symmetry

Bindings for core::conformation::symmetry namespace

class pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation

Bases: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation

Mirror symmetric conformation contains the same symminfo logic, but also includes special logic for mirror symmetries

Symmetry_Info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation) core::conformation::symmetry::SymmetryInfo

C++: core::conformation::symmetry::SymmetricConformation::Symmetry_Info() –> class std::shared_ptr<class core::conformation::symmetry::SymmetryInfo>

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(*args, **kwargs)

Overloaded function.

  1. append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

Apped a new residue after a given position in the pose

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.MirrorSymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None

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

  3. append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, 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.symmetry.MirrorSymmetricConformation, 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; clones this append to all copies

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void

apply_transformation(*args, **kwargs)

Overloaded function.

  1. apply_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

  2. apply_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int, rotationonly: bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Remap coordinate X from resid i’s frame to resid j’s frame

C++: core::conformation::symmetry::SymmetricConformation::apply_transformation(class numeric::xyzVector<double>, unsigned long, unsigned long, bool) –> class numeric::xyzVector<double>

apply_transformation_norecompute(*args, **kwargs)

Overloaded function.

  1. apply_transformation_norecompute(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

  2. apply_transformation_norecompute(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int, rotationonly: bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Remap coordinate X from resid i’s frame to resid j’s frame

assumes that the transformations are already computed (thus can be const)

C++: core::conformation::symmetry::SymmetricConformation::apply_transformation_norecompute(class numeric::xyzVector<double>, unsigned long, unsigned long, bool) const –> class numeric::xyzVector<double>

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, src: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.conformation.Conformation

virtual assignment operator

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

  1. assign(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, : pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation) -> pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation

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

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.symmetry.SymmetricConformation, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID, positions: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None

Symmetric batch_set_xyz

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.MirrorSymmetricConformation) pyrosetta.rosetta.core.conformation.Conformation

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation, seqpos1: int, atom_name1: str, seqpos2: int, atom_name2: str) None

Declare that a chemical bond exists between two residues

This updates all symmetry copies, so that each one has a chemical bond between the residues in question.

Frank DiMaio.

Rewritten by Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.MirrorSymmetricConformation, src: pyrosetta.rosetta.core.conformation.Conformation) None

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.MirrorSymmetricConformation) -> None

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

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

C++: core::conformation::symmetry::MirrorSymmetricConformation::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(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, fold_tree_in: pyrosetta.rosetta.core.kinematics.FoldTree) None

set the fold_tree

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation) pyrosetta.rosetta.utility.vector1_bool

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

get_residue_weight(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, resid1: int, resid2: int) float

C++: core::conformation::symmetry::MirrorSymmetricConformation::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

get_transformation(*args, **kwargs)

Overloaded function.

  1. get_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int) -> pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

  2. get_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int, input_is_subunit_id: bool) -> pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Get the transformation controlling resid i

C++: core::conformation::symmetry::SymmetricConformation::get_transformation(unsigned long, bool) const –> class numeric::HomogeneousTransform<double>

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.symmetry.MirrorSymmetricConformation, 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.symmetry.MirrorSymmetricConformation, 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.symmetry.MirrorSymmetricConformation, 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.symmetry.MirrorSymmetricConformation, 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

Append a new conformation by a jump; clones this append to all copies

C++: core::conformation::symmetry::MirrorSymmetricConformation::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(*args, **kwargs)

Overloaded function.

  1. prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

Prepend a new residue after a given position in the pose

C++: core::conformation::symmetry::SymmetricConformation::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

recalculate_transforms(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation) None

C++: core::conformation::symmetry::MirrorSymmetricConformation::recalculate_transforms() const –> 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.symmetry.MirrorSymmetricConformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, orient_backbone: bool) -> None

replace residue

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

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

C++: core::conformation::symmetry::MirrorSymmetricConformation::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

res_is_mirrored(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, seqpos: int) bool

Is this residue mirrored relative to the asymmetric unit?

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::symmetry::MirrorSymmetricConformation::res_is_mirrored(const unsigned long) const –> bool

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(*args, **kwargs)

Overloaded function.

  1. safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

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

safely_prepend_polymer_residue_before_seqpos(*args, **kwargs)

Overloaded function.

  1. safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.MirrorSymmetricConformation, other: pyrosetta.rosetta.core.conformation.Conformation) -> bool

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

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, setting: float) None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, setting: float) None

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

set_dof(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, id: pyrosetta.rosetta.core.id.DOF_ID, setting: float) None

DOF

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.MirrorSymmetricConformation, jump_number: int, new_jump: core::kinematics::Jump) -> None

JUMPS

set a jump

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

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

set a jump

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation, seqpos: int, setting: str) None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.MirrorSymmetricConformation, id: core::id::TorsionID, setting: float) None

BONDS/TORSIONS

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.MirrorSymmetricConformation, 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.symmetry.MirrorSymmetricConformation, 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

C++: core::conformation::symmetry::MirrorSymmetricConformation::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.symmetry.SymmetricConformation, id: pyrosetta.rosetta.core.id.AtomID, position: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Symmetric set_xyz

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, 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, in addition to ALL clones

C++: core::conformation::symmetry::SymmetricConformation::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

update_residue_identities(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation) None
Updates residue identities in symmetric subunits, ensuring that they are mirrored relative to the ASU in mirrored subunits

and identical to the ASU in non-mirrored subunits.

Assumes that the residue identities and variants (aside from D/L variants) already match. That is, if I have ASN at position 5 in my asymmetric unit, I either have ASN or DASN at the equivalent position in each symmetry copy. Safe to call repeatedly.

Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::symmetry::MirrorSymmetricConformation::update_residue_identities() –> 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.symmetry.SlideCriteriaType

Bases: pybind11_builtins.pybind11_object

Members:

CEN_DOCK_SCORE

FA_REP_SCORE

CONTACTS

TOTAL_NUM_CRITERIA

CEN_DOCK_SCORE = <SlideCriteriaType.CEN_DOCK_SCORE: 1>
CONTACTS = <SlideCriteriaType.CONTACTS: 3>
FA_REP_SCORE = <SlideCriteriaType.FA_REP_SCORE: 2>
TOTAL_NUM_CRITERIA = <SlideCriteriaType.TOTAL_NUM_CRITERIA: 4>
property name
class pyrosetta.rosetta.core.conformation.symmetry.SlideType

Bases: pybind11_builtins.pybind11_object

Members:

SEQUENTIAL

ORDERED_SEQUENTIAL

RANDOM

ORDERED_SEQUENTIAL = <SlideType.ORDERED_SEQUENTIAL: 2>
RANDOM = <SlideType.RANDOM: 3>
SEQUENTIAL = <SlideType.SEQUENTIAL: 1>
property name
class pyrosetta.rosetta.core.conformation.symmetry.SymDof

Bases: pybind11_builtins.pybind11_object

add_dof_from_string(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, dof_string: pyrosetta.rosetta.utility.vector1_std_string) None

C++: core::conformation::symmetry::SymDof::add_dof_from_string(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

allow_dof(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::allow_dof(int) const –> bool

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, src: pyrosetta.rosetta.core.conformation.symmetry.SymDof) pyrosetta.rosetta.core.conformation.symmetry.SymDof

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

has_dof(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof) bool

C++: core::conformation::symmetry::SymDof::has_dof() –> bool

has_range1(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range1(int) const –> bool

has_range1_lower(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range1_lower(int) const –> bool

has_range1_upper(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range1_upper(int) const –> bool

has_range2(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range2(int) const –> bool

has_range2_lower(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range2_lower(int) const –> bool

has_range2_upper(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::has_range2_upper(int) const –> bool

jump_direction(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) int

C++: core::conformation::symmetry::SymDof::jump_direction(int) const –> int

range1_lower(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) float

C++: core::conformation::symmetry::SymDof::range1_lower(int) const –> double

range1_upper(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) float

C++: core::conformation::symmetry::SymDof::range1_upper(int) const –> double

range2_is_bound(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) bool

C++: core::conformation::symmetry::SymDof::range2_is_bound(int) const –> bool

range2_lower(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) float

C++: core::conformation::symmetry::SymDof::range2_lower(int) const –> double

range2_upper(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int) float

C++: core::conformation::symmetry::SymDof::range2_upper(int) const –> double

read(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, dof_line: str) None

C++: core::conformation::symmetry::SymDof::read(std::string) –> void

set_allow_dof(self: pyrosetta.rosetta.core.conformation.symmetry.SymDof, df: int, newval: bool) None

C++: core::conformation::symmetry::SymDof::set_allow_dof(int, bool) –> void

class pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, src: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo

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

get_SlideCriteriaType(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType

C++: core::conformation::symmetry::SymSlideInfo::get_SlideCriteriaType() const –> enum core::conformation::symmetry::SlideCriteriaType

get_SlideCriteriaVal(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) str

C++: core::conformation::symmetry::SymSlideInfo::get_SlideCriteriaVal() const –> std::string

get_slide_order(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) pyrosetta.rosetta.std.vector_unsigned_long

C++: core::conformation::symmetry::SymSlideInfo::get_slide_order() const –> class std::vector<unsigned long, class std::allocator<unsigned long> >

get_slide_type(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) pyrosetta.rosetta.core.conformation.symmetry.SlideType

C++: core::conformation::symmetry::SymSlideInfo::get_slide_type() const –> enum core::conformation::symmetry::SlideType

set_SlideCriteriaType(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, score_criteria: pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType) None

C++: core::conformation::symmetry::SymSlideInfo::set_SlideCriteriaType(enum core::conformation::symmetry::SlideCriteriaType) –> void

set_SlideCriteriaVal(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, SlideCriteriaVal: str) None

C++: core::conformation::symmetry::SymSlideInfo::set_SlideCriteriaVal(std::string) –> void

set_slide_order(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, slide_order: pyrosetta.rosetta.std.vector_unsigned_long) None

C++: core::conformation::symmetry::SymSlideInfo::set_slide_order(class std::vector<unsigned long, class std::allocator<unsigned long> >) –> void

set_slide_type(self: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, slide_type: pyrosetta.rosetta.core.conformation.symmetry.SlideType) None

C++: core::conformation::symmetry::SymSlideInfo::set_slide_type(enum core::conformation::symmetry::SlideType) –> void

class pyrosetta.rosetta.core.conformation.symmetry.SymmData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, : pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.core.conformation.symmetry.SymmData

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

clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.core.conformation.symmetry.SymmData

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

components_moved_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, jname: str) pyrosetta.rosetta.utility.vector1_char

C++: core::conformation::symmetry::SymmData::components_moved_by_jump(const std::string &) const –> class utility::vector1<char, class std::allocator<char> >

get_anchor_residue(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) str

C++: core::conformation::symmetry::SymmData::get_anchor_residue() const –> const std::string &

get_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.utility.vector1_char

C++: core::conformation::symmetry::SymmData::get_components() const –> const class utility::vector1<char, class std::allocator<char> > &

get_dofs(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof

C++: core::conformation::symmetry::SymmData::get_dofs() const –> const class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > > &

get_include_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.utility.vector1_unsigned_long

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

get_interfaces(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_interfaces() const –> unsigned long

get_jump_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t

C++: core::conformation::symmetry::SymmData::get_jump_clones() const –> const class std::map<unsigned long, class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > > > > &

get_jump_name_to_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t

C++: core::conformation::symmetry::SymmData::get_jump_name_to_components() const –> const class std::map<std::string, class utility::vector1<char, class std::allocator<char> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<char, class std::allocator<char> > > > > &

get_jump_name_to_subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: core::conformation::symmetry::SymmData::get_jump_name_to_subunits() const –> const class std::map<std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &

get_jump_string_to_jump_num(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_unsigned_long

