conformation

Bindings for core::conformation namespace

class pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie, : pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

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

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

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.

  1. 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

  1. 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.

  1. 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(std::ostream &) const –> void

  1. show(self: pyrosetta.rosetta.core.conformation.Atom) -> None

Generate string representation of conformation::Atom to std::cout for debugging purposes.

C++: core::conformation::Atom::show() const –> void

type(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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.

  1. 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> &

  1. 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.AtomGraphEdgeData

Bases: pyrosetta.rosetta.core.conformation.PointGraphEdgeData

dsq(self: pyrosetta.rosetta.core.conformation.PointGraphEdgeData) float

C++: core::conformation::PointGraphEdgeData::dsq() –> double &

class pyrosetta.rosetta.core.conformation.AtomGraphVertexData

Bases: pyrosetta.rosetta.core.conformation.PointGraphVertexData

assign(self: pyrosetta.rosetta.core.conformation.AtomGraphVertexData, : pyrosetta.rosetta.core.conformation.AtomGraphVertexData) pyrosetta.rosetta.core.conformation.AtomGraphVertexData

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

atom_name(self: pyrosetta.rosetta.core.conformation.AtomGraphVertexData) str

C++: core::conformation::AtomGraphVertexData::atom_name() –> std::string &

atom_radius_squared(self: pyrosetta.rosetta.core.conformation.AtomGraphVertexData) float

C++: core::conformation::AtomGraphVertexData::atom_radius_squared() –> double &

residue_id(self: pyrosetta.rosetta.core.conformation.AtomGraphVertexData) int

C++: core::conformation::AtomGraphVertexData::residue_id() –> unsigned long &

xyz(self: pyrosetta.rosetta.core.conformation.PointGraphVertexData) pyrosetta.rosetta.numeric.xyzVector_double_t

Get a non-const reference to xyz data in order to set the data by reference.

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

class pyrosetta.rosetta.core.conformation.Conformation

Bases: pybind11_builtins.pybind11_object

A container of Residues and the kinematics to manage them

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: 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 &, const unsigned long, const bool) –> void

append_residue_by_bond(*args, **kwargs)

Overloaded function.

  1. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. append_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, build_ideal_geometry: bool) -> None

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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 &, const bool, int, unsigned long, int, const bool, const bool) –> void

append_residue_by_jump(*args, **kwargs)

Overloaded function.

  1. append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None

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

  3. 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

  4. 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 &, const unsigned long, const std::string &, const std::string &, const 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

backbone_torsion_angle_atoms(self: pyrosetta.rosetta.core.conformation.Conformation, 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 backbone atoms which define this backbone torsion

Returns TRUE to signal FAILURE

C++: core::conformation::Conformation::backbone_torsion_angle_atoms(const class core::id::TorsionID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, 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

bond_orientation(*args, **kwargs)

Overloaded function.

  1. bond_orientation(self: pyrosetta.rosetta.core.conformation.Conformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Return the normalized vector of the bond between these two atoms.

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

  1. bond_orientation(self: pyrosetta.rosetta.core.conformation.Conformation, torsion: core::id::TorsionID) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Return the normalized vector of the bond about which this torsion angle twists.

C++: core::conformation::Conformation::bond_orientation(const class core::id::TorsionID) const –> class numeric::xyzVector<double>

bonded_neighbor_all_res(*args, **kwargs)

Overloaded function.

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

  2. 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

  3. 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

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

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

Get all atoms bonded to another

If intra_res is false, we only find inter - residue neighbors

C++: core::conformation::Conformation::bonded_neighbor_all_res(const class core::id::AtomID &, bool, bool, 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.

  1. 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> > &

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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.

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

  2. 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(const unsigned long, const std::string &, const unsigned long, const std::string &) –> 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(const 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(const 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(const unsigned long, const 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(const 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.

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

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

  3. 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

Detect existing disulfides from the protein structure

using suggestions from the FileData (or not!)

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.

  1. 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

  1. 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

  1. 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

  1. 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) 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.

  1. 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 &

  1. 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) 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(const unsigned long) –> void

insert_conformation_by_jump(*args, **kwargs)

Overloaded function.

  1. 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

  2. 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

  3. 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

  4. 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

Calls residue append observers AFTER addition of all residues

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

insert_residue_by_bond(*args, **kwargs)

Overloaded function.

  1. insert_residue_by_bond(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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 &, const unsigned long, unsigned long, const bool, const std::string &, const std::string &, bool, const bool) –> void

insert_residue_by_jump(*args, **kwargs)

Overloaded function.

  1. insert_residue_by_jump(self: pyrosetta.rosetta.core.conformation.Conformation, new_rsd_in: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, anchor_pos: int) -> None

  2. 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

  3. 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

  4. 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 std::string &, const std::string &, 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_bonded(*args, **kwargs)

Overloaded function.

