conformation¶

Bindings for core::conformation namespace

class pyrosetta.rosetta.core.conformation.Atom¶

Bases: pybind11_builtins.pybind11_object

This atom class differs from the chameical::Atom, AtomType, and AtomTypeSet classes in that it only contains the information about the xyz coordinates. In the future, it might contain information about such things as B-factor. This information is generally initialized and set by conformation::Residue.

chemical::Atoms are stored in chemical::ResidueType (within its ResidueGraph);

conformation::Atoms are stored in conformation::Residue

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.conformation.Atom) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Atom, type_in: int, mm_type_in: int) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Atom, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t, type_in: int, mm_type_in: int) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Atom, arg0: pyrosetta.rosetta.core.conformation.Atom) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.conformation.Atom) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.conformation.Atom, : pyrosetta.rosetta.core.conformation.Atom) → pyrosetta.rosetta.core.conformation.Atom¶: C++: core::conformation::Atom::operator=(const class core::conformation::Atom &) –> class core::conformation::Atom &

mm_type(*args, **kwargs)¶

Overloaded function.

mm_type(self: pyrosetta.rosetta.core.conformation.Atom, mm_type_in: int) -> None

set the mm atom type number

C++: core::conformation::Atom::mm_type(const unsigned short) –> void

mm_type(self: pyrosetta.rosetta.core.conformation.Atom) -> int

get the mm atom type number

C++: core::conformation::Atom::mm_type() const –> unsigned short

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.core.conformation.Atom) -> None
show(self: pyrosetta.rosetta.core.conformation.Atom, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of conformation::Atom for debugging purposes.

C++: core::conformation::Atom::show(class std::basic_ostream<char> &) const –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.core.conformation.Atom, type_in: int) -> None

set the atom type number

C++: core::conformation::Atom::type(const unsigned short) –> void

type(self: pyrosetta.rosetta.core.conformation.Atom) -> int

Returns the AtomType number

C++: core::conformation::Atom::type() const –> unsigned short

xyz(*args, **kwargs)¶

Overloaded function.

xyz(self: pyrosetta.rosetta.core.conformation.Atom) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Returns the atom coordinates as an xyzVector

C++: core::conformation::Atom::xyz() const –> const class numeric::xyzVector<double> &

xyz(self: pyrosetta.rosetta.core.conformation.Atom, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Sets the atom coordinates using an xyzVector

C++: core::conformation::Atom::xyz(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.core.conformation.Conformation¶

Bases: pybind11_builtins.pybind11_object

A container of Residues and the kinematics to manage them

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.conformation.Conformation) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Conformation, arg0: pyrosetta.rosetta.core.conformation.Conformation) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.conformation.Conformation) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

aa(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.AA¶

Returns the AA enum for position <seqpos>

C++: core::conformation::Conformation::aa(unsigned long) const –> const enum core::chemical::AA &

add_parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation, newset: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → None¶

Add a (predefined) ParametersSet object (via its owning pointer)

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::add_parameters_set(class std::shared_ptr<class core::conformation::parametric::ParametersSet>) –> void

align_virtual_atoms_in_carbohydrate_residue(self: pyrosetta.rosetta.core.conformation.Conformation, sequence_position: int) → None¶

Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this: conformation.

C++: core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(const unsigned long) –> void

annotated_sequence(self: pyrosetta.rosetta.core.conformation.Conformation, show_all_variants: bool) → str¶

Returns the variant-tagged string representing the: residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]

C++: core::conformation::Conformation::annotated_sequence(bool) const –> std::string

append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) → None¶

glues to seqpos and perhaps also seqpos+1

C++: core::conformation::Conformation::append_polymer_residue_after_seqpos(const class core::conformation::Residue &, unsigned long, bool) –> void

append_residue_by_bond(*args, **kwargs)¶

Overloaded function.

append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int, start_new_chain: bool) -> None
append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool, connection_index: int, anchor_residue: int, anchor_connection_index: int, start_new_chain: bool, lookup_bond_length: bool) -> None

Append a new residue by a bond.

C++: core::conformation::Conformation::append_residue_by_bond(const class core::conformation::Residue &, bool, int, unsigned long, int, bool, bool) –> void

append_residue_by_jump(*args, **kwargs)¶

Overloaded function.

append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int, anchor_atom: str) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int, anchor_atom: str, root_atom: str) -> None
append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int, anchor_atom: str, root_atom: str, start_new_chain: bool) -> None

Append a new residue by a jump.

C++: core::conformation::Conformation::append_residue_by_jump(const class core::conformation::Residue &, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, bool) –> void

apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.conformation.Conformation, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::conformation::Conformation::apply_transform_Rx_plus_v(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void

assign(self: pyrosetta.rosetta.core.conformation.Conformation, src: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.conformation.Conformation¶

equals operator

C++: core::conformation::Conformation::operator=(const class core::conformation::Conformation &) –> class core::conformation::Conformation &

atom_is_backbone_norefold(self: pyrosetta.rosetta.core.conformation.Conformation, pos: int, atomno: int) → bool¶

returns true if atom is part of backbone.

C++: core::conformation::Conformation::atom_is_backbone_norefold(unsigned long, unsigned long) const –> bool

atom_tree(self: pyrosetta.rosetta.core.conformation.Conformation) → core::kinematics::AtomTree¶

Returns the conformation’s AtomTree

C++: core::conformation::Conformation::atom_tree() const –> const class core::kinematics::AtomTree &

atoms_are_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID) → bool¶

Helper method to determine whether two atoms have a chemical bond linking them.

Intended for internal use, but there’s really no reason not to make this a public method. This works for atoms within the same residue or in different residues. AMW went and made this a public method.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::atoms_are_bonded(const class core::id::AtomID &, const class core::id::AtomID &) const –> bool

batch_get_xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.utility.vector1_core_id_AtomID, position: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None¶: C++: core::conformation::Conformation::batch_get_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> void

batch_set_xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.utility.vector1_core_id_AtomID, position: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None¶: C++: core::conformation::Conformation::batch_set_xyz(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

block_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

block signals from being sent

C++: core::conformation::Conformation::block_signals() –> void

blocking_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

are signals being blocked?

C++: core::conformation::Conformation::blocking_signals() const –> bool

bond_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID) → float¶

Returns the bond angle defined by <atom[1-3]> through the AtomTree

C++: core::conformation::Conformation::bond_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> double

bond_length(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID) → float¶

Returns the bond length between <atom1> and <atom2> through the AtomTree

C++: core::conformation::Conformation::bond_length(const class core::id::AtomID &, const class core::id::AtomID &) const –> double

bonded_neighbor_all_res(*args, **kwargs)¶

Overloaded function.

bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Conformation, atomid: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

get all atoms bonded to another

C++: core::conformation::Conformation::bonded_neighbor_all_res(class core::id::AtomID, bool, bool) const –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

buffer_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

block signals from being sent and buffer them to be sent after unblocking

C++: core::conformation::Conformation::buffer_signals() –> void

buffering_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

are signals being blocked and buffered?

C++: core::conformation::Conformation::buffering_signals() const –> bool

chain_begin(self: pyrosetta.rosetta.core.conformation.Conformation, chain: int) → int¶

Returns the position number of the first residue in chain number <chain>

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_begin(unsigned long) const –> unsigned long

chain_end(self: pyrosetta.rosetta.core.conformation.Conformation, chain: int) → int¶

Returns the position number of the last residue in chain number <chain>

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_end(unsigned long) const –> unsigned long

chain_endings(*args, **kwargs)¶

Overloaded function.

chain_endings(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the list of (chain number) chain endings

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_endings() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

chain_endings(self: pyrosetta.rosetta.core.conformation.Conformation, endings: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Sets the list of (chain number) chain endings

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chain_endings(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

chains_from_termini(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Rederive the (chain number) chains from the termini/polymer status

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::chains_from_termini() –> void

check_valid_membrane(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Check that a new membrane position is valid

Given a new membrane normal/center pair, check that the newly constructed stub represents an orthogonal coordinate frame

C++: core::conformation::Conformation::check_valid_membrane() const –> void

clear(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

clear data

C++: core::conformation::Conformation::clear() –> void

clear_glycan_trees(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Safely detaches any tree observers and clears it to null.

C++: core::conformation::Conformation::clear_glycan_trees() –> void

clear_observers(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

clear all observers

C++: core::conformation::Conformation::clear_observers() –> void

clear_parameters_set_list(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Delete the list of ParametersSetOP objects.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::clear_parameters_set_list() –> void

clone(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.conformation.Conformation¶

clone the conformation

C++: core::conformation::Conformation::clone() const –> class std::shared_ptr<class core::conformation::Conformation>

const_residues(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t¶

Inefficient – constructs copy of residues_

C++: core::conformation::Conformation::const_residues() const –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

contains_carbohydrate_residues(*args, **kwargs)¶

Overloaded function.

contains_carbohydrate_residues(self: pyrosetta.rosetta.core.conformation.Conformation) -> bool

Return true if this conformation contains any carbohydrate residues.

C++: core::conformation::Conformation::contains_carbohydrate_residues() const –> bool

contains_carbohydrate_residues(self: pyrosetta.rosetta.core.conformation.Conformation, setting: bool) -> None

Set whether this conformation contains any carbohydrate residues.

C++: core::conformation::Conformation::contains_carbohydrate_residues(bool) –> void

copy_segment(self: pyrosetta.rosetta.core.conformation.Conformation, size: int, src: pyrosetta.rosetta.core.conformation.Conformation, begin: int, src_begin: int) → None¶

copy a stretch of coordinates/torsions from another Conformation

C++: core::conformation::Conformation::copy_segment(unsigned long, const class core::conformation::Conformation &, unsigned long, unsigned long) –> void

create_new_parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Create a new (empty) ParametersSet object and add its owning pointer

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::create_new_parameters_set() –> void

debug_pause(*args, **kwargs)¶

Overloaded function.

debug_pause(self: pyrosetta.rosetta.core.conformation.Conformation, flag: bool) -> None

wait for stdin after sending a GeneralEvent signal

C++: core::conformation::Conformation::debug_pause(bool) const –> void

debug_pause(self: pyrosetta.rosetta.core.conformation.Conformation) -> bool

waiting for stdin after sending a GeneralEvent signal?

C++: core::conformation::Conformation::debug_pause() const –> bool

debug_residue_torsions(*args, **kwargs)¶

Overloaded function.

debug_residue_torsions(self: pyrosetta.rosetta.core.conformation.Conformation) -> None
debug_residue_torsions(self: pyrosetta.rosetta.core.conformation.Conformation, verbose: bool) -> None

debugging

C++: core::conformation::Conformation::debug_residue_torsions(bool) const –> void

declare_chemical_bond(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos1: int, atom_name1: str, seqpos2: int, atom_name2: str) → None¶

Declare that a chemical bond exists between two residues

C++: core::conformation::Conformation::declare_chemical_bond(unsigned long, const class std::basic_string<char> &, unsigned long, const class std::basic_string<char> &) –> void

delete_chain_ending(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Deletes <seqpos> from the list of (chain number) chain endings

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::delete_chain_ending(unsigned long) –> void

delete_polymer_residue(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Delete polymer residue at the given sequence position

C++: core::conformation::Conformation::delete_polymer_residue(unsigned long) –> void

delete_residue_range_slow(self: pyrosetta.rosetta.core.conformation.Conformation, range_begin: int, range_end: int) → None¶

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue

C++: core::conformation::Conformation::delete_residue_range_slow(unsigned long, unsigned long) –> void

delete_residue_slow(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue

C++: core::conformation::Conformation::delete_residue_slow(unsigned long) –> void

detached_copy(self: pyrosetta.rosetta.core.conformation.Conformation, src: pyrosetta.rosetta.core.conformation.Conformation) → None¶

copy the other conformation into this, but make sure that the two: share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system).

C++: core::conformation::Conformation::detached_copy(const class core::conformation::Conformation &) –> void

detect_bonds(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶: C++: core::conformation::Conformation::detect_bonds() –> void

detect_disulfides(*args, **kwargs)¶

Overloaded function.

detect_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation) -> None
detect_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation, disulf_one: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
detect_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation, disulf_one: pyrosetta.rosetta.utility.vector1_unsigned_long, disulf_two: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::conformation::Conformation::detect_disulfides(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

detect_pseudobonds(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶: C++: core::conformation::Conformation::detect_pseudobonds() –> void

dof(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.DOF_ID) → float¶

Returns the AtomTree degree of freedom (DOF) <id>

C++: core::conformation::Conformation::dof(const class core::id::DOF_ID &) const –> double

dof_id_from_atom_ids(*args, **kwargs)¶

Overloaded function.

dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID, id4: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the torsion angle defined by these four atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the bond angle defined by these three atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID corresponding to the bond distance defined by these two atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class core::id::AtomID &, const class core::id::AtomID &) const –> class core::id::DOF_ID

dof_id_from_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) -> pyrosetta.rosetta.core.id.DOF_ID

Get the DOF_ID defined by these atoms.

C++: core::conformation::Conformation::dof_id_from_atom_ids(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) const –> class core::id::DOF_ID

dof_id_from_torsion_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID) → pyrosetta.rosetta.core.id.DOF_ID¶

Get the DOF_ID corresponding to this TorsionID.

