Welcome to PyRosetta’s documentation!¶
Contents:
-
rosetta.core.
DemoTesterFunction
((Base)arg1) → str :¶ - C++ signature :
- std::string DemoTesterFunction(DemoBase*)
-
rosetta.core.
Q_Test_CI1B
((__CPP_ContextIndependentOneBodyEnergy__)arg1) → None :¶ - C++ signature :
- void Q_Test_CI1B(boost::shared_ptr<core::scoring::methods::ContextIndependentOneBodyEnergy>)
-
rosetta.core.
Q_Test_EnergyMethodCreator
((__CPP_EnergyMethodCreator__)arg1) → None :¶ - C++ signature :
- void Q_Test_EnergyMethodCreator(boost::shared_ptr<core::scoring::methods::EnergyMethodCreator>)
-
rosetta.core.
Q_test_char_string_args_
((int)arg1) → None :¶ - C++ signature :
- void Q_test_char_string_args_(int)
Q_test_char_string_args_( (str)arg1) -> None :
- C++ signature :
- void Q_test_char_string_args_(std::string)
-
rosetta.core.
minirosetta_svn_url
() → str :¶ Read access to the svn / git url.
- C++ signature :
- std::string minirosetta_svn_url()
-
rosetta.core.
minirosetta_svn_version
() → str :¶ Read access to the svn / git version.
- C++ signature :
- std::string minirosetta_svn_version()
-
rosetta.core.
set_svn_version_and_url
((str)version, (str)url) → None :¶ Initialize this data from a lower-level library at startup to avoid relinking every time you update your svn / git version. This function should be called at most once.
- C++ signature :
- void set_svn_version_and_url(std::string,std::string)
-
class
rosetta.core.pose.
CrystInfo
¶ core/pose/CrystInfo.hh:27
-
A
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:43
- C++ signature :
- double A(core::pose::CrystInfo {lvalue})
- A( (CrystInfo)arg1, (float)Ain) -> None :
core/pose/CrystInfo.hh:44
- C++ signature :
- void A(core::pose::CrystInfo {lvalue},double)
-
B
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:45
- C++ signature :
- double B(core::pose::CrystInfo {lvalue})
- B( (CrystInfo)arg1, (float)Bin) -> None :
core/pose/CrystInfo.hh:46
- C++ signature :
- void B(core::pose::CrystInfo {lvalue},double)
-
C
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:47
- C++ signature :
- double C(core::pose::CrystInfo {lvalue})
- C( (CrystInfo)arg1, (float)Cin) -> None :
core/pose/CrystInfo.hh:48
- C++ signature :
- void C(core::pose::CrystInfo {lvalue},double)
-
alpha
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:50
- C++ signature :
- double alpha(core::pose::CrystInfo {lvalue})
- alpha( (CrystInfo)arg1, (float)alphain) -> None :
core/pose/CrystInfo.hh:51
- C++ signature :
- void alpha(core::pose::CrystInfo {lvalue},double)
-
beta
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:52
- C++ signature :
- double beta(core::pose::CrystInfo {lvalue})
- beta( (CrystInfo)arg1, (float)betain) -> None :
core/pose/CrystInfo.hh:53
- C++ signature :
- void beta(core::pose::CrystInfo {lvalue},double)
-
gamma
((CrystInfo)arg1) → float :¶ core/pose/CrystInfo.hh:54
- C++ signature :
- double gamma(core::pose::CrystInfo {lvalue})
- gamma( (CrystInfo)arg1, (float)gammain) -> None :
core/pose/CrystInfo.hh:55
- C++ signature :
- void gamma(core::pose::CrystInfo {lvalue},double)
-
spacegroup
((CrystInfo)arg1) → str :¶ core/pose/CrystInfo.hh:57
- C++ signature :
- std::string spacegroup(core::pose::CrystInfo {lvalue})
- spacegroup( (CrystInfo)arg1, (str)spacegroupin) -> None :
core/pose/CrystInfo.hh:58
- C++ signature :
- void spacegroup(core::pose::CrystInfo {lvalue},std::string)
-
-
class
rosetta.core.pose.
MiniPose
¶ lightweight version of the pose with stuff I need. not quite (silent_structs don’t necessarily have xyz). Kind of like a Conformation but without the overtree of an atom_tree. @remark 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.
-
atom_name
((MiniPose)arg1, (AtomID)atom_id) → str :¶ core/pose/MiniPose.hh:66
- C++ signature :
- std::string atom_name(core::pose::MiniPose {lvalue},core::id::AtomID)
-
atom_names_list
((MiniPose)arg1) → vec1_vec1_string :¶ core/pose/MiniPose.hh:54
- C++ signature :
- utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > > atom_names_list(core::pose::MiniPose {lvalue})
-
coords
((MiniPose)arg1) → object :¶ core/pose/MiniPose.hh:52
- C++ signature :
- utility::vector1<utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >, std::allocator<utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > > > coords(core::pose::MiniPose {lvalue})
-
fold_tree
((MiniPose)arg1) → FoldTree :¶ core/pose/MiniPose.hh:50
- C++ signature :
- core::kinematics::FoldTree fold_tree(core::pose::MiniPose {lvalue})
-
sequence
((MiniPose)arg1) → str :¶ core/pose/MiniPose.hh:62
- C++ signature :
- std::string sequence(core::pose::MiniPose {lvalue})
-
size
((MiniPose)arg1) → int :¶ core/pose/MiniPose.hh:58
- C++ signature :
- unsigned long size(core::pose::MiniPose {lvalue})
-
total_residue
((MiniPose)arg1) → int :¶ core/pose/MiniPose.hh:60
- C++ signature :
- unsigned long total_residue(core::pose::MiniPose {lvalue})
-
variant_types
((MiniPose)arg1, (int)seq_num) → vector1_string :¶ core/pose/MiniPose.hh:68
- C++ signature :
- utility::vector1<std::string, std::allocator<std::string> > variant_types(core::pose::MiniPose {lvalue},unsigned long)
-
variant_types_list
((MiniPose)arg1) → vec1_vec1_string :¶ core/pose/MiniPose.hh:56
- C++ signature :
- utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > > variant_types_list(core::pose::MiniPose {lvalue})
-
xyz
((MiniPose)arg1, (AtomID)atom_id) → xyzVector_Real :¶ core/pose/MiniPose.hh:64
- C++ signature :
- numeric::xyzVector<double> xyz(core::pose::MiniPose {lvalue},core::id::AtomID)
-
-
class
rosetta.core.pose.
PDBInfo
¶ 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 id 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().- @remarks 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.
-
add_reslabel
((PDBInfo)arg1, (int)res, (str)label) → None :¶ adds a label associated to a pose resid. [in] res residue in pose numbering [in] label string that is the “label”
- C++ signature :
- void add_reslabel(core::pose::PDBInfo {lvalue},unsigned long,std::string)
-
add_unrecognized_atom
((PDBInfo)arg1, (int)resnum, (str)resname, (str)atomname, (xyzVector_Real)coords, (float)temp) → None :¶ remembers info about atoms not read into the pose
- C++ signature :
- void add_unrecognized_atom(core::pose::PDBInfo {lvalue},unsigned long,std::string,std::string,numeric::xyzVector<double>,double)
-
alt_loc
((PDBInfo)arg1, (int)res, (int)atom_index) → 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++ signature :
- char alt_loc(core::pose::PDBInfo {lvalue},unsigned long,unsigned long)
- alt_loc( (PDBInfo)arg1, (int)res, (int)atom_index, (str)loc) -> None :
Sets the alternate location of the <atom_index> atom of pose residue <res> to <loc> : <loc> is an alternate location character
- C++ signature :
- void alt_loc(core::pose::PDBInfo {lvalue},unsigned long,unsigned long,char)
-
append_res
((PDBInfo)arg1, (int)res, (int)natoms[, (int)n=1]) → None :¶ Appends residue records given a pose residue number <res> [in] res residue to append after (in internal/pose numbering) [in] natoms number of atoms in type of appended residue [in] n number of residue records to append
- C++ signature :
- void append_res(core::pose::PDBInfo {lvalue},unsigned long,unsigned long [,unsigned long=1])
-
assign
((PDBInfo)arg1, (PDBInfo)info) → PDBInfo :¶ copy assignment
- C++ signature :
- core::pose::PDBInfo {lvalue} assign(core::pose::PDBInfo {lvalue},core::pose::PDBInfo)
-
attach_to
((PDBInfo)arg1, (Conformation)conf) → None :¶ Attaches the Conformation <conf> and begins observation example(s): See also:
Pose PDBInfo- C++ signature :
- void attach_to(core::pose::PDBInfo {lvalue},core::conformation::Conformation {lvalue})
-
chain
((PDBInfo)arg1, (int)res) → str :¶ - Returns the chain id for pose residue <res>
- example(s):
- pose.pdb_info().chain(3)
- See also:
- Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
- C++ signature :
- char chain(core::pose::PDBInfo {lvalue},unsigned long)
- chain( (PDBInfo)arg1, (int)res, (str)chain_id) -> None :
Sets the chain id of pose residue <res> to <chain_id> @remarks chain id should not be the empty record character, currently ‘^’ Returns the pdb insertion code of residue <res> example(s):
pose.pdb_info().chain(3,”R”)- See also:
- Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb
- C++ signature :
- void chain(core::pose::PDBInfo {lvalue},unsigned long,char)
-
clear_reslabel
((PDBInfo)arg1, (int)res) → None :¶ clean all the label(s) associated to a pose resid. [in] res residue in pose numbering
- C++ signature :
- void clear_reslabel(core::pose::PDBInfo {lvalue},unsigned long)
-
copy
((PDBInfo)arg1, (PDBInfo)input_info, (int)copy_from, (int)copy_to, (int)start_from) → None :¶ Copyies a section from PDBInfo <input_info> [in] input_info the PDBInfo to copy from [in] copy_from the first residue position in input_info to copy [in] copy_to the final residue position in input_info to copy [in] start_from the first residue position in this PDBInfo to
copy into- C++ signature :
- void copy(core::pose::PDBInfo {lvalue},core::pose::PDBInfo,unsigned long,unsigned long,unsigned long)
-
crystinfo
((PDBInfo)arg1) → CrystInfo :¶ Returns the pdb crystinfo
- C++ signature :
- core::pose::CrystInfo crystinfo(core::pose::PDBInfo {lvalue})
-
delete_res
((PDBInfo)arg1, (int)res[, (int)n=1]) → None :¶ Deletes <n> residue records starting from pose residue <res> [in] res residue to start deleting from (in internal/pose numbering) [in] n number of residue records to delete
- C++ signature :
- void delete_res(core::pose::PDBInfo {lvalue},unsigned long [,unsigned long=1])
-
detach_from
((PDBInfo)arg1) → None :¶ Detaches the Conformation and stops observation @remarks 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++ signature :
- void detach_from(core::pose::PDBInfo {lvalue})
-
static
empty_record
() → str :¶ Returns the chain id character specifying “empty record”, currently ‘^’
- C++ signature :
- char empty_record()
-
get_num_unrecognized_atoms
((PDBInfo)arg1) → int :¶ core/pose/PDBInfo.hh:1153
- C++ signature :
- unsigned long get_num_unrecognized_atoms(core::pose::PDBInfo {lvalue})
-
get_num_unrecognized_res
((PDBInfo)arg1) → int :¶ core/pose/PDBInfo.hh:1160
- C++ signature :
- unsigned long get_num_unrecognized_res(core::pose::PDBInfo {lvalue})
-
get_reslabels
((PDBInfo)arg1, (int)res) → vector1_string :¶ returns the pose(number) labels associated to the residue [in] res residue in pose numbering
- C++ signature :
- utility::vector1<std::string, std::allocator<std::string> > get_reslabels(core::pose::PDBInfo {lvalue},unsigned long)
-
get_unrecognized_atoms
((PDBInfo)arg1) → object :¶ remembers info about atoms not read into the pose
- C++ signature :
- utility::vector1<core::pose::UnrecognizedAtomRecord, std::allocator<core::pose::UnrecognizedAtomRecord> > get_unrecognized_atoms(core::pose::PDBInfo {lvalue})
-
get_unrecognized_res_name
((PDBInfo)arg1, (int)i) → str :¶ core/pose/PDBInfo.hh:1167
- C++ signature :
- std::string get_unrecognized_res_name(core::pose::PDBInfo {lvalue},unsigned long)
-
get_unrecognized_res_size
((PDBInfo)arg1, (int)i) → int :¶ core/pose/PDBInfo.hh:1174
- C++ signature :
- unsigned long get_unrecognized_res_size(core::pose::PDBInfo {lvalue},unsigned long)
-
header_information
((PDBInfo)arg1, (HeaderInformation)header_information) → None :¶ - For structures deposited into the protein databank, the
header information record stores the classfication, deposition date and the 4 character identification code. For now only allow initalizing it with copy and accessing it with a constant owning pointer. Note: The header information is only initialized if it is needed. Generally this requires using the -run:preserve_header options flag.
