residue in the given chain, (i.e. a residue on the given chain number is built directly from the jump) rather than logically upstream. If there’s more than one jump which builds the given chain, return the smallest numbered jump (even if it’s not the jump which best partions the chain on the FoldTree). If no jump directly builds the chain (unlikely), hard exit.
C++: core::pose::get_jump_id_from_chain_id(const unsigned long &, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_jump_ids_from_chain(*args, **kwargs)¶
Overloaded function.
get_jump_ids_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all the jump numbers for the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jumps here are the jumps which are directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. Return all jumps which build residues with the given chain letter. If no jumps directly builds residues with the given chain letters, return an empty vector.
The returned jump numbers are in sorted order
C++: core::pose::get_jump_ids_from_chain(const char &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
get_jump_ids_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Get all the jump numbers for the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jumps here are the jumps which are directly upstream of a residue with a given chain letter, (i.e. a residue with the given chain letter is built directly from the jump) rather than logically upstream. Return all jumps which build residues with the given chain letter. If no jumps directly builds residues with the given chain letters, return an empty vector.
The returned jump numbers are in sorted order
C++: core::pose::get_jump_ids_from_chain(const std::string &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_jump_ids_from_chain_ids(chain_ids: pyrosetta.rosetta.std.set_unsigned_long_t, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
Attempt to get jump IDs which correspond to the given chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The jumps here are the jumps which are directly upstream of a residue in the given chains, (i.e. a residue on the given chain number is built directly from the jump) rather than logically upstream. Return all jumps which build a given chain. If no jumps directly builds the given chains (unlikely), return an empty set.
C++: core::pose::get_jump_ids_from_chain_ids(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const class core::pose::Pose &) –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_pdb2pose_numbering_as_stdmap(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_std_string_unsigned_long ¶
Create std::map from PDBPoseMap
C++: core::pose::get_pdb2pose_numbering_as_stdmap(const class core::pose::Pose &) –> class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >
- pyrosetta.rosetta.core.pose.get_residues_from_chains(pose: pyrosetta.rosetta.core.pose.Pose, chain_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t ¶
Get all residues which correspond to the given chain numbers
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_residues_from_chains(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >
- pyrosetta.rosetta.core.pose.get_resnum_list(str: str, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
returns a resnum list directly from a string
C++: core::pose::get_resnum_list(const std::string &, const class core::pose::Pose &) –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_resnum_list_ordered(str: str, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
returns a resnum list directly from a string, preserving order
C++: core::pose::get_resnum_list_ordered(const std::string &, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_resnum_selector(tag_ptr: pyrosetta.rosetta.utility.tag.Tag, tag: str) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector ¶
- //
Extracts a list of residue numbers from a tag
//
The tag should contain a comma-separated list of numbers, in either
// pdb or rosetta format (
parse_resnum for details)
C++: core::pose::get_resnum_selector(class std::shared_ptr<const class utility::tag::Tag>, const std::string &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>
- pyrosetta.rosetta.core.pose.get_resnum_string(*args, **kwargs)¶
Overloaded function.
get_resnum_string(tag_ptr: pyrosetta.rosetta.utility.tag.Tag) -> str
get_resnum_string(tag_ptr: pyrosetta.rosetta.utility.tag.Tag, prefix: str) -> str
- DEPRECATED - provided for legacy usage only. Don’t use for new code.
Instead, just use a single option which uses the parse_resnum syntax to specify.
Checks for either/both of pdb_num/res_num in the tag, and pulls out the appropriate string
C++: core::pose::get_resnum_string(class std::shared_ptr<const class utility::tag::Tag>, const std::string &) –> std::string
get_resnum_string(tag_ptr: pyrosetta.rosetta.utility.tag.Tag, prefix: str, default_value: str) -> str
- DEPRECATED - provided for legacy usage only. Don’t use for new code.
Instead, just use a single option which uses parse_resnum syntax to specify
Checks for either/both of pdb_num/res_num in the tag, and pulls out the appropriate string
C++: core::pose::get_resnum_string(class std::shared_ptr<const class utility::tag::Tag>, const std::string &, const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.get_resnumber_from_reference_pose(refpose_name: str, refpose_number: int, refpose_offset: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
- Given the name of a ReferencePose object in the pose, a residue number in that reference pose, and a residue offset,
this function returns the Rosetta number of the corresponding residue in the pose. Should throw an error if the ReferencePose doesn’t exist in the pose, or 0 if no corresponding residue exists in the pose.
Vikram K. Mulligan, Baker laboratory (vmullig.edu)
C++: core::pose::get_resnumber_from_reference_pose(const std::string &, const unsigned long, const long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_resnums_for_chain(pose: pyrosetta.rosetta.core.pose.Pose, chain: str) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Get a vector of all residues numbers which are represented by this chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned residue numbers are in sorted order
C++: core::pose::get_resnums_for_chain(const class core::pose::Pose &, char) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_resnums_for_chain_id(pose: pyrosetta.rosetta.core.pose.Pose, chain_id: int) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Get a vector of all residues numbers which are represented by this chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The returned residue numbers are in sorted order
C++: core::pose::get_resnums_for_chain_id(const class core::pose::Pose &, unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.get_restype_for_pose(*args, **kwargs)¶
Overloaded function.
get_restype_for_pose(pose: pyrosetta.rosetta.core.pose.Pose, name: str) -> pyrosetta.rosetta.core.chemical.ResidueType
- Return the residue type in the correct
“mode” (fullatom, centroid …) the pose is in.
C++: core::pose::get_restype_for_pose(const class core::pose::Pose &, const std::string &) –> class std::shared_ptr<const class core::chemical::ResidueType>
get_restype_for_pose(pose: pyrosetta.rosetta.core.pose.Pose, name: str, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.ResidueType
- Return the residue type in the passed mode,
respecting any modification that pose may make.
C++: core::pose::get_restype_for_pose(const class core::pose::Pose &, const std::string &, enum core::chemical::TypeSetMode) –> class std::shared_ptr<const class core::chemical::ResidueType>
- pyrosetta.rosetta.core.pose.get_rsd_type_from_aa(*args, **kwargs)¶
Overloaded function.
get_rsd_type_from_aa(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, my_aa: pyrosetta.rosetta.core.chemical.AA, is_lower_terminus: bool, is_upper_terminus: bool) -> pyrosetta.rosetta.core.chemical.ResidueType
get_rsd_type_from_aa(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, my_aa: pyrosetta.rosetta.core.chemical.AA, is_lower_terminus: bool, is_upper_terminus: bool, metapatches: bool) -> pyrosetta.rosetta.core.chemical.ResidueType
use efficient residue type finder to find simplest residue type with this AA & requested termini.