C++: core::conformation::symmetry::SymmData::get_jump_string_to_jump_num() const –> const class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > > &

get_least_common_ancertor_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, jname1: str, jname2: str) str

C++: core::conformation::symmetry::SymmData::get_least_common_ancertor_jump(const std::string &, const std::string &) const –> const std::string &

get_least_common_ancertor_virtual(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, vname1: str, vname2: str) str

C++: core::conformation::symmetry::SymmData::get_least_common_ancertor_virtual(const std::string &, const std::string &) const –> const std::string &

get_num_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_num_components() const –> unsigned long

get_num_virtual(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_num_virtual() const –> unsigned long

get_output_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.utility.vector1_unsigned_long

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

get_parent_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, jname: str) str

C++: core::conformation::symmetry::SymmData::get_parent_jump(const std::string &) const –> const std::string &

get_parent_virtual(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, vname: str) str

C++: core::conformation::symmetry::SymmData::get_parent_virtual(const std::string &) const –> const std::string &

get_recenter(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) bool

C++: core::conformation::symmetry::SymmData::get_recenter() const –> bool

get_root(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_root() const –> unsigned long

get_rotation_matrix(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t

C++: core::conformation::symmetry::SymmData::get_rotation_matrix() const –> const class std::vector<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

get_score_multiply_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.utility.vector1_unsigned_long

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

get_score_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_score_subunit() const –> unsigned long

get_slide_info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo

C++: core::conformation::symmetry::SymmData::get_slide_info() const –> const class core::conformation::symmetry::SymSlideInfo &

get_subunit_name_to_component(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_char

C++: core::conformation::symmetry::SymmData::get_subunit_name_to_component() const –> const class std::map<std::string, char, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, char> > > &

get_subunit_num_to_virt_id(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: core::conformation::symmetry::SymmData::get_subunit_num_to_virt_id() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

get_subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) int

C++: core::conformation::symmetry::SymmData::get_subunits() const –> unsigned long

get_symmetry_name(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) str

C++: core::conformation::symmetry::SymmData::get_symmetry_name() const –> const std::string &

get_symmetry_type(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) str

C++: core::conformation::symmetry::SymmData::get_symmetry_type() const –> const std::string &

get_translation_matrix(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t

C++: core::conformation::symmetry::SymmData::get_translation_matrix() const –> const class std::vector<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

get_virt_id_to_subunit_chain(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_char

C++: core::conformation::symmetry::SymmData::get_virt_id_to_subunit_chain() const –> const class std::map<std::string, char, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, char> > > &

get_virt_id_to_subunit_num(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_unsigned_long

C++: core::conformation::symmetry::SymmData::get_virt_id_to_subunit_num() const –> const class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > > &

get_virt_id_to_subunit_residue(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::conformation::symmetry::SymmData::get_virt_id_to_subunit_residue() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

get_virtual_connects(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t

C++: core::conformation::symmetry::SymmData::get_virtual_connects() const –> const class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > &

get_virtual_coordinates(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_core_conformation_symmetry_VirtualCoordinate

C++: core::conformation::symmetry::SymmData::get_virtual_coordinates() const –> const class std::map<std::string, class core::conformation::symmetry::VirtualCoordinate, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::conformation::symmetry::VirtualCoordinate> > > &

get_virtual_id_to_num(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_std_string_unsigned_long

C++: core::conformation::symmetry::SymmData::get_virtual_id_to_num() const –> const class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > > &

get_virtual_num_to_id(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) pyrosetta.rosetta.std.map_unsigned_long_std_string

C++: core::conformation::symmetry::SymmData::get_virtual_num_to_id() const –> const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &

is_ancestor_virtual(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, ancestor: str, child: str) bool

C++: core::conformation::symmetry::SymmData::is_ancestor_virtual(const std::string &, const std::string &) const –> bool

read_symmetry_data_from_file(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, filename: str) None

C++: core::conformation::symmetry::SymmData::read_symmetry_data_from_file(std::string) –> void

read_symmetry_data_from_stream(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, infile: pyrosetta.rosetta.std.istream) None

C++: core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(std::istream &) –> void

sanity_check(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) None

C++: core::conformation::symmetry::SymmData::sanity_check() –> void

set_anchor_residue(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, anchor: str) None

C++: core::conformation::symmetry::SymmData::set_anchor_residue(std::string) –> void

set_interfaces(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, interfaces: int) None

C++: core::conformation::symmetry::SymmData::set_interfaces(unsigned long) –> void

set_rotation_matrix(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, rotation_matrices: pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t) None

C++: core::conformation::symmetry::SymmData::set_rotation_matrix(class std::vector<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > >) –> void

set_score_multiply_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, score_multiply_vector: pyrosetta.rosetta.utility.vector1_double) None

C++: core::conformation::symmetry::SymmData::set_score_multiply_subunit(class utility::vector1<double, class std::allocator<double> > &) –> void

set_slide_info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) None

C++: core::conformation::symmetry::SymmData::set_slide_info(const class core::conformation::symmetry::SymSlideInfo &) –> void

set_subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, num_subunits: int) None

C++: core::conformation::symmetry::SymmData::set_subunits(unsigned long) –> void

set_symm_transforms(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, symm_transforms: pyrosetta.rosetta.std.vector_std_vector_std_string_std_allocator_std_string_t) None

C++: core::conformation::symmetry::SymmData::set_symm_transforms(class std::vector<class std::vector<std::string, class std::allocator<std::string > >, class std::allocator<class std::vector<std::string, class std::allocator<std::string > > > >) –> void

set_symmetry_name(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, symm_name: str) None

C++: core::conformation::symmetry::SymmData::set_symmetry_name(std::string) –> void

set_symmetry_type(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, symm_type: str) None

C++: core::conformation::symmetry::SymmData::set_symmetry_type(std::string) –> void

set_translation_matrix(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, translation_matrices: pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t) None

C++: core::conformation::symmetry::SymmData::set_translation_matrix(class std::vector<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > >) –> void

show(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData) None

C++: core::conformation::symmetry::SymmData::show() –> void

subunits_moved_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmData, jname: str) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::conformation::symmetry::SymmData::subunits_moved_by_jump(const std::string &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceLoader

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader, : pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader) pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader

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

static classname() str

C++: core::conformation::symmetry::SymmDataLoader::classname() –> std::string

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: core::conformation::symmetry::SymmDataLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator, : pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator) pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator

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

create_resource_loader(self: pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator) pyrosetta.rosetta.basic.resource_manager.ResourceLoader

C++: core::conformation::symmetry::SymmDataLoaderCreator::create_resource_loader() const –> class std::shared_ptr<class basic::resource_manager::ResourceLoader>

loader_type(self: pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator) str

C++: core::conformation::symmetry::SymmDataLoaderCreator::loader_type() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: core::conformation::symmetry::SymmDataLoaderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation

Bases: pyrosetta.rosetta.core.conformation.Conformation

A symmetric conformation: has an additional data member “SymmetryInfo” class

Handles symmetrizing of some of the conformation-changing methods of Conformation

Symmetry_Info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation) core::conformation::symmetry::SymmetryInfo

C++: core::conformation::symmetry::SymmetricConformation::Symmetry_Info() –> class std::shared_ptr<class core::conformation::symmetry::SymmetryInfo>

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(*args, **kwargs)

Overloaded function.

  1. append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

Apped a new residue after a given position in the pose

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None

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

  3. append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, 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.symmetry.SymmetricConformation, 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; clones this append to all copies

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, v: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(const class numeric::xyzMatrix<double> &, const class numeric::xyzVector<double> &) –> void

apply_transformation(*args, **kwargs)

Overloaded function.

  1. apply_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

  2. apply_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int, rotationonly: bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Remap coordinate X from resid i’s frame to resid j’s frame

C++: core::conformation::symmetry::SymmetricConformation::apply_transformation(class numeric::xyzVector<double>, unsigned long, unsigned long, bool) –> class numeric::xyzVector<double>

apply_transformation_norecompute(*args, **kwargs)

Overloaded function.

  1. apply_transformation_norecompute(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

  2. apply_transformation_norecompute(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, Xin: pyrosetta.rosetta.numeric.xyzVector_double_t, residfrom: int, residto: int, rotationonly: bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t

Remap coordinate X from resid i’s frame to resid j’s frame

assumes that the transformations are already computed (thus can be const)

C++: core::conformation::symmetry::SymmetricConformation::apply_transformation_norecompute(class numeric::xyzVector<double>, unsigned long, unsigned long, bool) const –> class numeric::xyzVector<double>

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, src: pyrosetta.rosetta.core.conformation.Conformation) -> pyrosetta.rosetta.core.conformation.Conformation

virtual assignment operator

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

  1. assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, : pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation) -> pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation

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

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.symmetry.SymmetricConformation, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID, positions: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) None

Symmetric batch_set_xyz

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation) pyrosetta.rosetta.core.conformation.Conformation

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, seqpos1: int, atom_name1: str, seqpos2: int, atom_name2: str) None

Declare that a chemical bond exists between two residues

This updates all symmetry copies, so that each one has a chemical bond between the residues in question.

Frank DiMaio.

Rewritten by Vikram K. Mulligan (vmullig.edu).

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, src: pyrosetta.rosetta.core.conformation.Conformation) None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation) -> None

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

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

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, fold_tree_in: pyrosetta.rosetta.core.kinematics.FoldTree) -> None

set the fold_tree .. update symminfo if jump numbering changed

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

  1. fold_tree(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation) -> pyrosetta.rosetta.core.kinematics.FoldTree

FoldTree access

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

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.symmetry.SymmetricConformation) pyrosetta.rosetta.utility.vector1_bool

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

get_residue_weight(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid1: int, resid2: int) float

C++: core::conformation::symmetry::SymmetricConformation::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

get_transformation(*args, **kwargs)

Overloaded function.

  1. get_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int) -> pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

  2. get_transformation(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int, input_is_subunit_id: bool) -> pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Get the transformation controlling resid i

C++: core::conformation::symmetry::SymmetricConformation::get_transformation(unsigned long, bool) const –> class numeric::HomogeneousTransform<double>

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.symmetry.SymmetricConformation, 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.symmetry.SymmetricConformation, 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.symmetry.SymmetricConformation, 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.symmetry.SymmetricConformation, 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

Append a new conformation by a jump; clones this append to all copies

C++: core::conformation::symmetry::SymmetricConformation::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(*args, **kwargs)

Overloaded function.

  1. prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

Prepend a new residue after a given position in the pose

C++: core::conformation::symmetry::SymmetricConformation::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

recalculate_transforms(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation) None

C++: core::conformation::symmetry::SymmetricConformation::recalculate_transforms() const –> 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.symmetry.SymmetricConformation, seqpos: int, new_rsd: pyrosetta.rosetta.core.conformation.Residue, orient_backbone: bool) -> None

replace residue

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

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

C++: core::conformation::symmetry::SymmetricConformation::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(*args, **kwargs)

Overloaded function.

  1. safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. safely_append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

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

safely_prepend_polymer_residue_before_seqpos(*args, **kwargs)

Overloaded function.