C++: core::conformation::Conformation::dof_id_from_torsion_id(const class core::id::TorsionID &) const –> class core::id::DOF_ID

downstream_jump_stub(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → pyrosetta.rosetta.core.kinematics.Stub¶

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming

C++: core::conformation::Conformation::downstream_jump_stub(int) const –> class core::kinematics::Stub

empty(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

Returns true if this conformation does not have any residues

C++: core::conformation::Conformation::empty() const –> bool

fill_missing_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) → None¶: C++: core::conformation::Conformation::fill_missing_atoms(class core::id::AtomID_Map<bool>) –> void

fix_disulfides(self: pyrosetta.rosetta.core.conformation.Conformation, disulf_bonds: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None¶

Assigns disulfide bonds based on a pre-determined list

C++: core::conformation::Conformation::fix_disulfides(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

fold_tree(*args, **kwargs)¶

Overloaded function.

fold_tree(self: pyrosetta.rosetta.core.conformation.Conformation) -> core::kinematics::FoldTree

Returns the conformation’s FoldTree

C++: core::conformation::Conformation::fold_tree() const –> const class core::kinematics::FoldTree &

fold_tree(self: pyrosetta.rosetta.core.conformation.Conformation, fold_tree_in: core::kinematics::FoldTree) -> None

Sets the FoldTree to <fold_tree_in>

C++: core::conformation::Conformation::fold_tree(const class core::kinematics::FoldTree &) –> void

get_jump_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int, upstream_id: pyrosetta.rosetta.core.id.AtomID, downstream_id: pyrosetta.rosetta.core.id.AtomID) → bool¶

get two atoms connect by jump

C++: core::conformation::Conformation::get_jump_atom_ids(unsigned long, class core::id::AtomID &, class core::id::AtomID &) const –> bool

get_residue_mask(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.utility.vector1_bool¶

returns a mask of residues to be used in scoring

C++: core::conformation::Conformation::get_residue_mask() const –> class utility::vector1<bool, class std::allocator<bool> >

get_residue_weight(self: pyrosetta.rosetta.core.conformation.Conformation, : int, : int) → float¶

returns a residue-pair weight

C++: core::conformation::Conformation::get_residue_weight(unsigned long, unsigned long) const –> double

get_self_ptr(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.conformation.Conformation¶: C++: core::conformation::Conformation::get_self_ptr() –> class std::shared_ptr<class core::conformation::Conformation>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.std.weak_ptr_core_conformation_Conformation_t¶: C++: core::conformation::Conformation::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::Conformation>

get_stub_transform(self: pyrosetta.rosetta.core.conformation.Conformation, stub_id1: pyrosetta.rosetta.core.id.StubID, stub_id2: pyrosetta.rosetta.core.id.StubID) → pyrosetta.rosetta.core.kinematics.RT¶

get the transform between two stubs

C++: core::conformation::Conformation::get_stub_transform(const class core::id::StubID &, const class core::id::StubID &) const –> class core::kinematics::RT

get_torsion_angle_atom_ids(self: pyrosetta.rosetta.core.conformation.Conformation, tor_id: core::id::TorsionID, id1: pyrosetta.rosetta.core.id.AtomID, id2: pyrosetta.rosetta.core.id.AtomID, id3: pyrosetta.rosetta.core.id.AtomID, id4: pyrosetta.rosetta.core.id.AtomID) → bool¶

get four atoms which defined this torsion

C++: core::conformation::Conformation::get_torsion_angle_atom_ids(const class core::id::TorsionID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &) const –> bool

glycan_tree_set(self: pyrosetta.rosetta.core.conformation.Conformation) → core::conformation::carbohydrates::GlycanTreeSet¶

Get the glycan tree set. Nullptr if not present.

C++: core::conformation::Conformation::glycan_tree_set() const –> class std::shared_ptr<const class core::conformation::carbohydrates::GlycanTreeSet>

has_passport(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶: C++: core::conformation::Conformation::has_passport() const –> bool

insert_chain_ending(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Marks <seqpos> as the end of a new (chain number) chain

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::insert_chain_ending(unsigned long) –> void

insert_conformation_by_jump(*args, **kwargs)¶

Overloaded function.

insert_conformation_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, conf: pyrosetta.rosetta.core.conformation.Conformation, insert_seqpos: int, insert_jumppos: int, anchor_pos: int) -> None
insert_conformation_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, conf: pyrosetta.rosetta.core.conformation.Conformation, insert_seqpos: int, insert_jumppos: int, anchor_pos: int, anchor_jump_number: int) -> None
insert_conformation_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, conf: pyrosetta.rosetta.core.conformation.Conformation, insert_seqpos: int, insert_jumppos: int, anchor_pos: int, anchor_jump_number: int, anchor_atom: str) -> None
insert_conformation_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, conf: pyrosetta.rosetta.core.conformation.Conformation, insert_seqpos: int, insert_jumppos: int, anchor_pos: int, anchor_jump_number: int, anchor_atom: str, root_atom: str) -> None

Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump

C++: core::conformation::Conformation::insert_conformation_by_jump(const class core::conformation::Conformation &, unsigned long, unsigned long, unsigned long, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

insert_ideal_geometry_at_polymer_bond(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶: C++: core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(unsigned long) –> void

insert_ideal_geometry_at_residue_connection(self: pyrosetta.rosetta.core.conformation.Conformation, pos1: int, connid1: int) → None¶: C++: core::conformation::Conformation::insert_ideal_geometry_at_residue_connection(unsigned long, unsigned long) –> void

insert_residue_by_bond(*args, **kwargs)¶

Overloaded function.

insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool) -> None
insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, build_ideal_geometry: bool, anchor_atom: str, root_atom: str, new_chain: bool, lookup_bond_length: bool) -> None

Insert a new residue by jump. If new_chain is “true”, then seqpos must be the last: residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

C++: core::conformation::Conformation::insert_residue_by_bond(const class core::conformation::Residue &, unsigned long, unsigned long, bool, const class std::basic_string<char> &, const class std::basic_string<char> &, bool, bool) –> void

insert_residue_by_jump(*args, **kwargs)¶

Overloaded function.

insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None
insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str) -> None
insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str, root_atom: str) -> None
insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int, anchor_atom: str, root_atom: str, new_chain: bool) -> None

Insert a new residue by jump. If new_chain is “true”, then seqpos must be the last: residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

C++: core::conformation::Conformation::insert_residue_by_jump(const class core::conformation::Residue &, unsigned long, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, bool) –> void

inter_residue_connection_partner(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, connection_index: int) → pyrosetta.rosetta.core.id.AtomID¶

This returns the AtomID of the atom in the other residue to which the “connection_index”-th: connection of residue seqpos is connected to.

C++: core::conformation::Conformation::inter_residue_connection_partner(unsigned long, int) const –> class core::id::AtomID

is_centroid(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_centroid() const –> bool

is_fullatom(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_fullatom() const –> bool

is_membrane(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

convenience test for if the conformation contains information for a membrane protein

C++: core::conformation::Conformation::is_membrane() const –> bool

is_mixed_mode(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

convenience test for residue_type_set mode

C++: core::conformation::Conformation::is_mixed_mode() const –> bool

is_protected(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶: C++: core::conformation::Conformation::is_protected() const –> bool

jump(*args, **kwargs)¶

Overloaded function.

jump(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) -> pyrosetta.rosetta.core.kinematics.Jump

Returns the Jump with jump number <jump_number>

C++: core::conformation::Conformation::jump(int) const –> const class core::kinematics::Jump &

jump(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.core.kinematics.Jump

access a jump

C++: core::conformation::Conformation::jump(const class core::id::AtomID &) const –> const class core::kinematics::Jump &

jump_atom_id(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::conformation::Conformation::jump_atom_id(int) const –> class core::id::AtomID

membrane_info(self: pyrosetta.rosetta.core.conformation.Conformation) → core::conformation::membrane::MembraneInfo¶

Returns the const MembraneInfo object in conformation

Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data

C++: core::conformation::Conformation::membrane_info() –> class std::shared_ptr<class core::conformation::membrane::MembraneInfo>

modifiable_residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

modifiable_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.PoseResidueTypeSet
modifiable_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const): Modifications to this RTS won’t be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn’t have it already.

C++: core::conformation::Conformation::modifiable_residue_type_set_for_conf(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>

n_parameters_sets(self: pyrosetta.rosetta.core.conformation.Conformation) → int¶

Get the number of parameters sets defined for this Conformation.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::n_parameters_sets() const –> unsigned long

num_chains(self: pyrosetta.rosetta.core.conformation.Conformation) → int¶

Returns the number of chains

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::num_chains() const –> unsigned long

parameters_set(self: pyrosetta.rosetta.core.conformation.Conformation, index: int) → pyrosetta.rosetta.core.conformation.parametric.ParametersSet¶

Access one of the ParametersSets objects linked to this Conformation.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::parameters_set(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::ParametersSet>

pop_passport(self: pyrosetta.rosetta.core.conformation.Conformation) → core::environment::DofPassport¶: C++: core::conformation::Conformation::pop_passport() –> class std::shared_ptr<const class core::environment::DofPassport>

prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) → None¶

glues to seqpos and perhaps also seqpos-1

C++: core::conformation::Conformation::prepend_polymer_residue_before_seqpos(const class core::conformation::Residue &, unsigned long, bool) –> void

push_passport(self: pyrosetta.rosetta.core.conformation.Conformation, : core::environment::DofPassport) → None¶: C++: core::conformation::Conformation::push_passport(class std::shared_ptr<const class core::environment::DofPassport>) –> void

rebuild_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1

C++: core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(unsigned long) –> void

rebuild_polymer_bond_dependent_atoms_this_residue_only(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶

Rebuilds the atoms that are depenent on polymer bonds for the specified residue only.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only(unsigned long) –> void

rebuild_residue_connection_dependent_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, connid: int) → None¶: C++: core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(unsigned long, unsigned long) –> void

receive_observers_from(self: pyrosetta.rosetta.core.conformation.Conformation, src: pyrosetta.rosetta.core.conformation.Conformation) → None¶

fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation

C++: core::conformation::Conformation::receive_observers_from(const class core::conformation::Conformation &) –> void

replace_residue(*args, **kwargs)¶

Overloaded function.

replace_residue(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, orient_backbone: bool) -> None

replace residue

C++: core::conformation::Conformation::replace_residue(unsigned long, const class core::conformation::Residue &, bool) –> void

replace_residue(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, atom_pairs: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t) -> None

function to replace a residue based on superposition on the specified input atom pairs

C++: core::conformation::Conformation::replace_residue(unsigned long, const class core::conformation::Residue &, const class utility::vector1<struct std::pair<class std::basic_string<char>, class std::basic_string<char> >, class std::allocator<struct std::pair<class std::basic_string<char>, class std::basic_string<char> > > > &) –> void

reset_chain_endings(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Resets chain data so that the Conformation is marked as a single (chain number) chain

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Conformation::reset_chain_endings() –> void

reset_move_data(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

forget all the structure modifications

C++: core::conformation::Conformation::reset_move_data() –> void

reset_residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

reset_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, new_set: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> None
reset_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, new_set: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> None

Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS.

(If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.)

NOTE: You’re potentially in for a bunch of trouble if the passed in set isn’t a modified version of the value returned by modifiable_residue_type_set_for_conf() from this conformation. Also, a clone of the RTS is made, so subsequent edits to the RTS will not be reflected in the Conformation’s RTS

C++: core::conformation::Conformation::reset_residue_type_set_for_conf(class std::shared_ptr<const class core::chemical::PoseResidueTypeSet>, enum core::chemical::TypeSetMode) –> void

reset_structure_moved(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

reset the structure_moved_ bool

C++: core::conformation::Conformation::reset_structure_moved() const –> void

residue(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶

access one of the residues

this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.

update coordinates and torsions for this and all other residues before allowing read access

C++: core::conformation::Conformation::residue(unsigned long) const –> const class core::conformation::Residue &

residue_cop(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶

access one of the residues, using COP

C++: core::conformation::Conformation::residue_cop(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

residue_data(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache¶

Write access to the datacache array stored inside a Residue object. Although the Conformation

very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable.

The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a %Conformation) so that it can be used during scoring evaluation. Accessing the residue_data will trigger a coordinate (or torsion) update.

C++: core::conformation::Conformation::residue_data(unsigned long) –> class basic::datacache::BasicDataCache &

residue_type(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.ResidueType¶

access one of the residue’s types – avoids coord/torsion update

C++: core::conformation::Conformation::residue_type(unsigned long) const –> const class core::chemical::ResidueType &

residue_type_ptr(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → pyrosetta.rosetta.core.chemical.ResidueType¶

access one of the residue’s types as a COP – avoids coord/torsion update

C++: core::conformation::Conformation::residue_type_ptr(unsigned long) const –> class std::shared_ptr<const class core::chemical::ResidueType>

residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet
residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

Return the appropriate ResidueTypeSet for the Conformation: If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn’t have a specific PoseResidueTypeSet

C++: core::conformation::Conformation::residue_type_set_for_conf(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

residue_typeset_mode(*args, **kwargs)¶

Overloaded function.

residue_typeset_mode(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.TypeSetMode
residue_typeset_mode(self: pyrosetta.rosetta.core.conformation.Conformation, majority: bool) -> pyrosetta.rosetta.core.chemical.TypeSetMode

What mode of ResidueTypeSet is this Conformation made of?: If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes

C++: core::conformation::Conformation::residue_typeset_mode(bool) const –> enum core::chemical::TypeSetMode

safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) → None¶

glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary

C++: core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(const class core::conformation::Residue &, unsigned long, bool) –> void

safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) → None¶

glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary

C++: core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(const class core::conformation::Residue &, unsigned long, bool) –> void

same_type_as_me(*args, **kwargs)¶

Overloaded function.

same_type_as_me(self: pyrosetta.rosetta.core.conformation.Conformation, other: pyrosetta.rosetta.core.conformation.Conformation) -> bool
same_type_as_me(self: pyrosetta.rosetta.core.conformation.Conformation, other: pyrosetta.rosetta.core.conformation.Conformation, recurse: bool) -> bool

determine the type of the ConformationOP

C++: core::conformation::Conformation::same_type_as_me(const class core::conformation::Conformation &, bool) const –> bool

secstruct(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → str¶

Returns the secondary structure the position <seqpos>

character representing secondary structure; returns ‘L’ if the requested sequence position is larger than the length in the secondary structure array

C++: core::conformation::Conformation::secstruct(unsigned long) const –> char

sequence_matches(self: pyrosetta.rosetta.core.conformation.Conformation, other: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

do the names of all residues in this and src match?

C++: core::conformation::Conformation::sequence_matches(const class core::conformation::Conformation &) const –> bool

set_bond_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, setting: float) → None¶

Sets the bond angle defined by <atom[1-3]> to <setting>

C++: core::conformation::Conformation::set_bond_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, double) –> void

set_bond_length(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, setting: float) → None¶

Sets the cond length between <atom1> and <atom2> to <setting>

C++: core::conformation::Conformation::set_bond_length(const class core::id::AtomID &, const class core::id::AtomID &, double) –> void

set_dof(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.DOF_ID, setting: float) → None¶

Sets the AtomTree degree of freedom (DOF) <id> to <setting>

C++: core::conformation::Conformation::set_dof(const class core::id::DOF_ID &, double) –> void

set_jump(*args, **kwargs)¶

Overloaded function.

set_jump(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int, new_jump: pyrosetta.rosetta.core.kinematics.Jump) -> None

Sets the jump <jump_number> to <new_jump>

C++: core::conformation::Conformation::set_jump(int, const class core::kinematics::Jump &) –> void

set_jump(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID, new_jump: pyrosetta.rosetta.core.kinematics.Jump) -> None

set a jump

C++: core::conformation::Conformation::set_jump(const class core::id::AtomID &, const class core::kinematics::Jump &) –> void

set_jump_atom_stub_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.StubID) → None¶: C++: core::conformation::Conformation::set_jump_atom_stub_id(const class core::id::StubID &) –> void

set_membrane_info(self: pyrosetta.rosetta.core.conformation.Conformation, mem_info: core::conformation::membrane::MembraneInfo) → None¶

Setup a Membrane Info object in Conformation - pos & topology

Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.