C++: core::pose::get_rsd_type_from_aa(const class core::chemical::ResidueTypeSet &, const enum core::chemical::AA &, const bool &, const bool &, const bool) –> class std::shared_ptr<const class core::chemical::ResidueType>
- pyrosetta.rosetta.core.pose.get_score_line_string(pose: pyrosetta.rosetta.core.pose.Pose, key: str, val: str) bool ¶
C++: core::pose::get_score_line_string(const class core::pose::Pose &, const std::string &, std::string &) –> bool
- pyrosetta.rosetta.core.pose.get_sequence_len(sequence_in: str) int ¶
Get the real length of a annotated sequence
C++: core::pose::get_sequence_len(const std::string &) –> unsigned long
- pyrosetta.rosetta.core.pose.get_sha1_hash_excluding_chain(*args, **kwargs)¶
Overloaded function.
get_sha1_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> str
get_sha1_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> str
Get a value representing the position of all the atoms for residues which don’t have the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_sha1_hash_excluding_chain(const char &, const class core::pose::Pose &, const std::string &) –> std::string
get_sha1_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> str
get_sha1_hash_excluding_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> str
Get a value representing the position of all the atoms for residues which don’t have the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_sha1_hash_excluding_chain(const std::string &, const class core::pose::Pose &, const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.get_sha1_hash_excluding_chains(*args, **kwargs)¶
Overloaded function.
get_sha1_hash_excluding_chains(chains: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose) -> str
get_sha1_hash_excluding_chains(chains: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> str
Get a value representing the position of all the atoms for residues which don’t have the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_sha1_hash_excluding_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &, const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.get_sha1_hash_from_chain(*args, **kwargs)¶
Overloaded function.
get_sha1_hash_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> str
get_sha1_hash_from_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> str
Get a value representing the position of all the atoms for residues with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_sha1_hash_from_chain(const char &, const class core::pose::Pose &, const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.get_sha1_hash_from_chains(*args, **kwargs)¶
Overloaded function.
get_sha1_hash_from_chains(chains: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose) -> str
get_sha1_hash_from_chains(chains: pyrosetta.rosetta.utility.vector1_std_string, pose: pyrosetta.rosetta.core.pose.Pose, extra_label: str) -> str
Get a value representing the position of all the atoms for residues with the given chain letters
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::get_sha1_hash_from_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &, const std::string &) –> std::string
- pyrosetta.rosetta.core.pose.hasPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str) bool ¶
does this ExtraScore exist?
C++: core::pose::hasPoseExtraScore(const class core::pose::Pose &, const std::string &) –> bool
- pyrosetta.rosetta.core.pose.hasPoseExtraScore_str(pose: pyrosetta.rosetta.core.pose.Pose, name: str) bool ¶
does this (string) ExtraScore exist?
C++: core::pose::hasPoseExtraScore_str(const class core::pose::Pose &, const std::string &) –> bool
- pyrosetta.rosetta.core.pose.has_chain(*args, **kwargs)¶
Overloaded function.
has_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
Does the pose have a residue with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::has_chain(const std::string &, const class core::pose::Pose &) –> bool
has_chain(chain: str, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
Does the pose have a residue with the given chain letter
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::has_chain(const char &, const class core::pose::Pose &) –> bool
has_chain(chain_id: int, pose: pyrosetta.rosetta.core.pose.Pose) -> bool
Does the pose have a residue with the given chain number
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::has_chain(unsigned long, const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.core.pose.initialize_atomid_map(*args, **kwargs)¶
Overloaded function.
initialize_atomid_map(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: core::pose::initialize_atomid_map(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::pose::Pose &) –> void
initialize_atomid_map(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose: pyrosetta.rosetta.core.pose.Pose, value: pyrosetta.rosetta.core.id.AtomID) -> None
C++: core::pose::initialize_atomid_map(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::pose::Pose &, const class core::id::AtomID &) –> void
initialize_atomid_map(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> None
C++: core::pose::initialize_atomid_map(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::conformation::Conformation &) –> void
initialize_atomid_map(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation: pyrosetta.rosetta.core.conformation.Conformation, value: pyrosetta.rosetta.core.id.AtomID) -> None
C++: core::pose::initialize_atomid_map(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::conformation::Conformation &, const class core::id::AtomID &) –> void
- pyrosetta.rosetta.core.pose.initialize_atomid_map_AtomID(*args, **kwargs)¶
Overloaded function.
initialize_atomid_map_AtomID(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: core::pose::initialize_atomid_map_AtomID(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::pose::Pose &) –> void
initialize_atomid_map_AtomID(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose: pyrosetta.rosetta.core.pose.Pose, value: pyrosetta.rosetta.core.id.AtomID) -> None
C++: core::pose::initialize_atomid_map_AtomID(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::pose::Pose &, const class core::id::AtomID &) –> void
initialize_atomid_map_AtomID(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> None
C++: core::pose::initialize_atomid_map_AtomID(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::conformation::Conformation &) –> void
initialize_atomid_map_AtomID(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation: pyrosetta.rosetta.core.conformation.Conformation, value: pyrosetta.rosetta.core.id.AtomID) -> None
C++: core::pose::initialize_atomid_map_AtomID(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::conformation::Conformation &, const class core::id::AtomID &) –> void
- pyrosetta.rosetta.core.pose.initialize_disulfide_bonds(*args, **kwargs)¶
Overloaded function.
initialize_disulfide_bonds(pose: pyrosetta.rosetta.core.pose.Pose) -> None
detect and fix disulfide bonds
C++: core::pose::initialize_disulfide_bonds(class core::pose::Pose &) –> void
initialize_disulfide_bonds(pose: pyrosetta.rosetta.core.pose.Pose, fd: pyrosetta.rosetta.core.io.StructFileRep) -> None
detect and fix disulfide bonds
C++: core::pose::initialize_disulfide_bonds(class core::pose::Pose &, const class core::io::StructFileRep &) –> void
- pyrosetta.rosetta.core.pose.is_atom_axial_or_equatorial_to_ring(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, query_atom: int, ring_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.core.chemical.rings.AxEqDesignation ¶
Is the query atom in this pose residue axial or equatorial to the given ring or neither?
C++: core::pose::is_atom_axial_or_equatorial_to_ring(const class core::pose::Pose &, unsigned long, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> enum core::chemical::rings::AxEqDesignation
- pyrosetta.rosetta.core.pose.is_ideal_pose(pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if the <pose> geometry is ideal
The Pose to check.
- true if all pose positions have ideal bond lengths and angles
up to some very small epsilon
C++: core::pose::is_ideal_pose(const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.core.pose.is_ideal_position(seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
Returns true if the <pose> geometry is ideal in position <seqpos>
The Pose to check.