  1. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID) -> bool

  2. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID, virt: bool) -> bool

  3. is_bonded(self: pyrosetta.rosetta.core.conformation.Conformation, atomid1: pyrosetta.rosetta.core.id.AtomID, atomid2: pyrosetta.rosetta.core.id.AtomID, virt: bool, skip_canonical_and_solvent: bool) -> bool

Returns a boolean for two atomIDs to be bonded.

Uses bonded_neighbor_all_res, which iterates through residue connections. To speed up, we would need to turn the connects into a proper bonded graph

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

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.

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

Returns the Jump with jump number <jump_number>

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

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

  1. modifiable_residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

  2. 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) 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 &, const unsigned long, const 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(const 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 dependent 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(const 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.

  1. 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(const unsigned long, const class core::conformation::Residue &, const bool) –> void

  1. 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(const unsigned long, const class core::conformation::Residue &, const class utility::vector1<struct std::pair<std::string, std::string >, class std::allocator<struct std::pair<std::string, std::string > > > &) –> void

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.

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

  2. 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.

  1. residue_type_set_for_conf(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

  2. 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.

  1. residue_typeset_mode(self: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.chemical.TypeSetMode

  2. 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

resolve_partial_atom_id(self: pyrosetta.rosetta.core.conformation.Conformation, partial_id: core::id::PartialAtomID) pyrosetta.rosetta.core.id.AtomID

Resolve a partial atom ID into an AtomID that is specific for this %Conformation

C++: core::conformation::Conformation::resolve_partial_atom_id(const class core::id::PartialAtomID &) const –> class core::id::AtomID

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 &, const unsigned long, const 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 &, const unsigned long, const bool) –> void

same_type_as_me(*args, **kwargs)

Overloaded function.

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

  2. 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 &, const 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 &, const 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 &, const 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 &, const double) –> void

set_jump(*args, **kwargs)

Overloaded function.

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

Sets the jump <jump_number> to <new_jump>

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

  1. set_jump(self: pyrosetta.rosetta.core.conformation.Conformation, id: pyrosetta.rosetta.core.id.AtomID, new_jump: 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(const unsigned long, const 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: 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 &, const double) –> void

set_torsion_angle(*args, **kwargs)

Overloaded function.

  1. 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

  2. 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 &, const double, const 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.

  1. 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

  1. 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(std::ostream &) 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) 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]> in Radians

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: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t) 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.

  1. 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

  1. 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.

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

  2. 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) 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.ConformationKinWriter

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.ConformationKinWriter, : pyrosetta.rosetta.core.conformation.ConformationKinWriter) pyrosetta.rosetta.core.conformation.ConformationKinWriter

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

master(self: pyrosetta.rosetta.core.conformation.ConformationKinWriter, setting: str) None

C++: core::conformation::ConformationKinWriter::master(const std::string &) –> void

write_coords(*args, **kwargs)

Overloaded function.

  1. write_coords(self: pyrosetta.rosetta.core.conformation.ConformationKinWriter, ostr: pyrosetta.rosetta.std.ostream, conf: pyrosetta.rosetta.core.conformation.Conformation) -> None

  2. write_coords(self: pyrosetta.rosetta.core.conformation.ConformationKinWriter, ostr: pyrosetta.rosetta.std.ostream, conf: pyrosetta.rosetta.core.conformation.Conformation, is_instance: bool) -> None

Write out the coordinates for an entire conformation; this includes

inter-residue bonds that would be missed by the ResidueKinWriter.

C++: core::conformation::ConformationKinWriter::write_coords(std::ostream &, const class core::conformation::Conformation &, bool) const –> void

write_virtual_atoms(self: pyrosetta.rosetta.core.conformation.ConformationKinWriter, setting: bool) None

C++: core::conformation::ConformationKinWriter::write_virtual_atoms(bool) –> void

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

class pyrosetta.rosetta.core.conformation.ExactResidueMatcher

Bases: pyrosetta.rosetta.core.conformation.ResidueMatcher

assign(self: pyrosetta.rosetta.core.conformation.ExactResidueMatcher, : pyrosetta.rosetta.core.conformation.ExactResidueMatcher) pyrosetta.rosetta.core.conformation.ExactResidueMatcher

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

class pyrosetta.rosetta.core.conformation.PointGraphEdgeData

Bases: pybind11_builtins.pybind11_object

dsq(self: pyrosetta.rosetta.core.conformation.PointGraphEdgeData) float

C++: core::conformation::PointGraphEdgeData::dsq() –> double &

class pyrosetta.rosetta.core.conformation.PointGraphPy

Bases: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) -> None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::add_edge(unsigned long, unsigned long) –> void