- C++ signature :
- void header_information(core::pose::PDBInfo {lvalue},boost::shared_ptr<core::io::pdb::HeaderInformation>)
- header_information( (PDBInfo)arg1) -> HeaderInformation :
core/pose/PDBInfo.hh:542
- C++ signature :
- boost::shared_ptr<core::io::pdb::HeaderInformation const> header_information(core::pose::PDBInfo {lvalue})
- header_information( (PDBInfo)arg1) -> HeaderInformation :
core/pose/PDBInfo.hh:548
- C++ signature :
- boost::shared_ptr<core::io::pdb::HeaderInformation> header_information(core::pose::PDBInfo {lvalue})
-
icode
((PDBInfo)arg1, (int)res) → 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++ signature :
- char icode(core::pose::PDBInfo {lvalue},unsigned long)
- icode( (PDBInfo)arg1, (int)res, (str)ins_code) -> None :
Sets the insertion code of pose residue <res> to <ins_code> Returns the pdb insertion code of residue <res> example(s): See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb- C++ signature :
- void icode(core::pose::PDBInfo {lvalue},unsigned long,char)
-
is_het
((PDBInfo)arg1, (int)res, (int)atom_index) → 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++ signature :
- bool is_het(core::pose::PDBInfo {lvalue},unsigned long,unsigned long)
- is_het( (PDBInfo)arg1, (int)res, (int)atom_index, (bool)flag) -> 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++ signature :
- void is_het(core::pose::PDBInfo {lvalue},unsigned long,unsigned long,bool)
-
is_observing
((PDBInfo)arg1) → ConformationCAP :¶ 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++ signature :
- boost::weak_ptr<core::conformation::Conformation const> is_observing(core::pose::PDBInfo {lvalue})
-
modeltag
((PDBInfo)arg1) → str :¶ - Returns the model tag for a multi-model pdb
- example(s):
- pose.pdb_info().modeltag()
- See also:
- Pose PDBInfo
- C++ signature :
- std::string modeltag(core::pose::PDBInfo {lvalue})
- modeltag( (PDBInfo)arg1, (str)tag) -> None :
Sets the model tag for a multi-model pdb to <tag> example(s):
pose.pdb_info().modeltag(‘Number1’)- See also:
- Pose PDBInfo
- C++ signature :
- void modeltag(core::pose::PDBInfo {lvalue},std::string)
-
name
((PDBInfo)arg1) → str :¶ - Returns the pdb name
- example(s):
- pose.pdb_info().name()
- See also:
- Pose PDBInfo
- C++ signature :
- std::string name(core::pose::PDBInfo {lvalue})
- name( (PDBInfo)arg1, (str)s) -> None :
Sets the pdb name example(s):
pose.pdb_info().name(‘MyPDB’)- See also:
- Pose PDBInfo
- C++ signature :
- void name(core::pose::PDBInfo {lvalue},std::string)
-
natoms
((PDBInfo)arg1, (int)res) → 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++ signature :
- unsigned long natoms(core::pose::PDBInfo {lvalue},unsigned long)
-
nres
((PDBInfo)arg1) → int :¶ Returns the number of residues represented in PDBInfo example(s):
pose.pdb_info().nres()- See also:
- Pose PDBInfo
- C++ signature :
- unsigned long nres(core::pose::PDBInfo {lvalue})
-
number
((PDBInfo)arg1, (int)res) → 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++ signature :
- int number(core::pose::PDBInfo {lvalue},unsigned long)
- number( (PDBInfo)arg1, (int)res, (int)pdb_res) -> 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++ signature :
- void number(core::pose::PDBInfo {lvalue},unsigned long,int)
-
obsolete
((PDBInfo)arg1) → 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++ signature :
- bool obsolete(core::pose::PDBInfo {lvalue})
- obsolete( (PDBInfo)arg1, (bool)flag) -> 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++ signature :
- void obsolete(core::pose::PDBInfo {lvalue},bool)
-
occupancy
((PDBInfo)arg1, (int)res, (int)atom_index) → 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++ signature :
- double occupancy(core::pose::PDBInfo {lvalue},unsigned long,unsigned long)
- occupancy( (PDBInfo)arg1, (int)res, (int)atom_index, (float)occ) -> None :
Sets the occupancy of the <atom_index> atom of pose residue <res> to <occ>
- C++ signature :
- void occupancy(core::pose::PDBInfo {lvalue},unsigned long,unsigned long,double)
-
on_connection_change
((PDBInfo)arg1, (ConnectionEvent)event) → None :¶ Updates when connection to Conformation is changed
- C++ signature :
- void on_connection_change(core::pose::PDBInfo {lvalue},core::conformation::signals::ConnectionEvent)
-
on_identity_change
((PDBInfo)arg1, (IdentityEvent)event) → None :¶ Updates atom records when residue identity changes in Conformation
- C++ signature :
- void on_identity_change(core::pose::PDBInfo {lvalue},core::conformation::signals::IdentityEvent)
-
on_length_change
((PDBInfo)arg1, (LengthEvent)event) → None :¶ Updates residue and atom records when length changes in Conformation, obsoletes PDBInfo
- C++ signature :
- void on_length_change(core::pose::PDBInfo {lvalue},core::conformation::signals::LengthEvent)
-
pdb2pose
((PDBInfo)arg1, (str)chain, (int)res[, (str)icode=' ']) → int :¶ - Returns the pose numbering of the pdb residue with chain <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++ signature :
- unsigned long pdb2pose(core::pose::PDBInfo {lvalue},char,int [,char=’ ‘])
- pdb2pose( (PDBInfo)arg1) -> PDBPoseMap :
Returns the internally maintained PDBPoseMap example(s): See also:
Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb- C++ signature :
- core::pose::PDBPoseMap pdb2pose(core::pose::PDBInfo {lvalue})
-
pose2pdb
((PDBInfo)arg1, (int)res) → str :¶ Returns the pdb numbering string of pose residue <res> : pdb string contains the chainID 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++ signature :
- std::string pose2pdb(core::pose::PDBInfo {lvalue},unsigned long)
-
prepend_res
((PDBInfo)arg1, (int)res, (int)natoms[, (int)n=1]) → None :¶ Prepends residue records before given pose residue number <res> [in] res residue to prepend before (in internal/pose numbering) [in] natoms number of atoms in type of appended residue [in] n number of residue records to prepend
- C++ signature :
- void prepend_res(core::pose::PDBInfo {lvalue},unsigned long,unsigned long [,unsigned long=1])
-
rebuild_pdb2pose
((PDBInfo)arg1) → None :¶ rebuilds PDBPoseMap from scratch
- C++ signature :
- void rebuild_pdb2pose(core::pose::PDBInfo {lvalue})
-
remarks
((PDBInfo)arg1) → Remarks :¶ - Returns the pdb remarks (const)
- example(s):
- pose.pdb_info().remarks()
- See also:
- Pose PDBInfo
- C++ signature :
- core::pose::Remarks remarks(core::pose::PDBInfo {lvalue})
- remarks( (PDBInfo)arg1) -> 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++ signature :
- core::pose::Remarks {lvalue} remarks(core::pose::PDBInfo {lvalue})
- remarks( (PDBInfo)arg1, (Remarks)in) -> None :
Sets the pdb remarks to <in> example(s): See also:
Pose PDBInfo- C++ signature :
- void remarks(core::pose::PDBInfo {lvalue},core::pose::Remarks)
-
replace_res
((PDBInfo)arg1, (int)res, (int)natoms) → None :¶ “Replaces” residue record for pose residue <res> Leaves information in residue record untouched, but resizes and zeroes atom records for the residue. [in] res residue to replace [in] natoms number of atoms in type of residue
- C++ signature :
- void replace_res(core::pose::PDBInfo {lvalue},unsigned long,unsigned long)
-
replace_res_remap_bfactors
((PDBInfo)arg1, (int)res, (Residue)tgt) → None :¶ same as replace_res BUT remaps B factors from src to tgt
- C++ signature :
- void replace_res_remap_bfactors(core::pose::PDBInfo {lvalue},unsigned long,core::conformation::Residue)
-
res_haslabel
((PDBInfo)arg1, (int)res, (str)target_label) → bool :¶ uses std iterators to check if a residue has a label associated to it [in] res residue in pose numbering [in] target_label string to look for inside the labes associated to the residue
- C++ signature :
- bool res_haslabel(core::pose::PDBInfo {lvalue},unsigned long,std::string)
-
resize_atom_records
((PDBInfo)arg1, (int)res, (int)n[, (bool)zero=True]) → None :¶ - Ensures <n> atom records for residue <res> are available
: if <zero> is true, zero the atom records for this residue
- C++ signature :
- void resize_atom_records(core::pose::PDBInfo {lvalue},unsigned long,unsigned long [,bool=True])
- resize_atom_records( (PDBInfo)arg1, (int)n [, (bool)zero=True]) -> None :
Ensures <n> atom records for residue <res> are available : if <zero> is true, zero the atom records for this residue
- C++ signature :
- void resize_atom_records(core::pose::PDBInfo {lvalue},unsigned long [,bool=True])
- resize_atom_records( (PDBInfo)arg1, (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++ signature :
- void resize_atom_records(core::pose::PDBInfo {lvalue},core::pose::Pose)
-
resize_residue_records
((PDBInfo)arg1, (int)n) → 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. @warning 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++ signature :
- void resize_residue_records(core::pose::PDBInfo {lvalue},unsigned long)
-
set_chains
((PDBInfo)arg1, (str)id) → None :¶ Sets all residue chain ids to the character <id>
- C++ signature :
- void set_chains(core::pose::PDBInfo {lvalue},char)
-
set_crystinfo
((PDBInfo)arg1, (CrystInfo)crystinfoin) → None :¶ Sets the pdb crystinfo
- C++ signature :
- void set_crystinfo(core::pose::PDBInfo {lvalue},core::pose::CrystInfo)
-
set_resinfo
((PDBInfo)arg1, (int)res, (str)chain_id, (int)pdb_res[, (str)ins_code=' ']) → None :¶ Sets the chain id, pdb sequence residue numbering, and insertion code for pose residue <res> to <chain_id> , <pdb_res> , and <ins_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++ signature :
- void set_resinfo(core::pose::PDBInfo {lvalue},unsigned long,char,int [,char=’ ‘])
-
show
((PDBInfo)arg1, (OStream)out) → 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++ signature :
- void show(core::pose::PDBInfo {lvalue},std::ostream {lvalue})
-
temperature
((PDBInfo)arg1, (int)res, (int)atom_index) → 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++ signature :
- double temperature(core::pose::PDBInfo {lvalue},unsigned long,unsigned long)
- temperature( (PDBInfo)arg1, (int)res, (int)atom_index, (float)t) -> None :
Sets the temperature of the <atom_index> atom of pose residue <res> to <t>
- C++ signature :
- void temperature(core::pose::PDBInfo {lvalue},unsigned long,unsigned long,double)
-
tighten_memory
((PDBInfo)arg1) → None :¶ Tightens memory usage
- C++ signature :
- void tighten_memory(core::pose::PDBInfo {lvalue})
-
class
rosetta.core.pose.
PDBPoseMap
¶ 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.