- true if position seqpos has ideal bond lengths and angles
up to some very small epsilon
C++: core::pose::is_ideal_position(unsigned long, const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.core.pose.is_lower_terminus(pose: pyrosetta.rosetta.core.pose.Pose, resid: int) bool ¶
checks to see if this is a lower chain ending more intelligently than just checking residue variants
C++: core::pose::is_lower_terminus(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.is_position_conserved_residue(pose: pyrosetta.rosetta.core.pose.Pose, residue: int) bool ¶
- Returns true if <residue> is positionally conserved, false otherwise
Based on the POSITION_CONSERVED_RESIDUES annotation stored in the Pose DataCache
C++: core::pose::is_position_conserved_residue(const class core::pose::Pose &, unsigned long) –> bool
- pyrosetta.rosetta.core.pose.is_referencepose_number(str: str, refpose_string: str, refpose_resnumber: int, refpose_offset: int) bool ¶
Is a string of the format “refpose(<refposename>,<refposenumber>)” or “refpose(<refposename>,<refposenumber>)+/-<number>”?
If this successfully determines that this is a string of this format, it populates the refpose_string, refpose_resnumber,
and refpose_offset variables with the name of the ReferencePose, the number of the residue in the reference pose, and the +/- offset number parsed from this string.
Vikram K. Mulligan, Baker laboratory (vmullig.edu)
C++: core::pose::is_referencepose_number(const std::string &, std::string &, unsigned long &, long &) –> bool
- pyrosetta.rosetta.core.pose.is_upper_terminus(pose: pyrosetta.rosetta.core.pose.Pose, resid: int) bool ¶
checks to see if this is a lower chain ending more intelligently than just checking residue variants
C++: core::pose::is_upper_terminus(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.jumps_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, jumps: pyrosetta.rosetta.std.set_int_t) None ¶
- Retrieves jump information from <pose>, storing the result in <jumps>.
Jumps are keyed by their jump id.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::jumps_from_pose(const class core::pose::Pose &, class std::set<int, struct std::less<int>, class std::allocator<int> > &) –> void
- pyrosetta.rosetta.core.pose.just_modeling_RNA(sequence: str) bool ¶
C++: core::pose::just_modeling_RNA(const std::string &) –> bool
- pyrosetta.rosetta.core.pose.make_atom_map(p: pyrosetta.rosetta.core.pose.Pose, m: pyrosetta.rosetta.core.pose.PoseCoordPickMode) pyrosetta.rosetta.core.id.AtomID_Map_double_t ¶
C++: core::pose::make_atom_map(const class core::pose::Pose &, enum core::pose::PoseCoordPickMode) –> class core::id::AtomID_Map<double>
- pyrosetta.rosetta.core.pose.make_pose_from_saccharide_sequence(*args, **kwargs)¶
Overloaded function.
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool) -> None
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool, idealize_linkages: bool) -> None
- Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet
<residue_set> and store it in <pose>.
C++: core::pose::make_pose_from_saccharide_sequence(class core::pose::Pose &, const std::string &, const class core::chemical::ResidueTypeSet &, const bool, const bool) –> void
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str) -> None
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str) -> None
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str, auto_termini: bool) -> None
make_pose_from_saccharide_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str, auto_termini: bool, idealize_linkages: bool) -> None
- Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name
<type_set_name> and store it in <pose>.
C++: core::pose::make_pose_from_saccharide_sequence(class core::pose::Pose &, const std::string &, const std::string &, const bool, const bool) –> void
- pyrosetta.rosetta.core.pose.make_pose_from_sequence(*args, **kwargs)¶
Overloaded function.
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, requested_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, requested_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, auto_termini: bool) -> None
- Creates a Pose from the annotated protein sequence <sequence>
with ResidueTypeSet <residue_set> and stores it in <pose>
- : any existing data in <pose> is cleared, auto_termini
mark position 1, last_residue with lower, upper termini; default true
- example(s):
make_pose_from_sequence(pose,”THANKSEVAN”,core::chemical::FA_STANDARD)
- See also:
Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence
C++: core::pose::make_pose_from_sequence(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >, const bool) –> void
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool, metapatches: bool) -> None
C++: core::pose::make_pose_from_sequence(class core::pose::Pose &, const std::string &, const class core::chemical::ResidueTypeSet &, const bool, const bool) –> void
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool, metapatches: bool) -> None
C++: core::pose::make_pose_from_sequence(class core::pose::Pose &, const std::string &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, const bool, const bool) –> void
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str, auto_termini: bool) -> None
make_pose_from_sequence(pose: pyrosetta.rosetta.core.pose.Pose, sequence: str, type_set_name: str, auto_termini: bool, metapatches: bool) -> None
- Creates a Pose from the annotated protein sequence <sequence>
with the desired <type_set_name> and stores it in <pose>
- : any existing data in <pose> is cleared, auto_termini
mark position 1, last_residue with lower, upper termini; default true
C++: core::pose::make_pose_from_sequence(class core::pose::Pose &, const std::string &, const std::string &, const bool, const bool) –> void
- pyrosetta.rosetta.core.pose.make_rid_posenum(resnum: int) pyrosetta.rosetta.core.pose.ResidueIndexDescription ¶
Convenience function for converting a Size (Pose numbered) into a ResidueIndexDescription
C++: core::pose::make_rid_posenum(unsigned long) –> class std::shared_ptr<const class core::pose::ResidueIndexDescription>
- pyrosetta.rosetta.core.pose.mass(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: core::pose::mass(unsigned long, const unsigned long, const class core::pose::Pose &) –> double
- pyrosetta.rosetta.core.pose.named_atom_id_to_atom_id(*args, **kwargs)¶
Overloaded function.