  1. safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int) -> None

  2. safely_prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seqpos: int, build_ideal_geometry: bool) -> None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, other: pyrosetta.rosetta.core.conformation.Conformation) -> bool

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

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, setting: float) None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, setting: float) None

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

set_dof(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, id: pyrosetta.rosetta.core.id.DOF_ID, setting: float) None

DOF

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, jump_number: int, new_jump: core::kinematics::Jump) -> None

JUMPS

set a jump

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

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

set a jump

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, seqpos: int, setting: str) None

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, id: core::id::TorsionID, setting: float) None

BONDS/TORSIONS

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, 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.symmetry.SymmetricConformation, 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

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, id: pyrosetta.rosetta.core.id.AtomID, position: pyrosetta.rosetta.numeric.xyzVector_double_t) None

Symmetric set_xyz

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetricConformation, 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, in addition to ALL clones

C++: core::conformation::symmetry::SymmetricConformation::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.symmetry.SymmetryInfo

Bases: pybind11_builtins.pybind11_object

add_bb_clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, base_pos: int, clone_pos: int) None

C++: core::conformation::symmetry::SymmetryInfo::add_bb_clone(const unsigned long, const unsigned long) –> void

add_chi_clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, base_pos: int, clone_pos: int) None

C++: core::conformation::symmetry::SymmetryInfo::add_chi_clone(const unsigned long, const unsigned long) –> void

add_jump_clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, base_pos: int, clone_jump: int, wt: float) None

C++: core::conformation::symmetry::SymmetryInfo::add_jump_clone(const unsigned long, const unsigned long, const double) –> void

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, : pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

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

atom_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: pyrosetta.rosetta.core.id.AtomID) bool

C++: core::conformation::symmetry::SymmetryInfo::atom_is_independent(const class core::id::AtomID &) const –> bool

bb_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) pyrosetta.rosetta.utility.vector1_unsigned_long

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

bb_follows(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) int

C++: core::conformation::symmetry::SymmetryInfo::bb_follows(const unsigned long) const –> unsigned long

bb_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) bool

C++: core::conformation::symmetry::SymmetryInfo::bb_is_independent(const unsigned long) const –> bool

chi_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) pyrosetta.rosetta.utility.vector1_unsigned_long

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

chi_follows(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) int

C++: core::conformation::symmetry::SymmetryInfo::chi_follows(const unsigned long) const –> unsigned long

chi_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) bool

C++: core::conformation::symmetry::SymmetryInfo::chi_is_independent(const unsigned long) const –> bool

clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo

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

contiguous_monomers(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) bool

C++: core::conformation::symmetry::SymmetryInfo::contiguous_monomers() const –> bool

dependent_atoms(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: pyrosetta.rosetta.core.id.AtomID) pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: core::conformation::symmetry::SymmetryInfo::dependent_atoms(const class core::id::AtomID &) const –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

dependent_dofs(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: pyrosetta.rosetta.core.id.DOF_ID, conf: pyrosetta.rosetta.core.conformation.Conformation) pyrosetta.rosetta.utility.vector1_core_id_DOF_ID

Returns a list of dofs that depend on id. Inefficient – creates list anew each time.

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

dependent_torsions(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: core::id::TorsionID) pyrosetta.rosetta.utility.vector1_core_id_TorsionID

Returns a list of dofs that depend on id. Inefficient – creates list anew each time.

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

deriv_multiply(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res1: int, res2: int) float

C++: core::conformation::symmetry::SymmetryInfo::deriv_multiply(const unsigned long, const unsigned long) const –> double

dof_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: pyrosetta.rosetta.core.id.DOF_ID, conf: pyrosetta.rosetta.core.conformation.Conformation) bool

C++: core::conformation::symmetry::SymmetryInfo::dof_is_independent(const class core::id::DOF_ID &, const class core::conformation::Conformation &) const –> bool

equivalent_residue_on_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, subunit_index: int, residue_id: int) int
What is the equivalent residue on a particular subunit for the given residue? The

logic here mimics the logic in subunit index in terms of subunit numbering.

C++: core::conformation::symmetry::SymmetryInfo::equivalent_residue_on_subunit(unsigned long, unsigned long) const –> unsigned long

fa_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) bool

C++: core::conformation::symmetry::SymmetryInfo::fa_is_independent(const unsigned long) const –> bool

get_asymmetric_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res: int) int

C++: core::conformation::symmetry::SymmetryInfo::get_asymmetric_seqpos(const unsigned long) const –> unsigned long

get_component(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, i: int) str

C++: core::conformation::symmetry::SymmetryInfo::get_component(unsigned long) const –> char

get_component_bounds(*args, **kwargs)

Overloaded function.

  1. get_component_bounds(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t

C++: core::conformation::symmetry::SymmetryInfo::get_component_bounds() const –> const class std::map<char, struct std::pair<unsigned long, unsigned long>, struct std::less<char>, class std::allocator<struct std::pair<const char, struct std::pair<unsigned long, unsigned long> > > > &

  1. get_component_bounds(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, c: str) -> Tuple[int, int]

C++: core::conformation::symmetry::SymmetryInfo::get_component_bounds(char) const –> const struct std::pair<unsigned long, unsigned long> &

get_component_lower_bound(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, c: str) int

C++: core::conformation::symmetry::SymmetryInfo::get_component_lower_bound(char) const –> unsigned long

get_component_of_residue(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, ir: int) str

C++: core::conformation::symmetry::SymmetryInfo::get_component_of_residue(unsigned long) const –> char

get_component_upper_bound(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, c: str) int

C++: core::conformation::symmetry::SymmetryInfo::get_component_upper_bound(char) const –> unsigned long

get_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.utility.vector1_char

C++: core::conformation::symmetry::SymmetryInfo::get_components() const –> const class utility::vector1<char, class std::allocator<char> > &

get_dof_derivative_weight(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: pyrosetta.rosetta.core.id.DOF_ID, conf: pyrosetta.rosetta.core.conformation.Conformation) float

C++: core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(const class core::id::DOF_ID &, const class core::conformation::Conformation &) const –> double

get_dofs(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof

C++: core::conformation::symmetry::SymmetryInfo::get_dofs() const –> const class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > > &

get_jump_name(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, i: int) str

C++: core::conformation::symmetry::SymmetryInfo::get_jump_name(unsigned long) const –> std::string

get_jump_name_to_components(*args, **kwargs)

Overloaded function.

  1. get_jump_name_to_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t

C++: core::conformation::symmetry::SymmetryInfo::get_jump_name_to_components() const –> const class std::map<std::string, class utility::vector1<char, class std::allocator<char> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<char, class std::allocator<char> > > > > &

  1. get_jump_name_to_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, jname: str) -> pyrosetta.rosetta.utility.vector1_char

C++: core::conformation::symmetry::SymmetryInfo::get_jump_name_to_components(const std::string &) const –> const class utility::vector1<char, class std::allocator<char> > &

get_jump_name_to_subunits(*args, **kwargs)

Overloaded function.