-
assign
((PDBPoseMap)arg1, (PDBPoseMap)m) → PDBPoseMap :¶ copy assignment
- C++ signature :
- core::pose::PDBPoseMap {lvalue} assign(core::pose::PDBPoseMap {lvalue},core::pose::PDBPoseMap)
-
clear
((PDBPoseMap)arg1) → None :¶ clear the current mapping data
- C++ signature :
- void clear(core::pose::PDBPoseMap {lvalue})
-
conditional_erase
((PDBPoseMap)arg1, (str)chain, (int)pdb_res, (str)ins_code, (int)pose_res) → bool :¶ remove mapping for pdb residue key only if Pose residue matches [in] chain chain id [in] pdb_res pdb residue numbering [in] ins_code insertion code, use ‘ ‘ if no insertion code [in] pose_res the mapped Pose residue true if key-value pair erase, false otherwise
- C++ signature :
- bool conditional_erase(core::pose::PDBPoseMap {lvalue},char,int,char,unsigned long)
-
erase
((PDBPoseMap)arg1, (str)chain, (int)pdb_res, (str)ins_code) → None :¶ forcibly remove mapping for pdb residue key [in] chain chain id [in] pdb_res pdb residue numbering [in] ins_code insertion code, use ‘ ‘ if no insertion code
- C++ signature :
- void erase(core::pose::PDBPoseMap {lvalue},char,int,char)
-
fill
((PDBPoseMap)arg1, (PDBInfo)info) → None :¶ fill with corresponding pdb -> pose residue mapping does not clear any currently existing mapping data
- C++ signature :
- void fill(core::pose::PDBPoseMap {lvalue},core::pose::PDBInfo)
-
find
((PDBPoseMap)arg1, (str)chain, (int)pdb_res[, (str)ins_code=' ']) → int :¶ lookup pose numbering [in] chain chain id [in] pdb_res pdb residue numbering [in] ins_code insertion code pose numbering for residue, returns 0 if not found
- C++ signature :
- unsigned long find(core::pose::PDBPoseMap {lvalue},char,int [,char=’ ‘])
-
insert
((PDBPoseMap)arg1, (str)chain, (int)pdb_res, (str)ins_code, (int)pose_res) → None :¶ insert pdb -> pose number mapping [in] chain chain id [in] pdb_res pdb residue numbering [in] ins_code insertion code, use ‘ ‘ if no insertion code [in] pose_res pose numbering for residue @remarks if the chain is equal to the PDBInfo’s empty record character,
the insertion will be skipped- C++ signature :
- void insert(core::pose::PDBPoseMap {lvalue},char,int,char,unsigned long)
-
size
((PDBPoseMap)arg1) → int :¶ number of mappings
- C++ signature :
- unsigned long size(core::pose::PDBPoseMap {lvalue})
-
-
class
rosetta.core.pose.
Pose
¶ - A molecular system including residues, kinematics, and energies
- 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:
- to update the xyz coordinates in response to changes to internal degrees of freedom, and
- to update internal coordinates when the user modifes the xyz (Cartesian) coords,
- Scoring:
- to keep track of what parts of the structure have changed since the last score evaluation, and
- 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.energies Pose.fold_tree Pose.pdb_info Pose.residue Pose.sequence Pose.total_residue-
aa
((Pose)arg1, (int)seqpos) → AA :¶ Returns the chemical::AA of the residue at <seqpos> example(s):
pose.aa(17)- See also:
- Pose
- Pose.Residue
- Pose.sequence Residue
- C++ signature :
- core::chemical::AA aa(core::pose::Pose {lvalue},unsigned long)
-
add_constraint
((Pose)arg1, (__CPP_Constraint__)cst) → Constraint :¶ adding a constraint is done by cloning the input constraint. A const copy is then returned
- C++ signature :
- boost::shared_ptr<core::scoring::constraints::Constraint const> add_constraint(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::constraints::Constraint const>)
-
add_constraints
((Pose)arg1, (object)csts) → object :¶ core/pose/Pose.hh:350
- C++ signature :
- utility::vector1<boost::shared_ptr<core::scoring::constraints::Constraint const>, std::allocator<boost::shared_ptr<core::scoring::constraints::Constraint const> > > add_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::scoring::constraints::Constraint const>, std::allocator<boost::shared_ptr<core::scoring::constraints::Constraint const> > >)
-
alpha
((Pose)arg1, (int)pos) → 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++ signature :
- double alpha(core::pose::Pose {lvalue},unsigned long)
-
annotated_sequence
((Pose)arg1[, (bool)show_all_variants=False]) → 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.total_residue
Residue
- C++ signature :
- std::string annotated_sequence(core::pose::Pose {lvalue} [,bool=False])
-
append_polymer_residue_after_seqpos
((Pose)arg1, (Residue)new_rsd, (int)seqpos, (bool)build_ideal_geometry) → None :¶ glues to seqpos and perhaps also seqpos+1
- C++ signature :
- void append_polymer_residue_after_seqpos(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long,bool)
-
append_pose_by_jump
((Pose)arg1, (Pose)src, (int)jump_anchor_residue[, (str)jump_anchor_atom=''[, (str)jump_root_atom='']]) → None :¶ Appends source pose conformation to pose by a new jump
- C++ signature :
- void append_pose_by_jump(core::pose::Pose {lvalue},core::pose::Pose,unsigned long [,std::string=’’ [,std::string=’‘]])
-
append_residue_by_bond
((Pose)arg1, (Residue)new_rsd[, (bool)build_ideal_geometry=False[, (int)connection=0[, (int)anchor_residue=0[, (int)anchor_connection=0[, (bool)start_new_chain=False[, (bool)lookup_bond_length=False]]]]]]) → 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++ signature :
- void append_residue_by_bond(core::pose::Pose {lvalue},core::conformation::Residue [,bool=False [,int=0 [,unsigned long=0 [,int=0 [,bool=False [,bool=False]]]]]])
-
append_residue_by_jump
((Pose)arg1, (Residue)new_rsd, (int)jump_anchor_residue[, (str)jump_anchor_atom=''[, (str)jump_root_atom=''[, (bool)start_new_chain=False]]]) → None :¶ - Appends <new_rsd> (a residue) to pose by a new jump
- C++ signature :
- void append_residue_by_jump(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long [,std::string=’’ [,std::string=’’ [,bool=False]]])
-
apply_transform_Rx_plus_v
((Pose)arg1, (xyzMatrix_Real)R, (xyzVector_Real)v) → None :¶ Apply a transform of the Rx + v form, where R is a rotation matrix and v is a translation vector.
- C++ signature :
- void apply_transform_Rx_plus_v(core::pose::Pose {lvalue},numeric::xyzMatrix<double>,numeric::xyzVector<double>)
-
assign
((Pose)arg1, (Pose)src) → Pose :¶ Copies <src> into the pose example(s):
test_pose.assign(pose)- See also:
- Pose
- C++ signature :
- core::pose::Pose {lvalue} assign(core::pose::Pose {lvalue},core::pose::Pose)
-
atom_tree
((Pose)arg1) → AtomTree :¶ Returns the pose AtomTree
- C++ signature :
- core::kinematics::AtomTree atom_tree(core::pose::Pose {lvalue})
-
batch_get_xyz
((Pose)arg1, (vector1_AtomID)ids, (vector1_xyzVector_Real)points) → None :¶ Gets the locations (xyz) of pose AtomIDs in <ids>
- C++ signature :
- void batch_get_xyz(core::pose::Pose {lvalue},utility::vector1<core::id::AtomID, std::allocator<core::id::AtomID> >,utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > > {lvalue})
-
batch_set_xyz
((Pose)arg1, (vector1_AtomID)ids, (vector1_xyzVector_Real)points) → None :¶ Sets the locations (xyz) of pose AtomIDs in <ids> to mathcing PointPositions in <points>
- C++ signature :
- void batch_set_xyz(core::pose::Pose {lvalue},utility::vector1<core::id::AtomID, std::allocator<core::id::AtomID> >,utility::vector1<numeric::xyzVector<double>, std::allocator<numeric::xyzVector<double> > >)
-
beta
((Pose)arg1, (int)seqpos) → 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++ signature :
- double beta(core::pose::Pose {lvalue},unsigned long)
-
center
((Pose)arg1) → None :¶ Sets pose coordinates such that the pose center is at the Euclidean origin
- C++ signature :
- void center(core::pose::Pose {lvalue})
-
chain
((Pose)arg1, (int)seqpos) → int :¶ Returns the chain number of residue <seqpos> example(s):
pose.chain(3)- See also:
- Pose Pose.annotated_sequence
- Pose.chain_sequence
- Pose.fold_tree Pose.sequence FoldTree
- C++ signature :
- int chain(core::pose::Pose {lvalue},unsigned long)
-
chain_sequence
((Pose)arg1, (int)chain_in) → str :¶ Returns the sequence for the chain <chain_in> Example(s):
pose.chain_sequence(1)- See also:
- Pose Pose.chain Pose.residue Pose.sequence
- C++ signature :
- std::string chain_sequence(core::pose::Pose {lvalue},unsigned long)
-
chi
((Pose)arg1, (int)chino, (int)seqpos) → 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++ signature :
- double chi(core::pose::Pose {lvalue},int,unsigned long)
- chi( (Pose)arg1, (int)seqpos) -> 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++ signature :
- double chi(core::pose::Pose {lvalue},unsigned long)
-
clear
((Pose)arg1) → None :¶ Empty the pose contents example(s):
pose.clear()- See also:
- Pose Pose.assign Pose.empty
- C++ signature :
- void clear(core::pose::Pose {lvalue})
-
clone
((Pose)arg1) → Pose :¶ clone the conformation
- C++ signature :
- boost::shared_ptr<core::pose::Pose> clone(core::pose::Pose {lvalue})
-
conformation
((Pose)arg1) → Conformation :¶ Returns the pose Conformation (const-access)
- example(s):
- pose.Conformation()
- See also:
- Pose Conformation
- C++ signature :
- core::conformation::Conformation conformation(core::pose::Pose {lvalue})
- conformation( (Pose)arg1) -> Conformation :
Returns the pose Conformation (non-const access)
- C++ signature :
- core::conformation::Conformation {lvalue} conformation(core::pose::Pose {lvalue})
-
conformation_ptr
((Pose)arg1) → Conformation :¶ Returns the pose Conformation pointer (const access)
- C++ signature :
- boost::shared_ptr<core::conformation::Conformation const> conformation_ptr(core::pose::Pose {lvalue})
- conformation_ptr( (Pose)arg1) -> __CPP_Conformation__ :
Returns the pose Conformation pointer (const access)
- C++ signature :
- boost::shared_ptr<core::conformation::Conformation> {lvalue} conformation_ptr(core::pose::Pose {lvalue})
-
constraint_set
((Pose)arg1) → ConstraintSet :¶ core/pose/Pose.hh:343
- C++ signature :
- boost::shared_ptr<core::scoring::constraints::ConstraintSet const> constraint_set(core::pose::Pose {lvalue})
- constraint_set( (Pose)arg1, (__CPP_ConstraintSet__)) -> None :
core/pose/Pose.hh:370
- C++ signature :
- void constraint_set(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::constraints::ConstraintSet>)
-
copy_segment
((Pose)arg1, (int)size, (Pose)src, (int)begin, (int)src_begin) → None :¶ Copy a stretch of coordinates/torsions from <src> to pose
- C++ signature :
- void copy_segment(core::pose::Pose {lvalue},unsigned long,core::pose::Pose,unsigned long,unsigned long)
-
data
((Pose)arg1) → BasicDataCache :¶ - BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh
- C++ signature :
- basic::datacache::BasicDataCache data(core::pose::Pose {lvalue})
- data( (Pose)arg1) -> BasicDataCache :
BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh
- C++ signature :
- basic::datacache::BasicDataCache {lvalue} data(core::pose::Pose {lvalue})
-
delete_polymer_residue
((Pose)arg1, (int)seqpos) → None :¶ core/pose/Pose.hh:518
- C++ signature :
- void delete_polymer_residue(core::pose::Pose {lvalue},unsigned long)
-
delta
((Pose)arg1, (int)pos) → 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++ signature :
- double delta(core::pose::Pose {lvalue},unsigned long)
-
dof
((Pose)arg1, (DOF_ID)id) → float :¶ Returns the value of the AtomTree DOF <id>
- See also:
- Pose DOF_ID
- C++ signature :
- double dof(core::pose::Pose {lvalue},core::id::DOF_ID)
-
dump_pdb
((Pose)arg1, (str)file_name[, (str)tag='1']) → bool :¶ - Export pose data to the PDB file <file_name>
- example(s):
- pose.dump_pdb(‘new_01.pdb’)
- See also:
- Pose pose_from_pdb
- C++ signature :
- bool dump_pdb(core::pose::Pose {lvalue},std::string [,std::string=‘1’])
- dump_pdb( (Pose)arg1, (OStream)out [, (str)tag=‘1’]) -> None :
core/pose/Pose.hh:1351
- C++ signature :
- void dump_pdb(core::pose::Pose {lvalue},std::ostream {lvalue} [,std::string=‘1’])
- dump_pdb( (Pose)arg1, (OStream)out, (vector1_Size)residue_indices [, (str)tag=‘1’]) -> None :
for writing a specified subset of residues in pdb format
- C++ signature :
- void dump_pdb(core::pose::Pose {lvalue},std::ostream {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> > [,std::string=‘1’])
-
dump_scored_pdb
((Pose)arg1, (str)file_name, (ScoreFunction)scorefxn[, (str)tag='1']) → None :¶ Export pose data to the PDB file <file_name>, add some score output
- C++ signature :
- void dump_scored_pdb(core::pose::Pose {lvalue},std::string,core::scoring::ScoreFunction [,std::string=‘1’])
-
empty
((Pose)arg1) → bool :¶ Returns true if there are no residues in the conformation example(s):
pose.empty()- See also:
- Pose Pose.clear