C++: core::conformation::Conformation::set_membrane_info(class std::shared_ptr<class core::conformation::membrane::MembraneInfo>) –> void

set_noncanonical_connection(self: pyrosetta.rosetta.core.conformation.Conformation, res_id_lower: int, lr_conn_id: int, res_id_upper: int, ur_conn_id: int) → None¶

Create an arbitrary covalent connection between two residues.

C++: core::conformation::Conformation::set_noncanonical_connection(unsigned long, unsigned long, unsigned long, unsigned long) –> void

set_polymeric_connection(self: pyrosetta.rosetta.core.conformation.Conformation, res_id_lower: int, res_id_upper: int) → None¶

identify polymeric connections

C++: core::conformation::Conformation::set_polymeric_connection(unsigned long, unsigned long) –> void

set_secstruct(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, setting: str) → None¶

Sets the secondary structure of the position <seqpos> to <setting>

Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.

C++: core::conformation::Conformation::set_secstruct(unsigned long, char) –> void

set_stub_transform(self: pyrosetta.rosetta.core.conformation.Conformation, stub_id1: pyrosetta.rosetta.core.id.StubID, stub_id2: pyrosetta.rosetta.core.id.StubID, target_rt: pyrosetta.rosetta.core.kinematics.RT) → None¶

Set the transform between two stubs – only works if there’s a jump between the two sets of stubatoms

C++: core::conformation::Conformation::set_stub_transform(const class core::id::StubID &, const class core::id::StubID &, const class core::kinematics::RT &) –> void

set_torsion(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID, setting: float) → None¶

Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump

C++: core::conformation::Conformation::set_torsion(const class core::id::TorsionID &, double) –> void

set_torsion_angle(*args, **kwargs)¶

Overloaded function.

set_torsion_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, setting: float) -> None
set_torsion_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, setting: float, quiet: bool) -> None

Sets the torsion angle defined by <atom[1-4]> to <setting>

C++: core::conformation::Conformation::set_torsion_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, double, bool) –> void

set_xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID, position: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::conformation::Conformation::set_xyz(const class core::id::AtomID &, const class numeric::xyzVector<double> &) –> void

setup_glycan_trees(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Setup glycan trees and attach length observer.

C++: core::conformation::Conformation::setup_glycan_trees() –> void

sever_chemical_bond(self: pyrosetta.rosetta.core.conformation.Conformation, seqpos1: int, res1_resconn_index: int, seqpos2: int, res2_resconn_index: int) → None¶

Sever the chemical bond between two residues by stating that the: connections for those residues are “incomplete” (i.e. in a state where these residues are not ready to be scored).

C++: core::conformation::Conformation::sever_chemical_bond(unsigned long, unsigned long, unsigned long, unsigned long) –> void

show_residue_connections(*args, **kwargs)¶

Overloaded function.

show_residue_connections(self: pyrosetta.rosetta.core.conformation.Conformation) -> None

Show residue connections for debugging purposes.

C++: core::conformation::Conformation::show_residue_connections() const –> void

show_residue_connections(self: pyrosetta.rosetta.core.conformation.Conformation, os: pyrosetta.rosetta.std.ostream) -> None

Show residue connections for debugging purposes.

C++: core::conformation::Conformation::show_residue_connections(class std::basic_ostream<char> &) const –> void

size(self: pyrosetta.rosetta.core.conformation.Conformation) → int¶

Returns the number of residues in the Conformation

C++: core::conformation::Conformation::size() const –> unsigned long

structure_moved(self: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

has the structure moved since the last call to reset_move_data or reset_structure_moved

C++: core::conformation::Conformation::structure_moved() const –> bool

stub_from_id(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.StubID) → pyrosetta.rosetta.core.kinematics.Stub¶: C++: core::conformation::Conformation::stub_from_id(const class core::id::StubID &) const –> class core::kinematics::Stub

torsion(self: pyrosetta.rosetta.core.conformation.Conformation, id: core::id::TorsionID) → float¶

Return the torsion angle OR rigid-body offset for <id>

C++: core::conformation::Conformation::torsion(const class core::id::TorsionID &) const –> double

torsion_angle(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → float¶

Returns the torsion angle defined by <atom[1-4]>

C++: core::conformation::Conformation::torsion_angle(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) const –> double

unblock_signals(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶

allow signals to be sent

C++: core::conformation::Conformation::unblock_signals() –> void

update_actcoord(self: pyrosetta.rosetta.core.conformation.Conformation, resid: int) → None¶: C++: core::conformation::Conformation::update_actcoord(unsigned long) –> void

update_actcoords(self: pyrosetta.rosetta.core.conformation.Conformation) → None¶: C++: core::conformation::Conformation::update_actcoords() –> void

update_domain_map(self: pyrosetta.rosetta.core.conformation.Conformation, domain_map: ObjexxFCL::FArray1D<int>) → None¶

Generate a domain_map from the current dof/xyz moved data

C++: core::conformation::Conformation::update_domain_map(class ObjexxFCL::FArray1D<int> &) const –> void

update_membrane_position(self: pyrosetta.rosetta.core.conformation.Conformation, center: pyrosetta.rosetta.numeric.xyzVector_double_t, normal: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Update Normal, Center in the Membrane

Sets the center and normal coordinates to the appropriate parameters and checks for a valid stub prior to returning.

C++: core::conformation::Conformation::update_membrane_position(class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> void

update_noncanonical_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int, lr_conn_id: int, upper_seqpos: int, ur_conn_id: int) → None¶

Update the connection status between the lower_seqpos residue’s lr_conn_id connection ID and: the upper_seqpos residue’s ur_conn_id connection ID.

C++: core::conformation::Conformation::update_noncanonical_connection(unsigned long, unsigned long, unsigned long, unsigned long) –> void

update_orbital_coords(*args, **kwargs)¶

Overloaded function.

update_orbital_coords(self: pyrosetta.rosetta.core.conformation.Conformation, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: core::conformation::Conformation::update_orbital_coords(class core::conformation::Residue &) const –> void

update_orbital_coords(self: pyrosetta.rosetta.core.conformation.Conformation, resid: int) -> None

C++: core::conformation::Conformation::update_orbital_coords(unsigned long) –> void

update_polymeric_connection(*args, **kwargs)¶

Overloaded function.

update_polymeric_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int) -> None
update_polymeric_connection(self: pyrosetta.rosetta.core.conformation.Conformation, lower_seqpos: int, update_connection_dep_atoms: bool) -> None

Update the polymer connection status between lower_seqpos and lower_seqpos+1: based on chainID’s and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated.

C++: core::conformation::Conformation::update_polymeric_connection(unsigned long, bool) –> void

upstream_jump_stub(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → pyrosetta.rosetta.core.kinematics.Stub¶

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming

C++: core::conformation::Conformation::upstream_jump_stub(int) const –> class core::kinematics::Stub

xyz(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

access xyz coordinates of an atom

C++: core::conformation::Conformation::xyz(const class core::id::AtomID &) const –> const class numeric::xyzVector<double> &

class pyrosetta.rosetta.core.conformation.DefaultCubeHash¶

Bases: pyrosetta.rosetta.std.unary_function_numeric_xyzTriple_unsigned_long_unsigned_long_t

uses default boost::hash combine to hash Cubes

__call__(self: pyrosetta.rosetta.core.conformation.DefaultCubeHash, key: pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t) → int¶

return hash value given CubeKey

C++: core::conformation::DefaultCubeHash::operator()(const class numeric::xyzTriple<unsigned long> &) const –> unsigned long

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.conformation.DefaultCubeHash) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class pyrosetta.rosetta.core.conformation.Residue¶

Bases: pybind11_builtins.pybind11_object

Instance Residue class, used for placed residues and rotamers

This class is designed to be lightweight. It holds a const-reference (“rsd_type_”)

to a ResidueType object for access to information common to all instances of a single type, e.g., Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:

a vector1 of Atoms, which holds the positions (and also the atom-types for

fast access during scoring);

the sequence position and chain number, both integers

(See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.)

the backbone, side-chain, and internal ring (if applicable) torsion angles (of course backbone torsions are

not unique to a rotamer, and the chi angles are derivable from the coordinates, but storing them in the residue is convenient for scoring purposes).

the coordinates of an interaction center or centroid, used e.g., in the

knowledge-based full-atom pair term (“actcoord_”). Maybe this will also hold the centroid position for centroid-mode scoring??

Haro_index(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s aromatic hydrogens

: AtomIndices == vector1< Size >

example(s):

residue.Haro_index()

See also:

Residue Residue.atoms Residue.Hpol_index Pose

C++: core::conformation::Residue::Haro_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpol_index(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s polar hydrogens

: AtomIndices == vector1< Size >

example(s):

residue.Hpol_index()

See also:

Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Residue.Hpos_polar Pose

C++: core::conformation::Residue::Hpol_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_apolar(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s apolar hydrogens

: AtomIndices == vector1< Size >

example(s):

residue.Hpos_apolar()

See also:

Residue Residue.atoms Residue.Hpol_index() Residue.Hpos_polar Pose

C++: core::conformation::Residue::Hpos_apolar() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_polar(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s polar hydrogens

: AtomIndices == vector1< Size >

example(s):

residue.Hpos_polar()

See also:

Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Pose

C++: core::conformation::Residue::Hpos_polar() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_polar_sc(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s polar sidechain hydrogens

: AtomIndices == vector1< Size >

example(s):

residue.Hpos_polar_sc()

See also:

Residue Residue.atoms Residue.Hpol_index Residue.Hpos_polar Pose

C++: core::conformation::Residue::Hpos_polar_sc() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

RNA_info(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.rna.RNA_Info¶

Return the RNA_residueType object. This is RNA specific.

C++: core::conformation::Residue::RNA_info() const –> const class core::chemical::rna::RNA_Info &

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.conformation.Residue, rsd_type_in: pyrosetta.rosetta.core.chemical.ResidueType, dummy_arg: bool) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Residue, rsd_type_in: pyrosetta.rosetta.core.chemical.ResidueType, dummy_arg: bool) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Residue, arg0: pyrosetta.rosetta.core.chemical.ResidueType, arg1: pyrosetta.rosetta.core.conformation.Residue, arg2: core::conformation::Conformation) -> None

doc

__init__(self: pyrosetta.rosetta.core.conformation.Residue, rsd_type_in: pyrosetta.rosetta.core.chemical.ResidueType, current_rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation, preserve_c_beta: bool) -> None
__init__(self: pyrosetta.rosetta.core.conformation.Residue, arg0: pyrosetta.rosetta.core.conformation.Residue) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.conformation.Residue) → str¶

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

aa(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.AA¶

Returns this residue’s AA type, if any: Used for knowledge-based scores, dunbrack, etc. could be “aa_unk” AA is enumeration

C++: core::conformation::Residue::aa() const –> const enum core::chemical::AA &

abase2(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → int¶

Returns the atom index of the <atomno> atom’s second base atom: note: abase2 is this atom’s first bonded neighbor other than this atom’s base atom (unless it has only one neighbor)

C++: core::conformation::Residue::abase2(const int) const –> unsigned long

accpt_pos(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s h-bond acceptor atoms

: AtomIndices == vector1< Size >

example(s):

residue.accpt_pos()

See also:

Residue Residue.accpt_pos_sc Residue.atoms Pose

C++: core::conformation::Residue::accpt_pos() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

accpt_pos_sc(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s sidechain h-bond acceptor atoms

: AtomIndices == vector1< Size >

example(s):

residue.accpt_pos_sc()

See also:

Residue Residue.accpt_pos Residue.atoms Pose

C++: core::conformation::Residue::accpt_pos_sc() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

actcoord(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Returns the coordinates used for pairE calculations (amino acids only)

C++: core::conformation::Residue::actcoord() –> class numeric::xyzVector<double> &

actcoord_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of atoms that will be used to define this residue’s actcoord.

C++: core::conformation::Residue::actcoord_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

actual_residue_connection(self: pyrosetta.rosetta.core.conformation.Residue, resconnid: int) → pyrosetta.rosetta.core.chemical.ResConnID¶

Get the residue connection.: How is this different than residue_connection?

C++: core::conformation::Residue::actual_residue_connection(unsigned long) const –> class core::chemical::ResConnID

all_bb_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s backbone atoms

: heavyatoms and hydrogens, AtomIndices == vector1< Size >

example(s):

residue.all_bb_atoms()

See also:

Residue Residue.atoms Pose

C++: core::conformation::Residue::all_bb_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

annotated_name(*args, **kwargs)¶

Overloaded function.

annotated_name(self: pyrosetta.rosetta.core.conformation.Residue) -> str
annotated_name(self: pyrosetta.rosetta.core.conformation.Residue, show_all_variants: bool) -> str

Returns this residue’s 1-letter representation, including: details in square brackets. E.g., H[HIS_D]

C++: core::conformation::Residue::annotated_name(const bool) const –> std::string

apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.conformation.Residue, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Applies a transform of the form Rx + v, where R is a rotation: matrix, V is a vector, and x is the original position in xyz space

C++: core::conformation::Residue::apply_transform_Rx_plus_v(class numeric::xyzMatrix<double>, class numeric::xyzVector<double>) –> void

atom(*args, **kwargs)¶

Overloaded function.

atom(self: pyrosetta.rosetta.core.conformation.Residue, atm_index: int) -> pyrosetta.rosetta.core.conformation.Atom

Returns this residue’s Atom with index number <atm_index> (non-const)

: Atom object is xyz and atom_type

example(s):

residue.atom(3)

See also:

Residue Residue.atoms Pose

C++: core::conformation::Residue::atom(const unsigned long) –> class core::conformation::Atom &

atom(self: pyrosetta.rosetta.core.conformation.Residue, atm_name: str) -> pyrosetta.rosetta.core.conformation.Atom

Returns this residue’s Atom with name <atm_name> (non-const)

: Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you

need a specific atom

example(s):: residue.atom(3)
See also:: Residue Residue.atoms Pose

C++: core::conformation::Residue::atom(const class std::basic_string<char> &) –> class core::conformation::Atom &

atom_base(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → int¶

Returns the atom index of the <atomno> atom’s base atom

C++: core::conformation::Residue::atom_base(const int) const –> unsigned long

atom_begin(self: pyrosetta.rosetta.core.conformation.Residue) → __gnu_cxx::__normal_iterator<core::conformation::Atom*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >¶

begin interator, to iterate over atoms

C++: core::conformation::Residue::atom_begin() –> class __gnu_cxx::__normal_iterator<class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >

atom_depends_on_lower(*args, **kwargs)¶

Overloaded function.

atom_depends_on_lower(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) -> bool
atom_depends_on_lower(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int, recursive: bool) -> bool

Does this atom depend on the LOWER_CONNECT?