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int, edge_data: core::conformation::PointGraphEdgeData) -> None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::add_edge(unsigned long, unsigned long, const class core::conformation::PointGraphEdgeData &) –> void

assign(self: pyrosetta.rosetta.core.conformation.PointGraphPy, : pyrosetta.rosetta.core.conformation.PointGraphPy) pyrosetta.rosetta.core.conformation.PointGraphPy

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

drop_all_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::drop_all_edges() –> void

edge_exists(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) bool

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::edge_exists(unsigned long, unsigned long) –> bool

get_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::get_edge(unsigned long, unsigned long) –> class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *

get_vertex(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, index: int) pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::get_vertex(unsigned long) –> class utility::graph::UEVertex<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &

num_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_edges() const –> unsigned long

num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_vertices() const –> unsigned long

set_num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, num_vertices: int) None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::set_num_vertices(unsigned long) –> void

class pyrosetta.rosetta.core.conformation.PointGraphVertexData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.PointGraphVertexData, : pyrosetta.rosetta.core.conformation.PointGraphVertexData) pyrosetta.rosetta.core.conformation.PointGraphVertexData

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

xyz(self: pyrosetta.rosetta.core.conformation.PointGraphVertexData) pyrosetta.rosetta.numeric.xyzVector_double_t

Get a non-const reference to xyz data in order to set the data by reference.

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

class pyrosetta.rosetta.core.conformation.PseudoBond

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.PseudoBond, rhs: pyrosetta.rosetta.core.conformation.PseudoBond) pyrosetta.rosetta.core.conformation.PseudoBond

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

lr(*args, **kwargs)

Overloaded function.

  1. lr(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> int

C++: core::conformation::PseudoBond::lr() const –> unsigned long

  1. lr(self: pyrosetta.rosetta.core.conformation.PseudoBond, : int) -> None

C++: core::conformation::PseudoBond::lr(unsigned long) –> void

lr_conn_id(*args, **kwargs)

Overloaded function.

  1. lr_conn_id(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> int

C++: core::conformation::PseudoBond::lr_conn_id() const –> unsigned long

  1. lr_conn_id(self: pyrosetta.rosetta.core.conformation.PseudoBond, : int) -> None

C++: core::conformation::PseudoBond::lr_conn_id(unsigned long) –> void

lr_resconnid(*args, **kwargs)

Overloaded function.

  1. lr_resconnid(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> pyrosetta.rosetta.core.chemical.ResConnID

C++: core::conformation::PseudoBond::lr_resconnid() const –> class core::chemical::ResConnID

  1. lr_resconnid(self: pyrosetta.rosetta.core.conformation.PseudoBond, : pyrosetta.rosetta.core.chemical.ResConnID) -> None

C++: core::conformation::PseudoBond::lr_resconnid(class core::chemical::ResConnID) –> void

nbonds(*args, **kwargs)

Overloaded function.

  1. nbonds(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> int

C++: core::conformation::PseudoBond::nbonds() const –> unsigned long

  1. nbonds(self: pyrosetta.rosetta.core.conformation.PseudoBond, : int) -> None

C++: core::conformation::PseudoBond::nbonds(unsigned long) –> void

ur(*args, **kwargs)

Overloaded function.

  1. ur(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> int

C++: core::conformation::PseudoBond::ur() const –> unsigned long

  1. ur(self: pyrosetta.rosetta.core.conformation.PseudoBond, : int) -> None

C++: core::conformation::PseudoBond::ur(unsigned long) –> void

ur_conn_id(*args, **kwargs)

Overloaded function.

  1. ur_conn_id(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> int

C++: core::conformation::PseudoBond::ur_conn_id() const –> unsigned long

  1. ur_conn_id(self: pyrosetta.rosetta.core.conformation.PseudoBond, : int) -> None

C++: core::conformation::PseudoBond::ur_conn_id(unsigned long) –> void

ur_resconnid(*args, **kwargs)

Overloaded function.