- Pose.sequence
- Pose.total_residue
- C++ signature :
- bool empty(core::pose::Pose {lvalue})
-
energies
((Pose)arg1) → Energies :¶ Returns the pose Energies (const-access)
- example(s):
- pose.energies()
- See also:
- Pose Energies PDBInfo ScoreFunction create_score_function
- C++ signature :
- core::scoring::Energies energies(core::pose::Pose {lvalue})
- energies( (Pose)arg1) -> Energies :
Returns the pose Energies (non-const access)
- C++ signature :
- core::scoring::Energies {lvalue} energies(core::pose::Pose {lvalue})
-
epsilon
((Pose)arg1, (int)seqpos) → 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++ signature :
- double epsilon(core::pose::Pose {lvalue},unsigned long)
-
fold_tree
((Pose)arg1) → FoldTree :¶ - Returns the pose FoldTree
- example(s):
- pose.fold_tree()
- See also:
- Pose FoldTree
- C++ signature :
- core::kinematics::FoldTree fold_tree(core::pose::Pose {lvalue})
- fold_tree( (Pose)arg1, (FoldTree)fold_tree_in) -> None :
Sets the pose FoldTree to <fold_tree_in> example(s):
pose.fold_tree( foldtree )- See also:
- Pose pose.fold_tree FoldTree
- C++ signature :
- void fold_tree(core::pose::Pose {lvalue},core::kinematics::FoldTree)
-
gamma
((Pose)arg1, (int)seqpos) → 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++ signature :
- double gamma(core::pose::Pose {lvalue},unsigned long)
-
get_self_ptr
((Pose)arg1) → Pose :¶ self pointers
- C++ signature :
- boost::shared_ptr<core::pose::Pose const> get_self_ptr(core::pose::Pose {lvalue})
- get_self_ptr( (Pose)arg1) -> Pose :
core/pose/Pose.hh:209
- C++ signature :
- boost::shared_ptr<core::pose::Pose> get_self_ptr(core::pose::Pose {lvalue})
-
get_self_weak_ptr
((Pose)arg1) → PoseCAP :¶ core/pose/Pose.hh:210
- C++ signature :
- boost::weak_ptr<core::pose::Pose const> get_self_weak_ptr(core::pose::Pose {lvalue})
- get_self_weak_ptr( (Pose)arg1) -> PoseAP :
core/pose/Pose.hh:211
- C++ signature :
- boost::weak_ptr<core::pose::Pose> get_self_weak_ptr(core::pose::Pose {lvalue})
-
has_dof
((Pose)arg1, (DOF_ID)id) → bool :¶ Returns true if pose has DOF <id> See also:
Pose DOF_ID- C++ signature :
- bool has_dof(core::pose::Pose {lvalue},core::id::DOF_ID)
-
insert_residue_by_bond
((Pose)arg1, (Residue)new_rsd_in, (int)seqpos, (int)anchor_pos[, (bool)build_ideal_geometry=False[, (str)anchor_atom=''[, (str)root_atom=''[, (bool)new_chain=False[, (bool)lookup_bond_length=False]]]]]) → None :¶ This code sorely belongs in Pose.cc Adds <new_rsd_in> to pose at <seqpos>
- C++ signature :
- void insert_residue_by_bond(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long,unsigned long [,bool=False [,std::string=’’ [,std::string=’’ [,bool=False [,bool=False]]]]])
-
insert_residue_by_jump
((Pose)arg1, (Residue)new_rsd_in, (int)seqpos, (int)anchor_pos[, (str)anchor_atomno=''[, (str)root_atomno='']]) → None :¶ This code sorely belongs in Pose.cc Adds <new_rsd_in> to pose at <seqpos>
- C++ signature :
- void insert_residue_by_jump(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long,unsigned long [,std::string=’’ [,std::string=’‘]])
-
is_centroid
((Pose)arg1) → bool :¶ Returns true if pose is ResidueType centroid convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) example(s):
pose.is_centroid()- See also:
- Pose Pose.is_fullatom Residue ResidueType
this is nt a good test –Doug
- C++ signature :
- bool is_centroid(core::pose::Pose {lvalue})
-
is_fullatom
((Pose)arg1) → bool :¶ Returns true if pose is ResidueType fullatom convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) example(s):
pose.is_fullatom()- See also:
- Pose Pose.is_centroid Residue ResidueType
this is nt a good test –Doug
- C++ signature :
- bool is_fullatom(core::pose::Pose {lvalue})
-
jump
((Pose)arg1, (int)jump_number) → Jump :¶ - Returns the pose FoldTree Jump <jump_number>
- example(s):
- pose.jump(1)
- See also:
- Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge Jump
- C++ signature :
- core::kinematics::Jump jump(core::pose::Pose {lvalue},int)
- jump( (Pose)arg1, (AtomID)id) -> Jump :
Returns the pose FoldTree Jump <id> example(s):
pose.set_jump(R5N)- See also:
- Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge AtomID
- C++ signature :
- core::kinematics::Jump jump(core::pose::Pose {lvalue},core::id::AtomID)
-
metric
((Pose)arg1, (str)calculator_name, (str)key, (MetricValueBase)val) → None :¶ core/pose/Pose.hh:401
- C++ signature :
- void metric(core::pose::Pose {lvalue},std::string,std::string,basic::MetricValueBase {lvalue})
-
n_residue
((Pose)arg1) → int :¶ Returns the number of residues in the pose conformation example(s):
pose.n_residue()- See also:
- Pose Pose.sequence Pose.total_residue
- C++ signature :
- unsigned long n_residue(core::pose::Pose {lvalue})
-
num_jump
((Pose)arg1) → int :¶ Returns the number of jumps in the pose FoldTree example(s):
pose.num_jump()- See also:
- Pose Pose.jump Pose.set_jump FoldTree Jump
- C++ signature :
- unsigned long num_jump(core::pose::Pose {lvalue})
-
observer_cache
((Pose)arg1) → ObserverCache :¶ ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh
- C++ signature :
- core::pose::datacache::ObserverCache observer_cache(core::pose::Pose {lvalue})
- observer_cache( (Pose)arg1) -> ObserverCache :
ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh
- C++ signature :
- core::pose::datacache::ObserverCache {lvalue} observer_cache(core::pose::Pose {lvalue})
-
omega
((Pose)arg1, (int)seqpos) → float :¶ Returns the omega torsion angle of residue <seqpos> assumes the residue is an amino acid or monosaccharide example(s):
pose.omega(3)- See also:
- Pose Pose.residue Pose.set_omega Residue
- C++ signature :
- double omega(core::pose::Pose {lvalue},unsigned long)
-
pdb_info
((Pose)arg1) → PDBInfo :¶ - Returns the pose PDBInfo (const)
- example(s):
- pose.pdb_info()
- See also:
- Pose Energies PDBInfo
ScoreFunction pose_from_pdb NULL if no PDBInfo instance exists, the pdb info instance otherwise
- C++ signature :
- boost::shared_ptr<core::pose::PDBInfo const> pdb_info(core::pose::Pose {lvalue})
- pdb_info( (Pose)arg1) -> PDBInfo :
Returns the pose PDBInfo NULL if no PDBInfo instance exists, the PDBInfo instance otherwise
- C++ signature :
- boost::shared_ptr<core::pose::PDBInfo> pdb_info(core::pose::Pose {lvalue})
- pdb_info( (Pose)arg1, (PDBInfo)new_info) -> PDBInfo :
Sets pose PDBInfo to <new_info> [in] <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++ signature :
- boost::shared_ptr<core::pose::PDBInfo> pdb_info(core::pose::Pose {lvalue},boost::shared_ptr<core::pose::PDBInfo>)
-
phi
((Pose)arg1, (int)seqpos) → float :¶ Returns the phi torsion angle of residue <seqpos> assumes the residue is an amino acid or monosaccharide
- example(s):
- pose.phi(1)
- See also:
- Pose Pose.residue Pose.set_phi Residue
- C++ signature :
- double phi(core::pose::Pose {lvalue},unsigned long)
-
prepend_polymer_residue_before_seqpos
((Pose)arg1, (Residue)new_rsd, (int)seqpos, (bool)build_ideal_geometry) → None :¶ glues to seqpos and perhaps also seqpos-1
- C++ signature :
- void prepend_polymer_residue_before_seqpos(core::pose::Pose {lvalue},core::conformation::Residue,unsigned long,bool)
-
print_metric
((Pose)arg1, (str)calculator_name, (str)key) → str :¶ core/pose/Pose.hh:404
- C++ signature :
- std::string print_metric(core::pose::Pose {lvalue},std::string,std::string)
-
psi
((Pose)arg1, (int)seqpos) → float :¶ Returns the psi torsion angle of residue <seqpos> 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++ signature :
- double psi(core::pose::Pose {lvalue},unsigned long)
-
remove_constraint
((Pose)arg1, (__CPP_Constraint__)cst[, (bool)object_comparison=False]) → bool :¶ re object_comparison see comment for ConstraintSet::remove_constraint function
- C++ signature :
- bool remove_constraint(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::constraints::Constraint const> [,bool=False])
-
remove_constraints
((Pose)arg1, (object)csts[, (bool)object_comparison=False]) → bool :¶ re object_comparison see comment for ConstraintSet::remove_constraint function
- C++ signature :
- bool remove_constraints(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::scoring::constraints::Constraint const>, std::allocator<boost::shared_ptr<core::scoring::constraints::Constraint const> > > [,bool=False])
- remove_constraints( (Pose)arg1) -> bool :
core/pose/Pose.hh:367
- C++ signature :
- bool remove_constraints(core::pose::Pose {lvalue})
-
replace_residue
((Pose)arg1, (int)seqpos, (Residue)new_rsd_in, (bool)orient_backbone) → None :¶ Replaces the residue at <seqpos> with <new_rsd_in>
- C++ signature :
- void replace_residue(core::pose::Pose {lvalue},unsigned long,core::conformation::Residue,bool)
- replace_residue( (Pose)arg1, (int)seqpos, (Residue)new_rsd_in, (vector1_pair_string_string)atom_pairs) -> 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++ signature :
- void replace_residue(core::pose::Pose {lvalue},int,core::conformation::Residue,utility::vector1<std::pair<std::string, std::string>, std::allocator<std::pair<std::string, std::string> > >)
-
residue
((Pose)arg1, (int)seqpos) → 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.total_residue Residue ResidueType
- C++ signature :
- core::conformation::Residue residue(core::pose::Pose {lvalue},unsigned long)
-
residue_type
((Pose)arg1, (int)seqpos) → 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.sequence Pose.total_residue Residue ResidueType
- C++ signature :
- core::chemical::ResidueType residue_type(core::pose::Pose {lvalue},unsigned long)
-
scoring_begin
((Pose)arg1, (ScoreFunction)info) → None :¶ Called by ScoreFunction at the beginning of scoring
- C++ signature :
- void scoring_begin(core::pose::Pose {lvalue},core::scoring::ScoreFunction)
-
scoring_end
((Pose)arg1, (ScoreFunction)scorefxn) → None :¶ Called by ScoreFunction at the end of scoring
- C++ signature :
- void scoring_end(core::pose::Pose {lvalue},core::scoring::ScoreFunction)
-
secstruct
((Pose)arg1, (int)seqpos) → 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 ‘S’ = strand or sheet ‘E’ = loop JKL: is this correct? DsspDesignOperations says that H = helix, E = strand, and L = loop example(s):
pose.secstruct(3)- See also:
- Pose Pose.residue Pose.set_secstruct Residue
- C++ signature :
- char secstruct(core::pose::Pose {lvalue},unsigned long)
- secstruct( (Pose)arg1) -> str :
Returns a string representing pose secondary structure example(s):
pose.secstruct()- See also:
- Pose Pose.residue Pose.set_secstruct Residue
- C++ signature :
- std::string secstruct(core::pose::Pose {lvalue})
-
sequence
((Pose)arg1) → 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.total_residue
- C++ signature :
- std::string sequence(core::pose::Pose {lvalue})
-
set_alpha
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_alpha(core::pose::Pose {lvalue},unsigned long,double)
-
set_beta
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_beta(core::pose::Pose {lvalue},unsigned long,double)
-
set_chi
((Pose)arg1, (int)chino, (int)seqpos, (float)setting) → 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++ signature :
- void set_chi(core::pose::Pose {lvalue},int,unsigned long,double)
- set_chi( (Pose)arg1, (int)seqpos, (float)setting) -> 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++ signature :
- void set_chi(core::pose::Pose {lvalue},unsigned long,double)
-
set_delta
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_delta(core::pose::Pose {lvalue},unsigned long,double)
-
set_dof
((Pose)arg1, (DOF_ID)id, (float)setting) → None :¶ Sets the value of the AtomTree DOF <id> See also:
Pose DOF_ID- C++ signature :
- void set_dof(core::pose::Pose {lvalue},core::id::DOF_ID,double)
-
set_epsilon
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_epsilon(core::pose::Pose {lvalue},unsigned long,double)
-
set_gamma
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_gamma(core::pose::Pose {lvalue},unsigned long,double)
-
set_jump
((Pose)arg1, (int)jump_number, (Jump)new_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++ signature :
- void set_jump(core::pose::Pose {lvalue},int,core::kinematics::Jump)
- set_jump( (Pose)arg1, (AtomID)id, (Jump)new_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++ signature :
- void set_jump(core::pose::Pose {lvalue},core::id::AtomID,core::kinematics::Jump)
-
set_new_conformation
((Pose)arg1, (__CPP_Conformation__)new_conformation) → None :¶ Now that the conformation_ member data is an owning pointer, and we have derived classes of Conformation.