If recursive is set to true (the default), the dependencies are traced back and the function returns true if ANY atom that this atom depends on is dependent on LOWER_CONNECT. If false, only the immediate stub1, stub2, and stub3 atoms are checked.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::Residue::atom_depends_on_lower(const unsigned long, const bool) const –> bool

atom_depends_on_upper(*args, **kwargs)¶

Overloaded function.

atom_depends_on_upper(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) -> bool
atom_depends_on_upper(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int, recursive: bool) -> bool

Does this atom depend on the UPPER_CONNECT?

If recursive is set to true (the default), the dependencies are traced back and the function returns true if ANY atom that this atom depends on is dependent on UPPER_CONNECT. If false, only the immediate stub1, stub2, and stub3 atoms are checked.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::Residue::atom_depends_on_upper(const unsigned long, const bool) const –> bool

atom_end(self: pyrosetta.rosetta.core.conformation.Residue) → __gnu_cxx::__normal_iterator<core::conformation::Atom*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >¶

end interator, to iterate over atoms

C++: core::conformation::Residue::atom_end() –> class __gnu_cxx::__normal_iterator<class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >

atom_index(self: pyrosetta.rosetta.core.conformation.Residue, atm: str) → int¶

Returns the index number of the <atm> in this residue

example: residue.atom_index(“CA”) returns 2 for a normal amino acid

example(s):: residue.atom_index(“CA”)
See also:: Residue AtomType Pose

C++: core::conformation::Residue::atom_index(const class std::basic_string<char> &) const –> unsigned long

atom_is_backbone(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → bool¶

Returns true if this residue’s atom with index number <atomno> is a backbone atom

example(s):

residue.atom_is_backbone(3)

See also:

Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

C++: core::conformation::Residue::atom_is_backbone(const int) const –> bool

atom_is_hydrogen(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → bool¶

Returns true if this residue’s atom with index number <atomno> is a hydrogen

example(s):

residue.atom_is_backbone(3)

See also:

Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

C++: core::conformation::Residue::atom_is_hydrogen(const unsigned long) const –> bool

atom_is_polar_hydrogen(self: pyrosetta.rosetta.core.conformation.Residue, ind: int) → bool¶

Is a particular atom a polar hydrogen?

C++: core::conformation::Residue::atom_is_polar_hydrogen(unsigned long) const –> bool

atom_name(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → str¶: Returns the name of this residue’s atom with index number <atm>

C++: core::conformation::Residue::atom_name(const int) const –> const std::string &

atom_type(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → pyrosetta.rosetta.core.chemical.AtomType¶

Returns the AtomType of this residue’s atom with index number <atomno>

example(s):

residue.atom_type(3)

See also:

Residue Residue.atom_index AtomType Pose

C++: core::conformation::Residue::atom_type(const int) const –> const class core::chemical::AtomType &

atom_type_index(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → int¶

Returns the atom_type_index of this residue’s atom with index number <atomno>

atom_type_index is used to query this atom’s AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType

example(s):: residue.atom_type_index(3)
See also:: Residue Residue.atom_index AtomType Pose

C++: core::conformation::Residue::atom_type_index(const unsigned long) const –> unsigned long

atom_type_set(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.AtomTypeSet¶

Returns the AtomTypeSet of this residue

example(s):

residue.atom_type_set()

See also:

Residue Residue.atom_type_index AtomType Pose

C++: core::conformation::Residue::atom_type_set() const –> const class core::chemical::AtomTypeSet &

atomic_charge(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → float¶

Returns the atom charge of this residue’s atom with index number <atomno>

example(s):

residue.atomic_charge(3)

See also:

Residue Residue.atom_index Pose

C++: core::conformation::Residue::atomic_charge(const int) const –> double

atoms(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_core_conformation_Atom¶

Returns this residue’s Atoms (non-const), a vector1 of Atom objects

example(s):

residue.atoms()

See also:

Residue Pose

C++: core::conformation::Residue::atoms() –> class utility::vector1<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > &

atoms_with_orb_index(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::conformation::Residue::atoms_with_orb_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

attached_H_begin(*args, **kwargs)¶

Overloaded function.

attached_H_begin(self: pyrosetta.rosetta.core.conformation.Residue, atom: int) -> int

Returns the index number of the first hydrogen attached to the atom

with index number <atom>

example(s):: residue.attached_H_begin()
See also:: Residue Residue.atom Residue.atoms Residue.attached_H_end Pose

C++: core::conformation::Residue::attached_H_begin(const int) const –> unsigned long

attached_H_begin(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the AtomIndices of the first hydrogen attached to each heavyatom

example(s):

residue.attached_H_begin()

See also:

Residue Residue.atom Residue.atoms Residue.attached_H_end Residue.nheavyatoms Pose

C++: core::conformation::Residue::attached_H_begin() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

attached_H_end(*args, **kwargs)¶

Overloaded function.

attached_H_end(self: pyrosetta.rosetta.core.conformation.Residue, atom: int) -> int

Returns the index number of the last hydrogen attached to the atom

with index number <atom>

example(s):: residue.attached_H_end()
See also:: Residue Residue.atom Residue.atoms Residue.attached_H_begin Pose

C++: core::conformation::Residue::attached_H_end(const int) const –> unsigned long

attached_H_end(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the AtomIndices of the last hydrogen attached to each heavyatom

example(s):

residue.attached_H_end()

See also:

Residue Residue.atom Residue.atoms Residue.attached_H_begin Residue.nheavyatoms Pose

C++: core::conformation::Residue::attached_H_end() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

backbone_aa(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.AA¶

Returns this residue’s backbone_aa type, if any.

This is used for noncanonical alpha-amino acids that are templated on canonicals.

For example, 4,5-dihydroxyisoleucine uses the ramachandran and p_aa_pp scoring of isoleucine.

C++: core::conformation::Residue::backbone_aa() const –> const enum core::chemical::AA &

bonded_neighbor(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices for all bonded neighbor atoms of <atm>

C++: core::conformation::Residue::bonded_neighbor(const int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

bonded_orbitals(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::conformation::Residue::bonded_orbitals(const int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

build_atom_ideal(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int, conformation: core::conformation::Conformation) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Return coordinates for building an atom from ideal internal coordinates,: used for building missing atoms

C++: core::conformation::Residue::build_atom_ideal(const int, const class core::conformation::Conformation &) const –> class numeric::xyzVector<double>

build_orbital_xyz(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::conformation::Residue::build_orbital_xyz(const unsigned long) const –> class numeric::xyzVector<double>

carbohydrate_info(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo¶

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

C++: core::conformation::Residue::carbohydrate_info() const –> class std::shared_ptr<const class core::chemical::carbohydrates::CarbohydrateInfo>

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.core.conformation.Residue) -> int

Returns this residue’s chain id

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Residue::chain() const –> unsigned long

chain(self: pyrosetta.rosetta.core.conformation.Residue, setting: int) -> None

Sets this residue’s chain id

Don’t call directly – In almost all situations, this should be set by the owning Conformation

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

C++: core::conformation::Residue::chain(const unsigned long) –> void

chi(*args, **kwargs)¶

Overloaded function.

chi(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_double

Returns the chi torsion angles of this residue (non-const)

C++: core::conformation::Residue::chi() –> class utility::vector1<double, class std::allocator<double> > &

chi(self: pyrosetta.rosetta.core.conformation.Residue, chis: pyrosetta.rosetta.utility.vector1_double) -> None

Sets the chi torsion angles of this residue

CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.

example(s):

See also:

Residue Pose Pose.set_chi

C++: core::conformation::Residue::chi(const class utility::vector1<double, class std::allocator<double> > &) –> void

chi(self: pyrosetta.rosetta.core.conformation.Residue, chino: int) -> float

get a specific chi torsion angle

example(s):

residue.chi(1)

See also:

Residue Pose Pose.chi

C++: core::conformation::Residue::chi(const unsigned long) const –> double

chi_atoms(*args, **kwargs)¶

Overloaded function.

chi_atoms(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Returns the AtomIndices of each set of four atoms defining each chi angle

C++: core::conformation::Residue::chi_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

chi_atoms(self: pyrosetta.rosetta.core.conformation.Residue, chino: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the AtomIndices of the four atoms defining this residue’s <chino> chi angle

C++: core::conformation::Residue::chi_atoms(const int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

chi_rotamers(self: pyrosetta.rosetta.core.conformation.Residue, chino: int) → pyrosetta.rosetta.utility.vector1_std_pair_double_double_t¶

Returns the chi rotamers available for this residue’s chi angle <chino>

C++: core::conformation::Residue::chi_rotamers(const unsigned long) const –> const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &

clear_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue) → None¶: C++: core::conformation::Residue::clear_residue_connections() –> void

clone(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue¶

Copy this residue( allocate actual memory for it )

C++: core::conformation::Residue::clone() const –> class std::shared_ptr<class core::conformation::Residue>

clone_flipping_chirality(self: pyrosetta.rosetta.core.conformation.Residue, residue_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.conformation.Residue¶

Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.

Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues. The passed ResidueTypeSet is the ResidueTypeSet you want the mirrored type to come from.

This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart. It assumes that you’ve already mirrored all of the coordinates, and just allows you to generate a replacement residue of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms, variant types, etc.).

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::clone_flipping_chirality(const class core::chemical::ResidueTypeSet &) const –> class std::shared_ptr<class core::conformation::Residue>

connect_atom(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of this residue’s atom connected to the <other> Residue

example(s):

See also:

Residue Residue.atom Residue.atoms Residue.lower_connect_atom Residue.upper_connect_atom Pose

C++: core::conformation::Residue::connect_atom(const class core::conformation::Residue &) const –> unsigned long

connect_map(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) → pyrosetta.rosetta.core.chemical.ResConnID¶: C++: core::conformation::Residue::connect_map(unsigned long) const –> class core::chemical::ResConnID

connect_map_size(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the size (number of elements) in the connect_map_ object.

C++: core::conformation::Residue::connect_map_size() const –> unsigned long

connected_residue_at_lower(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the residue number of a residue connected to this residue

at this residue’s lower_connect.

This function returns 0 if this residue lacks a lower_connect

or if it’s not connected to anything at its lower_connect.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::connected_residue_at_lower() const –> unsigned long

connected_residue_at_resconn(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) → int¶

Returns the residue number of a residue connected to this residue

at this residue’s connection resconn_index.

For example, in a normally-connected pose made of alpha-amino

acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6. Exactly the same as residue_connection_partner

C++: core::conformation::Residue::connected_residue_at_resconn(const unsigned long) const –> unsigned long

connected_residue_at_upper(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the residue number of a residue connected to this residue

at this residue’s upper_connect.

This function returns 0 if this residue lacks an upper_connect

or if it’s not connected to anything at its upper_connect.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::connected_residue_at_upper() const –> unsigned long

connection_distance(self: pyrosetta.rosetta.core.conformation.Residue, conf: core::conformation::Conformation, resconn_index: int, matchpoint: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶

Distance between a potential residue connection match and the position of the expected atom

C++: core::conformation::Residue::connection_distance(const class core::conformation::Conformation &, const unsigned long, const class numeric::xyzVector<double> &) const –> double

connection_incomplete(self: pyrosetta.rosetta.core.conformation.Residue, resconnid: int) → bool¶: C++: core::conformation::Residue::connection_incomplete(unsigned long) const –> bool

connections_match(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if ???

C++: core::conformation::Residue::connections_match(const class core::conformation::Residue &) const –> bool

connections_to_residue(*args, **kwargs)¶

Overloaded function.

connections_to_residue(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the vector1 of resconn ids that connect this residue to other

C++: core::conformation::Residue::connections_to_residue(const class core::conformation::Residue &) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

connections_to_residue(self: pyrosetta.rosetta.core.conformation.Residue, other_resid: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the vector1 of resconn ids that connect this residue to other

C++: core::conformation::Residue::connections_to_residue(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

copy_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue, src_rsd: pyrosetta.rosetta.core.conformation.Residue) → None¶

attempt to take residue connection info from src_rsd

C++: core::conformation::Residue::copy_residue_connections(const class core::conformation::Residue &) –> void

copy_residue_connections_from(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue) → None¶: C++: core::conformation::Residue::copy_residue_connections_from(const class core::conformation::Residue &) –> void

create_residue(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue¶

Returns a ResidueOP for creating a copy of residue, same as clone(): Temporary hack until Residue hierarchy is worked out

C++: core::conformation::Residue::create_residue() const –> class std::shared_ptr<class core::conformation::Residue>

create_rotamer(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue¶

Returns a ResidueOP for creating a rotamer of this residue: Temporary hack until Residue hierarchy is worked out

C++: core::conformation::Residue::create_rotamer() const –> class std::shared_ptr<class core::conformation::Residue>

cut_bond_neighbor(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

atom indices for bonded neighbors to which atom-tree connections are disallowed.

C++: core::conformation::Residue::cut_bond_neighbor(const int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

data(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.basic.datacache.BasicDataCache¶

BasicDataCache indexed by enum in residue_datacache.hh. Beware, this: will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this %Residue – the datacache is created just-in-time

C++: core::conformation::Residue::data() const –> const class basic::datacache::BasicDataCache &

data_ptr(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.basic.datacache.BasicDataCache¶

BasicDataCache indexed by enum in residue_datacache.hh

C++: core::conformation::Residue::data_ptr() const –> class std::shared_ptr<const class basic::datacache::BasicDataCache>

fill_missing_atoms(*args, **kwargs)¶

Overloaded function.

fill_missing_atoms(self: pyrosetta.rosetta.core.conformation.Residue, missing: pyrosetta.rosetta.utility.vector1_bool, conformation: core::conformation::Conformation) -> bool
fill_missing_atoms(self: pyrosetta.rosetta.core.conformation.Residue, missing: pyrosetta.rosetta.utility.vector1_bool, conformation: core::conformation::Conformation, fail: bool) -> bool

Builds coordinates for atoms missing from this residue

assuming ideal internal coordinates

If fail is false, will return true if we can fill all the missing atoms, and false if we can’t.

missing is passed by non-const ref: it will be updated for the atoms which are filled. (If fail is false, it will end up all false, or you’ll get a utility_exit()

C++: core::conformation::Residue::fill_missing_atoms(class utility::vector1<bool, class std::allocator<bool> > &, const class core::conformation::Conformation &, bool) –> bool

first_adjacent_heavy_atom(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) → int¶

Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.

