| | |
- AddPyMolObserver(...)
- AddPyMolObserver( (Pose)p [, (bool)keep_history=False [, (float)update_interval=0]]) -> PyMolObserver :
Helper function that create PyMolObserver Object and add it to the give Pose.
This is the most likely the only function that you need to call...
C++ signature :
boost::shared_ptr<protocols::moves::PyMolObserver> AddPyMolObserver(core::pose::Pose {lvalue} [,bool=False [,double=0]])
- AddPyMolObserver_to_conformation(...)
- AddPyMolObserver_to_conformation( (Pose)p [, (bool)keep_history=False [, (float)update_interval=0]]) -> PyMolObserver :
Helper function that create PyMolObserver Object and add it to the give Pose conformation object so pymol only updates on conformation changes.
C++ signature :
boost::shared_ptr<protocols::moves::PyMolObserver> AddPyMolObserver_to_conformation(core::pose::Pose {lvalue} [,bool=False [,double=0]])
- AddPyMolObserver_to_energies(...)
- AddPyMolObserver_to_energies( (Pose)p [, (bool)keep_history=False [, (float)update_interval=0]]) -> PyMolObserver :
Helper function that create PyMolObserver Object and add it to the give Pose energies object so pymol only updates on energy changes.
C++ signature :
boost::shared_ptr<protocols::moves::PyMolObserver> AddPyMolObserver_to_energies(core::pose::Pose {lvalue} [,bool=False [,double=0]])
- Broker_main(...)
- Broker_main() -> None :
Initiates AbrelaxMover using the job distribution (jd2)
C++ signature :
void Broker_main()
- CA_gdtmm(...)
- CA_gdtmm( (Pose)pose1, (Pose)pose2, (object)residue_selection) -> float :
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
C++ signature :
double CA_gdtmm(core::pose::Pose,core::pose::Pose,std::list<unsigned long, std::allocator<unsigned long> >)
CA_gdtmm( (Pose)pose1, (Pose)pose2, (object)residue_selection, (float)m_1_1, (float)m_2_2, (float)m_3_3, (float)m_4_3, (float)m_7_4) -> float :
core/scoring/rms_util.hh:452
C++ signature :
double CA_gdtmm(core::pose::Pose,core::pose::Pose,std::list<unsigned long, std::allocator<unsigned long> >,double {lvalue},double {lvalue},double {lvalue},double {lvalue},double {lvalue})
CA_gdtmm( (Pose)pose1, (Pose)pose2, (float)m_1_1, (float)m_2_2, (float)m_3_3, (float)m_4_3, (float)m_7_4) -> float :
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2. Also returns the
five components of the gdtmm score.
C++ signature :
double CA_gdtmm(core::pose::Pose,core::pose::Pose,double {lvalue},double {lvalue},double {lvalue},double {lvalue},double {lvalue})
CA_gdtmm( (Pose)pose1, (Pose)pose2) -> float :
Calculate gdtmm score based on the C-alpha positions in pose1 and pose2.
C++ signature :
double CA_gdtmm(core::pose::Pose,core::pose::Pose)
CA_gdtmm( (Pose)pose1, (Pose)pose2, (map_Size_Size)residues) -> float :
Compute the CA RMSD between two poses.
C++ signature :
double CA_gdtmm(core::pose::Pose,core::pose::Pose,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
- CA_gdttm(...)
- CA_gdttm( (Pose)pose1, (Pose)pose2, (float)gdttm_score, (float)gdtha_score) -> None :
core/scoring/rms_util.hh:494
C++ signature :
void CA_gdttm(core::pose::Pose,core::pose::Pose,double {lvalue},double {lvalue})
CA_gdttm( (Pose)pose1, (Pose)pose2, (float)gdttm_score, (float)gdtha_score, (map_Size_Size)residues) -> None :
core/scoring/rms_util.hh:486
C++ signature :
void CA_gdttm(core::pose::Pose,core::pose::Pose,double {lvalue},double {lvalue},std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
CA_gdttm( (Pose)pose1, (Pose)pose2, (float)gdttm_score, (float)gdtha_score, (object)residue_selection) -> None :
Calculate gdttm score based on the C-alpha positions in pose1 and pose2.
C++ signature :
void CA_gdttm(core::pose::Pose,core::pose::Pose,double {lvalue},double {lvalue},std::list<unsigned long, std::allocator<unsigned long> >)
- CA_maxsub(...)