- C++ signature :
- void set_new_conformation(core::pose::Pose {lvalue},boost::shared_ptr<core::conformation::Conformation const>)
-
set_new_energies_object
((Pose)arg1, (__CPP_Energies__)energies) → None :¶ Now that the energies_ member data is an owning pointer, and we have derived classes of Energies.
- C++ signature :
- void set_new_energies_object(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::Energies>)
-
set_omega
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_omega(core::pose::Pose {lvalue},unsigned long,double)
-
set_phi
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_phi(core::pose::Pose {lvalue},unsigned long,double)
-
set_psi
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_psi(core::pose::Pose {lvalue},unsigned long,double)
-
set_ring_conformation
((Pose)arg1, (int)seqpos, (RingConformer)conformer) → None :¶ Set the given residue’s ring conformation, if appropriate.
- C++ signature :
- void set_ring_conformation(core::pose::Pose {lvalue},unsigned long,core::chemical::RingConformer)
-
set_secstruct
((Pose)arg1, (int)seqpos, (str)setting) → 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++ signature :
- void set_secstruct(core::pose::Pose {lvalue},unsigned long,char)
-
set_theta
((Pose)arg1, (int)seqpos, (float)setting) → None :¶ Sets the theta torsion angle of beta-amino acid residue <seqpos> to <setting> <setting> must be in degrees, assumes residue is a beta-amino acid. example(s):
pose.set_theta(21, 58.9)- See also:
- Pose Pose.theta Pose.residue Residue
Vikram K. Mulligan (vmullig@uw.edu)
- C++ signature :
- void set_theta(core::pose::Pose {lvalue},unsigned long,double)
-
set_torsion
((Pose)arg1, (TorsionID)id, (float)setting) → None :¶ Sets the Conformation torsion angle identified by <id> to <setting> See also:
Pose TorsionID- C++ signature :
- void set_torsion(core::pose::Pose {lvalue},core::id::TorsionID,double)
-
set_xyz
((Pose)arg1, (AtomID)id, (xyzVector_Real)point) → None :¶ - Sets the location (xyz) of pose AtomID <id> to
the PointPosition <point> See also:
Pose Pose.residue Pose.xyz Residue- C++ signature :
- void set_xyz(core::pose::Pose {lvalue},core::id::AtomID,numeric::xyzVector<double>)
- set_xyz( (Pose)arg1, (NamedAtomID)id, (xyzVector_Real)point) -> None :
Sets the location (xyz) of pose NamedAtomID <id> to the PointPosition <point> See also:
Pose Pose.residue Pose.xyz Residue- C++ signature :
- void set_xyz(core::pose::Pose {lvalue},core::id::NamedAtomID,numeric::xyzVector<double>)
-
set_zeta
((Pose)arg1, (int)seqpos, (float)setting) → 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++ signature :
- void set_zeta(core::pose::Pose {lvalue},unsigned long,double)
-
split_by_chain
((Pose)arg1) → vector1_PoseOP :¶ Returns a vector of poses with one element per chain of the original pose
- C++ signature :
- utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > split_by_chain(core::pose::Pose {lvalue})
- split_by_chain( (Pose)arg1, (int)chain_id) -> Pose :
core/pose/Pose.hh:305
- C++ signature :
- boost::shared_ptr<core::pose::Pose> split_by_chain(core::pose::Pose {lvalue},unsigned long)
-
stub_from_id
((Pose)arg1, (NamedStubID)id) → Stub :¶ core/pose/Pose.hh:1290
- C++ signature :
- core::kinematics::Stub stub_from_id(core::pose::Pose {lvalue},core::id::NamedStubID)
-
theta
((Pose)arg1, (int)seqpos) → float :¶ Returns the theta torsion angle of beta-amino acid residue <seqpos> assumes residue is a beta-amino acid. example(s):
pose.theta(21)- See also:
- Pose Pose.set_theta Pose.residue Residue
Vikram K. Mulligan (vmullig@uw.edu)
- C++ signature :
- double theta(core::pose::Pose {lvalue},unsigned long)
-
torsion
((Pose)arg1, (TorsionID)id) → float :¶ Returns the Conformation torsion angle identified by <id>
- See also:
- Pose TorsionID
- C++ signature :
- double torsion(core::pose::Pose {lvalue},core::id::TorsionID)
-
total_atoms
((Pose)arg1) → int :¶ - Returns the total number of atoms in the pose conformation
- example:
- pose.total_atoms()
- C++ signature :
- unsigned long total_atoms(core::pose::Pose {lvalue})
- total_atoms( (Pose)arg1, (int)nres) -> int :
Returns the total number of atoms in the pose up to a particular residue
- C++ signature :
- unsigned long total_atoms(core::pose::Pose {lvalue},unsigned long)
-
total_residue
((Pose)arg1) → int :¶ Returns the number of residues in the pose conformation example(s):
pose.total_residue()- See also:
- Pose Pose.n_residue Pose.sequence
- C++ signature :
- unsigned long total_residue(core::pose::Pose {lvalue})
-
transfer_constraint_set
((Pose)arg1, (Pose)pose) → None :¶ core/pose/Pose.hh:372
- C++ signature :
- void transfer_constraint_set(core::pose::Pose {lvalue},core::pose::Pose)
-
update_actcoord
((Pose)arg1, (int)resid) → None :¶ Updates the action coordinates for pose residue <resid>
- C++ signature :
- void update_actcoord(core::pose::Pose {lvalue},unsigned long)
-
update_actcoords
((Pose)arg1) → None :¶ Called by PairEPotential to update the action coordinates for all residues
- C++ signature :
- void update_actcoords(core::pose::Pose {lvalue})
-
update_orbital_coords
((Pose)arg1, (int)resid) → None :¶ core/pose/Pose.hh:1320
- C++ signature :
- void update_orbital_coords(core::pose::Pose {lvalue},unsigned long)
-
update_pose_chains_from_pdb_chains
((Pose)arg1) → None :¶ Updates the pose chain IDs to match the pdb chain IDs.
- C++ signature :
- void update_pose_chains_from_pdb_chains(core::pose::Pose {lvalue})
-
update_residue_neighbors
((Pose)arg1) → None :¶ Updates neighbor links in the pose Energies object
- C++ signature :
- void update_residue_neighbors(core::pose::Pose {lvalue})
-
xyz
((Pose)arg1, (AtomID)id) → xyzVector_Real :¶ - 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++ signature :
- numeric::xyzVector<double> xyz(core::pose::Pose {lvalue},core::id::AtomID)
- xyz( (Pose)arg1, (NamedAtomID)id) -> xyzVector_Real :
Returns the location (xyz) of pose NamedAtomID <id> Tutorial soon... See also:
Pose Pose.residue NamedAtomID Residue Residue.xyz- C++ signature :
- numeric::xyzVector<double> xyz(core::pose::Pose {lvalue},core::id::NamedAtomID)
-
zeta
((Pose)arg1, (int)seqpos) → 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++ signature :
- double zeta(core::pose::Pose {lvalue},unsigned long)
-
class
rosetta.core.pose.
PoseCoordPickMode
¶ core/pose/xyzStripeHashPose.fwd.hh:19
-
rosetta.core.pose.
QQQ_PosePyObserverTesterFunction
() → None :¶ - C++ signature :
- void QQQ_PosePyObserverTesterFunction()
-
class
rosetta.core.pose.
RemarkInfo
¶ core/pose/Remarks.hh:32
-
class
rosetta.core.pose.
Remarks
¶ core/pose/Remarks.hh:50
-
class
rosetta.core.pose.
SingletonBase_T_core_chemical_ChemicalManager_T
¶ SingletonBase is meant to serve as a base class for singleton classes in Rosetta handling the initialization of the singleton in a thread-safe way. The derived class must a) implement a private, static function: T * create_singleton_instance() so that the SingletonBase class can invoke this function, and b) declare the SingletonBase class to be a friend, so that it can invoke this function The .cc file in which the derived singleton must be put will need to include the definitions for the two static data members, instance_ and singleton_mutex_.
-
static
get_instance
() → ChemicalManager :¶ Safely instantiate a singleton class in a (possibly) multithreaded context. In the non-multithreaded case, this simply checks the singleton’s instance member; in the multithreaded case, it checks the instance member, then it obtains the singleton’s instance-creation mutex, then it checks the instance member again, to ensure that no other thread has already created the instance, it creates the instance, and then it releases the mutex.
- C++ signature :
- core::chemical::ChemicalManager* get_instance()
-
static
-
class
rosetta.core.pose.
UnrecognizedAtomRecord
¶ info about an atom in a unrecognized res (not in pose, but we want to remember it)
-
atom_name
((UnrecognizedAtomRecord)arg1) → str :¶ core/pose/PDBInfo.hh:75
- C++ signature :
- std::string atom_name(core::pose::UnrecognizedAtomRecord {lvalue})
-
coords
((UnrecognizedAtomRecord)arg1) → xyzVector_Real :¶ core/pose/PDBInfo.hh:76
- C++ signature :
- numeric::xyzVector<double> coords(core::pose::UnrecognizedAtomRecord {lvalue})
-
res_name
((UnrecognizedAtomRecord)arg1) → str :¶ core/pose/PDBInfo.hh:74
- C++ signature :
- std::string res_name(core::pose::UnrecognizedAtomRecord {lvalue})
-
res_num
((UnrecognizedAtomRecord)arg1) → int :¶ core/pose/PDBInfo.hh:73
- C++ signature :
- unsigned long res_num(core::pose::UnrecognizedAtomRecord {lvalue})
-
temp
((UnrecognizedAtomRecord)arg1) → float :¶ core/pose/PDBInfo.hh:77
- C++ signature :
- double temp(core::pose::UnrecognizedAtomRecord {lvalue})
-
-
rosetta.core.pose.
addVirtualResAsRoot
((xyzVector_Real)xyz, (Pose)pose) → None :¶ - Adds a virtual residue to the end of the pose at the specified location.
Roots the structure on this residue.