  1. ur_resconnid(self: pyrosetta.rosetta.core.conformation.PseudoBond) -> pyrosetta.rosetta.core.chemical.ResConnID

C++: core::conformation::PseudoBond::ur_resconnid() const –> class core::chemical::ResConnID

  1. ur_resconnid(self: pyrosetta.rosetta.core.conformation.PseudoBond, : pyrosetta.rosetta.core.chemical.ResConnID) -> None

C++: core::conformation::PseudoBond::ur_resconnid(class core::chemical::ResConnID) –> void

class pyrosetta.rosetta.core.conformation.PseudoBondCollection

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection, : pyrosetta.rosetta.core.conformation.PseudoBondCollection) pyrosetta.rosetta.core.conformation.PseudoBondCollection

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

clone_with_new_sequence_numbering(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection, old2new: pyrosetta.rosetta.utility.vector1_int) pyrosetta.rosetta.core.conformation.PseudoBondCollection

C++: core::conformation::PseudoBondCollection::clone_with_new_sequence_numbering(const class utility::vector1<int, class std::allocator<int> > &) const –> class std::shared_ptr<const class core::conformation::PseudoBondCollection>

iter_begin(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection) __gnu_cxx::__normal_iterator<core::conformation::PseudoBond const*, std::vector<core::conformation::PseudoBond, std::allocator<core::conformation::PseudoBond> > >

C++: core::conformation::PseudoBondCollection::iter_begin() const –> class __gnu_cxx::__normal_iterator<const class core::conformation::PseudoBond *, class std::vector<class core::conformation::PseudoBond, class std::allocator<class core::conformation::PseudoBond> > >

iter_end(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection) __gnu_cxx::__normal_iterator<core::conformation::PseudoBond const*, std::vector<core::conformation::PseudoBond, std::allocator<core::conformation::PseudoBond> > >

C++: core::conformation::PseudoBondCollection::iter_end() const –> class __gnu_cxx::__normal_iterator<const class core::conformation::PseudoBond *, class std::vector<class core::conformation::PseudoBond, class std::allocator<class core::conformation::PseudoBond> > >

push_back(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection, : pyrosetta.rosetta.core.conformation.PseudoBond) None

C++: core::conformation::PseudoBondCollection::push_back(const class core::conformation::PseudoBond &) –> void

size(self: pyrosetta.rosetta.core.conformation.PseudoBondCollection) int

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

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 &

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 unsigned long) 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.

  1. annotated_name(self: pyrosetta.rosetta.core.conformation.Residue) -> str

  2. 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.

  1. 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 &

  1. 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 std::string &) –> 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 unsigned long) 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(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) bool

Does this atom depend on the LOWER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Vikram K. Mulligan (vmullig.edu).

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

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

Does this atom depend on the UPPER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::Residue::atom_depends_on_upper(const unsigned long) 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 std::string &) 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 unsigned long) 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 unsigned long) 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 unsigned long) 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 unsigned long) 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.

  1. 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 unsigned long) const –> unsigned long

  1. 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.

  1. 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 unsigned long) const –> unsigned long

  1. 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 unsigned long) 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 unsigned long) 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.

  1. 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

  1. 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.

  1. 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> > &

  1. 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

  1. 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.

  1. 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> > > > &

  1. 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 unsigned long) 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.

  1. 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> > &

  1. 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(*args, **kwargs)

Overloaded function.

  1. copy_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue, src_rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. copy_residue_connections(self: pyrosetta.rosetta.core.conformation.Residue, src_rsd: pyrosetta.rosetta.core.conformation.Residue, suppress_warnings: bool) -> None

Attempt to take residue connection info from src_rsd

If suppress_warnings is true, we don’t warn if residue connections on other residues are invalidated by a change of residue connection numbering in this residue. (Useful if we’re calling this function from a context in which we know that we’re going to update residue connections after the function call.) Note that warnings are never suppressed if high verbosity is set (TR.Debug.visible() == true).

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

Return a COP to the data cache

Might be a null pointer if the cache has not been initialized

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

fill_missing_atoms(*args, **kwargs)

Overloaded function.

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

  2. 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_atoms_exocyclic_to_ring_atom(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) pyrosetta.rosetta.utility.vector1_unsigned_long

Get a list of exocyclic atoms connected to a given ring atom.

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

get_hydrogens_bonded_to_ring_atom(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) pyrosetta.rosetta.utility.vector1_unsigned_long

Get a list of hydrogen atoms connected to a given ring atom.

C++: core::conformation::Residue::get_hydrogens_bonded_to_ring_atom(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>

get_substituents_to_ring_atom(self: pyrosetta.rosetta.core.conformation.Residue, atom_index: int) pyrosetta.rosetta.utility.vector1_unsigned_long

Get a list of substituent atoms connected to a given ring atom.

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

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 std::string &) const –> bool

has_incomplete_connection(*args, **kwargs)

Overloaded function.

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

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

  1. 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 std::string &) 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 unsigned long) 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_TNA(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns true if this residue is a TNA residue

C++: core::conformation::Residue::is_TNA() 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_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is an aramid

C++: core::conformation::Residue::is_aramid() 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.

  1. 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)

See Also:

For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)

first check if it is polymer upper or lower connected to the other residue. then check if it is boned to the other residue through non-polymer connection.