C++: core::conformation::Residue::first_adjacent_heavy_atom(const unsigned long) const –> unsigned long

first_sidechain_atom(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of the first sidechain heavyatom

example(s):

residue.first_sidechain_atom()

See also:

Residue Residue.atom Residue.atoms Residue.last_backbone_atom Pose

C++: core::conformation::Residue::first_sidechain_atom() const –> unsigned long

first_sidechain_hydrogen(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of the first sidechain hydrogen

example(s):

residue.first_sidechain_hydrogen()

See also:

Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

C++: core::conformation::Residue::first_sidechain_hydrogen() const –> unsigned long

get_adjacent_heavy_atoms(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Get a list of heavy atoms connected to a given atom.

C++: core::conformation::Residue::get_adjacent_heavy_atoms(const unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_metal_binding_atoms(self: pyrosetta.rosetta.core.conformation.Residue, metal_binding_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Gets the AtomIndices of the atoms in this residue that can bind to metals

: AtomIndices == vector1< Size >

: Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::get_metal_binding_atoms(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_pseudobonds_to_residue(self: pyrosetta.rosetta.core.conformation.Residue, resid: int) → core::conformation::PseudoBondCollection¶: C++: core::conformation::Residue::get_pseudobonds_to_residue(unsigned long) const –> class std::shared_ptr<const class core::conformation::PseudoBondCollection>

get_self_ptr(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::conformation::Residue::get_self_ptr() –> class std::shared_ptr<class core::conformation::Residue>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.std.weak_ptr_core_conformation_Residue_t¶: C++: core::conformation::Residue::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::Residue>

has(self: pyrosetta.rosetta.core.conformation.Residue, atm: str) → bool¶

Returns true if this residue has an atom named <atm>

C++: core::conformation::Residue::has(const class std::basic_string<char> &) const –> bool

has_incomplete_connection(*args, **kwargs)¶

Overloaded function.

has_incomplete_connection(self: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: core::conformation::Residue::has_incomplete_connection() const –> bool

has_incomplete_connection(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) -> bool

Returns true is <atomno> has complete connectivity?

C++: core::conformation::Residue::has_incomplete_connection(const unsigned long) const –> bool

has_lower_connect(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if residue has a valid lower connection.

example(s):

residue.has_lower_connect()

C++: core::conformation::Residue::has_lower_connect() const –> bool

has_property(self: pyrosetta.rosetta.core.conformation.Residue, property: str) → bool¶

Return true if the residue has <property>.

C++: core::conformation::Residue::has_property(const class std::basic_string<char> &) const –> bool

has_sc_orbitals(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue has side chain orbitals

C++: core::conformation::Residue::has_sc_orbitals() const –> bool

has_shadow_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Return true if and only if this residue’s type has shadow atoms.

C++: core::conformation::Residue::has_shadow_atoms() const –> bool

has_upper_connect(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if residue has a valid upper connection.

example(s):

residue.has_upper_connect()

C++: core::conformation::Residue::has_upper_connect() const –> bool

has_variant_type(self: pyrosetta.rosetta.core.conformation.Residue, variant_type: pyrosetta.rosetta.core.chemical.VariantType) → bool¶

Generic variant access

C++: core::conformation::Residue::has_variant_type(const enum core::chemical::VariantType) const –> bool

heavyAtoms_end(self: pyrosetta.rosetta.core.conformation.Residue) → __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >¶: C++: core::conformation::Residue::heavyAtoms_end() const –> class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >

heavyatom_has_polar_hydrogens(self: pyrosetta.rosetta.core.conformation.Residue, ind: int) → bool¶

Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom)

C++: core::conformation::Residue::heavyatom_has_polar_hydrogens(unsigned long) const –> bool

heavyatom_is_an_acceptor(self: pyrosetta.rosetta.core.conformation.Residue, ind: int) → bool¶

Is a particular atom a heavy atom acceptor?

C++: core::conformation::Residue::heavyatom_is_an_acceptor(unsigned long) const –> bool

icoor(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → pyrosetta.rosetta.core.chemical.AtomICoor¶

Returns the internal coordinates of this residue’s atom with index number <atm>

C++: core::conformation::Residue::icoor(const int) const –> const class core::chemical::AtomICoor &

inter_residue_connection_partner(self: pyrosetta.rosetta.core.conformation.Residue, connid: int, conformation: core::conformation::Conformation) → core::id::AtomID¶

This returns the AtomID of the atom in the other residue to which the “connection_index”-th: connection of residue seqpos is connected to.

C++: core::conformation::Residue::inter_residue_connection_partner(int, const class core::conformation::Conformation &) const –> class core::id::AtomID

is_DNA(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a DNA residue

C++: core::conformation::Residue::is_DNA() const –> bool

is_NA(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a nucleic acid

C++: core::conformation::Residue::is_NA() const –> bool

is_RNA(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a RNA residue

C++: core::conformation::Residue::is_RNA() const –> bool

is_apolar(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

true if the residue is apolar

: apolar is classified as NOT polar, aromatic, or charged

C++: core::conformation::Residue::is_apolar() const –> bool

is_aromatic(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue is aromatic

C++: core::conformation::Residue::is_aromatic() const –> bool

is_bonded(*args, **kwargs)¶

Overloaded function.

is_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) -> bool

Am I bonded to other?: Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)

C++: core::conformation::Residue::is_bonded(const class core::conformation::Residue &) const –> bool

is_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other_index: int) -> bool

Am I bonded to other?: Looks at all residue connections as opposed to doing arithmetic

C++: core::conformation::Residue::is_bonded(const unsigned long) const –> bool

is_branch_point(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Return true if the residue is a branch point variant.

C++: core::conformation::Residue::is_branch_point() const –> bool

is_carbohydrate(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a carbohydrate

C++: core::conformation::Residue::is_carbohydrate() const –> bool

is_charged(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue is charged

C++: core::conformation::Residue::is_charged() const –> bool

is_coarse(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

residue is coarse (used for RNA right now)

C++: core::conformation::Residue::is_coarse() const –> bool

is_d_rna(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a D-RNA residue

C++: core::conformation::Residue::is_d_rna() const –> bool

is_l_rna(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a L-RNA residue

C++: core::conformation::Residue::is_l_rna() const –> bool

is_ligand(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a ligand

C++: core::conformation::Residue::is_ligand() const –> bool

is_lower_terminus(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue has a lower terminus variant

C++: core::conformation::Residue::is_lower_terminus() const –> bool

is_metal(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::is_metal() const –> bool

is_metalbinding(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::is_metalbinding() const –> bool

is_peptoid(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns if this residue is a peptoid

C++: core::conformation::Residue::is_peptoid() const –> bool

is_polar(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue is polar

C++: core::conformation::Residue::is_polar() const –> bool

is_polymer(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a polymer

C++: core::conformation::Residue::is_polymer() const –> bool

is_polymer_bonded(*args, **kwargs)¶

Overloaded function.

is_polymer_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) -> bool

Am I polymer bonded to other?

C++: core::conformation::Residue::is_polymer_bonded(const class core::conformation::Residue &) const –> bool

is_polymer_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other_index: int) -> bool

Am I polymer-bonded to other? checks lower and upper connections

C++: core::conformation::Residue::is_polymer_bonded(const unsigned long) const –> bool

is_protein(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is an amino acid

C++: core::conformation::Residue::is_protein() const –> bool

is_pseudo_bonded(*args, **kwargs)¶

Overloaded function.

is_pseudo_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) -> bool

Do I have any pseudobonds to other?

C++: core::conformation::Residue::is_pseudo_bonded(const class core::conformation::Residue &) const –> bool

is_pseudo_bonded(self: pyrosetta.rosetta.core.conformation.Residue, other_index: int) -> bool

Do I have any pseudobonds to other?

C++: core::conformation::Residue::is_pseudo_bonded(const unsigned long) const –> bool

is_purine(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a purine

C++: core::conformation::Residue::is_purine() const –> bool

is_pyrimidine(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a pyrimidine

C++: core::conformation::Residue::is_pyrimidine() const –> bool

is_repulsive(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → bool¶

Check if atom is repulsive.

C++: core::conformation::Residue::is_repulsive(const unsigned long &) const –> bool

is_similar_aa(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the aa residue types are the same

C++: core::conformation::Residue::is_similar_aa(const class core::conformation::Residue &) const –> bool

is_similar_rotamer(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the chi angles of another residue all fall within 5 deg

C++: core::conformation::Residue::is_similar_rotamer(const class core::conformation::Residue &) const –> bool

is_sri(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Is this one of SRI’s special heteropolymer building blocks?

C++: core::conformation::Residue::is_sri() const –> bool

is_surface(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if this residue is a surface residue

C++: core::conformation::Residue::is_surface() const –> bool

is_terminus(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if the residue has a terminus variant

C++: core::conformation::Residue::is_terminus() const –> bool

is_triazolemer(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Returns true if and only if this residue is a triazolemer

C++: core::conformation::Residue::is_triazolemer() const –> bool

is_upper_terminus(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Return true if the residue has an upper terminus variant

C++: core::conformation::Residue::is_upper_terminus() const –> bool

is_virtual(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) → bool¶

Check if atom is virtual.

C++: core::conformation::Residue::is_virtual(const unsigned long &) const –> bool

is_virtual_residue(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Check if residue is virtual.

C++: core::conformation::Residue::is_virtual_residue() const –> bool

last_backbone_atom(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of the last backbone heavyatom

The heavyatoms come first in atom ordering,

first backbone then sidechain, hydrogens follow the order of their attached heavyatom.

example(s):

residue.last_backbone_atom()

See also:

Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

C++: core::conformation::Residue::last_backbone_atom() const –> unsigned long

lower_connect(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.ResidueConnection¶

Returns this residue’s lower_connection: a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue

C++: core::conformation::Residue::lower_connect() const –> const class core::chemical::ResidueConnection &

lower_connect_atom(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of this residue’s atom which connects to: the residue before it in sequence

: polymers only, example: for an amino acid, residue.lower_connect_atom() = atom_index(“N”)

example(s):

residue.lower_connect_atom()

See also:

Residue Residue.atom Residue.atoms Residue.upper_connect_atom Pose

C++: core::conformation::Residue::lower_connect_atom() const –> unsigned long

mainchain_atom(self: pyrosetta.rosetta.core.conformation.Residue, i: int) → int¶

Returns the atom index of the residue’s ith mainchain atom

C++: core::conformation::Residue::mainchain_atom(const unsigned long) const –> unsigned long

mainchain_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the AtomIndices of this residue’s mainchain atoms

C++: core::conformation::Residue::mainchain_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

mainchain_torsion(self: pyrosetta.rosetta.core.conformation.Residue, torsion: int) → float¶

Returns a specific mainchain torsion angle for this residue

example: mainchain_torsion(2) will be the psi angle for an amino acid

example(s):: residue.mainchain_torsion(2)
See also:: Residue Pose Pose.omega Pose.phi Pose.psi

C++: core::conformation::Residue::mainchain_torsion(const unsigned long) const –> double

mainchain_torsions(*args, **kwargs)¶

Overloaded function.

mainchain_torsions(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_double

Returns the mainchain torsion angles of this residue (non-const)

C++: core::conformation::Residue::mainchain_torsions() –> class utility::vector1<double, class std::allocator<double> > &

mainchain_torsions(self: pyrosetta.rosetta.core.conformation.Residue, torsions: pyrosetta.rosetta.utility.vector1_double) -> None

Sets the mainchain torsion angles of this residue to <torsions>

example(s):

residue.mainchain_torsions()

See also:

Residue Pose Pose.set_omega Pose.set_phi Pose.set_psi

C++: core::conformation::Residue::mainchain_torsions(const class utility::vector1<double, class std::allocator<double> > &) –> void

mark_connect_incomplete(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) → None¶: C++: core::conformation::Residue::mark_connect_incomplete(unsigned long) –> void

mirrored_relative_to_type(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

Is this residue mirrored relative to its coordinates in the ResidueType?

Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.

C++: core::conformation::Residue::mirrored_relative_to_type() const –> bool

mm_atom_name(self: pyrosetta.rosetta.core.conformation.Residue, atom: int) → str¶

Returns the mm_atom_name of this residue’s atom with index number <atom>

C++: core::conformation::Residue::mm_atom_name(const int) const –> const std::string &

n_bonded_neighbor_all_res(*args, **kwargs)¶

Overloaded function.

n_bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int) -> int
n_bonded_neighbor_all_res(self: pyrosetta.rosetta.core.conformation.Residue, atomno: int, virt: bool) -> int

Returns the number of atoms bonded to <atomno> in all residues?

C++: core::conformation::Residue::n_bonded_neighbor_all_res(const unsigned long, bool) const –> unsigned long

n_current_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of ResidueConnections on this residue

including polymeric residue connections.: This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!!

C++: core::conformation::Residue::n_current_residue_connections() const –> unsigned long

n_hbond_acceptors(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

number of hbond_donors

C++: core::conformation::Residue::n_hbond_acceptors() const –> unsigned long

n_hbond_donors(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

number of hbond_donors

C++: core::conformation::Residue::n_hbond_donors() const –> unsigned long

n_mainchain_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of the residue’s mainchain atoms

C++: core::conformation::Residue::n_mainchain_atoms() const –> unsigned long

n_non_polymeric_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of non-polymeric ResidueConnections on this residue

C++: core::conformation::Residue::n_non_polymeric_residue_connections() const –> unsigned long

n_nus(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Return the number of nu (internal ring) angles this residue has.

Example: residue.n_nus() See also:

Residue Residue.nu Residue.nus Pose.set_ring_conformation Pose Pose.nu

C++: core::conformation::Residue::n_nus() const –> unsigned long

n_orbitals(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of orbitals in this residue

C++: core::conformation::Residue::n_orbitals() const –> unsigned long

n_polymeric_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of polymeric ResidueConnections on this residue

C++: core::conformation::Residue::n_polymeric_residue_connections() const –> unsigned long

n_possible_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of ResidueConnections on this residue

including polymeric residue connections.: This is the total number of possible connections from the ResidueType

C++: core::conformation::Residue::n_possible_residue_connections() const –> unsigned long

n_virtual_atoms(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of virtual atoms in this residue.

This calls the function with the same name in ResidueType, which counts virts on the fly (memory-efficient, performance-poor). This being the case, don’t call this function repeatedly! Call it once, and store the return value!

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::n_virtual_atoms() const –> unsigned long

na_analogue(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.AA¶

Returns the nucleic acid type to be used for fragment sampling.