named_atom_id_to_atom_id(named_atom_id: pyrosetta.rosetta.core.id.NamedAtomID, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.id.AtomID
named_atom_id_to_atom_id(named_atom_id: pyrosetta.rosetta.core.id.NamedAtomID, pose: pyrosetta.rosetta.core.pose.Pose, raise_exception: bool) -> pyrosetta.rosetta.core.id.AtomID
C++: core::pose::named_atom_id_to_atom_id(const class core::id::NamedAtomID &, const class core::pose::Pose &, bool) –> class core::id::AtomID
- pyrosetta.rosetta.core.pose.named_stub_id_to_stub_id(named_stub_id: pyrosetta.rosetta.core.id.NamedStubID, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.StubID ¶
C++: core::pose::named_stub_id_to_stub_id(const class core::id::NamedStubID &, const class core::pose::Pose &) –> class core::id::StubID
- pyrosetta.rosetta.core.pose.noncanonical_atom_count(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
count the number of non-canonical amino acids in thepose
C++: core::pose::noncanonical_atom_count(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.noncanonical_chi_count(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
count the number of non-canonical chi angles in the pose
C++: core::pose::noncanonical_chi_count(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.noncanonical_residue_count(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
count the number of non-canonical residues in the pose
C++: core::pose::noncanonical_residue_count(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.nres_protein(pose: pyrosetta.rosetta.core.pose.Pose) int ¶
Number of protein residues in the pose
No virtuals, membrane residues or embedding residues counted
C++: core::pose::nres_protein(const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.num_atoms(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
C++: core::pose::num_atoms(unsigned long, const unsigned long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.num_chi_angles(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
C++: core::pose::num_chi_angles(unsigned long, const unsigned long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.num_hbond_acceptors(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
C++: core::pose::num_hbond_acceptors(unsigned long, const unsigned long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.num_hbond_donors(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
C++: core::pose::num_hbond_donors(unsigned long, const unsigned long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.num_heavy_atoms(begin: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose) int ¶
C++: core::pose::num_heavy_atoms(unsigned long, const unsigned long, const class core::pose::Pose &) –> unsigned long
- pyrosetta.rosetta.core.pose.parse_PDBnum_icode(token: str, fname: str, lineno: int, PDBnum: int, icode: str) None ¶
- Take the string “token” and try to interpret it as a PDB identifier in the form of an
integer as well as an optional insertion code. For example the string “25A” would be interpretted as the residue 25 with the insertion code “A.” Throws an exception if the input string is misformatted.
C++: core::pose::parse_PDBnum_icode(const std::string &, const std::string &, const unsigned long, int &, char &) –> void
- pyrosetta.rosetta.core.pose.parse_resnum(*args, **kwargs)¶
Overloaded function.
parse_resnum(resnum: str) -> pyrosetta.rosetta.core.pose.ResidueIndexDescription
parse_resnum(resnum: str, check_for_refpose: bool) -> pyrosetta.rosetta.core.pose.ResidueIndexDescription
Creates a ResidueIndexDescription from a string
- Recognizes three forms of numbering:
Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID. IMPORTANT: This does not currently handle insertion codes.
Reference pose numbers. These have the form refpose([refpose name], [refpose number]).
In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say “refpose(state1,17)+3”, which means three residues past the residue correpsonding to residue 17 in the reference pose called “state1”.
- a ResidueIndexDescription that will yield a residue number when applied to pose.
Returns a nullptr if there’s an error with parsing the string
C++: core::pose::parse_resnum(const std::string &, const bool) –> class std::shared_ptr<const class core::pose::ResidueIndexDescription>
parse_resnum(resnum: str, pose: pyrosetta.rosetta.core.pose.Pose) -> int
parse_resnum(resnum: str, pose: pyrosetta.rosetta.core.pose.Pose, check_for_refpose: bool) -> int
Extracts a residue number from a string.
- Recognizes three forms of numbering:
Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID. IMPORTANT: This does not currently handle insertion codes.
Reference pose numbers. These have the form refpose([refpose name], [refpose number]).
In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say “refpose(state1,17)+3”, which means three residues past the residue correpsonding to residue 17 in the reference pose called “state1”.
the rosetta residue number for the string, or 0 upon an error
C++: core::pose::parse_resnum(const std::string &, const class core::pose::Pose &, const bool) –> unsigned long
- pyrosetta.rosetta.core.pose.parse_sequence(sequence_in: str, fullname_list: pyrosetta.rosetta.utility.vector1_std_string, oneletter_to_fullname_index: pyrosetta.rosetta.std.vector_unsigned_long, one_letter_sequence: str) None ¶
Parse the input annotated sequence
C++: core::pose::parse_sequence(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class std::vector<unsigned long, class std::allocator<unsigned long> > &, std::string &) –> void
- pyrosetta.rosetta.core.pose.partition_pose_by_jump(src: pyrosetta.rosetta.core.pose.Pose, jump_number: int, partner1: pyrosetta.rosetta.core.pose.Pose, partner2: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_int ¶
C++: core::pose::partition_pose_by_jump(const class core::pose::Pose &, const int, class core::pose::Pose &, class core::pose::Pose &) –> class utility::vector1<int, class std::allocator<int> >
- pyrosetta.rosetta.core.pose.pdb_to_pose(*args, **kwargs)¶
Overloaded function.
pdb_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, pdb_res: pyrosetta.rosetta.utility.vector1_int) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn’t find it. – rhiju
C++: core::pose::pdb_to_pose(const class core::pose::Pose &, const class utility::vector1<int, class std::allocator<int> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
pdb_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, pdb_res: Tuple[pyrosetta.rosetta.utility.vector1_int, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]) -> pyrosetta.rosetta.utility.vector1_unsigned_long
Convert PDB numbering/chain to pose numbering. Must exist somewhere else, but I couldn’t find it. – rhiju
C++: core::pose::pdb_to_pose(const class core::pose::Pose &, const class std::tuple<class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<std::string, class std::allocator<std::string > > > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
pdb_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, res_num: int) -> int
pdb_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, res_num: int, chain: str) -> int
Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn’t find it. – rhiju
C++: core::pose::pdb_to_pose(const class core::pose::Pose &, const int, const char) –> unsigned long
- pyrosetta.rosetta.core.pose.pdbslice(*args, **kwargs)¶
Overloaded function.
pdbslice(new_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose, slice_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Create a subpose of the src pose – figures out a reasonable fold tree.
C++: core::pose::pdbslice(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, slice_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Create a subpose of the src pose – figures out a reasonable fold tree.
C++: core::pose::pdbslice(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- pyrosetta.rosetta.core.pose.pose_from_saccharide_sequence(*args, **kwargs)¶
Overloaded function.
pose_from_saccharide_sequence(sequence: str) -> pyrosetta.rosetta.core.pose.Pose
pose_from_saccharide_sequence(sequence: str, type_set_name: str) -> pyrosetta.rosetta.core.pose.Pose
pose_from_saccharide_sequence(sequence: str, type_set_name: str, auto_termini: bool) -> pyrosetta.rosetta.core.pose.Pose
pose_from_saccharide_sequence(sequence: str, type_set_name: str, auto_termini: bool, idealize_linkages: bool) -> pyrosetta.rosetta.core.pose.Pose
- Return a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name
<type_set_name>.