- C++ signature :
- void addVirtualResAsRoot(numeric::xyzVector<double>,core::pose::Pose {lvalue})
- addVirtualResAsRoot( (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++ signature :
- void addVirtualResAsRoot(core::pose::Pose {lvalue})
-
rosetta.core.pose.
add_comment
((Pose)pose, (str)key, (str)val) → 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++ signature :
- void add_comment(core::pose::Pose {lvalue},std::string,std::string)
-
rosetta.core.pose.
add_lower_terminus_type_to_pose_residue
((Pose)pose, (int)seqpos) → None :¶ core/pose/util.hh:436
- C++ signature :
- void add_lower_terminus_type_to_pose_residue(core::pose::Pose {lvalue},unsigned long)
-
rosetta.core.pose.
add_score_line_string
((Pose)pose, (str)key, (str)val) → None :¶ Dumps a pdb with comments at end of file 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++ signature :
- void add_score_line_string(core::pose::Pose {lvalue},std::string,std::string)
-
rosetta.core.pose.
add_upper_terminus_type_to_pose_residue
((Pose)pose, (int)seqpos) → None :¶ core/pose/util.hh:443
- C++ signature :
- void add_upper_terminus_type_to_pose_residue(core::pose::Pose {lvalue},unsigned long)
-
rosetta.core.pose.
add_variant_type_to_pose_residue
((Pose)pose, (VariantType)variant_type, (int)seqpos) → None :¶ Construct a variant of an existing pose residue.
- C++ signature :
- void add_variant_type_to_pose_residue(core::pose::Pose {lvalue},core::chemical::VariantType,unsigned long)
-
rosetta.core.pose.
add_variant_type_to_residue
((Residue)old_rsd, (VariantType)variant_type, (Pose)pose) → Residue :¶ Construct a variant of an existing residue.
- C++ signature :
- boost::shared_ptr<core::conformation::Residue> add_variant_type_to_residue(core::conformation::Residue,core::chemical::VariantType,core::pose::Pose)
-
rosetta.core.pose.
annotated_to_oneletter_sequence
((str)annotated_seq) → str :¶ Returns the oneletter_sequence that corresponds to the given annotated sequence.
- C++ signature :
- std::string annotated_to_oneletter_sequence(std::string)
-
rosetta.core.pose.
append_pose_to_pose
((Pose)pose1, (Pose)pose2[, (bool)new_chain=True]) → None :¶ Append residues of pose2 to pose1.
- C++ signature :
- void append_pose_to_pose(core::pose::Pose {lvalue},core::pose::Pose [,bool=True])
-
rosetta.core.pose.
append_subpose_to_pose
((Pose)pose1, (Pose)pose2, (int)start_res, (int)end_res[, (bool)new_chain=True]) → None :¶ Append specified residues of pose2 to pose1.
- C++ signature :
- void append_subpose_to_pose(core::pose::Pose {lvalue},core::pose::Pose,unsigned long,unsigned long [,bool=True])
-
rosetta.core.pose.
atom_id_to_named_atom_id
((AtomID)atom_id, (Pose)pose) → NamedAtomID :¶ core/pose/util.hh:353
- C++ signature :
- core::id::NamedAtomID atom_id_to_named_atom_id(core::id::AtomID,core::pose::Pose)
-
rosetta.core.pose.
canonical_atom_count
((Pose)pose) → int :¶ count the number of canonical amino acid atoms in the pose
- C++ signature :
- unsigned long canonical_atom_count(core::pose::Pose)
-
rosetta.core.pose.
canonical_residue_count
((Pose)pose) → int :¶ count the number of canonical residues in the pose
- C++ signature :
- unsigned long canonical_residue_count(core::pose::Pose)
-
rosetta.core.pose.
center_of_mass
((Pose)pose, (int)start, (int)stop) → xyzVector_Real :¶ core/pose/util.hh:669
- C++ signature :
- numeric::xyzVector<double> center_of_mass(core::pose::Pose,int,int)
-
rosetta.core.pose.
clearPoseExtraScore
((Pose)pose, (str)name) → None :¶ core/pose/util.hh:170
- C++ signature :
- void clearPoseExtraScore(core::pose::Pose {lvalue},std::string)
-
rosetta.core.pose.
clearPoseExtraScores
((Pose)pose) → None :¶ core/pose/util.hh:174
- C++ signature :
- void clearPoseExtraScores(core::pose::Pose {lvalue})
-
rosetta.core.pose.
compare_atom_coordinates
((Pose)lhs, (Pose)rhs[, (int)n_dec_places=3]) → 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@gmail.com [in] lhs one pose to compare [in] rhs one pose to compare [in] n_dec_places number of decimal places to compare for the coordinates (remember == doesn’t work for float); defaults to 3 which is PDB accuracy
- C++ signature :
- bool compare_atom_coordinates(core::pose::Pose,core::pose::Pose [,unsigned long=3])
-
rosetta.core.pose.
compare_binary_protein_silent_struct
((Pose)lhs, (Pose)rhs) → bool :¶ this function compares poses for equality up to the information stored in the binary protein silent struct format.
- C++ signature :
- bool compare_binary_protein_silent_struct(core::pose::Pose,core::pose::Pose)
-
rosetta.core.pose.
conf2pdb_chain
((Pose)pose) → object :¶ get Conformation chain -> PDBInfo chain mapping @remarks Any chains whose PDBInfo chain records are marked entirely as
PDBInfo::empty_record() will be mapped to that character. Note that Conformation -> PDBInfo is always unique, but the reverse may not be true.- the mapping if PDBInfo available and chains appear consistent,
- otherwise returns an empty mapping
- C++ signature :
- std::map<int, char, std::less<int>, std::allocator<std::pair<int const, char> > > conf2pdb_chain(core::pose::Pose)
-
rosetta.core.pose.
convert_from_std_map
((object)atom_map, (Pose)pose) → AtomID_Map_T_core_id_AtomID_T :¶ core/pose/util.hh:687
- C++ signature :
- core::id::AtomID_Map<core::id::AtomID> convert_from_std_map(std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >,core::pose::Pose)
-
rosetta.core.pose.
correctly_add_cutpoint_variants
((Pose)pose, (int)cutpoint_res[, (bool)check_fold_tree=True]) → None :¶ core/pose/util.hh:696
- C++ signature :
- void correctly_add_cutpoint_variants(core::pose::Pose {lvalue},unsigned long [,bool=True])
- correctly_add_cutpoint_variants( (Pose)pose) -> None :
Add cutpoint variants to all residues annotated as cutpoints in the pose.
- C++ signature :
- void correctly_add_cutpoint_variants(core::pose::Pose {lvalue})
-
rosetta.core.pose.
create_subpose
((Pose)src, (vector1_Size)positions, (FoldTree)f, (Pose)pose) → None :¶ Create a subpose of the src pose. PDBInfo is set as NULL.
- C++ signature :
- void create_subpose(core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> >,core::kinematics::FoldTree,core::pose::Pose {lvalue})
-
rosetta.core.pose.
delete_comment
((Pose)pose, (str)key) → None :¶ Deletes the entry in the STRING_MAP associated with the given key.
- C++ signature :
- void delete_comment(core::pose::Pose {lvalue},std::string)
-
rosetta.core.pose.
dump_comment_pdb
((str)file_name, (Pose)pose) → None :¶ dumps pose+ comments to pdb file
- C++ signature :
- void dump_comment_pdb(std::string,core::pose::Pose)
-
rosetta.core.pose.
energy_from_pose
((Pose)pose, (str)sc_type) → float :¶ core/pose/util.hh:387
- C++ signature :
- double energy_from_pose(core::pose::Pose,std::string)
- energy_from_pose( (Pose)pose, (ScoreType)sc_type) -> float :
core/pose/util.hh:383
- C++ signature :
- double energy_from_pose(core::pose::Pose,core::scoring::ScoreType)
-
rosetta.core.pose.
extract_tag_from_pose
((Pose)pose) → str :¶ Returns a string giving the pose’s tag if there is such a thing or “UnknownTag” otherwise.
- C++ signature :
- std::string extract_tag_from_pose(core::pose::Pose {lvalue})
-
rosetta.core.pose.
getPoseExtraScore
((Pose)pose, (str)name, (str)value) → bool :¶ core/pose/util.hh:181
- C++ signature :
- bool getPoseExtraScore(core::pose::Pose,std::string,std::string {lvalue})
- getPoseExtraScore( (Pose)pose, (str)name) -> float :
core/pose/util.hh:154
- C++ signature :
- double getPoseExtraScore(core::pose::Pose,std::string)
- getPoseExtraScore( (Pose)pose, (str)name, (float)value) -> bool :
getters/setters for things in the Pose DataCache
- C++ signature :
- bool getPoseExtraScore(core::pose::Pose,std::string,double {lvalue})
-
rosetta.core.pose.
get_all_comments
((Pose)pose) → map_string_string :¶ Gets a map< string, string > representing comments about the Pose in the form of key-value pairs.
- C++ signature :
- std::map<std::string, std::string, std::less<std::string>, std::allocator<std::pair<std::string const, std::string> > > get_all_comments(core::pose::Pose)
-
rosetta.core.pose.
get_all_score_line_strings
((Pose)pose) → map_string_string :¶ Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs.
- C++ signature :
- std::map<std::string, std::string, std::less<std::string>, std::allocator<std::pair<std::string const, std::string> > > get_all_score_line_strings(core::pose::Pose)
-
rosetta.core.pose.
get_center_of_mass
((Pose)pose) → xyzVector_Real :¶ Get center of mass of a pose.
- C++ signature :
- numeric::xyzVector<double> get_center_of_mass(core::pose::Pose)
-
rosetta.core.pose.
get_chain_from_chain_id
((int)chain_id, (Pose)pose) → str :¶ core/pose/util.hh:508
- C++ signature :
- char get_chain_from_chain_id(unsigned long,core::pose::Pose)
-
rosetta.core.pose.
get_chain_from_jump_id
((int)jump_id, (Pose)pose) → str :¶ core/pose/util.hh:526
- C++ signature :
- char get_chain_from_jump_id(unsigned long,core::pose::Pose)
-
rosetta.core.pose.
get_chain_id_from_chain
((str)chain, (Pose)pose) → int :¶ core/pose/util.hh:496
- C++ signature :
- unsigned long get_chain_id_from_chain(char,core::pose::Pose)
- get_chain_id_from_chain( (str)chain, (Pose)pose) -> int :
core/pose/util.hh:493
- C++ signature :
- unsigned long get_chain_id_from_chain(std::string,core::pose::Pose)
-
rosetta.core.pose.
get_chain_id_from_jump_id
((int)jump_id, (Pose)pose) → int :¶ core/pose/util.hh:523
- C++ signature :
- unsigned long get_chain_id_from_jump_id(unsigned long,core::pose::Pose)
-
rosetta.core.pose.
get_chain_ids_from_chain
((str)chain, (Pose)pose) → vector1_Size :¶ core/pose/util.hh:502
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_chain_ids_from_chain(char,core::pose::Pose)
- get_chain_ids_from_chain( (str)chain, (Pose)pose) -> vector1_Size :
core/pose/util.hh:499
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_chain_ids_from_chain(std::string,core::pose::Pose)
-
rosetta.core.pose.
get_chain_ids_from_chains
((vector1_string)chains, (Pose)pose) → vector1_Size :¶ core/pose/util.hh:505
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_chain_ids_from_chains(utility::vector1<std::string, std::allocator<std::string> >,core::pose::Pose)
-
rosetta.core.pose.
get_chain_residues
((Pose)pose, (int)chain_id) → object :¶ core/pose/util.hh:529
- C++ signature :
- utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > > get_chain_residues(core::pose::Pose,unsigned long)
-
rosetta.core.pose.
get_comment
((Pose)pose, (str)key, (str)val) → 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++ signature :
- bool get_comment(core::pose::Pose,std::string,std::string {lvalue})
-
rosetta.core.pose.
get_hash_excluding_chain
((str)chain, (Pose)pose) → int :¶ core/pose/util.hh:572
- C++ signature :
- unsigned long get_hash_excluding_chain(char,core::pose::Pose)
-
rosetta.core.pose.
get_hash_from_chain
((str)chain, (Pose)pose) → int :¶ core/pose/util.hh:569
- C++ signature :
- unsigned long get_hash_from_chain(char,core::pose::Pose)
-
rosetta.core.pose.
get_jump_id_from_chain
((str)chain, (Pose)pose) → int :¶ core/pose/util.hh:514
- C++ signature :
- unsigned long get_jump_id_from_chain(char,core::pose::Pose)
- get_jump_id_from_chain( (str)chain, (Pose)pose) -> int :
core/pose/util.hh:511
- C++ signature :
- unsigned long get_jump_id_from_chain(std::string,core::pose::Pose)
-
rosetta.core.pose.
get_jump_id_from_chain_id
((int)chain_id, (Pose)pose) → int :¶ core/pose/util.hh:488
- C++ signature :
- unsigned long get_jump_id_from_chain_id(unsigned long,core::pose::Pose)
-
rosetta.core.pose.