C++: core::conformation::Residue::na_analogue() const –> const enum core::chemical::AA &

name(self: pyrosetta.rosetta.core.conformation.Residue) → str¶

Returns this residue’s ResidueType name

: for proteins, this will be the amino acid type and variant type

C++: core::conformation::Residue::name() const –> const std::string &

name1(self: pyrosetta.rosetta.core.conformation.Residue) → str¶

Returns this residue’s 1-letter representation

: for proteins, this will be the 1-letter amino acid code

C++: core::conformation::Residue::name1() const –> char

name3(self: pyrosetta.rosetta.core.conformation.Residue) → str¶

Returns this residue’s 3-letter representation

: for proteins, this will be the 3-letter amino acid code

C++: core::conformation::Residue::name3() const –> const std::string &

natoms(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of atoms in this residue

example(s):

residue.natoms()

See also:

Residue Pose

C++: core::conformation::Residue::natoms() const –> unsigned long

nbr_atom(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of this residue’s atom used as a center for neighbor definition: example: C-beta atom for some amino acids

C++: core::conformation::Residue::nbr_atom() const –> unsigned long

nbr_atom_xyz(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::conformation::Residue::nbr_atom_xyz() const –> const class numeric::xyzVector<double> &

nbr_radius(self: pyrosetta.rosetta.core.conformation.Residue) → float¶

Returns the distance cutoff value used as a radius for neighbor definition

C++: core::conformation::Residue::nbr_radius() const –> double

nbrs(self: pyrosetta.rosetta.core.conformation.Residue, atm: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Convenience synonym for bonded_neighbor

C++: core::conformation::Residue::nbrs(const int) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

nchi(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of chi angles this residue has

example(s):

residue.nchi()

See also:

Residue Pose Pose.chi Pose.set_chi

C++: core::conformation::Residue::nchi() const –> unsigned long

nheavyatoms(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the number of heavyatoms in this residue

example(s):

residue.nheavyatoms()

See also:

Residue Pose

C++: core::conformation::Residue::nheavyatoms() const –> unsigned long

nonconst_data(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.basic.datacache.BasicDataCache¶

BasicDataCache indexed by enum in residue_datacache.hh. Beware, this: will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this %Residue – the datacache is created just-in-time

C++: core::conformation::Residue::nonconst_data() –> class basic::datacache::BasicDataCache &

nonconst_data_ptr(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.basic.datacache.BasicDataCache¶

BasicDataCache indexed by enum in residue_datacache.hh

C++: core::conformation::Residue::nonconst_data_ptr() –> class std::shared_ptr<class basic::datacache::BasicDataCache>

nu(self: pyrosetta.rosetta.core.conformation.Residue, index: int) → float¶

Get a specific nu (internal ring) torsion angle by index.

Example: residue.nu(1) See also:

Residue Residue.nus Residue.n_nus Pose.set_ring_conformation Pose Pose.nu

It is intentional that there is no set_nu() function; nu angles should only be modified together.

Use Pose.set_ring_conformation() instead.

C++: core::conformation::Residue::nu(const unsigned long) const –> double

nu_atoms(*args, **kwargs)¶

Overloaded function.

nu_atoms(self: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Return the AtomIndices of each set of four atoms defining each nu angle.

C++: core::conformation::Residue::nu_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

nu_atoms(self: pyrosetta.rosetta.core.conformation.Residue, index: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return the AtomIndices of the four atoms defining the specified nu angle.

C++: core::conformation::Residue::nu_atoms(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> >

nus(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_double¶

Return the nu (internal ring) torsion angles of this residue. (non-const)

C++: core::conformation::Residue::nus() –> class utility::vector1<double, class std::allocator<double> > &

orbital_name(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int) → str¶: C++: core::conformation::Residue::orbital_name(const int) const –> const std::string &

orbital_type(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int) → pyrosetta.rosetta.core.chemical.orbitals.OrbitalType¶: C++: core::conformation::Residue::orbital_type(const int) const –> const class core::chemical::orbitals::OrbitalType &

orbital_type_index(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int) → int¶: C++: core::conformation::Residue::orbital_type_index(const unsigned long) const –> unsigned long

orbital_xyz(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::conformation::Residue::orbital_xyz(const unsigned long) const –> const class numeric::xyzVector<double> &

orient_onto_residue(*args, **kwargs)¶

Overloaded function.

orient_onto_residue(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue) -> None

Orient our coords onto those of <src>, using the atoms from select_orient_atoms

C++: core::conformation::Residue::orient_onto_residue(const class core::conformation::Residue &) –> void

orient_onto_residue(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, atom_pairs: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t) -> None

C++: core::conformation::Residue::orient_onto_residue(const class core::conformation::Residue &, const class utility::vector1<struct std::pair<class std::basic_string<char>, class std::basic_string<char> >, class std::allocator<struct std::pair<class std::basic_string<char>, class std::basic_string<char> > > > &) –> void

orient_onto_residue_peptoid(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation) → None¶

Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide

C++: core::conformation::Residue::orient_onto_residue_peptoid(const class core::conformation::Residue &, const class core::conformation::Conformation &) –> void

path_distance(*args, **kwargs)¶

Overloaded function.

path_distance(self: pyrosetta.rosetta.core.conformation.Residue, atom: int) -> pyrosetta.rosetta.utility.vector1_int

Returns the shortest path distance from <atom> to any other atom in this residue

example(s):

See also:

Residue Residue.atom Residue.atoms Pose

C++: core::conformation::Residue::path_distance(int) const –> const class utility::vector1<int, class std::allocator<int> > &

path_distance(self: pyrosetta.rosetta.core.conformation.Residue, at1: int, at2: int) -> int

Returns the number of bonds separating atom <at1> from <at2>

example(s):

See also:

Residue Residue.atom Residue.atoms Residue.path_distance Pose

C++: core::conformation::Residue::path_distance(int, int) const –> int

path_distances(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t¶

Returns the shortest path distance for any atom pair in this residue

example: path_distances()[atom1][atom2]

example(s):

See also:: Residue Residue.atom Residue.atoms Residue.path_distance Pose

C++: core::conformation::Residue::path_distances() const –> const class utility::vector1<class utility::vector1<int, class std::allocator<int> >, class std::allocator<class utility::vector1<int, class std::allocator<int> > > > &

place(*args, **kwargs)¶

Overloaded function.

place(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation) -> None
place(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation, preserve_c_beta: bool) -> None

Place this rotamer at the sequence position occupied by <src>: by reorienting the ideal side chain coordinates to match

C++: core::conformation::Residue::place(const class core::conformation::Residue &, const class core::conformation::Conformation &, bool) –> void

polymeric_oriented_sequence_distance(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the sequence separation distance between this residue and <other>: positive if the other residue is downstream in sequence

C++: core::conformation::Residue::polymeric_oriented_sequence_distance(const class core::conformation::Residue &) const –> int

polymeric_sequence_distance(self: pyrosetta.rosetta.core.conformation.Residue, other: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the sequence separation distance between this residue and <other>

: magnitude of distance only

C++: core::conformation::Residue::polymeric_sequence_distance(const class core::conformation::Residue &) const –> unsigned long

pseudobonds(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t¶: C++: core::conformation::Residue::pseudobonds() const –> const class std::map<unsigned long, class std::shared_ptr<const class core::conformation::PseudoBondCollection>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::shared_ptr<const class core::conformation::PseudoBondCollection> > > > &

requires_actcoord(self: pyrosetta.rosetta.core.conformation.Residue) → bool¶

does this residue require an actcoord?

C++: core::conformation::Residue::requires_actcoord() const –> bool

residue_connect_atom_index(self: pyrosetta.rosetta.core.conformation.Residue, resconn_id: int) → int¶: C++: core::conformation::Residue::residue_connect_atom_index(const unsigned long) const –> unsigned long

residue_connection(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) → pyrosetta.rosetta.core.chemical.ResidueConnection¶

Returns this residue’s ResidueConnection: a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue

C++: core::conformation::Residue::residue_connection(const int) const –> const class core::chemical::ResidueConnection &

residue_connection_conn_id(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) → int¶

Returns the connection id on the OTHER residue connected to this residue at this residue’s

connection resconn_index.

For example, if this were a normally-connected alpha amino acid, residue_connection_conn_id(1) would return 2, since the first connection in this residue is attached to the second connection in the previous residue.

C++: core::conformation::Residue::residue_connection_conn_id(const unsigned long) const –> unsigned long

residue_connection_partner(*args, **kwargs)¶

Overloaded function.

residue_connection_partner(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int) -> int

Returns the residue number of a residue connected to this residue

at this residue’s connection resconn_index.

For example, in a normally-connected pose made of alpha-amino

acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6.

C++: core::conformation::Residue::residue_connection_partner(const unsigned long) const –> unsigned long

residue_connection_partner(self: pyrosetta.rosetta.core.conformation.Residue, resconn_index: int, otherres: int, other_connid: int) -> None

set a connection to this residue by adding its partner’s residue number

C++: core::conformation::Residue::residue_connection_partner(const unsigned long, const unsigned long, const unsigned long) –> void

ring_conformer(*args, **kwargs)¶

Overloaded function.

ring_conformer(self: pyrosetta.rosetta.core.conformation.Residue, ring_num: int) -> pyrosetta.rosetta.core.chemical.rings.RingConformer
ring_conformer(self: pyrosetta.rosetta.core.conformation.Residue, ring_num: int, limit: float) -> pyrosetta.rosetta.core.chemical.rings.RingConformer

Return the current RingConformer of this residue’s nth ring.

C++: core::conformation::Residue::ring_conformer(const unsigned long, double) const –> const struct core::chemical::rings::RingConformer &

select_orient_atoms(self: pyrosetta.rosetta.core.conformation.Residue, center: int, nbr1: int, nbr2: int) → None¶

Selects three atoms for orienting this residue

C++: core::conformation::Residue::select_orient_atoms(unsigned long &, unsigned long &, unsigned long &) const –> void

seqpos(*args, **kwargs)¶

Overloaded function.

seqpos(self: pyrosetta.rosetta.core.conformation.Residue) -> int

Returns the sequence position of this residue

C++: core::conformation::Residue::seqpos() const –> unsigned long

seqpos(self: pyrosetta.rosetta.core.conformation.Residue, setting: int) -> None

Sets this residue’s sequence position to <setting>

C++: core::conformation::Residue::seqpos(const unsigned long) –> void

set_all_chi(self: pyrosetta.rosetta.core.conformation.Residue, chis: pyrosetta.rosetta.utility.vector1_double) → None¶

Sets all of this residue’s chi angles using the set_chi function: (wrapper function)

C++: core::conformation::Residue::set_all_chi(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_all_nu(self: pyrosetta.rosetta.core.conformation.Residue, nus: pyrosetta.rosetta.utility.vector1_double, taus: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: core::conformation::Residue::set_all_nu(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_all_ring_nu(self: pyrosetta.rosetta.core.conformation.Residue, start: int, end: int, nus: pyrosetta.rosetta.utility.vector1_double, taus: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: core::conformation::Residue::set_all_ring_nu(unsigned long, unsigned long, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_chi(self: pyrosetta.rosetta.core.conformation.Residue, chino: int, setting: float) → None¶

Sets this residue’s chi angle <chino> to <setting>: assuming that changes propagate according to the atom_base tree

C++: core::conformation::Residue::set_chi(const int, const double) –> void

set_d(self: pyrosetta.rosetta.core.conformation.Residue, chino: int, setting: float) → None¶

bondlength analog to set_chi: like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

fpd

C++: core::conformation::Residue::set_d(const int, const double) –> void

set_mirrored_relative_to_type(self: pyrosetta.rosetta.core.conformation.Residue, setting: bool) → None¶

Set whether this residue is mirrored relative to its coordinates in the ResidueType.

Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.

C++: core::conformation::Residue::set_mirrored_relative_to_type(const bool) –> void

set_orbital_xyz(self: pyrosetta.rosetta.core.conformation.Residue, orbital_index: int, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::conformation::Residue::set_orbital_xyz(const unsigned long, const class numeric::xyzVector<double> &) –> void

set_pseudobonds_to_residue(self: pyrosetta.rosetta.core.conformation.Residue, resid: int, pbs: core::conformation::PseudoBondCollection) → None¶: C++: core::conformation::Residue::set_pseudobonds_to_residue(unsigned long, class std::shared_ptr<const class core::conformation::PseudoBondCollection>) –> void

set_tau(self: pyrosetta.rosetta.core.conformation.Residue, nuno: int, setting: float) → None¶

set_theta for nus

C++: core::conformation::Residue::set_tau(const unsigned long, const double) –> void

set_theta(self: pyrosetta.rosetta.core.conformation.Residue, chino: int, setting: float) → None¶

bondangle analog to set_chi: same idea as set_d

fpd

C++: core::conformation::Residue::set_theta(const int, const double) –> void

set_xyz(*args, **kwargs)¶

Overloaded function.

set_xyz(self: pyrosetta.rosetta.core.conformation.Residue, atm_index: int, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Sets the position of this residue’s atom with index number <atm_index>

example(s):

See also:

Residue Residue.atom Residue.atoms Residue.xyz Pose

C++: core::conformation::Residue::set_xyz(const unsigned long, const class numeric::xyzVector<double> &) –> void

set_xyz(self: pyrosetta.rosetta.core.conformation.Residue, atm_name: str, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Sets the position of this residue’s atom with name <atm_name>

example(s):

See also:

Residue Residue.atom Residue.atoms Residue.xyz Pose

C++: core::conformation::Residue::set_xyz(const class std::basic_string<char> &, const class numeric::xyzVector<double> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.core.conformation.Residue) -> None
show(self: pyrosetta.rosetta.core.conformation.Residue, output: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.core.conformation.Residue, output: pyrosetta.rosetta.std.ostream, output_atomic_details: bool) -> None

Generate string representation of Residue for debugging purposes.

C++: core::conformation::Residue::show(class std::basic_ostream<char> &, bool) const –> void

sidechainAtoms_begin(self: pyrosetta.rosetta.core.conformation.Residue) → __gnu_cxx::__normal_iterator<core::conformation::Atom const*, std::vector<core::conformation::Atom, std::allocator<core::conformation::Atom> > >¶

should be safe, given the atom ordering rules?