- CA_maxsub( (Pose)pose1, (Pose)pose2, (object)residue_selection [, (float)rms=4.0]) -> int :
core/scoring/rms_util.hh:393
C++ signature :
int CA_maxsub(core::pose::Pose,core::pose::Pose,std::list<unsigned long, std::allocator<unsigned long> > [,double=4.0])
CA_maxsub( (Pose)pose1, (Pose)pose2 [, (float)rms=4.0]) -> int :
Calculates a C-alpha maxsub-based superposition between pose1 and pose2, returns
the number of residues superimposed past a certain threshold. See maxsub.hh and maxsub.cc
for more information.
C++ signature :
int CA_maxsub(core::pose::Pose,core::pose::Pose [,double=4.0])
- CA_rmsd(...)
- CA_rmsd( (Pose)pose1, (Pose)pose2, (object)residue_selection) -> float :
core/scoring/rms_util.hh:331
C++ signature :
double CA_rmsd(core::pose::Pose,core::pose::Pose,std::list<unsigned long, std::allocator<unsigned long> >)
CA_rmsd( (Pose)pose1, (Pose)pose2, (int)start, (int)end, (vector1_Size)exclude) -> float :
core/scoring/rms_util.hh:323
C++ signature :
double CA_rmsd(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,utility::vector1<unsigned long, std::allocator<unsigned long> >)
CA_rmsd( (Pose)pose1, (Pose)pose2 [, (int)start=1 [, (int)end=0]]) -> float :
Compute rmsd for residues between start and end.
If start and end aren't specified, use the entire pose.
C++ signature :
double CA_rmsd(core::pose::Pose,core::pose::Pose [,unsigned long=1 [,unsigned long=0]])
CA_rmsd( (Pose)pose1, (Pose)pose2, (map_Size_Size)residues) -> float :
Compute the CA RMSD between two poses.
C++ signature :
double CA_rmsd(core::pose::Pose,core::pose::Pose,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
- CA_rmsd_symmetric(...)
- CA_rmsd_symmetric( (Pose)pose1, (Pose)pose2) -> float :
core/scoring/rms_util.hh:534
C++ signature :
double CA_rmsd_symmetric(core::pose::Pose,core::pose::Pose)
- DOF_type_is_rb(...)
- DOF_type_is_rb( (DOF_Type)t) -> bool :
//////////////////////////////////////////////////////////////////////////
C++ signature :
bool DOF_type_is_rb(core::id::DOF_Type)
- MembraneEmbed_from_pose(...)
- MembraneEmbed_from_pose( (Pose)pose) -> MembraneEmbed :
Add Const Membrane Embedding to the pose cache
C++ signature :
core::scoring::MembraneEmbed MembraneEmbed_from_pose(core::pose::Pose)
- MembraneTopology_from_pose(...)
- MembraneTopology_from_pose( (Pose)pose) -> MembraneTopology :
core/scoring/MembraneTopology.hh:262
C++ signature :
core::scoring::MembraneTopology MembraneTopology_from_pose(core::pose::Pose)
- Membrane_FAEmbed_from_pose(...)
- Membrane_FAEmbed_from_pose( (Pose)) -> Membrane_FAEmbed :
Grab Const MP Fa Embedding data from the pose cache
C++ signature :
core::scoring::Membrane_FAEmbed Membrane_FAEmbed_from_pose(core::pose::Pose)
- QQQ_CreateMinMover(...)
- QQQ_CreateMinMover() -> Mover :
C++ signature :
boost::shared_ptr<protocols::moves::Mover> QQQ_CreateMinMover()
- QQQ_SubclassTester(...)
- QQQ_SubclassTester( (__CPP_Mover__)arg1) -> None :
C++ signature :
void QQQ_SubclassTester(boost::shared_ptr<protocols::moves::Mover>)
- QQQ_SubclassTester2(...)
- QQQ_SubclassTester2( (__CPP_Mover__)arg1, (Pose)arg2) -> None :
C++ signature :
void QQQ_SubclassTester2(boost::shared_ptr<protocols::moves::Mover>,boost::shared_ptr<core::pose::Pose>)
- Relax_main(...)
- Relax_main( (bool)) -> int :
protocols/relax/relax_main.hh:24
C++ signature :
int Relax_main(bool)
- aa_from_name(...)
- aa_from_name( (str)name) -> AA :
///////////////////////////////////////////////////////
Give an AA string name, return its enum type.
///////////////////////////////////////////////////////
C++ signature :
core::chemical::AA aa_from_name(std::string)
- aa_from_oneletter_code(...)
- aa_from_oneletter_code( (str)onelettercode) -> AA :
////////////////////////////////////////////////////////
give a 1 letter code and return the string name
////////////////////////////////////////////////////////
C++ signature :
core::chemical::AA aa_from_oneletter_code(char)
- addScoresForLoopParts(...)