get_jump_ids_from_chain
((str)chain, (Pose)pose) → vector1_Size :¶ core/pose/util.hh:520
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_jump_ids_from_chain(std::string,core::pose::Pose)
- get_jump_ids_from_chain( (str)chain, (Pose)pose) -> vector1_Size :
core/pose/util.hh:517
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_jump_ids_from_chain(char,core::pose::Pose)
-
rosetta.core.pose.
get_jump_ids_from_chain_ids
((set_Size)chain_ids, (Pose)pose) → set_Size :¶ core/pose/util.hh:485
- C++ signature :
- std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > get_jump_ids_from_chain_ids(std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >,core::pose::Pose)
-
rosetta.core.pose.
get_resnum
((Tag)tag_ptr, (Pose)pose[, (str)prefix='']) → int :¶ core/pose/selection.hh:37
- C++ signature :
- unsigned long get_resnum(boost::shared_ptr<utility::tag::Tag const>,core::pose::Pose [,std::string=’‘])
-
rosetta.core.pose.
get_resnum_list
((str)str, (Pose)pose) → set_Size :¶ returns a resnum list directly from a string
- C++ signature :
- std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> > get_resnum_list(std::string,core::pose::Pose)
- get_resnum_list( (Tag)tag_ptr, (str)tag, (Pose)pose) -> vector1_Size :
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 (@see parse_resnum for details)- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_resnum_list(boost::shared_ptr<utility::tag::Tag const>,std::string,core::pose::Pose)
-
rosetta.core.pose.
get_resnum_list_ordered
((str)str, (Pose)pose) → vector1_Size :¶ returns a resnum list directly from a string, preserving order
- C++ signature :
- utility::vector1<unsigned long, std::allocator<unsigned long> > get_resnum_list_ordered(std::string,core::pose::Pose)
-
rosetta.core.pose.
get_score_line_string
((Pose)pose, (str)key, (str)val) → bool :¶ core/pose/util.hh:250
- C++ signature :
- bool get_score_line_string(core::pose::Pose,std::string,std::string {lvalue})
-
rosetta.core.pose.
get_sequence_len
((str)sequence_in) → int :¶ Get the real length of a annotated sequence
- C++ signature :
- unsigned long get_sequence_len(std::string)
-
rosetta.core.pose.
get_sha1_hash_excluding_chain
((str)chain, (Pose)pose) → str :¶ core/pose/util.hh:574
- C++ signature :
- std::string get_sha1_hash_excluding_chain(char,core::pose::Pose)
-
rosetta.core.pose.
hasPoseExtraScore
((Pose)pose, (str)name) → bool :¶ core/pose/util.hh:159
- C++ signature :
- bool hasPoseExtraScore(core::pose::Pose,std::string)
-
rosetta.core.pose.
has_chain
((int)chain_id, (Pose)pose) → bool :¶ core/pose/util.hh:482
- C++ signature :
- bool has_chain(unsigned long,core::pose::Pose)
- has_chain( (str)chain, (Pose)pose) -> bool :
core/pose/util.hh:479
- C++ signature :
- bool has_chain(char,core::pose::Pose)
- has_chain( (str)chain, (Pose)pose) -> bool :
core/pose/util.hh:476
- C++ signature :
- bool has_chain(std::string,core::pose::Pose)
-
rosetta.core.pose.
initialize_atomid_map
((AtomID_Map_T_core_id_AtomID_T)atom_map, (Conformation)conformation, (AtomID)value) → None :¶ Initialize an AtomID_Map for a given Conformation using a specified fill value
- C++ signature :
- void initialize_atomid_map(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Conformation,core::id::AtomID)
- initialize_atomid_map( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Conformation)conformation) -> None :
Initialize an AtomID_Map for a given Conformation using the AtomID_Map’s current default fill values
- C++ signature :
- void initialize_atomid_map(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Conformation)
- initialize_atomid_map( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Pose)pose, (AtomID)value) -> None :
Initialize an AtomID_Map for a given Pose using a specified fill value
- C++ signature :
- void initialize_atomid_map(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::pose::Pose,core::id::AtomID)
- initialize_atomid_map( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Pose)pose) -> None :
Initialize an AtomID_Map for a given Pose using the AtomID_Map’s current default fill values
- C++ signature :
- void initialize_atomid_map(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::pose::Pose)
-
rosetta.core.pose.
initialize_atomid_map_AtomID
((AtomID_Map_T_core_id_AtomID_T)atom_map, (Conformation)conformation, (AtomID)value) → None :¶ core/pose/util.tmpl.hh:379
- C++ signature :
- void initialize_atomid_map_AtomID(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Conformation,core::id::AtomID)
- initialize_atomid_map_AtomID( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Conformation)conformation) -> None :
core/pose/util.tmpl.hh:376
- C++ signature :
- void initialize_atomid_map_AtomID(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Conformation)
- initialize_atomid_map_AtomID( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Pose)pose, (AtomID)value) -> None :
core/pose/util.tmpl.hh:372
- C++ signature :
- void initialize_atomid_map_AtomID(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::pose::Pose,core::id::AtomID)
- initialize_atomid_map_AtomID( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Pose)pose) -> None :
core/pose/util.tmpl.hh:369
- C++ signature :
- void initialize_atomid_map_AtomID(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::pose::Pose)
-
rosetta.core.pose.
initialize_disulfide_bonds
((Pose)pose) → None :¶ detect and fix disulfide bonds
- C++ signature :
- void initialize_disulfide_bonds(core::pose::Pose {lvalue})
-
rosetta.core.pose.
is_ideal_pose
((Pose)pose) → bool :¶ Returns true if the <pose> geometry is ideal [in] pose The Pose to check. true if all pose positions have ideal bond lengths and angles
up to some very small epsilon- C++ signature :
- bool is_ideal_pose(core::pose::Pose)
-
rosetta.core.pose.
is_ideal_position
((int)seqpos, (Pose)pose) → bool :¶ Returns true if the <pose> geometry is ideal in position <seqpos> [in] pose The Pose to check. true if position seqpos has ideal bond lengths and angles
up to some very small epsilon- C++ signature :
- bool is_ideal_position(unsigned long,core::pose::Pose)
-
rosetta.core.pose.
is_lower_terminus
((Pose)pose, (int)resid) → bool :¶ checks to see if this is a lower chain ending more intelligently than just checking residue variants
- C++ signature :
- bool is_lower_terminus(core::pose::Pose,unsigned long)
-
rosetta.core.pose.
is_position_conserved_residue
((Pose)pose, (int)residue) → bool :¶ Returns true if <residue> is positionally conserved, false otherwise
- C++ signature :
- bool is_position_conserved_residue(core::pose::Pose,unsigned long)
-
rosetta.core.pose.
is_upper_terminus
((Pose)pose, (int)resid) → bool :¶ checks to see if this is a lower chain ending more intelligently than just checking residue variants
- C++ signature :
- bool is_upper_terminus(core::pose::Pose,unsigned long)
-
rosetta.core.pose.
jumps_from_pose
((Pose)pose, (set_int)jumps) → None :¶ Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id.
- C++ signature :
- void jumps_from_pose(core::pose::Pose,std::set<int, std::less<int>, std::allocator<int> >*)
-
rosetta.core.pose.
make_atom_map
((Pose)p, (PoseCoordPickMode)m) → AtomID_Map_T_double_T :¶ core/pose/xyzStripeHashPose.hh:29
- C++ signature :
- core::id::AtomID_Map<double> make_atom_map(core::pose::Pose,core::pose::PoseCoordPickMode)
-
rosetta.core.pose.
make_pose_from_saccharide_sequence
((Pose)pose, (str)sequence[, (str)type_set_name='fa_standard'[, (bool)auto_termini=True]]) → 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++ signature :
- void make_pose_from_saccharide_sequence(core::pose::Pose {lvalue},std::string [,std::string=’fa_standard’ [,bool=True]])
- make_pose_from_saccharide_sequence( (Pose)pose, (str)sequence, (ResidueTypeSet)residue_set [, (bool)auto_termini=True]) -> None :
Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and store it in <pose>.
- C++ signature :
- void make_pose_from_saccharide_sequence(core::pose::Pose {lvalue},std::string,core::chemical::ResidueTypeSet [,bool=True])
-
rosetta.core.pose.
make_pose_from_sequence
((Pose)pose, (str)sequence, (str)type_set_name[, (bool)auto_termini=True]) → 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++ signature :
- void make_pose_from_sequence(core::pose::Pose {lvalue},std::string,std::string [,bool=True])
- make_pose_from_sequence( (Pose)pose, (str)sequence, (ResidueTypeSet)residue_set [, (bool)auto_termini=True]) -> None :
core/pose/annotated_sequence.hh:85
- C++ signature :
- void make_pose_from_sequence(core::pose::Pose {lvalue},std::string,core::chemical::ResidueTypeSet [,bool=True])
- make_pose_from_sequence( (Pose)pose, (object)requested_types [, (bool)auto_termini=True]) -> 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”,”fa_standard”)- See also:
- Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence
- C++ signature :
- void make_pose_from_sequence(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > > [,bool=True])
-
rosetta.core.pose.
mass
((int)begin, (int)end, (Pose)pose) → float :¶ core/pose/util.hh:566
- C++ signature :
- double mass(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
named_atom_id_to_atom_id
((NamedAtomID)named_atom_id, (Pose)pose[, (bool)raise_exception=True]) → AtomID :¶ core/pose/util.hh:360
- C++ signature :
- core::id::AtomID named_atom_id_to_atom_id(core::id::NamedAtomID,core::pose::Pose [,bool=True])
-
rosetta.core.pose.
named_stub_id_to_stub_id
((NamedStubID)named_stub_id, (Pose)pose) → StubID :¶ core/pose/util.hh:372
- C++ signature :
- core::id::StubID named_stub_id_to_stub_id(core::id::NamedStubID,core::pose::Pose)
-
rosetta.core.pose.
noncanonical_atom_count
((Pose)pose) → int :¶ count the number of non-canonical amino acids in thepose
- C++ signature :
- unsigned long noncanonical_atom_count(core::pose::Pose)
-
rosetta.core.pose.
noncanonical_chi_count
((Pose)pose) → int :¶ count the number of non-canonical chi angles in the pose
- C++ signature :
- unsigned long noncanonical_chi_count(core::pose::Pose)
-
rosetta.core.pose.
noncanonical_residue_count
((Pose)pose) → int :¶ count the number of non-canonical residues in the pose
- C++ signature :
- unsigned long noncanonical_residue_count(core::pose::Pose)
-
rosetta.core.pose.
nres_protein
((Pose)pose) → int :¶ Number of protein residues in the pose No virtuals, membrane residues or embedding residues counted
- C++ signature :
- unsigned long nres_protein(core::pose::Pose)
-
rosetta.core.pose.
num_atoms
((int)begin, (int)end, (Pose)pose) → int :¶ core/pose/util.hh:541
- C++ signature :
- unsigned long num_atoms(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
num_chi_angles
((int)begin, (int)end, (Pose)pose) → int :¶ core/pose/util.hh:559
- C++ signature :
- unsigned long num_chi_angles(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
num_hbond_acceptors
((int)begin, (int)end, (Pose)pose) → int :¶ core/pose/util.hh:547
- C++ signature :
- unsigned long num_hbond_acceptors(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
num_hbond_donors
((int)begin, (int)end, (Pose)pose) → int :¶ core/pose/util.hh:553
- C++ signature :
- unsigned long num_hbond_donors(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
num_heavy_atoms
((int)begin, (int)end, (Pose)pose) → int :¶ core/pose/util.hh:535
- C++ signature :
- unsigned long num_heavy_atoms(unsigned long,unsigned long,core::pose::Pose)
-
rosetta.core.pose.
parse_resnum
((str)resnum, (Pose)pose) → int :¶ Extracts a residue number from a string. @detail Recognizes two 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.
the rosetta residue number for the string, or 0 upon an error
- C++ signature :
- unsigned long parse_resnum(std::string,core::pose::Pose)
-
rosetta.core.pose.
parse_sequence
((str)sequence_in, (vector1_string)fullname_list, (std_vector_Size)oneletter_to_fullname_index, (str)one_letter_sequence) → None :¶ Parse the input annotated sequence
- C++ signature :
- void parse_sequence(std::string,utility::vector1<std::string, std::allocator<std::string> > {lvalue},std::vector<unsigned long, std::allocator<unsigned long> > {lvalue},std::string {lvalue})
-
rosetta.core.pose.
partition_pose_by_jump
((Pose)src, (int)jump_number, (Pose)partner1, (Pose)partner2) → None :¶ core/pose/util.hh:125
- C++ signature :
- void partition_pose_by_jump(core::pose::Pose,int,core::pose::Pose {lvalue},core::pose::Pose {lvalue})
-
rosetta.core.pose.
pdbslice
((Pose)pose, (vector1_Size)slice_res) → None :¶ Create a subpose of the src pose – figures out a reasonable fold tree.