C++: core::pose::pose_from_saccharide_sequence(const std::string &, const std::string &, const bool, const bool) –> class std::shared_ptr<class core::pose::Pose>
- pyrosetta.rosetta.core.pose.pose_max_nbr_radius(pose: pyrosetta.rosetta.core.pose.Pose) float ¶
returns a Distance
C++: core::pose::pose_max_nbr_radius(const class core::pose::Pose &) –> double
- pyrosetta.rosetta.core.pose.pose_residue_is_terminal(pose: pyrosetta.rosetta.core.pose.Pose, resid: int) bool ¶
returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants
C++: core::pose::pose_residue_is_terminal(const class core::pose::Pose &, const unsigned long) –> bool
- pyrosetta.rosetta.core.pose.pose_to_pdb(pose: pyrosetta.rosetta.core.pose.Pose, pose_res: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Convert pose numbering to pdb numbering. Must exist somewhere else, but I couldn’t find it. – rhiju
C++: core::pose::pose_to_pdb(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.radius_of_gyration(pose: pyrosetta.rosetta.core.pose.Pose, center_of_mass: pyrosetta.rosetta.numeric.xyzVector_double_t, residues: pyrosetta.rosetta.utility.vector1_bool) float ¶
Get the radius of gyration of the selected residues
WARNING: Despite the name, this function only calculates with a single coordinate per residue (the Calpha/neighbor atom)
- Requires the center_of_mass as an input because often people will want
both com and rg and this ensures that we only calculate com once.
C++: core::pose::radius_of_gyration(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const class utility::vector1<bool, class std::allocator<bool> > &) –> double
- pyrosetta.rosetta.core.pose.read_comment_pdb(file_name: str, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Reads the comments from the pdb file and adds it into comments
C++: core::pose::read_comment_pdb(const std::string &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.read_psipred_ss2_file(*args, **kwargs)¶
Overloaded function.
read_psipred_ss2_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> pyrosetta.rosetta.utility.vector1_char
C++: core::pose::read_psipred_ss2_file(const class core::pose::Pose &, const std::string &) –> class utility::vector1<char, class std::allocator<char> >
read_psipred_ss2_file(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_char
C++: core::pose::read_psipred_ss2_file(const class core::pose::Pose &) –> class utility::vector1<char, class std::allocator<char> >
- pyrosetta.rosetta.core.pose.remove_ligand_canonical_residues(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues.
C++: core::pose::remove_ligand_canonical_residues(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.remove_lower_terminus_type_from_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
C++: core::pose::remove_lower_terminus_type_from_pose_residue(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.remove_nonprotein_residues(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).
C++: core::pose::remove_nonprotein_residues(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.remove_upper_terminus_type_from_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) None ¶
C++: core::pose::remove_upper_terminus_type_from_pose_residue(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.remove_variant_type_from_pose_residue(pose: pyrosetta.rosetta.core.pose.Pose, variant_type: pyrosetta.rosetta.core.chemical.VariantType, seqpos: int) None ¶
Construct a non-variant of an existing pose residue.
C++: core::pose::remove_variant_type_from_pose_residue(class core::pose::Pose &, const enum core::chemical::VariantType, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.remove_variant_type_from_residue(old_rsd: pyrosetta.rosetta.core.conformation.Residue, variant_type: pyrosetta.rosetta.core.chemical.VariantType, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.conformation.Residue ¶
Remove variant from an existing residue.
C++: core::pose::remove_variant_type_from_residue(const class core::conformation::Residue &, const enum core::chemical::VariantType, const class core::pose::Pose &) –> class std::shared_ptr<class core::conformation::Residue>
- pyrosetta.rosetta.core.pose.remove_virtual_residues(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Removes all virtual residues from <pose>
C++: core::pose::remove_virtual_residues(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.renumber_pdbinfo_based_on_conf_chains(*args, **kwargs)¶
Overloaded function.
renumber_pdbinfo_based_on_conf_chains(pose: pyrosetta.rosetta.core.pose.Pose) -> bool
renumber_pdbinfo_based_on_conf_chains(pose: pyrosetta.rosetta.core.pose.Pose, fix_chains: bool) -> bool
renumber_pdbinfo_based_on_conf_chains(pose: pyrosetta.rosetta.core.pose.Pose, fix_chains: bool, start_from_existing_numbering: bool) -> bool
renumber_pdbinfo_based_on_conf_chains(pose: pyrosetta.rosetta.core.pose.Pose, fix_chains: bool, start_from_existing_numbering: bool, keep_insertion_codes: bool) -> bool
renumber_pdbinfo_based_on_conf_chains(pose: pyrosetta.rosetta.core.pose.Pose, fix_chains: bool, start_from_existing_numbering: bool, keep_insertion_codes: bool, rotate_chain_ids: bool) -> bool
renumber PDBInfo based on Conformation chains; each chain starts from 1
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
The Pose to modify.
- If true, the procedure will attempt to fix any empty record
characters it finds in the PDBInfo. (default true)
- If true, will attempt to start each
chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)
- If true, will maintain insertion codes and
will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)
- If true, allows support for more than 26 pdb chains
by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)
- If fixing chains and there is only one chain and the PDBInfo exists
but all records are marked as empty, will renumber and set the PDBInfo chain to ‘A’.
true if renumbering successful, false otherwise
C++: core::pose::renumber_pdbinfo_based_on_conf_chains(class core::pose::Pose &, bool, const bool, const bool, const bool) –> bool
- pyrosetta.rosetta.core.pose.reorder_root_partition_res(root_partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, fixed_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: core::pose::reorder_root_partition_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- pyrosetta.rosetta.core.pose.replace_pose_residue_copying_existing_coordinates(*args, **kwargs)¶
Overloaded function.
replace_pose_residue_copying_existing_coordinates(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, new_rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None
C++: core::pose::replace_pose_residue_copying_existing_coordinates(class core::pose::Pose &, const unsigned long, const class core::chemical::ResidueType &) –> void
replace_pose_residue_copying_existing_coordinates(pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, new_rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, mapping: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: core::pose::replace_pose_residue_copying_existing_coordinates(class core::pose::Pose &, const unsigned long, const class core::chemical::ResidueType &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- pyrosetta.rosetta.core.pose.reroot(pose: pyrosetta.rosetta.core.pose.Pose, root_partition_res: pyrosetta.rosetta.utility.vector1_unsigned_long, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, preferred_root_res: pyrosetta.rosetta.utility.vector1_unsigned_long, fixed_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
C++: core::pose::reroot(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- pyrosetta.rosetta.core.pose.res_in_chain(pose: pyrosetta.rosetta.core.pose.Pose, resnum: int, chain: str) bool ¶
Does this residue number have this chain letter?
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
C++: core::pose::res_in_chain(const class core::pose::Pose &, unsigned long, const std::string &) –> bool
- pyrosetta.rosetta.core.pose.residue_center_of_mass(*args, **kwargs)¶
Overloaded function.
residue_center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_bool) -> int
C++: core::pose::residue_center_of_mass(const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >) –> int
residue_center_of_mass(pose: pyrosetta.rosetta.core.pose.Pose, start: int, stop: int) -> int
C++: core::pose::residue_center_of_mass(const class core::pose::Pose &, const int, const int) –> int
- pyrosetta.rosetta.core.pose.residue_types_from_saccharide_sequence(sequence: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
Return a list of carbohydrate ResidueTypes corresponding to an annotated, linear, IUPAC polysaccharide sequence.
an annotated IUPAC polysaccharide sequence, e.g., “alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-D-Glcp”
the desired residue set
a 1-indexed vector of ResidueType owning pointers, in Rosetta order.