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

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

Am I bonded to other?

Looks at all residue connections as opposed to doing arithmetic

See Also:

For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)

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 property

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

is_meta_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a meta aramid

C++: core::conformation::Residue::is_meta_aramid() 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_ortho_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is an ortho aramid

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

is_para_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a para aramid

C++: core::conformation::Residue::is_para_aramid() 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.

  1. 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

  1. 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_post_methylene_meta_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene meta aramid

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

is_post_methylene_ortho_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene ortho aramid

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

is_post_methylene_para_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene para aramid

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

is_pre_methylene_meta_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a pre methylene meta aramid

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

is_pre_methylene_ortho_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a pre methylene ortho aramid

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

is_pre_methylene_para_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a pre methylene para aramid

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

is_pre_methylene_post_methylene_meta_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene meta aramid

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

is_pre_methylene_post_methylene_ortho_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene ortho aramid

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

is_pre_methylene_post_methylene_para_aramid(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns if this residue is a post methylene para aramid

C++: core::conformation::Residue::is_pre_methylene_post_methylene_para_aramid() 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.

  1. 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

  1. 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.

A misnomer; this should really be called “is_repulsive_atom()”. ~Labonte

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 property

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 property

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.

AMW TODO: somehow SWA spends literally 3.7% of its time calling this function.

A misnomer; this should really be called “is_virtual_atom()”. ~Labonte

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

is_water(self: pyrosetta.rosetta.core.conformation.Residue) bool

Returns true if this residue is water

C++: core::conformation::Residue::is_water() 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.

  1. 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> > &

  1. 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

misplaced(self: pyrosetta.rosetta.core.conformation.Residue) bool

Return whether or not the Residue was incorrectly oriented and placed within the polymer when created.

C++: core::conformation::Residue::misplaced() 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 unsigned long) const –> const std::string &

n_bonded_neighbor_all_res(*args, **kwargs)

Overloaded function.

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

  2. 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 unsigned long) 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

Return an OP to the datacache

Will create new one if not already initialized

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.

  1. 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> > > >

  1. 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 unsigned long) 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 unsigned long) 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_location(*args, **kwargs)

Overloaded function.

  1. orient_onto_location(self: pyrosetta.rosetta.core.conformation.Residue, center: int, nbr1: int, nbr2: int, center_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t, nbr1_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t, nbr2_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Orients residue object onto atom locations

Orients onto the atom numbers center, nbr1, nbr2.

C++: core::conformation::Residue::orient_onto_location(unsigned long, unsigned long, unsigned long, class numeric::xyzVector<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> void

  1. orient_onto_location(self: pyrosetta.rosetta.core.conformation.Residue, center_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t, nbr1_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t, nbr2_locaton: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Orients residue object onto atom locations

Orients using default orient atoms taken from select_orient_atoms

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

orient_onto_residue(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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<std::string, std::string >, class std::allocator<struct std::pair<std::string, std::string > > > &) –> 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.

  1. 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(unsigned long) const –> const class utility::vector1<int, class std::allocator<int> > &

  1. 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(unsigned long, unsigned long) 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.

  1. place(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation) -> bool

  2. place(self: pyrosetta.rosetta.core.conformation.Residue, src: pyrosetta.rosetta.core.conformation.Residue, conformation: core::conformation::Conformation, preserve_c_beta: bool) -> bool

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) –> bool

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 unsigned long) 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.

  1. 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

  1. 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

resolve_partial_atom_id(self: pyrosetta.rosetta.core.conformation.Residue, partial_id: core::id::PartialAtomID) core::id::AtomID

Resolve a partial atom ID into an AtomID for this residue

C++: core::conformation::Residue::resolve_partial_atom_id(const class core::id::PartialAtomID &) const –> class core::id::AtomID

ring_conformer(*args, **kwargs)

Overloaded function.

  1. ring_conformer(self: pyrosetta.rosetta.core.conformation.Residue, ring_num: int) -> pyrosetta.rosetta.core.chemical.rings.RingConformer

  2. 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.

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

Returns the sequence position of this residue

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

  1. 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.

  1. 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

  1. 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 std::string &, const class numeric::xyzVector<double> &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.conformation.Residue) -> None

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

  3. 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(std::ostream &, 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.

  1. 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> &

  1. 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 std::string &) 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

static create_residue(*args, **kwargs)

Overloaded function.