- C++ signature :
- void pdbslice(core::pose::Pose {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >)
- pdbslice( (Pose)new_pose, (Pose)pose, (vector1_Size)slice_res) -> None :
Create a subpose of the src pose – figures out a reasonable fold tree.
- C++ signature :
- void pdbslice(core::pose::Pose {lvalue},core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> >)
-
rosetta.core.pose.
pose_from_saccharide_sequence
((str)sequence[, (str)type_set_name='fa_standard'[, (bool)auto_termini=True]]) → Pose :¶ Return a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name>.
- C++ signature :
- boost::shared_ptr<core::pose::Pose> pose_from_saccharide_sequence(std::string [,std::string=’fa_standard’ [,bool=True]])
-
rosetta.core.pose.
pose_max_nbr_radius
((Pose)pose) → float :¶ returns a Distance
- C++ signature :
- double pose_max_nbr_radius(core::pose::Pose)
-
rosetta.core.pose.
pose_residue_is_terminal
((Pose)pose, (int)resid) → bool :¶ returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants
- C++ signature :
- bool pose_residue_is_terminal(core::pose::Pose,unsigned long)
-
rosetta.core.pose.
read_comment_pdb
((str)file_name, (Pose)pose) → None :¶ Reads the comments from the pdb file and adds it into comments
- C++ signature :
- void read_comment_pdb(std::string,core::pose::Pose {lvalue})
-
rosetta.core.pose.
read_psipred_ss2_file
((Pose)pose) → vector1_char :¶ core/pose/util.hh:141
- C++ signature :
- utility::vector1<char, std::allocator<char> > read_psipred_ss2_file(core::pose::Pose)
-
rosetta.core.pose.
remove_ligand_canonical_residues
((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++ signature :
- void remove_ligand_canonical_residues(core::pose::Pose {lvalue})
-
rosetta.core.pose.
remove_lower_terminus_type_from_pose_residue
((Pose)pose, (int)seqpos) → None :¶ core/pose/util.hh:450
- C++ signature :
- void remove_lower_terminus_type_from_pose_residue(core::pose::Pose {lvalue},unsigned long)
-
rosetta.core.pose.
remove_nonprotein_residues
((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++ signature :
- void remove_nonprotein_residues(core::pose::Pose {lvalue})
-
rosetta.core.pose.
remove_upper_terminus_type_from_pose_residue
((Pose)pose, (int)seqpos) → None :¶ core/pose/util.hh:457
- C++ signature :
- void remove_upper_terminus_type_from_pose_residue(core::pose::Pose {lvalue},unsigned long)
-
rosetta.core.pose.
remove_variant_type_from_pose_residue
((Pose)pose, (VariantType)variant_type, (int)seqpos) → None :¶ Construct a non-variant of an existing pose residue.
- C++ signature :
- void remove_variant_type_from_pose_residue(core::pose::Pose {lvalue},core::chemical::VariantType,unsigned long)
-
rosetta.core.pose.
remove_variant_type_from_residue
((Residue)old_rsd, (VariantType)variant_type, (Pose)pose) → Residue :¶ Remove variant from an existing residue.
- C++ signature :
- boost::shared_ptr<core::conformation::Residue> remove_variant_type_from_residue(core::conformation::Residue,core::chemical::VariantType,core::pose::Pose)
-
rosetta.core.pose.
remove_virtual_residues
((Pose)pose) → None :¶ Removes all virtual residues from <pose>
- C++ signature :
- void remove_virtual_residues(core::pose::Pose*)
-
rosetta.core.pose.
renumber_pdbinfo_based_on_conf_chains
((Pose)pose[, (bool)fix_chains=True[, (bool)start_from_existing_numbering=True[, (bool)keep_insertion_codes=False[, (bool)rotate_chain_ids=False]]]]) → bool :¶ renumber PDBInfo based on Conformation chains; each chain starts from 1 [in,out] pose The Pose to modify. [in] fix_chains If true, the procedure will attempt to fix any empty record
characters it finds in the PDBInfo. (default true)- [in] start_from_existing_numbering 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)
- [in] keep_insertion_codes 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)
- [in] rotate_chain_ids 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)
- @remarks 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++ signature :
- bool renumber_pdbinfo_based_on_conf_chains(core::pose::Pose {lvalue} [,bool=True [,bool=True [,bool=False [,bool=False]]]])
-
rosetta.core.pose.
replace_pose_residue_copying_existing_coordinates
((Pose)pose, (int)seqpos, (ResidueType)new_rsd_type) → None :¶ core/pose/util.hh:405
- C++ signature :
- void replace_pose_residue_copying_existing_coordinates(core::pose::Pose {lvalue},unsigned long,core::chemical::ResidueType)
-
rosetta.core.pose.
residue_center_of_mass
((Pose)pose, (int)start, (int)stop) → int :¶ core/pose/util.hh:676
- C++ signature :
- int residue_center_of_mass(core::pose::Pose,int,int)
-
rosetta.core.pose.
residue_types_from_saccharide_sequence
((str)sequence, (ResidueTypeSet)residue_set) → object :¶ Return a list of carbohydrate ResidueTypes corresponding to an annotated, linear, IUPAC polysaccharide sequence.
- C++ signature :
- utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > > residue_types_from_saccharide_sequence(std::string,core::chemical::ResidueTypeSet)
-
rosetta.core.pose.
residue_types_from_sequence
((str)sequence_in, (ResidueTypeSet)residue_set[, (bool)auto_termini=True]) → object :¶ return a list of ResidueTypes corresponding to an annotated protein sequence [in] sequence_in an annotated sequence [in] residue_set the desired residue set [in] auto_termini mark position 1, last_residue with lower, upper termini; default true
- C++ signature :
- utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > > residue_types_from_sequence(std::string,core::chemical::ResidueTypeSet [,bool=True])
-
rosetta.core.pose.
return_nearest_residue
((Pose)pose, (int)begin, (int)end, (xyzVector_Real)center) → int :¶ core/pose/util.hh:684
- C++ signature :
- int return_nearest_residue(core::pose::Pose,int,int,numeric::xyzVector<double>)
-
rosetta.core.pose.
sequence_map_from_pdbinfo
((Pose)first, (Pose)second) → 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++ signature :
- core::id::SequenceMapping sequence_map_from_pdbinfo(core::pose::Pose,core::pose::Pose)
-
rosetta.core.pose.
setPoseExtraScore
((Pose)pose, (str)name, (str)value) → None :¶ core/pose/util.hh:187
- C++ signature :
- void setPoseExtraScore(core::pose::Pose {lvalue},std::string,std::string)
- setPoseExtraScore( (Pose)pose, (str)name, (float)value) -> None :
core/pose/util.hh:165
- C++ signature :
- void setPoseExtraScore(core::pose::Pose {lvalue},std::string,double)
-
rosetta.core.pose.
set_ss_from_phipsi
((Pose)pose) → None :¶ Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that
- C++ signature :
- void set_ss_from_phipsi(core::pose::Pose {lvalue})
-
rosetta.core.pose.
setup_dof_mask_from_move_map
((MoveMap)mm, (Pose)pose, (object)dof_mask) → None :¶ convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer
- C++ signature :
- void setup_dof_mask_from_move_map(core::kinematics::MoveMap,core::pose::Pose,core::id::DOF_ID_Map<bool> {lvalue})
-
rosetta.core.pose.
setup_dof_to_torsion_map
((Pose)pose, (object)dof_map) → None :¶ set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID)
- C++ signature :
- void setup_dof_to_torsion_map(core::pose::Pose,core::id::DOF_ID_Map<core::id::TorsionID> {lvalue})
-
rosetta.core.pose.
sort_pose_by_score
((Pose)pose1, (Pose)pose2) → bool :¶ core/pose/util.hh:379
- C++ signature :
- bool sort_pose_by_score(boost::shared_ptr<core::pose::Pose>,boost::shared_ptr<core::pose::Pose>)
-
rosetta.core.pose.
stub_id_to_named_stub_id
((StubID)stub_id, (Pose)pose) → NamedStubID :¶ core/pose/util.hh:366
- C++ signature :
- core::id::NamedStubID stub_id_to_named_stub_id(core::id::StubID,core::pose::Pose)
-
rosetta.core.pose.
swap_transform
((int)jump_num, (RT)xform, (Pose)pose) → None :¶ Updates the rigid-body transform of the specified jump in <pose>
- C++ signature :
- void swap_transform(unsigned long,core::kinematics::RT,core::pose::Pose*)
-
rosetta.core.pose.
tag_from_pose
((Pose)pose) → str :¶ - C++ signature :
- std::string tag_from_pose(core::pose::Pose)
-
rosetta.core.pose.
tag_into_pose
((Pose)pose, (str)tag) → None :¶ core/pose/util.hh:376
- C++ signature :
- void tag_into_pose(core::pose::Pose {lvalue},std::string)
-
rosetta.core.pose.
total_energy_from_pose
((Pose)pose) → float :¶ core/pose/util.hh:389
- C++ signature :
- double total_energy_from_pose(core::pose::Pose)
-
rosetta.core.pose.
transfer_jumps
((Pose)srcpose, (Pose)tgtpose) → None :¶ core/pose/util.hh:398
- C++ signature :
- void transfer_jumps(core::pose::Pose,core::pose::Pose {lvalue})
-
rosetta.core.pose.
transfer_phi_psi
((Pose)srcpose, (Pose)tgtpose) → None :¶ core/pose/util.hh:395
- C++ signature :
- void transfer_phi_psi(core::pose::Pose,core::pose::Pose {lvalue})
- transfer_phi_psi( (Pose)srcpose, (Pose)tgtpose, (int)ir, (int)jr) -> None :
core/pose/util.hh:392
- C++ signature :
- void transfer_phi_psi(core::pose::Pose,core::pose::Pose {lvalue},unsigned long,unsigned long)
-
class
rosetta.core.pose.
xyzStripeHashPose
¶ core/pose/xyzStripeHashPose.hh:31
-
add_pose
((xyzStripeHashPose)arg1, (Pose)p, (AtomID_Map_T_double_T)amap) → None :¶ core/pose/xyzStripeHashPose.hh:56
- C++ signature :
- void add_pose(core::pose::xyzStripeHashPose {lvalue},core::pose::Pose,core::id::AtomID_Map<double>)
- add_pose( (xyzStripeHashPose)arg1, (Pose)p [, (PoseCoordPickMode)m=rosetta.core.pose.PoseCoordPickMode.PoseCoordPickMode_BB]) -> None :
core/pose/xyzStripeHashPose.hh:61
- C++ signature :
- void add_pose(core::pose::xyzStripeHashPose {lvalue},core::pose::Pose [,core::pose::PoseCoordPickMode=rosetta.core.pose.PoseCoordPickMode.PoseCoordPickMode_BB])
-
static
extract_pose_balls
((Pose)p, (vector1_numeric_geometry_hashing_Ball)balls[, (PoseCoordPickMode)m=rosetta.core.pose.PoseCoordPickMode.PoseCoordPickMode_BB]) → None :¶ core/pose/xyzStripeHashPose.hh:71
- C++ signature :
- void extract_pose_balls(core::pose::Pose,utility::vector1<numeric::geometry::hashing::Ball, std::allocator<numeric::geometry::hashing::Ball> > {lvalue} [,core::pose::PoseCoordPickMode=rosetta.core.pose.PoseCoordPickMode.PoseCoordPickMode_BB])
- extract_pose_balls( (Pose)p, (vector1_numeric_geometry_hashing_Ball)balls, (AtomID_Map_T_double_T)amap) -> None :
core/pose/xyzStripeHashPose.hh:78
- C++ signature :
- void extract_pose_balls(core::pose::Pose,utility::vector1<numeric::geometry::hashing::Ball, std::allocator<numeric::geometry::hashing::Ball> > {lvalue},core::id::AtomID_Map<double>)
-
init_posehash
((xyzStripeHashPose)arg1) → None :¶ core/pose/xyzStripeHashPose.hh:64
- C++ signature :
- void init_posehash(core::pose::xyzStripeHashPose {lvalue})
-