That is, the first residue will be the reducing end (the last residue in the sequence), and all branches will be consecutive, with earlier branches earlier in set of residue types.
Format for <sequence>:
Prefixes apply to the residue to which they are attached, below indicated by residue n. Residues are listed from N to 1, where N is the total number of residues in the saccharide. The sequence is parsed by reading to the next hyphen, so hyphens are crucial. Linkage indication: “(a->x)-” specifies the linkage of residue n, where a is the anomeric carbon number of residue (n+1) and x is the oxygen number of residue n. The first residue listed in the annotated sequence (residue N) need not have the linkage prefix. A ->4) ResidueType will automatically be assigned by default if not specified. Anomer indication: The strings “alpha-” or “beta-” are supplied next, which determines the stereochemistry of the anomeric carbon of the residue to which it is prefixed. An alpha ResidueType will automatically be assigned by default. Stereochemical indication: “L-” or “D-” specifies whether residue n is an L- or D-sugar. The default is “D-“. 3-Letter code: A three letter code (in sentence case) MUST be supplied next. This specifies the “base sugar name”, e.g., Glc is for glucose. (A list of all recognized 3-letter codes for sugars can be found in the database.) 1-Letter suffix: If no suffix follows, residue n will be linear. If a letter is present, it indicates the ring size, where “f” is furanose, “p” is pyranose, and “s” is septanose. Branches are indicated using nested brackets and are best explained by example: beta-D-Galp-(1->4)-[alpha-L-Fucp-(1->3)]-D-GlcpNAc is: beta-D-Galp-(1->4)-D-GlcpNAc
alpha-L-Fucp-(1->3)
make_pose_from_saccharide_sequence() will generate a pose with a proper lower terminus. glycosylate_pose() will append the fragment by bond.
C++: core::pose::residue_types_from_saccharide_sequence(const std::string &, const class core::chemical::ResidueTypeSet &) –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- pyrosetta.rosetta.core.pose.residue_types_from_sequence(*args, **kwargs)¶
Overloaded function.
residue_types_from_sequence(sequence_in: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
residue_types_from_sequence(sequence_in: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
residue_types_from_sequence(sequence_in: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, auto_termini: bool, metapatches: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
return a list of ResidueTypes corresponding to an annotated protein sequence
an annotated sequence
the desired residue set
mark position 1, last_residue with lower, upper termini; default true
C++: core::pose::residue_types_from_sequence(const std::string &, const class core::chemical::ResidueTypeSet &, const bool, const bool) –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- pyrosetta.rosetta.core.pose.return_nearest_residue(*args, **kwargs)¶
Overloaded function.
return_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, residues: pyrosetta.rosetta.utility.vector1_bool, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> int
C++: core::pose::return_nearest_residue(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class numeric::xyzVector<double>) –> int
return_nearest_residue(pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int, center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> int
C++: core::pose::return_nearest_residue(const class core::pose::Pose &, const int, const int, class numeric::xyzVector<double>) –> int
- pyrosetta.rosetta.core.pose.saved_native_pose(*args, **kwargs)¶
Overloaded function.
saved_native_pose(data_map: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.pose.Pose
saved_native_pose(data_map: pyrosetta.rosetta.basic.datacache.DataMap, resource_str: str) -> pyrosetta.rosetta.core.pose.Pose
- Retrieve the native pose from the DataMap which is added through the OptionsCollection
during RosettaScript parsing as a resource.
If the resource is not present, will return a nullptr.
C++: core::pose::saved_native_pose(class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<const class core::pose::Pose>
- pyrosetta.rosetta.core.pose.saved_reference_pose(*args, **kwargs)¶
Overloaded function.
saved_reference_pose(in_tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.pose.Pose
saved_reference_pose(in_tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap, tag_str: str) -> pyrosetta.rosetta.core.pose.Pose
C++: core::pose::saved_reference_pose(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<class core::pose::Pose>
- pyrosetta.rosetta.core.pose.sequence_map_from_pdbinfo(first: pyrosetta.rosetta.core.pose.Pose, second: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.SequenceMapping ¶
- Create a sequence map of first pose onto the second, matching the PDBInfo
If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching.
C++: core::pose::sequence_map_from_pdbinfo(const class core::pose::Pose &, const class core::pose::Pose &) –> class core::id::SequenceMapping
- pyrosetta.rosetta.core.pose.setPoseExtraScore(*args, **kwargs)¶
Overloaded function.
setPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: float) -> None
Set a core::Real in the pose datacache, that will be output as a score in the scorefile.
C++: core::pose::setPoseExtraScore(class core::pose::Pose &, const std::string &, double) –> void
setPoseExtraScore(pose: pyrosetta.rosetta.core.pose.Pose, name: str, value: str) -> None
Set a string in the pose datacache, that will be output as a score in the scorefile.
C++: core::pose::setPoseExtraScore(class core::pose::Pose &, const std::string &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.set_bb_torsion(torsion_id: int, pose: pyrosetta.rosetta.core.pose.Pose, sequence_position: int, new_angle: float) None ¶
- Set the BB torsion, phi, psi, omega (see core::types).
Works with carbohydrates. Think about moving this to pose itself.