C++: core::conformation::Residue::sidechainAtoms_begin() const –> class __gnu_cxx::__normal_iterator<const class core::conformation::Atom *, class std::vector<class core::conformation::Atom, class std::allocator<class core::conformation::Atom> > >

type(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.ResidueType¶

Returns this residue’s ResidueType

example(s):

residue.type()

See also:

Residue Residue.type_ptr Residue.atom_type

C++: core::conformation::Residue::type() const –> const class core::chemical::ResidueType &

type_ptr(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.ResidueType¶

Returns this residue’s ResidueType as a COP

example(s):

residue.typei_ptr()

See also:

Residue Residue.type Residue.atom_type

C++: core::conformation::Residue::type_ptr() const –> class std::shared_ptr<const class core::chemical::ResidueType>

update_actcoord(self: pyrosetta.rosetta.core.conformation.Residue) → None¶

Updates actcoord for this residue

C++: core::conformation::Residue::update_actcoord() –> void

update_connections_to_other_residue(self: pyrosetta.rosetta.core.conformation.Residue, other_rsd: pyrosetta.rosetta.core.conformation.Residue) → None¶

Search through the other residue for connections to this residue, and

ensure that this residue’s connect_map is up to date with that residue’s connection indices (and residue number).

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::Residue::update_connections_to_other_residue(const class core::conformation::Residue &) –> void

update_nus(self: pyrosetta.rosetta.core.conformation.Residue) → None¶

Calculate the set of nu dihedrals from the xyz coordinates and store them.

C++: core::conformation::Residue::update_nus() –> void

update_orbital_coords(self: pyrosetta.rosetta.core.conformation.Residue) → None¶: C++: core::conformation::Residue::update_orbital_coords() –> void

update_sequence_numbering(self: pyrosetta.rosetta.core.conformation.Residue, old2new: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Updates the sequence numbers for this residue and the numbers: stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped

C++: core::conformation::Residue::update_sequence_numbering(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

upper_connect(self: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.chemical.ResidueConnection¶

Returns this residue’s upper_connection: a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue

C++: core::conformation::Residue::upper_connect() const –> const class core::chemical::ResidueConnection &

upper_connect_atom(self: pyrosetta.rosetta.core.conformation.Residue) → int¶

Returns the index number of this residue’s atom which connects to: the residue after it in sequence

: polymers only, example: for an amino acid, residue.upper_connect_atom() = atom_index(“C”)

example(s):

residue.upper_connect_atom()

See also:

Residue Residue.atom Residue.atoms Residue.lower_connect_atom Pose

C++: core::conformation::Residue::upper_connect_atom() const –> unsigned long

xyz(*args, **kwargs)¶

Overloaded function.

xyz(self: pyrosetta.rosetta.core.conformation.Residue, atm_index: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Returns the position of this residue’s atom with index number <atm_index>

: position is a Vector

example(s):

residue.xyz(3)

See also:

Residue Residue.atom Residue.atoms Residue.set_xyz Pose

C++: core::conformation::Residue::xyz(const unsigned long) const –> const class numeric::xyzVector<double> &

xyz(self: pyrosetta.rosetta.core.conformation.Residue, atm_name: str) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Returns the position of this residue’s atom with name <atm_name>

: position is a Vector

example(s):

residue.xyz(“CA”)

See also:

Residue Residue.atom Residue.atoms Residue.set_xyz Pose

C++: core::conformation::Residue::xyz(const class std::basic_string<char> &) const –> const class numeric::xyzVector<double> &

class pyrosetta.rosetta.core.conformation.ResidueFactory¶

Bases: pybind11_builtins.pybind11_object

a collection of functions making a single residue

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.core.conformation.ResidueFactory) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

create_residue(*args, **kwargs)¶

Overloaded function.

create_residue(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.conformation.Residue

creates residue of desired type, coords are ideal values in some default spatial orientation

C++: core::conformation::ResidueFactory::create_residue(const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::conformation::Residue>

create_residue(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, current_rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.conformation.Residue
create_residue(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, current_rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: pyrosetta.rosetta.core.conformation.Conformation, preserve_c_beta: bool) -> pyrosetta.rosetta.core.conformation.Residue

rotamer-style creation, uses backbone of existing residue (current_rsd)

C++: core::conformation::ResidueFactory::create_residue(const class core::chemical::ResidueType &, const class core::conformation::Residue &, const class core::conformation::Conformation &, bool) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.core.conformation.add_lower_terminus_type_to_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶: C++: core::conformation::add_lower_terminus_type_to_conformation_residue(class core::conformation::Conformation &, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.add_upper_terminus_type_to_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶: C++: core::conformation::add_upper_terminus_type_to_conformation_residue(class core::conformation::Conformation &, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.add_variant_type_to_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, variant_type: pyrosetta.rosetta.core.chemical.VariantType, seqpos: int) → None¶

Construct a variant of an existing conformation residue.

C++: core::conformation::add_variant_type_to_conformation_residue(class core::conformation::Conformation &, const enum core::chemical::VariantType, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.all_atom_center(residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Get the center of the Residue

This computes an equally-weighted, all-atom (including virtuals and hydrogens) center

C++: core::conformation::all_atom_center(const class core::conformation::Residue &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.conformation.atom_id_to_named_atom_id(atom_id: pyrosetta.rosetta.core.id.AtomID, rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.id.NamedAtomID¶: C++: core::conformation::atom_id_to_named_atom_id(const class core::id::AtomID &, const class core::conformation::Residue &) –> class core::id::NamedAtomID

pyrosetta.rosetta.core.conformation.break_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, res1: int, res2: int) → None¶

Breaks a disulfide bond.

Vikram K. Mulligan, Baker lab (vmullig.edu).

C++: core::conformation::break_disulfide(class core::conformation::Conformation &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.build_chemical_edge(edge: pyrosetta.rosetta.core.kinematics.Edge, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) → None¶

build a sub atom-tree for a chemical edge and attach it to main atom-tree

C++: core::conformation::build_chemical_edge(const class core::kinematics::Edge &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

pyrosetta.rosetta.core.conformation.build_jump_edge(edge: pyrosetta.rosetta.core.kinematics.Edge, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) → None¶

build a sub atom-tree for a jump edge and attach it to main atom-tree

C++: core::conformation::build_jump_edge(const class core::kinematics::Edge &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

pyrosetta.rosetta.core.conformation.build_polymer_edge(edge: pyrosetta.rosetta.core.kinematics.Edge, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) → None¶

build a sub atom-tree for a polymer edge and attach it to main atom-tree

C++: core::conformation::build_polymer_edge(const class core::kinematics::Edge &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

pyrosetta.rosetta.core.conformation.build_residue_tree(*args, **kwargs)¶

Overloaded function.

build_residue_tree(root_atomno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, atom_ptr: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t, root_atom_is_jump_atom: bool) -> None

build the tree of atoms for this residue, anchored at root_atomno

C++: core::conformation::build_residue_tree(const int, const class core::conformation::Residue &, class utility::vector1<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > &, const bool) –> void

build_residue_tree(residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, rsd: pyrosetta.rosetta.core.conformation.Residue, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, atom_ptr: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_kinematics_tree_Atom_t) -> None

build_residue_tree function that uses the foldtree info

also used in build_tree to build the residue tree for the root residue

C++: core::conformation::build_residue_tree(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::conformation::Residue &, const class core::kinematics::FoldTree &, class utility::vector1<class std::shared_ptr<class core::kinematics::tree::Atom>, class std::allocator<class std::shared_ptr<class core::kinematics::tree::Atom> > > &) –> void

pyrosetta.rosetta.core.conformation.build_tree(fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) → None¶: C++: core::conformation::build_tree(const class core::kinematics::FoldTree &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

pyrosetta.rosetta.core.conformation.change_cys_state(index: int, cys_type_name3: str, conf: pyrosetta.rosetta.core.conformation.Conformation) → bool¶

Switch the disulfide state of a disulfide-forming residue (e.g. CYS->CYD or CYD->CYS or

DCYD->DCYS or DCYS->DCYD or whatnot).

Position of the residue to replace.

The 3-letter name of the cys type to use: either CYS: or CYD. DEPRECATED and kept only for backward-compatibility.

The conformation to modify

true if the replacement was successful, false otherwise.

C++: core::conformation::change_cys_state(const unsigned long, const class std::basic_string<char> &, class core::conformation::Conformation &) –> bool

pyrosetta.rosetta.core.conformation.char_valid_as_torsion_bin(torbin: str) → bool¶

returns true if the input character represents a valid torsion bin

C++: core::conformation::char_valid_as_torsion_bin(char) –> bool

pyrosetta.rosetta.core.conformation.check_good_cutpoint_neighbour(thisres: pyrosetta.rosetta.core.conformation.Residue, other_res: pyrosetta.rosetta.core.conformation.Residue) → None¶

Given two residues, check that they are compatible types to be connected via a cutpoint.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::check_good_cutpoint_neighbour(const class core::conformation::Residue &, const class core::conformation::Residue &) –> void

pyrosetta.rosetta.core.conformation.cis_omega_torsion_bin(torbin: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → bool¶: C++: core::conformation::cis_omega_torsion_bin(enum core::conformation::ppo_torsion_bin) –> bool

pyrosetta.rosetta.core.conformation.copy_residue_coordinates_and_rebuild_missing_atoms(*args, **kwargs)¶

Overloaded function.

copy_residue_coordinates_and_rebuild_missing_atoms(source_rsd: pyrosetta.rosetta.core.conformation.Residue, target_rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: pyrosetta.rosetta.core.conformation.Conformation, preserve_only_sidechain_dihedrals: bool) -> None

Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.

If preserve_only_sidechain_dihedrals is true, then this function only copies mainchain coordinates,

and rebuilds all sidechain coordinates from scratch, setting side-chain dihedrals based on the source residue. Otherwise, if false, it copies all the atoms that it can from the source residue, then rebuilds the rest.

Vikram K. Mulligan (vmullig.edu)

C++: core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class core::conformation::Conformation &, const bool) –> void

copy_residue_coordinates_and_rebuild_missing_atoms(source_rsd: pyrosetta.rosetta.core.conformation.Residue, target_rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> None

Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.

C++: core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class core::conformation::Conformation &) –> void

pyrosetta.rosetta.core.conformation.disulfide_bonds(conformation: pyrosetta.rosetta.core.conformation.Conformation, disulfides: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None¶

Generate a list of all disulfide bonds in the conformation

C++: core::conformation::disulfide_bonds(const class core::conformation::Conformation &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

pyrosetta.rosetta.core.conformation.find_neighbors_restricted(*args, **kwargs)¶

Overloaded function.

find_neighbors_restricted(point_graph: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, neighbor_cutoff: float, residue_selection: pyrosetta.rosetta.utility.vector1_bool) -> None
find_neighbors_restricted(point_graph: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, neighbor_cutoff: float, residue_selection: pyrosetta.rosetta.utility.vector1_bool, strategy: pyrosetta.rosetta.core.conformation.Strategy) -> None

C++: core::conformation::find_neighbors_restricted(class std::shared_ptr<class utility::graph::UpperEdgeGraph<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> >, double, const class utility::vector1<bool, class std::allocator<bool> > &, enum core::conformation::Strategy) –> void

pyrosetta.rosetta.core.conformation.form_disulfide(*args, **kwargs)¶

Overloaded function.

form_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int) -> None
form_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int, preserve_d_residues: bool) -> None
form_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int, preserve_d_residues: bool, force_d_residues: bool) -> None

Introduce cysteines at the specified location and define a disulfide bond between them.

Does not do the repacking & minimization required to place the disulfide correctly.

C++: core::conformation::form_disulfide(class core::conformation::Conformation &, unsigned long, unsigned long, const bool, const bool) –> void

pyrosetta.rosetta.core.conformation.form_disulfide_helper(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, preserve_d_residues: bool, force_d_residues: bool) → None¶

Helper function for the form_disulfide function.

This function ensures that as a residue is mutated to a disulfide-bonding residue type, all other variant types are preserved; it is used to avoid code duplication.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

C++: core::conformation::form_disulfide_helper(class core::conformation::Conformation &, const unsigned long, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, const bool, const bool) –> void

pyrosetta.rosetta.core.conformation.get_anchor_and_root_atoms(anchor_rsd: pyrosetta.rosetta.core.conformation.Residue, root_rsd: pyrosetta.rosetta.core.conformation.Residue, edge: pyrosetta.rosetta.core.kinematics.Edge, anchor_atomno: int, root_atomno: int) → None¶

Use this routine to deduce atom indices of connect atoms in the tree

C++: core::conformation::get_anchor_and_root_atoms(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::kinematics::Edge &, unsigned long &, unsigned long &) –> void

pyrosetta.rosetta.core.conformation.get_anchor_atomno(*args, **kwargs)¶

Overloaded function.

get_anchor_atomno(anchor_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) -> int

Get the atom-index of the atom to which the residue at position seqpos should be anchored.

C++: core::conformation::get_anchor_atomno(const class core::conformation::Residue &, const unsigned long, const class core::kinematics::FoldTree &) –> int

get_anchor_atomno(rsd: pyrosetta.rosetta.core.conformation.Residue, dir: int) -> int

get anchor atom to which the atom-tree of next residue in the edge is attached.

C++: core::conformation::get_anchor_atomno(const class core::conformation::Residue &, const int) –> int

pyrosetta.rosetta.core.conformation.get_chemical_root_and_anchor_atomnos(rsd_anchor: pyrosetta.rosetta.core.conformation.Residue, rsd_root: pyrosetta.rosetta.core.conformation.Residue, anchor_atom_no: int, root_atom_no: int) → None¶: C++: core::conformation::get_chemical_root_and_anchor_atomnos(const class core::conformation::Residue &, const class core::conformation::Residue &, unsigned long &, unsigned long &) –> void

pyrosetta.rosetta.core.conformation.get_disulf_partner(conformation: pyrosetta.rosetta.core.conformation.Conformation, res_index: int) → int¶

Gets a disulfide-forming residue’s partner in the disulfide bond.

Vikram K. Mulligan, Baker lab (vmullig.edu).

C++: core::conformation::get_disulf_partner(const class core::conformation::Conformation &, const unsigned long) –> unsigned long

pyrosetta.rosetta.core.conformation.get_root_atomno(rsd: pyrosetta.rosetta.core.conformation.Residue, dir: int) → int¶: C++: core::conformation::get_root_atomno(const class core::conformation::Residue &, const int) –> int

pyrosetta.rosetta.core.conformation.get_root_residue_root_atomno(rsd: pyrosetta.rosetta.core.conformation.Residue, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) → int¶: C++: core::conformation::get_root_residue_root_atomno(const class core::conformation::Residue &, const class core::kinematics::FoldTree &) –> unsigned long

pyrosetta.rosetta.core.conformation.get_second_atom_from_connection(resno: int, atomno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, conformation: pyrosetta.rosetta.core.conformation.Conformation, conn_id: int) → bool¶

Given a residue and a connection id, get the heavyatom adjacent to the atom that makes that connection.