  1. 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>

  1. 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

  2. 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

  3. 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, allow_alternate_backbone_matching: 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, bool) –> class std::shared_ptr<class core::conformation::Residue>

class pyrosetta.rosetta.core.conformation.ResidueKinWriter

Bases: pybind11_builtins.pybind11_object

animate(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::animate(bool) –> void

assign(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, : pyrosetta.rosetta.core.conformation.ResidueKinWriter) pyrosetta.rosetta.core.conformation.ResidueKinWriter

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

dominant(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::dominant(bool) –> void

group(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::group(bool) –> void

master(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: str) None

C++: core::conformation::ResidueKinWriter::master(const std::string &) –> void

write_apolar_hydrogens(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::write_apolar_hydrogens(bool) –> void

write_backbone_hydrogens(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::write_backbone_hydrogens(bool) –> void

write_hydrogens(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None
Calling this function with the setting “true”, turns on polar, apolar, and backbone hydrogen writing.

Calling this function with the setting “false”, turns off polar, apolar, and backbone hydrogen writing.

C++: core::conformation::ResidueKinWriter::write_hydrogens(bool) –> void

write_kin_header(*args, **kwargs)

Overloaded function.

  1. write_kin_header(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, ostr: pyrosetta.rosetta.std.ostream, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. write_kin_header(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, ostr: pyrosetta.rosetta.std.ostream, rsd: pyrosetta.rosetta.core.conformation.Residue, atom_to_center_on: int) -> None

  3. write_kin_header(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, ostr: pyrosetta.rosetta.std.ostream, rsd: pyrosetta.rosetta.core.conformation.Residue, atom_to_center_on: int, which_kin: int) -> None

write the header for the kinemage to center on this residue

C++: core::conformation::ResidueKinWriter::write_kin_header(std::ostream &, const class core::conformation::Residue &, unsigned long, unsigned long) const –> void

write_polar_hydrogens(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::write_polar_hydrogens(bool) –> void

write_rsd_coords(*args, **kwargs)

Overloaded function.

  1. write_rsd_coords(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, ostr: pyrosetta.rosetta.std.ostream, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. write_rsd_coords(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, ostr: pyrosetta.rosetta.std.ostream, rsd: pyrosetta.rosetta.core.conformation.Residue, is_instance: bool) -> None

Write out the coordinates for a particular residue; the kinemage tag

is assumed to have been writen already.

C++: core::conformation::ResidueKinWriter::write_rsd_coords(std::ostream &, const class core::conformation::Residue &, bool) const –> void

write_virtual_atoms(self: pyrosetta.rosetta.core.conformation.ResidueKinWriter, setting: bool) None

C++: core::conformation::ResidueKinWriter::write_virtual_atoms(bool) –> void

class pyrosetta.rosetta.core.conformation.ResidueMatcher

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.ResidueMatcher, : pyrosetta.rosetta.core.conformation.ResidueMatcher) pyrosetta.rosetta.core.conformation.ResidueMatcher

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

class pyrosetta.rosetta.core.conformation.RotamerSetBase

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, : pyrosetta.rosetta.core.conformation.RotamerSetBase) pyrosetta.rosetta.core.conformation.RotamerSetBase

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

data(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) pyrosetta.rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh

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

get_n_residue_types(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) int

C++: core::conformation::RotamerSetBase::get_n_residue_types() const –> unsigned long

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, which_restype: int) int

C++: core::conformation::RotamerSetBase::get_n_rotamers_for_residue_type(unsigned long) const –> unsigned long

get_residue_type_begin(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, which_restype: int) int

C++: core::conformation::RotamerSetBase::get_residue_type_begin(unsigned long) const –> unsigned long

get_residue_type_index_for_rotamer(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, which_rotamer: int) int
Rotamers i to i+j of all the same residue type are grouped together.

This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

C++: core::conformation::RotamerSetBase::get_residue_type_index_for_rotamer(unsigned long) const –> unsigned long

get_trie(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, method_enum_id: int) pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

C++: core::conformation::RotamerSetBase::get_trie(unsigned long) const –> class std::shared_ptr<const class core::conformation::AbstractRotamerTrie>

nonconst_rotamer(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

mutatable access to a single rotamer in the set.

C++: core::conformation::RotamerSetBase::nonconst_rotamer(unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

num_rotamers(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) int

C++: core::conformation::RotamerSetBase::num_rotamers() const –> unsigned long

resid(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) int

C++: core::conformation::RotamerSetBase::resid() const –> unsigned long

rotamer(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

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

rotamer_ref(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, rot_id: int) pyrosetta.rosetta.core.conformation.Residue

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

store_trie(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, method_enum_id: int, trie: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) None

C++: core::conformation::RotamerSetBase::store_trie(unsigned long, class std::shared_ptr<class core::conformation::AbstractRotamerTrie>) –> void

class pyrosetta.rosetta.core.conformation.Strategy

Bases: pybind11_builtins.pybind11_object

Members:

NAIVE

AUTOMATIC

OCTREE

THREEDGRID

STRIPEHASH

AUTOMATIC = <Strategy.AUTOMATIC: 1>
NAIVE = <Strategy.NAIVE: 0>
OCTREE = <Strategy.OCTREE: 2>
STRIPEHASH = <Strategy.STRIPEHASH: 4>
THREEDGRID = <Strategy.THREEDGRID: 3>
property name
class pyrosetta.rosetta.core.conformation.UltraLightResidue

Bases: pybind11_builtins.pybind11_object

align_to_residue(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, other_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) None

C++: core::conformation::UltraLightResidue::align_to_residue(const class core::conformation::UltraLightResidue &) –> void

assign(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, : pyrosetta.rosetta.core.conformation.UltraLightResidue) pyrosetta.rosetta.core.conformation.UltraLightResidue

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

center(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) pyrosetta.rosetta.numeric.xyzVector_double_t

get centerpoint of residue

C++: core::conformation::UltraLightResidue::center() const –> class numeric::xyzVector<double>

coords_vector(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

get const ref to residue coords

C++: core::conformation::UltraLightResidue::coords_vector() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

heavy_coords_vector(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

get const ref to residue heavy atom coords

C++: core::conformation::UltraLightResidue::heavy_coords_vector() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

max_dist_to_center(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) float

Return the maximum distance from any atom to the center.

C++: core::conformation::UltraLightResidue::max_dist_to_center() const –> double

natoms(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) int

return number of atoms in ultralight residue

C++: core::conformation::UltraLightResidue::natoms() const –> unsigned long

residue(self: pyrosetta.rosetta.core.conformation.UltraLightResidue) pyrosetta.rosetta.core.conformation.Residue

return a constant pointer to the base residue

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

set_coords(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, input_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None

get const ref to residue coords

C++: core::conformation::UltraLightResidue::set_coords(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

slide(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t) None

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

transform(*args, **kwargs)

Overloaded function.

  1. transform(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, rotation_matrix: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::conformation::UltraLightResidue::transform(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void

  1. transform(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, rotation_matrix: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, group_center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::conformation::UltraLightResidue::transform(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double>) –> void

update_conformation(self: pyrosetta.rosetta.core.conformation.UltraLightResidue, conformation: pyrosetta.rosetta.core.conformation.Conformation) None

update conformation with current coords. Slow.

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

class pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher

Bases: pyrosetta.rosetta.core.conformation.ResidueMatcher

assign(self: pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher, : pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher) pyrosetta.rosetta.core.conformation.WatsonCrickResidueMatcher

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

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.

  1. 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

  1. 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 std::string &, 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.

  1. 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

  1. 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

  1. copy_residue_coordinates_and_rebuild_missing_atoms(source_rsd: pyrosetta.rosetta.core.conformation.Residue, target_rsd: pyrosetta.rosetta.core.conformation.Residue, mapping: pyrosetta.rosetta.utility.vector1_unsigned_long, conf: pyrosetta.rosetta.core.conformation.Conformation) -> None

Fills coords of target_rsd with coords from source_rsd using the provided mapping, rebuilds others

The mapping is indexed by target_rsd atom index, giving source_rsd index or zero for not present.

C++: core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(const class core::conformation::Residue &, class core::conformation::Residue &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, 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_bond_torsion_with_nearest_orientation(conf: pyrosetta.rosetta.core.conformation.Conformation, torsions: pyrosetta.rosetta.utility.vector1_core_id_TorsionID, query_torsion: core::id::TorsionID) core::id::TorsionID

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

pyrosetta.rosetta.core.conformation.find_neighbors_restricted(*args, **kwargs)

Overloaded function.

  1. 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

  2. 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.

  1. form_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int) -> None

  2. form_disulfide(conformation: pyrosetta.rosetta.core.conformation.Conformation, lower_res: int, upper_res: int, preserve_d_residues: bool) -> None

  3. 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.

  1. 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

  1. 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_residue_from_name(*args, **kwargs)

Overloaded function.

  1. get_residue_from_name(name: str) -> pyrosetta.rosetta.core.conformation.Residue

  2. get_residue_from_name(name: str, residue_type_set: str) -> pyrosetta.rosetta.core.conformation.Residue

Returns a new residue based on a name

C++: core::conformation::get_residue_from_name(const std::string &, const std::string &) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.core.conformation.get_residue_from_name1(*args, **kwargs)

Overloaded function.