  1. get_jump_name_to_subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: core::conformation::symmetry::SymmetryInfo::get_jump_name_to_subunits() const –> const class std::map<std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &

  1. get_jump_name_to_subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, jname: str) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::conformation::symmetry::SymmetryInfo::get_jump_name_to_subunits(const std::string &) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_jump_num(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, i: str) int

C++: core::conformation::symmetry::SymmetryInfo::get_jump_num(std::string) const –> unsigned long

get_njumps_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::get_njumps_subunit() const –> unsigned long

get_nres_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::get_nres_subunit() const –> unsigned long

get_num_components(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::get_num_components() const –> const unsigned long &

get_slide_info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo

C++: core::conformation::symmetry::SymmetryInfo::get_slide_info() const –> class core::conformation::symmetry::SymSlideInfo

get_subunit_name_to_component(*args, **kwargs)

Overloaded function.

  1. get_subunit_name_to_component(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> pyrosetta.rosetta.std.map_std_string_char

C++: core::conformation::symmetry::SymmetryInfo::get_subunit_name_to_component() const –> const class std::map<std::string, char, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, char> > > &

  1. get_subunit_name_to_component(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, vname: str) -> str

C++: core::conformation::symmetry::SymmetryInfo::get_subunit_name_to_component(const std::string &) const –> char

get_use_symmetry(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) bool

C++: core::conformation::symmetry::SymmetryInfo::get_use_symmetry() const –> bool

independent_residues(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) pyrosetta.rosetta.utility.vector1_bool

C++: core::conformation::symmetry::SymmetryInfo::independent_residues() const –> class utility::vector1<bool, class std::allocator<bool> >

init_defaults(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) None

C++: core::conformation::symmetry::SymmetryInfo::init_defaults() –> void

initialize(*args, **kwargs)

Overloaded function.

  1. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) -> None

  2. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces: int) -> None

  3. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces: int, type: str) -> None

C++: core::conformation::symmetry::SymmetryInfo::initialize(const unsigned long, const unsigned long, const unsigned long, const unsigned long, class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > >, const unsigned long, class utility::vector1<double, class std::allocator<double> >, class core::conformation::symmetry::SymSlideInfo, const unsigned long, const std::string &) –> void

  1. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, jump_clones: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo) -> None

  2. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, jump_clones: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces: int) -> None

  3. initialize(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_monomer: int, njump_monomer: int, N: int, num_virtual: int, jump_clones: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof, score_subunit: int, score_multiply: pyrosetta.rosetta.utility.vector1_double, slide_info: pyrosetta.rosetta.core.conformation.symmetry.SymSlideInfo, num_interfaces: int, type: str) -> None

C++: core::conformation::symmetry::SymmetryInfo::initialize(const unsigned long, const unsigned long, const unsigned long, const unsigned long, class std::map<unsigned long, class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > > > >, class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > >, const unsigned long, class utility::vector1<double, class std::allocator<double> >, class core::conformation::symmetry::SymSlideInfo, const unsigned long, const std::string &) –> void

interface_number(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res1: int, res2: int) int

C++: core::conformation::symmetry::SymmetryInfo::interface_number(const unsigned long, const unsigned long) const –> unsigned long

is_asymmetric_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res: int) bool

C++: core::conformation::symmetry::SymmetryInfo::is_asymmetric_seqpos(const unsigned long) const –> bool

is_virtual(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) bool

C++: core::conformation::symmetry::SymmetryInfo::is_virtual(const unsigned long) const –> bool

jump_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, base_jump: int) pyrosetta.rosetta.utility.vector1_unsigned_long

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

jump_follows(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) int

C++: core::conformation::symmetry::SymmetryInfo::jump_follows(const unsigned long) const –> unsigned long

jump_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) bool

C++: core::conformation::symmetry::SymmetryInfo::jump_is_independent(const unsigned long) const –> bool

last_independent_residue(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::last_independent_residue() const –> unsigned long

map_symmetric_res_pairs(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res1: int, res2: int, conf: pyrosetta.rosetta.core.conformation.Conformation) pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t

C++: core::conformation::symmetry::SymmetryInfo::map_symmetric_res_pairs(unsigned long, unsigned long, const class core::conformation::Conformation &) const –> class std::vector<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

num_bb_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_bb_clones() const –> unsigned long

num_chi_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_chi_clones() const –> unsigned long

num_independent_residues(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_independent_residues() const –> unsigned long

num_interfaces(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_interfaces() const –> unsigned long

num_jump_clones(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_jump_clones() const –> unsigned long

num_slidablejumps(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_slidablejumps() const –> unsigned long

num_total_residues(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_total_residues() const –> unsigned long

num_total_residues_with_pseudo(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_total_residues_with_pseudo() const –> unsigned long

num_total_residues_without_pseudo(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo() const –> unsigned long

num_virtuals(*args, **kwargs)

Overloaded function.