Chooses mainchain over non-mainchain, and heavyatoms over non-heavyatoms. Returns true for FAILURE.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::get_second_atom_from_connection(unsigned long &, unsigned long &, const class core::conformation::Residue &, const class core::conformation::Conformation &, const unsigned long &) –> bool

pyrosetta.rosetta.core.conformation.get_torsion_bin(*args, **kwargs)¶

Overloaded function.

get_torsion_bin(phi: float, psi: float) -> pyrosetta.rosetta.core.conformation.ppo_torsion_bin
get_torsion_bin(phi: float, psi: float, omega: float) -> pyrosetta.rosetta.core.conformation.ppo_torsion_bin

determine the torsion bin for a given phi/psi/omega combination, assuming that omega is 180 if not specified

Amelie Stein (amelie.stein.edu)

Wed May 2 11:18:29 PDT 2012

C++: core::conformation::get_torsion_bin(double, double, double) –> enum core::conformation::ppo_torsion_bin

pyrosetta.rosetta.core.conformation.idealize_hydrogens(res: pyrosetta.rosetta.core.conformation.Residue, conf: pyrosetta.rosetta.core.conformation.Conformation) → None¶: C++: core::conformation::idealize_hydrogens(class core::conformation::Residue &, const class core::conformation::Conformation &) –> void

pyrosetta.rosetta.core.conformation.idealize_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Idealize backbone and sidechain at seqpos

C++: core::conformation::idealize_position(const unsigned long, class core::conformation::Conformation &) –> void

pyrosetta.rosetta.core.conformation.insert_ideal_bonds_at_polymer_junction(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) → None¶

Sets the two bond angles and the bond length across the junction, rebuilds dependent atoms (eg O,H)

C++: core::conformation::insert_ideal_bonds_at_polymer_junction(const unsigned long, class core::conformation::Conformation &) –> void

pyrosetta.rosetta.core.conformation.insert_ideal_mainchain_bonds(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) → None¶: C++: core::conformation::insert_ideal_mainchain_bonds(const unsigned long, class core::conformation::Conformation &) –> void

pyrosetta.rosetta.core.conformation.insert_residue_into_atom_tree(new_rsd: pyrosetta.rosetta.core.conformation.Residue, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_tree: core::kinematics::AtomTree) → None¶

Inserts/ appends new residue subtree into an existing atomtree

The foldtree must already have been changed to reflect the new residue

The sequence position of the new residue is deduced from new_rsd.seqpos()

This function handles renumbering of the atomtree if necessary

C++: core::conformation::insert_residue_into_atom_tree(const class core::conformation::Residue &, const class core::kinematics::FoldTree &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::kinematics::AtomTree &) –> void

pyrosetta.rosetta.core.conformation.inv_virtual_type_for_conf(conformation: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.chemical.ResidueType¶

Return the appropritate ResidueType for the inverse virtual residue for the

“mode” (fullatom, centroid …) the conformation is in.

When at all possible, use core::pose::get_restype_for_pose() instead, as that can use more pose-specific residue type information, if any.

C++: core::conformation::inv_virtual_type_for_conf(const class core::conformation::Conformation &) –> class std::shared_ptr<const class core::chemical::ResidueType>

pyrosetta.rosetta.core.conformation.is_atom_axial_or_equatorial_to_ring(residue: pyrosetta.rosetta.core.conformation.Residue, query_atom: int, ring_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.core.chemical.rings.AxEqDesignation¶

Is the query atom in this residue axial or equatorial to the given ring or neither?

C++: core::conformation::is_atom_axial_or_equatorial_to_ring(const class core::conformation::Residue &, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> enum core::chemical::rings::AxEqDesignation

pyrosetta.rosetta.core.conformation.is_disulfide_bond(conformation: pyrosetta.rosetta.core.conformation.Conformation, residueA_pos: int, residueB_pos: int) → bool¶

Find whether there is a disulfide defined between two residues

C++: core::conformation::is_disulfide_bond(const class core::conformation::Conformation &, unsigned long, unsigned long) –> bool

pyrosetta.rosetta.core.conformation.is_ideal_position(*args, **kwargs)¶

Overloaded function.

is_ideal_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> bool
is_ideal_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation, theta_epsilon: float) -> bool
is_ideal_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation, theta_epsilon: float, D_epsilon: float) -> bool

Return true if position contains an ideal geometry up to some epsilon

sequence position

conformation object

permitted deviation from ideal bond angles, in Radians

permitted deviation from ideal bond length

conformation is needed for context of polymer nbrs

C++: core::conformation::is_ideal_position(const unsigned long, const class core::conformation::Conformation &, double, double) –> bool

pyrosetta.rosetta.core.conformation.map_char_to_torsion_bin(torbin: str) → pyrosetta.rosetta.core.conformation.ppo_torsion_bin¶

returns the torsion bin that the input character represents

C++: core::conformation::map_char_to_torsion_bin(char) –> enum core::conformation::ppo_torsion_bin

pyrosetta.rosetta.core.conformation.map_string_to_torsion_bin_string(torstring: str) → pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin¶

convert a string of characters into a vector of the internally recognized ppo_torsion_bin enumeration

utility::excn::EXCN_MsgException if any of the input characters in this string are invalid

C++: core::conformation::map_string_to_torsion_bin_string(const class std::basic_string<char> &) –> class utility::vector0<enum core::conformation::ppo_torsion_bin, class std::allocator<enum core::conformation::ppo_torsion_bin> >

pyrosetta.rosetta.core.conformation.map_torsion_bin_to_char(torbin: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → str¶

convert a torsion bin to a character s.t. that character can be converted back to a torsion bin

C++: core::conformation::map_torsion_bin_to_char(enum core::conformation::ppo_torsion_bin) –> char

pyrosetta.rosetta.core.conformation.named_atom_id_to_atom_id(atom_id: pyrosetta.rosetta.core.id.NamedAtomID, rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.id.AtomID¶: C++: core::conformation::named_atom_id_to_atom_id(const class core::id::NamedAtomID &, const class core::conformation::Residue &) –> class core::id::AtomID

pyrosetta.rosetta.core.conformation.orient_residue_for_ideal_bond(*args, **kwargs)¶

Overloaded function.

orient_residue_for_ideal_bond(moving_rsd: pyrosetta.rosetta.core.conformation.Residue, moving_connection: pyrosetta.rosetta.core.chemical.ResidueConnection, fixed_rsd: pyrosetta.rosetta.core.conformation.Residue, fixed_connection: pyrosetta.rosetta.core.chemical.ResidueConnection, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> None
orient_residue_for_ideal_bond(moving_rsd: pyrosetta.rosetta.core.conformation.Residue, moving_connection: pyrosetta.rosetta.core.chemical.ResidueConnection, fixed_rsd: pyrosetta.rosetta.core.conformation.Residue, fixed_connection: pyrosetta.rosetta.core.chemical.ResidueConnection, conformation: pyrosetta.rosetta.core.conformation.Conformation, lookup_bond_length: bool) -> None

C++: core::conformation::orient_residue_for_ideal_bond(class core::conformation::Residue &, const class core::chemical::ResidueConnection &, const class core::conformation::Residue &, const class core::chemical::ResidueConnection &, const class core::conformation::Conformation &, bool) –> void

pyrosetta.rosetta.core.conformation.position_of_atom_on_ring(residue: pyrosetta.rosetta.core.conformation.Residue, query_atom: int, ring_atoms: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶

What is the attachment position of the query atom on the given ring?

C++: core::conformation::position_of_atom_on_ring(const class core::conformation::Residue &, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

class pyrosetta.rosetta.core.conformation.ppo_torsion_bin¶

Bases: pybind11_builtins.pybind11_object

Enumeration representing the different phi/psi/omega torsion bins

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) -> bool
__eq__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → int¶

__init__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: int) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) -> bool
__ne__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: int) -> bool

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.conformation.ppo_torsion_bin, arg0: tuple) → None¶

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

pyrosetta.rosetta.core.conformation.promote_sameresidue_child_of_jump_atom(*args, **kwargs)¶

Overloaded function.

promote_sameresidue_child_of_jump_atom(edge: pyrosetta.rosetta.core.kinematics.Edge, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_pointer: pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t) -> None

Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list

C++: core::conformation::promote_sameresidue_child_of_jump_atom(const class core::kinematics::Edge &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::id::AtomID_Map<class std::shared_ptr<class core::kinematics::tree::Atom> > &) –> void

promote_sameresidue_child_of_jump_atom(edge: pyrosetta.rosetta.core.kinematics.Edge, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_tree: core::kinematics::AtomTree) -> None

Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list

C++: core::conformation::promote_sameresidue_child_of_jump_atom(const class core::kinematics::Edge &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::kinematics::AtomTree &) –> void

pyrosetta.rosetta.core.conformation.remap_cis_omega_torsion_bins_to_trans(torbin: pyrosetta.rosetta.core.conformation.ppo_torsion_bin) → pyrosetta.rosetta.core.conformation.ppo_torsion_bin¶: C++: core::conformation::remap_cis_omega_torsion_bins_to_trans(enum core::conformation::ppo_torsion_bin) –> enum core::conformation::ppo_torsion_bin

pyrosetta.rosetta.core.conformation.remove_lower_terminus_type_from_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶: C++: core::conformation::remove_lower_terminus_type_from_conformation_residue(class core::conformation::Conformation &, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.remove_upper_terminus_type_from_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int) → None¶: C++: core::conformation::remove_upper_terminus_type_from_conformation_residue(class core::conformation::Conformation &, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.remove_variant_type_from_conformation_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, variant_type: pyrosetta.rosetta.core.chemical.VariantType, seqpos: int) → None¶

Construct a non-variant of an existing conformation residue.

C++: core::conformation::remove_variant_type_from_conformation_residue(class core::conformation::Conformation &, const enum core::chemical::VariantType, const unsigned long) –> void

pyrosetta.rosetta.core.conformation.replace_conformation_residue_copying_existing_coordinates(conformation: pyrosetta.rosetta.core.conformation.Conformation, seqpos: int, new_rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::conformation::replace_conformation_residue_copying_existing_coordinates(class core::conformation::Conformation &, const unsigned long, const class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.core.conformation.replace_residue_in_atom_tree(new_rsd: pyrosetta.rosetta.core.conformation.Residue, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, atom_tree: core::kinematics::AtomTree) → None¶

Helper function for conformation routines

C++: core::conformation::replace_residue_in_atom_tree(const class core::conformation::Residue &, const class core::kinematics::FoldTree &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, class core::kinematics::AtomTree &) –> void

pyrosetta.rosetta.core.conformation.residue_point_graph_from_conformation(conformation: pyrosetta.rosetta.core.conformation.Conformation, pg: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) → None¶: C++: core::conformation::residue_point_graph_from_conformation(const class core::conformation::Conformation &, class utility::graph::UpperEdgeGraph<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &) –> void

pyrosetta.rosetta.core.conformation.set_chi_according_to_coordinates(rotamer: pyrosetta.rosetta.core.conformation.Residue) → None¶

rotamer chi-update from coords useful for building rotamers from coordinates

C++: core::conformation::set_chi_according_to_coordinates(class core::conformation::Residue &) –> void

pyrosetta.rosetta.core.conformation.setup_corresponding_atoms(atom_map: pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → None¶

set up a map to match mainchain atoms from residue1 to residue2

C++: core::conformation::setup_corresponding_atoms(class core::id::AtomID_Map<class core::id::AtomID> &, const class core::conformation::Residue &, const class core::conformation::Residue &) –> void

pyrosetta.rosetta.core.conformation.show_atom_tree(atom: core::kinematics::tree::Atom, conf: pyrosetta.rosetta.core.conformation.Conformation, os: pyrosetta.rosetta.std.ostream) → None¶: C++: core::conformation::show_atom_tree(const class core::kinematics::tree::Atom &, const class core::conformation::Conformation &, class std::basic_ostream<char> &) –> void

pyrosetta.rosetta.core.conformation.stub_id_to_named_stub_id(stub_id: pyrosetta.rosetta.core.id.StubID, rsd: pyrosetta.rosetta.core.conformation.Residue) → core::id::NamedStubID¶: C++: core::conformation::stub_id_to_named_stub_id(const class core::id::StubID &, const class core::conformation::Residue &) –> class core::id::NamedStubID

pyrosetta.rosetta.core.conformation.update_cutpoint_virtual_atoms_if_connected(*args, **kwargs)¶

Overloaded function.

update_cutpoint_virtual_atoms_if_connected(conformation: pyrosetta.rosetta.core.conformation.Conformation, cutpoint_res: int) -> None
update_cutpoint_virtual_atoms_if_connected(conformation: pyrosetta.rosetta.core.conformation.Conformation, cutpoint_res: int, recurse: bool) -> None

Given a conformation and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this

position has either of these variant types, and if it does, determine whether it’s connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it’s bonded.

Requires a little bit of special-casing for gamma-amino acids. Throws an exception if the residue to which a CUTPOINT_LOWER is bonded does not have an “N” and a “CA” or “C4”. Safe to call repeatedly, or if cutpoint variant types are absent; in these cases, the function does nothing.

By default, this function calls itself again once on residues to which this residue is connected, to update their geometry. Set recurse=false to disable this.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::update_cutpoint_virtual_atoms_if_connected(class core::conformation::Conformation &, const unsigned long, bool) –> void

pyrosetta.rosetta.core.conformation.upper_is_symm_equivalent_of_lower(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int) → bool¶

Another helper function for the form_disulfide function.

Returns true if and only if the conformation is symmetric and upper_res is a symmetric copy of lower_res.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

C++: core::conformation::upper_is_symm_equivalent_of_lower(const class core::conformation::Conformation &, const unsigned long, const unsigned long) –> bool

pyrosetta.rosetta.core.conformation.virtual_type_for_conf(conformation: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.chemical.ResidueType¶

Return the appropritate ResidueType for the virtual residue for the

“mode” (fullatom, centroid …) the conformation is in.

When at all possible, use core::pose::virtual_type_for_pose() instead, as that can use more pose-specific residue type information, if any.

C++: core::conformation::virtual_type_for_conf(const class core::conformation::Conformation &) –> class std::shared_ptr<const class core::chemical::ResidueType>

pyrosetta.rosetta.core.conformation.write_kinemage_header(ostr: pyrosetta.rosetta.std.ostream, kin_number: int, title: str, ctr: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::conformation::write_kinemage_header(class std::basic_ostream<char> &, const unsigned long, const class std::basic_string<char> &, const class numeric::xyzVector<double> &) –> void