  1. get_residue_from_name1(name1: str) -> pyrosetta.rosetta.core.conformation.Residue

  2. get_residue_from_name1(name1: str, is_lower_terminus: bool) -> pyrosetta.rosetta.core.conformation.Residue

  3. get_residue_from_name1(name1: str, is_lower_terminus: bool, is_upper_terminus: bool) -> pyrosetta.rosetta.core.conformation.Residue

  4. get_residue_from_name1(name1: str, is_lower_terminus: bool, is_upper_terminus: bool, d_aa: bool) -> pyrosetta.rosetta.core.conformation.Residue

  5. get_residue_from_name1(name1: str, is_lower_terminus: bool, is_upper_terminus: bool, d_aa: bool, residue_type_set: str) -> pyrosetta.rosetta.core.conformation.Residue

Returns a new residue based on a name1

C++: core::conformation::get_residue_from_name1(char, bool, bool, bool, const std::string &) –> class std::shared_ptr<class core::conformation::Residue>

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_rt_from_residue_pair(res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) core::kinematics::RT

Get stub mapping that maps residue 1 to residue 2

Coordinate frames for each defined by orient_atoms which defaults to

C++: core::conformation::get_rt_from_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &) –> class core::kinematics::RT

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_stub_from_residue(res: pyrosetta.rosetta.core.conformation.Residue) core::kinematics::Stub

Get stub from orient_atoms

This defaults to a stub with CA, N, C for canonical amino acids

C++: core::conformation::get_stub_from_residue(const class core::conformation::Residue &) –> class core::kinematics::Stub

pyrosetta.rosetta.core.conformation.get_torsion_bin(*args, **kwargs)

Overloaded function.

  1. get_torsion_bin(phi: float, psi: float) -> pyrosetta.rosetta.core.conformation.ppo_torsion_bin

  2. 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_partial_atom_ids_for_mainchain_torsion(res: pyrosetta.rosetta.core.conformation.Residue, mainchain_torsion: int, atoms: pyrosetta.rosetta.std.set_core_id_PartialAtomID_t) None
For a given mainchain torsion, report the partial atom IDs that

define it, inserting these partial atom IDs into a std::set (to avoid redundancy perhaps with other torsions that also depend on the same atoms).

C++: core::conformation::insert_partial_atom_ids_for_mainchain_torsion(const class core::conformation::Residue &, const unsigned long, class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> > &) –> 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(residue: pyrosetta.rosetta.core.conformation.Residue, query_atom: int) pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Is the query atom in this residue axial or equatorial or neither?

C++: core::conformation::is_atom_axial_or_equatorial(const class core::conformation::Residue &, unsigned long) –> enum core::chemical::rings::AxEqDesignation

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.

  1. is_ideal_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> bool

  2. is_ideal_position(seqpos: int, conformation: pyrosetta.rosetta.core.conformation.Conformation, theta_epsilon: float) -> bool

  3. 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 std::string &) –> 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.

  1. 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

  2. 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?

The Residue containing the atoms in question.

The index of the atom in question.

The position on the ring as an integer. 0 means that the query atom is not attached to the ring.

If a member of the ring is selected as a query atom, this function returns 0.

If a non-ring atom is connected to two ring atoms, the (numerically) lower ring position is returned.

Labonte <JWLabonte.edu>

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

Members:

ppo_torbin_A

ppo_torbin_B

ppo_torbin_E

ppo_torbin_G

ppo_torbin_a

ppo_torbin_b

ppo_torbin_e

ppo_torbin_g

ppo_torbin_X

ppo_torbin_U

n_ppo_torsion_bins

n_ppo_torsion_bins = <ppo_torsion_bin.ppo_torbin_U: 10>
property name
ppo_torbin_A = <ppo_torsion_bin.ppo_torbin_A: 1>
ppo_torbin_B = <ppo_torsion_bin.ppo_torbin_B: 2>
ppo_torbin_E = <ppo_torsion_bin.ppo_torbin_E: 3>
ppo_torbin_G = <ppo_torsion_bin.ppo_torbin_G: 4>
ppo_torbin_U = <ppo_torsion_bin.ppo_torbin_U: 10>
ppo_torbin_X = <ppo_torsion_bin.ppo_torbin_X: 9>
ppo_torbin_a = <ppo_torsion_bin.ppo_torbin_a: 5>
ppo_torbin_b = <ppo_torsion_bin.ppo_torbin_b: 6>
ppo_torbin_e = <ppo_torsion_bin.ppo_torbin_e: 7>
ppo_torbin_g = <ppo_torsion_bin.ppo_torbin_g: 8>
pyrosetta.rosetta.core.conformation.promote_sameresidue_child_of_jump_atom(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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 &, std::ostream &) –> 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.

  1. update_cutpoint_virtual_atoms_if_connected(conformation: pyrosetta.rosetta.core.conformation.Conformation, cutpoint_res: int) -> None

  2. 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(std::ostream &, const unsigned long, const std::string &, const class numeric::xyzVector<double> &) –> void