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: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → None¶

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

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

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

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

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

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

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

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

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

append_polymer_residue_after_seqpos(*args, **kwargs)¶

Overloaded function.

append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int) -> None
append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int, 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, bool) –> void

append_residue_by_bond(*args, **kwargs)¶

Overloaded function.

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

Append a new residue by a bond.

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

append_residue_by_jump(*args, **kwargs)¶

Overloaded function.

append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None
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
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
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 &, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, bool) –> void

apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.conformation.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.

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
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.

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
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.

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 &

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

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

bonded_neighbor_all_res(*args, **kwargs)¶

Overloaded function.

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

get all atoms bonded to another

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

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

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

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

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

are signals being blocked and buffered?

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

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

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

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

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

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

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

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

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

chain_endings(*args, **kwargs)¶

Overloaded function.

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

Returns the list of (chain number) chain endings

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

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

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

Sets the list of (chain number) chain endings

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

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

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

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

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

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

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

Check that a new membrane position is valid

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

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

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

clear data

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

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

Safely detaches any tree observers and clears it to null.

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

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

clear all observers

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

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

Delete the list of ParametersSetOP objects.

Vikram K. Mulligan (vmullig.edu)

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

clone(self: pyrosetta.rosetta.core.conformation.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.

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

Return true if this conformation contains any carbohydrate residues.

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

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

Set whether this conformation contains any carbohydrate residues.

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

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

copy a stretch of coordinates/torsions from another Conformation

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

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

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

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

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

debug_pause(*args, **kwargs)¶

Overloaded function.

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

wait for stdin after sending a GeneralEvent signal

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

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

waiting for stdin after sending a GeneralEvent signal?

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

debug_residue_torsions(*args, **kwargs)¶

Overloaded function.

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

debugging

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

declare_chemical_bond(self: pyrosetta.rosetta.core.conformation.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(unsigned long, const class std::basic_string<char> &, unsigned long, const class std::basic_string<char> &) –> void

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

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

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

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

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

Delete polymer residue at the given sequence position

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

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

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

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

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

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

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

detached_copy(self: pyrosetta.rosetta.core.conformation.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.

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

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

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

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

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

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

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

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

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

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

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

Get the DOF_ID defined by these atoms.

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

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

Get the DOF_ID corresponding to this TorsionID.

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

downstream_jump_stub(self: pyrosetta.rosetta.core.conformation.Conformation, jump_number: int) → 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(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶

Get the transformation controlling resid i

C++: core::conformation::symmetry::SymmetricConformation::get_transformation(unsigned long) –> 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(unsigned long) –> void

insert_conformation_by_jump(*args, **kwargs)¶

Overloaded function.

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
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
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
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 &, unsigned long, unsigned long, unsigned long, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

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

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

insert_residue_by_bond(*args, **kwargs)¶

Overloaded function.

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

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

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

insert_residue_by_jump(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

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

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

convenience test for residue_type_set mode

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

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

convenience test for residue_type_set mode

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

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

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

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

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

convenience test for residue_type_set mode

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

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

jump(*args, **kwargs)¶

Overloaded function.

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

Returns the Jump with jump number <jump_number>

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

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

access a jump

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

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

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

Returns the const MembraneInfo object in conformation

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

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

modifiable_residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

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

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

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

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

Get the number of parameters sets defined for this Conformation.

Vikram K. Mulligan (vmullig.edu)

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

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

Returns the number of chains

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

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

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

Access one of the ParametersSets objects linked to this Conformation.

Vikram K. Mulligan (vmullig.edu)

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

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

prepend_polymer_residue_before_seqpos(*args, **kwargs)¶

Overloaded function.

prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int) -> None
prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int, 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, bool) –> void

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

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

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

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

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

Rebuilds the atoms that are 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(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() –> void

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

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

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

replace_residue(*args, **kwargs)¶

Overloaded function.

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

replace residue

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

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

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.

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

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

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

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

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

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

reset the structure_moved_ bool

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

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

access one of the residues

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

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

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

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

access one of the residues, using COP

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

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

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

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

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

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

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

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

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

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

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

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

residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

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

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

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

residue_typeset_mode(*args, **kwargs)¶

Overloaded function.

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

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

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

safely_append_polymer_residue_after_seqpos(*args, **kwargs)¶

Overloaded function.

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

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

safely_prepend_polymer_residue_before_seqpos(*args, **kwargs)¶

Overloaded function.

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

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

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 &, 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 &, 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 &, 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 &, double) –> void

set_jump(*args, **kwargs)¶

Overloaded function.

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(int, const class core::kinematics::Jump &) –> void

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(unsigned long, char) –> void

set_stub_transform(self: pyrosetta.rosetta.core.conformation.Conformation, stub_id1: pyrosetta.rosetta.core.id.StubID, stub_id2: pyrosetta.rosetta.core.id.StubID, target_rt: 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 &, double) –> void

set_torsion_angle(*args, **kwargs)¶

Overloaded function.

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
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 &, double, 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.

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

Show residue connections for debugging purposes.

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

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

Show residue connections for debugging purposes.