C++: core::pose::set_bb_torsion(unsigned long, class core::pose::Pose &, unsigned long, double) –> void
- pyrosetta.rosetta.core.pose.set_bfactors_from_atom_id_map(pose: pyrosetta.rosetta.core.pose.Pose, bfactors: pyrosetta.rosetta.core.id.AtomID_Map_double_t) None ¶
Set bfactors in a pose PDBInfo
C++: core::pose::set_bfactors_from_atom_id_map(class core::pose::Pose &, const class core::id::AtomID_Map<double> &) –> void
- pyrosetta.rosetta.core.pose.set_output_res_and_chain(extended_pose: pyrosetta.rosetta.core.pose.Pose, output_resnum_and_chain_and_segid: Tuple[pyrosetta.rosetta.utility.vector1_int, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]) None ¶
C++: core::pose::set_output_res_and_chain(class core::pose::Pose &, const class std::tuple<class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<std::string, class std::allocator<std::string > > > &) –> void
- pyrosetta.rosetta.core.pose.set_reasonable_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: core::pose::set_reasonable_fold_tree(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.set_ss_from_phipsi(pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Analyzes <pose> residue phi/psi sets and guesses the secondary
structure, ideally dssp should be used for that
C++: core::pose::set_ss_from_phipsi(class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.setup_dof_mask_from_move_map(mm: core::kinematics::MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, dof_mask: pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t) None ¶
convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer
C++: core::pose::setup_dof_mask_from_move_map(const class core::kinematics::MoveMap &, const class core::pose::Pose &, class core::id::DOF_ID_Map<bool> &) –> void
- pyrosetta.rosetta.core.pose.setup_dof_to_torsion_map(pose: pyrosetta.rosetta.core.pose.Pose, dof_map: pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) None ¶
set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID)
C++: core::pose::setup_dof_to_torsion_map(const class core::pose::Pose &, class core::id::DOF_ID_Map<class core::id::TorsionID> &) –> void
- pyrosetta.rosetta.core.pose.show_adjacent_nt_connections(pose: pyrosetta.rosetta.core.pose.Pose, res: int) None ¶
C++: core::pose::show_adjacent_nt_connections(const class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.core.pose.sort_pose_by_score(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: core::pose::sort_pose_by_score(const class std::shared_ptr<class core::pose::Pose> &, const class std::shared_ptr<class core::pose::Pose> &) –> bool
- pyrosetta.rosetta.core.pose.stepwise_addable_pose_residue(n: int, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: core::pose::stepwise_addable_pose_residue(const unsigned long, const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.core.pose.stepwise_addable_residue(n: int, non_standard_residue_map: pyrosetta.rosetta.std.map_unsigned_long_std_string) bool ¶
C++: core::pose::stepwise_addable_residue(const unsigned long, const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &) –> bool
- pyrosetta.rosetta.core.pose.stub_id_to_named_stub_id(stub_id: pyrosetta.rosetta.core.id.StubID, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.NamedStubID ¶
C++: core::pose::stub_id_to_named_stub_id(const class core::id::StubID &, const class core::pose::Pose &) –> class core::id::NamedStubID
- pyrosetta.rosetta.core.pose.swap_transform(jump_num: int, xform: pyrosetta.rosetta.core.kinematics.RT, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Updates the rigid-body transform of the specified jump in <pose>
C++: core::pose::swap_transform(unsigned long, const class core::kinematics::RT &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.tag_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) str ¶
C++: core::pose::tag_from_pose(const class core::pose::Pose &) –> std::string
- pyrosetta.rosetta.core.pose.tag_into_pose(pose: pyrosetta.rosetta.core.pose.Pose, tag: str) None ¶
C++: core::pose::tag_into_pose(class core::pose::Pose &, const std::string &) –> void
- pyrosetta.rosetta.core.pose.total_energy_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: core::pose::total_energy_from_pose(const class core::pose::Pose &) –> double
- pyrosetta.rosetta.core.pose.transfer_jumps(srcpose: pyrosetta.rosetta.core.pose.Pose, tgtpose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: core::pose::transfer_jumps(const class core::pose::Pose &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.transfer_phi_psi(*args, **kwargs)¶
Overloaded function.
transfer_phi_psi(srcpose: pyrosetta.rosetta.core.pose.Pose, tgtpose: pyrosetta.rosetta.core.pose.Pose, ir: int, jr: int) -> None
C++: core::pose::transfer_phi_psi(const class core::pose::Pose &, class core::pose::Pose &, unsigned long, unsigned long) –> void
transfer_phi_psi(srcpose: pyrosetta.rosetta.core.pose.Pose, tgtpose: pyrosetta.rosetta.core.pose.Pose) -> None
C++: core::pose::transfer_phi_psi(const class core::pose::Pose &, class core::pose::Pose &) –> void
- pyrosetta.rosetta.core.pose.update_cutpoint_virtual_atoms_if_connected(*args, **kwargs)¶
Overloaded function.
update_cutpoint_virtual_atoms_if_connected(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int) -> None
update_cutpoint_virtual_atoms_if_connected(pose: pyrosetta.rosetta.core.pose.Pose, cutpoint_res: int, recurse: bool) -> None
- Given a pose and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this
position has either of these variant types, and if it does, determine whether it’s connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it’s bonded.
Requires a little bit of special-casing for gamma-amino acids. Throws an exception if the residue to which a CUTPOINT_LOWER is bonded does not have an “N” and a “CA” or “C4”. Safe to call repeatedly, or if cutpoint variant types are absent; in these cases, the function does nothing.
By default, this function calls itself again once on residues to which this residue is connected, to update their geometry. Set recurse=false to disable this.
Vikram K. Mulligan (vmullig.edu).
C++: core::pose::update_cutpoint_virtual_atoms_if_connected(class core::pose::Pose &, const unsigned long, bool) –> void
- pyrosetta.rosetta.core.pose.virtual_type_for_pose(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Return the appropritate ResidueType for the virtual residue for the i
“mode” (fullatom, centroid …) the pose is in.
C++: core::pose::virtual_type_for_pose(const class core::pose::Pose &) –> class std::shared_ptr<const class core::chemical::ResidueType>
- class pyrosetta.rosetta.core.pose.xyzStripeHashPose¶
Bases:
xyzStripeHash
- add_pose(*args, **kwargs)¶
Overloaded function.
add_pose(self: pyrosetta.rosetta.core.pose.xyzStripeHashPose, p: pyrosetta.rosetta.core.pose.Pose, amap: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> None
C++: core::pose::xyzStripeHashPose::add_pose(const class core::pose::Pose &, const class core::id::AtomID_Map<double> &) –> void
add_pose(self: pyrosetta.rosetta.core.pose.xyzStripeHashPose, p: pyrosetta.rosetta.core.pose.Pose) -> None
add_pose(self: pyrosetta.rosetta.core.pose.xyzStripeHashPose, p: pyrosetta.rosetta.core.pose.Pose, m: pyrosetta.rosetta.core.pose.PoseCoordPickMode) -> None
C++: core::pose::xyzStripeHashPose::add_pose(const class core::pose::Pose &, enum core::pose::PoseCoordPickMode) –> void
- assign(self: pyrosetta.rosetta.core.pose.xyzStripeHashPose, : pyrosetta.rosetta.core.pose.xyzStripeHashPose) pyrosetta.rosetta.core.pose.xyzStripeHashPose ¶
C++: core::pose::xyzStripeHashPose::operator=(const class core::pose::xyzStripeHashPose &) –> class core::pose::xyzStripeHashPose &
- ball(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, ib: int) pyrosetta.rosetta.numeric.geometry.hashing.Ball ¶
C++: numeric::geometry::hashing::xyzStripeHash::ball(const unsigned long &) const –> const struct numeric::geometry::hashing::Ball &
- clash(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v_in: pyrosetta.rosetta.numeric.xyzVector_float_t) bool ¶
C++: numeric::geometry::hashing::xyzStripeHash::clash(const class numeric::xyzVector<float> &) const –> bool
- clash_amount(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v_in: pyrosetta.rosetta.numeric.xyzVector_float_t) float ¶
C++: numeric::geometry::hashing::xyzStripeHash::clash_amount(const class numeric::xyzVector<float> &) const –> float
- clash_check_ball(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, b: pyrosetta.rosetta.numeric.geometry.hashing.Ball) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::clash_check_ball(const struct numeric::geometry::hashing::Ball &) const –> int
- clash_check_residue_pairs(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, test_balls: pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball, residue_pairs: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) bool ¶
C++: numeric::geometry::hashing::xyzStripeHash::clash_check_residue_pairs(const class utility::vector1<struct numeric::geometry::hashing::Ball, class std::allocator<struct numeric::geometry::hashing::Ball> > &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) const –> bool
- clash_not_resid(*args, **kwargs)¶
Overloaded function.