  1. num_virtuals(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> int

C++: core::conformation::symmetry::SymmetryInfo::num_virtuals() const –> unsigned long

  1. num_virtuals(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, setting: int) -> None

C++: core::conformation::symmetry::SymmetryInfo::num_virtuals(const unsigned long) –> void

read_silent_struct(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, filename: str) bool

C++: core::conformation::symmetry::SymmetryInfo::read_silent_struct(const std::string &) –> bool

reset_score_multiply_to_reasonable_default(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) bool

C++: core::conformation::symmetry::SymmetryInfo::reset_score_multiply_to_reasonable_default() –> bool

resize_asu(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres_new: int) None

C++: core::conformation::symmetry::SymmetryInfo::resize_asu(unsigned long) –> void

score_multiply(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res1: int, res2: int) float

C++: core::conformation::symmetry::SymmetryInfo::score_multiply(const unsigned long, const unsigned long) const –> double

score_multiply_factor(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::score_multiply_factor() const –> unsigned long

set_dofs(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) None

C++: core::conformation::symmetry::SymmetryInfo::set_dofs(const class std::map<unsigned long, class core::conformation::symmetry::SymDof, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class core::conformation::symmetry::SymDof> > > &) –> void

set_flat_score_multiply(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nres: int, factor: int) None

C++: core::conformation::symmetry::SymmetryInfo::set_flat_score_multiply(const unsigned long, const unsigned long) –> void

set_jump_name(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, i: int, : str) None

C++: core::conformation::symmetry::SymmetryInfo::set_jump_name(unsigned long, std::string) –> void

set_multicomponent_info(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, num_components: int, components: pyrosetta.rosetta.utility.vector1_char, component_bounds: pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t, name2component: pyrosetta.rosetta.std.map_std_string_char, jname2component: pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t, jname2subunits: pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) None

C++: core::conformation::symmetry::SymmetryInfo::set_multicomponent_info(const unsigned long &, const class utility::vector1<char, class std::allocator<char> > &, const class std::map<char, struct std::pair<unsigned long, unsigned long>, struct std::less<char>, class std::allocator<struct std::pair<const char, struct std::pair<unsigned long, unsigned long> > > > &, const class std::map<std::string, char, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, char> > > &, const class std::map<std::string, class utility::vector1<char, class std::allocator<char> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<char, class std::allocator<char> > > > > &, const class std::map<std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &) –> void

set_nres_subunit(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, setting: int) None

C++: core::conformation::symmetry::SymmetryInfo::set_nres_subunit(const unsigned long) –> void

set_score_multiply(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, res: int, factor: int) None

C++: core::conformation::symmetry::SymmetryInfo::set_score_multiply(const unsigned long, const unsigned long) –> void

set_score_multiply_from_subunit_factors(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, score_multiply_vector_subunit: pyrosetta.rosetta.utility.vector1_double, nres_subunit: int, n_subunits: int) None

C++: core::conformation::symmetry::SymmetryInfo::set_score_multiply_from_subunit_factors(const class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const unsigned long) –> void

set_use_symmetry(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, setting: bool) None

C++: core::conformation::symmetry::SymmetryInfo::set_use_symmetry(bool) –> void

subunit_index(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, seqpos: int) int

What subunit does a particular residue come from?

C++: core::conformation::symmetry::SymmetryInfo::subunit_index(const unsigned long) const –> unsigned long

subunits(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) int

C++: core::conformation::symmetry::SymmetryInfo::subunits() const –> unsigned long

torsion_changes_move_other_monomers(*args, **kwargs)

Overloaded function.

  1. torsion_changes_move_other_monomers(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> bool

C++: core::conformation::symmetry::SymmetryInfo::torsion_changes_move_other_monomers() const –> bool

  1. torsion_changes_move_other_monomers(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, setting: bool) -> None

C++: core::conformation::symmetry::SymmetryInfo::torsion_changes_move_other_monomers(const bool) –> void

torsion_is_independent(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, id: core::id::TorsionID) bool

C++: core::conformation::symmetry::SymmetryInfo::torsion_is_independent(const class core::id::TorsionID &) const –> bool

update_nmonomer_jumps(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, nmonomer_new: int) None

C++: core::conformation::symmetry::SymmetryInfo::update_nmonomer_jumps(unsigned long) –> void

update_score_multiply_factor(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) None

C++: core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor() –> void

write_silent_struct(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, filename: str) bool

C++: core::conformation::symmetry::SymmetryInfo::write_silent_struct(const std::string &) –> bool

class pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform, : pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform) pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform

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

clone(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform) pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform

Clone operator.

Copy this object and return an owning pointer to the copy.

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

ht(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform) pyrosetta.rosetta.numeric.HomogeneousTransform_double_t

Get the HomogeneousTransform matrix.

C++: core::conformation::symmetry::SymmetryTransform::ht() const –> const class numeric::HomogeneousTransform<double> &

mirror_z(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform) bool

Get whether this HomogeneousTransform mirrors aout the z-axis or not.

C++: core::conformation::symmetry::SymmetryTransform::mirror_z() const –> bool

set_mirror_z(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform, val: bool) None

Set whether this HomogeneousTransform mirrors about the z-axis or not.

C++: core::conformation::symmetry::SymmetryTransform::set_mirror_z(const bool) –> void

class pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate

Bases: pybind11_builtins.pybind11_object

add_coordinate_from_string(*args, **kwargs)

Overloaded function.

  1. add_coordinate_from_string(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate, coords: pyrosetta.rosetta.utility.vector1_std_string) -> None

  2. add_coordinate_from_string(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate, coords: pyrosetta.rosetta.utility.vector1_std_string, coord_start: int) -> None

C++: core::conformation::symmetry::VirtualCoordinate::add_coordinate_from_string(class utility::vector1<std::string, class std::allocator<std::string > >, unsigned long) –> void

assign(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate, src: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate) pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate

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

get_mirror_z(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate) bool

C++: core::conformation::symmetry::VirtualCoordinate::get_mirror_z() const –> bool

get_origin(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::symmetry::VirtualCoordinate::get_origin() –> class numeric::xyzVector<double> &

get_x(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::symmetry::VirtualCoordinate::get_x() –> class numeric::xyzVector<double> &

get_y(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::symmetry::VirtualCoordinate::get_y() –> class numeric::xyzVector<double> &

set_mirror_z(self: pyrosetta.rosetta.core.conformation.symmetry.VirtualCoordinate, val: bool) None

C++: core::conformation::symmetry::VirtualCoordinate::set_mirror_z(bool) –> void

pyrosetta.rosetta.core.conformation.symmetry.calculate_inverting_virtuals(ft: pyrosetta.rosetta.core.kinematics.FoldTree, conf: pyrosetta.rosetta.core.conformation.Conformation, symm_info: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, mirrored_subs: pyrosetta.rosetta.utility.vector1_bool, mirrored_jumps: pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t) None