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

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

Returns the number of residues in the Conformation

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

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

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

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

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

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

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

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

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

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

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

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

allow signals to be sent

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

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

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

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

Generate a domain_map from the current dof/xyz moved data

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

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

Update Normal, Center in the Membrane

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

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

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

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

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

update_orbital_coords(*args, **kwargs)¶

Overloaded function.

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

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

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

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

update_polymeric_connection(*args, **kwargs)¶

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.core.conformation.symmetry.SlideType¶

Bases: pybind11_builtins.pybind11_object

Members:

SEQUENTIAL

ORDERED_SEQUENTIAL

RANDOM

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: pyrosetta.rosetta.core.conformation.parametric.ParametersSet) → None¶

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

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

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

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

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

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

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

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

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

append_polymer_residue_after_seqpos(*args, **kwargs)¶

Overloaded function.

append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int) -> None
append_polymer_residue_after_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int, 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, bool) –> void

append_residue_by_bond(*args, **kwargs)¶

Overloaded function.

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

Append a new residue by a bond.

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

append_residue_by_jump(*args, **kwargs)¶

Overloaded function.

append_residue_by_jump(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, anchor_residue: int) -> None
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
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
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 &, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, bool) –> void

apply_transform_Rx_plus_v(self: pyrosetta.rosetta.core.conformation.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.

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
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.

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
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.

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 &

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

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

bonded_neighbor_all_res(*args, **kwargs)¶

Overloaded function.

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

get all atoms bonded to another

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

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

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

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

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

are signals being blocked and buffered?

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

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

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

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

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

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

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

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

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

chain_endings(*args, **kwargs)¶

Overloaded function.

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

Returns the list of (chain number) chain endings

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

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

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

Sets the list of (chain number) chain endings

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

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

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

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

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

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

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

Check that a new membrane position is valid

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

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

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

clear data

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

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

Safely detaches any tree observers and clears it to null.

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

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

clear all observers

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

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

Delete the list of ParametersSetOP objects.

Vikram K. Mulligan (vmullig.edu)

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

clone(self: pyrosetta.rosetta.core.conformation.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.

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

Return true if this conformation contains any carbohydrate residues.

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

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

Set whether this conformation contains any carbohydrate residues.

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

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

copy a stretch of coordinates/torsions from another Conformation

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

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

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

to the current Conformation object.

Vikram K. Mulligan (vmullig.edu)

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

debug_pause(*args, **kwargs)¶

Overloaded function.

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

wait for stdin after sending a GeneralEvent signal

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

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

waiting for stdin after sending a GeneralEvent signal?

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

debug_residue_torsions(*args, **kwargs)¶

Overloaded function.

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

debugging

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

declare_chemical_bond(self: pyrosetta.rosetta.core.conformation.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(unsigned long, const class std::basic_string<char> &, unsigned long, const class std::basic_string<char> &) –> void

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

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

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

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

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

Delete polymer residue at the given sequence position

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

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

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

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

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

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

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

detached_copy(self: pyrosetta.rosetta.core.conformation.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.

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

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

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

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

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

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

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

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

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

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

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

Get the DOF_ID defined by these atoms.

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

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

Get the DOF_ID corresponding to this TorsionID.

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

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

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

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

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

Returns true if this conformation does not have any residues

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

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

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

Assigns disulfide bonds based on a pre-determined list

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

fold_tree(*args, **kwargs)¶

Overloaded function.

fold_tree(self: pyrosetta.rosetta.core.conformation.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

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(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, resid: int) → pyrosetta.rosetta.numeric.HomogeneousTransform_double_t¶

Get the transformation controlling resid i

C++: core::conformation::symmetry::SymmetricConformation::get_transformation(unsigned long) –> 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(unsigned long) –> void

insert_conformation_by_jump(*args, **kwargs)¶

Overloaded function.

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
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
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
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 &, unsigned long, unsigned long, unsigned long, unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

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

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

insert_residue_by_bond(*args, **kwargs)¶

Overloaded function.

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

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

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

insert_residue_by_jump(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

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

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

convenience test for residue_type_set mode

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

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

convenience test for residue_type_set mode

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

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

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

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

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

convenience test for residue_type_set mode

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

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

jump(*args, **kwargs)¶

Overloaded function.

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

Returns the Jump with jump number <jump_number>

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

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

access a jump

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

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

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

Returns the const MembraneInfo object in conformation

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

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

modifiable_residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

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

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

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

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

Get the number of parameters sets defined for this Conformation.

Vikram K. Mulligan (vmullig.edu)

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

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

Returns the number of chains

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

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

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

Access one of the ParametersSets objects linked to this Conformation.

Vikram K. Mulligan (vmullig.edu)

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

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

prepend_polymer_residue_before_seqpos(*args, **kwargs)¶

Overloaded function.

prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int) -> None
prepend_polymer_residue_before_seqpos(self: pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation, new_rsd: pyrosetta.rosetta.core.conformation.Residue, seq_pos: int, 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, bool) –> void

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

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

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

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

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

Rebuilds the atoms that are 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(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() –> void

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

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

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

replace_residue(*args, **kwargs)¶

Overloaded function.

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

replace residue

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

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

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

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

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

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

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

forget all the structure modifications

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

reset_residue_type_set_for_conf(*args, **kwargs)¶

Overloaded function.

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