clash_not_resid(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v_in: pyrosetta.rosetta.numeric.xyzVector_float_t, resid: int) -> bool
clash_not_resid(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v_in: pyrosetta.rosetta.numeric.xyzVector_float_t, resid: int, resid2: int) -> bool
C++: numeric::geometry::hashing::xyzStripeHash::clash_not_resid(const class numeric::xyzVector<float> &, const int &, const int &) const –> bool
- clash_raw(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v: pyrosetta.rosetta.numeric.xyzVector_float_t) bool ¶
C++: numeric::geometry::hashing::xyzStripeHash::clash_raw(const class numeric::xyzVector<float> &) const –> bool
- class const_iterator¶
Bases:
pybind11_object
- arrow(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator) pyrosetta.rosetta.numeric.xyzVector_float_t ¶
C++: numeric::geometry::hashing::xyzStripeHash::const_iterator::operator->() –> const class numeric::xyzVector<float> *
- dereference(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator) pyrosetta.rosetta.numeric.xyzVector_float_t ¶
C++: numeric::geometry::hashing::xyzStripeHash::const_iterator::operator*() –> const class numeric::xyzVector<float> &
- radius(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash.const_iterator) float ¶
C++: numeric::geometry::hashing::xyzStripeHash::const_iterator::radius() –> float
- debug_pdb(*args, **kwargs)¶
Overloaded function.
debug_pdb(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) -> str
debug_pdb(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, x: pyrosetta.rosetta.numeric.xyzTransform_double_t) -> str
C++: numeric::geometry::hashing::xyzStripeHash::debug_pdb(const class numeric::xyzTransform<double> &) const –> std::string
- static extract_pose_balls(*args, **kwargs)¶
Overloaded function.
extract_pose_balls(p: pyrosetta.rosetta.core.pose.Pose, balls: pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball) -> None
extract_pose_balls(p: pyrosetta.rosetta.core.pose.Pose, balls: pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball, m: pyrosetta.rosetta.core.pose.PoseCoordPickMode) -> None
C++: core::pose::xyzStripeHashPose::extract_pose_balls(const class core::pose::Pose &, class utility::vector1<struct numeric::geometry::hashing::Ball, class std::allocator<struct numeric::geometry::hashing::Ball> > &, enum core::pose::PoseCoordPickMode) –> void
extract_pose_balls(p: pyrosetta.rosetta.core.pose.Pose, balls: pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball, amap: pyrosetta.rosetta.core.id.AtomID_Map_double_t) -> None
C++: core::pose::xyzStripeHashPose::extract_pose_balls(const class core::pose::Pose &, class utility::vector1<struct numeric::geometry::hashing::Ball, class std::allocator<struct numeric::geometry::hashing::Ball> > &, const class core::id::AtomID_Map<double> &) –> void
- fill_pairs(*args, **kwargs)¶
Overloaded function.
fill_pairs(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v: pyrosetta.rosetta.numeric.xyzVector_float_t, ir: int, pairs: pyrosetta.rosetta.utility.vector1_std_pair_int_int_t) -> None
fill_pairs(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v: pyrosetta.rosetta.numeric.xyzVector_float_t, ir: int, pairs: pyrosetta.rosetta.utility.vector1_std_pair_int_int_t, maxd2: float) -> None
C++: numeric::geometry::hashing::xyzStripeHash::fill_pairs(const class numeric::xyzVector<float> &, const int &, class utility::vector1<struct std::pair<int, int>, class std::allocator<struct std::pair<int, int> > > &, float) const –> void
- grid_atoms(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) pyrosetta.rosetta.numeric.geometry.hashing.Ball ¶
C++: numeric::geometry::hashing::xyzStripeHash::grid_atoms() const –> const struct numeric::geometry::hashing::Ball *
- grid_size(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) float ¶
C++: numeric::geometry::hashing::xyzStripeHash::grid_size() const –> float
- grid_size2(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) float ¶
C++: numeric::geometry::hashing::xyzStripeHash::grid_size2() const –> float
- init(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, balls: pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball) None ¶
C++: numeric::geometry::hashing::xyzStripeHash::init(const class utility::vector1<struct numeric::geometry::hashing::Ball, class std::allocator<struct numeric::geometry::hashing::Ball> > &) –> void
- init_posehash(self: pyrosetta.rosetta.core.pose.xyzStripeHashPose) None ¶
C++: core::pose::xyzStripeHashPose::init_posehash() –> void
- class iter_base_numeric_geometry_hashing_xyzStripeHash_const_iterator_t¶
Bases:
pybind11_object
- natom(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::natom() const –> int
- nbcount(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v_in: pyrosetta.rosetta.numeric.xyzVector_float_t) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::nbcount(const class numeric::xyzVector<float> &) const –> int
- nbcount_raw(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, v: pyrosetta.rosetta.numeric.xyzVector_float_t) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::nbcount_raw(const class numeric::xyzVector<float> &) const –> int
- resi(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, ib: int) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::resi(const unsigned long &) const –> unsigned long
- sanity_check(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) bool ¶
C++: numeric::geometry::hashing::xyzStripeHash::sanity_check() const –> bool
- size(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::size() const –> unsigned long
- translation(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) pyrosetta.rosetta.numeric.xyzVector_float_t ¶
C++: numeric::geometry::hashing::xyzStripeHash::translation() const –> const class numeric::xyzVector<float> &
- translation_real(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) pyrosetta.rosetta.numeric.xyzVector_double_t ¶
C++: numeric::geometry::hashing::xyzStripeHash::translation_real() const –> class numeric::xyzVector<double>
- xdim(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::xdim() const –> int
- xyz(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash, ib: int) pyrosetta.rosetta.numeric.xyzVector_float_t ¶
C++: numeric::geometry::hashing::xyzStripeHash::xyz(const unsigned long &) const –> class numeric::xyzVector<float>
- ydim(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::ydim() const –> int
- zdim(self: pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash) int ¶
C++: numeric::geometry::hashing::xyzStripeHash::zdim() const –> int