A very specific helper function that counts the number of mirror ops from root->each subunit

C++: core::conformation::symmetry::calculate_inverting_virtuals(const class core::kinematics::FoldTree &, const class core::conformation::Conformation &, const class core::conformation::symmetry::SymmetryInfo &, class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<struct std::pair<bool, bool>, class std::allocator<struct std::pair<bool, bool> > > &) –> void

class pyrosetta.rosetta.core.conformation.symmetry.dof_type

Bases: pybind11_builtins.pybind11_object

Members:

X_DOF

Y_DOF

Z_DOF

X_ANGLE_DOF

Y_ANGLE_DOF

Z_ANGLE_DOF

X_ANGLE_DOF = <dof_type.X_ANGLE_DOF: 4>
X_DOF = <dof_type.X_DOF: 1>
Y_ANGLE_DOF = <dof_type.Y_ANGLE_DOF: 5>
Y_DOF = <dof_type.Y_DOF: 2>
Z_ANGLE_DOF = <dof_type.Z_ANGLE_DOF: 6>
Z_DOF = <dof_type.Z_DOF: 3>
property name
pyrosetta.rosetta.core.conformation.symmetry.get_asymm_unit_fold_tree(conf: pyrosetta.rosetta.core.conformation.Conformation) pyrosetta.rosetta.core.kinematics.FoldTree

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

pyrosetta.rosetta.core.conformation.symmetry.get_chain_id_string() str

C++: core::conformation::symmetry::get_chain_id_string() –> std::string

pyrosetta.rosetta.core.conformation.symmetry.is_mirror_symmetric(conf: pyrosetta.rosetta.core.conformation.Conformation) bool

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

pyrosetta.rosetta.core.conformation.symmetry.is_symmetric(*args, **kwargs)

Overloaded function.

  1. is_symmetric(conf: pyrosetta.rosetta.core.conformation.Conformation) -> bool

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

  1. is_symmetric(symminfo: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo) -> bool

C++: core::conformation::symmetry::is_symmetric(const class core::conformation::symmetry::SymmetryInfo &) –> bool

pyrosetta.rosetta.core.conformation.symmetry.recenter(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData) None

C++: core::conformation::symmetry::recenter(class core::conformation::Conformation &, class core::conformation::symmetry::SymmData &) –> void

pyrosetta.rosetta.core.conformation.symmetry.replaced_symmetric_foldtree_with_new_monomer(symm_f: pyrosetta.rosetta.core.kinematics.FoldTree, symmetry_info: pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo, monomer_f: pyrosetta.rosetta.core.kinematics.FoldTree) pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(class core::kinematics::FoldTree, class core::conformation::symmetry::SymmetryInfo, class core::kinematics::FoldTree) –> class core::kinematics::FoldTree

pyrosetta.rosetta.core.conformation.symmetry.residue_center_of_mass(conformation: pyrosetta.rosetta.core.conformation.Conformation, start: int, stop: int) int

C++: core::conformation::symmetry::residue_center_of_mass(const class core::conformation::Conformation &, const int, const int) –> int

pyrosetta.rosetta.core.conformation.symmetry.return_nearest_residue(conformation: pyrosetta.rosetta.core.conformation.Conformation, begin: int, end: int, center: pyrosetta.rosetta.numeric.xyzVector_double_t) int

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

pyrosetta.rosetta.core.conformation.symmetry.set_asymm_unit_fold_tree(p: pyrosetta.rosetta.core.conformation.Conformation, f: pyrosetta.rosetta.core.kinematics.FoldTree) None

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

pyrosetta.rosetta.core.conformation.symmetry.set_fold_tree_from_symm_data(*args, **kwargs)

Overloaded function.

  1. set_fold_tree_from_symm_data(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData) -> pyrosetta.rosetta.core.kinematics.FoldTree

  2. set_fold_tree_from_symm_data(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData, conf2pdb_chain: pyrosetta.rosetta.std.map_unsigned_long_char) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::conformation::symmetry::set_fold_tree_from_symm_data(class core::conformation::Conformation &, class core::conformation::symmetry::SymmData &, class std::map<unsigned long, char, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, char> > >) –> class core::kinematics::FoldTree

pyrosetta.rosetta.core.conformation.symmetry.setup_symmetric_conformation(*args, **kwargs)

Overloaded function.

  1. setup_symmetric_conformation(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData) -> pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation

  2. setup_symmetric_conformation(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData, conf2pdb_chain: pyrosetta.rosetta.std.map_unsigned_long_char) -> pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation

C++: core::conformation::symmetry::setup_symmetric_conformation(class core::conformation::Conformation &, class core::conformation::symmetry::SymmData &, class std::map<unsigned long, char, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, char> > >) –> class std::shared_ptr<class core::conformation::symmetry::SymmetricConformation>

pyrosetta.rosetta.core.conformation.symmetry.shift_jump_numbers_in_dofs(src_conformation: pyrosetta.rosetta.core.conformation.Conformation, shift: int) None

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

pyrosetta.rosetta.core.conformation.symmetry.show_foldtree(symm_conf: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, symdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData, chain2range: pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t) str

C++: core::conformation::symmetry::show_foldtree(const class core::conformation::symmetry::SymmetricConformation &, const class core::conformation::symmetry::SymmData &, const class std::map<char, struct std::pair<unsigned long, unsigned long>, struct std::less<char>, class std::allocator<struct std::pair<const char, struct std::pair<unsigned long, unsigned long> > > > &) –> std::string

pyrosetta.rosetta.core.conformation.symmetry.symmetrize_fold_tree(conf: pyrosetta.rosetta.core.conformation.Conformation, f: pyrosetta.rosetta.core.kinematics.FoldTree) None
Converts an asymmetric foldtree (f) with virtual root into a

symmetric foldtree compatible with symmetric conformation (conf)

  • A symmetric conformation

  • An asymmetric foldtree. This foldtree MUST have a virtual root

This function does not require the symm data

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