- addScoresForLoopParts( (Pose)pose, (Loops)loops, (ScoreFunction)scorefxn, (Pose)native_pose, (int)nloops) -> None :
protocols/loops/util.hh:57
C++ signature :
void addScoresForLoopParts(core::pose::Pose {lvalue},protocols::loops::Loops,core::scoring::ScoreFunction,core::pose::Pose {lvalue},unsigned long)
- add_atom(...)
- add_atom( (int)atomno, (int)seqpos, (vec1_vec1_Size)links, (object)atom_ptr, (bool)add_jump_atom) -> Atom :
creat an atom and add it to the residue atom-tree based on information stored in links.
C++ signature :
boost::shared_ptr<core::kinematics::tree::Atom> add_atom(int,int,utility::vector1<utility::vector1<unsigned long, std::allocator<unsigned long> >, std::allocator<utility::vector1<unsigned long, std::allocator<unsigned long> > > >,utility::vector1<boost::shared_ptr<core::kinematics::tree::Atom>, std::allocator<boost::shared_ptr<core::kinematics::tree::Atom> > > {lvalue},bool)
- add_atom_type_set_parameters_from_command_line(...)
- add_atom_type_set_parameters_from_command_line( (str)atom_type_set_tag, (AtomTypeSet)atom_type_set) -> None :
Add additional parameter files not present in <atom-set-name>/extras.txt.
C++ signature :
void add_atom_type_set_parameters_from_command_line(std::string,core::chemical::AtomTypeSet {lvalue})
- add_coordinate_constraints_to_pose(...)
- add_coordinate_constraints_to_pose( (Pose)pose, (Pose)constraint_target_pose, (Loops)exclude_regions) -> None :
protocols/relax/Ramady.hh:27
C++ signature :
void add_coordinate_constraints_to_pose(core::pose::Pose {lvalue},core::pose::Pose,protocols::loops::Loops {lvalue})
- add_cutpoint_variants(...)
- add_cutpoint_variants( (Pose)pose) -> None :
///////////////////////////////////////////////////////////////////////////////
Add cutpoint variants to all the cutpoints in a Pose.
C++ signature :
void add_cutpoint_variants(core::pose::Pose {lvalue})
- add_loop_flank_residues_bb_to_movemap(...)
- add_loop_flank_residues_bb_to_movemap( (Loops)loops, (MoveMap)mm [, (int)flank_size=2]) -> None :
add flank stem residues to the loop movemap
C++ signature :
void add_loop_flank_residues_bb_to_movemap(protocols::loops::Loops,core::kinematics::MoveMap {lvalue} [,unsigned long=2])
- add_lower_terminus_type_to_conformation_residue(...)
- add_lower_terminus_type_to_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
core/conformation/util.hh:151
C++ signature :
void add_lower_terminus_type_to_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)
- add_single_cutpoint_variant(...)
- add_single_cutpoint_variant( (Pose)pose, (int)cutpoint) -> None :
Add cutpoint variants around a single cutpoint (defined by residue number).
C++ signature :
void add_single_cutpoint_variant(core::pose::Pose {lvalue},unsigned long)
add_single_cutpoint_variant( (Pose)pose, (Loop)loop) -> None :
Add cutpoint variants around a single cutpoint (defined by a Loop).
C++ signature :
void add_single_cutpoint_variant(core::pose::Pose {lvalue},protocols::loops::Loop)
- add_upper_terminus_type_to_conformation_residue(...)
- add_upper_terminus_type_to_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
core/conformation/util.hh:158
C++ signature :
void add_upper_terminus_type_to_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)
- add_variant_type_to_conformation_residue(...)
- add_variant_type_to_conformation_residue( (Conformation)conformation, (VariantType)variant_type, (int)seqpos) -> None :
Construct a variant of an existing conformation residue.
C++ signature :
void add_variant_type_to_conformation_residue(core::conformation::Conformation {lvalue},core::chemical::VariantType,unsigned long)
- add_virtual_residue_to_cterm(...)
- add_virtual_residue_to_cterm( (Pose)pose) -> None :
protocols/relax/cst_util.hh:52
C++ signature :
void add_virtual_residue_to_cterm(core::pose::Pose {lvalue})
- all_atom_rmsd(...)
- all_atom_rmsd( (Pose)pose1, (Pose)pose2, (object)residue_selection) -> float :
core/scoring/rms_util.hh:356
C++ signature :
double all_atom_rmsd(core::pose::Pose,core::pose::Pose,std::list<unsigned long, std::allocator<unsigned long> >)
all_atom_rmsd( (Pose)pose1, (Pose)pose2) -> float :
core/scoring/rms_util.hh:337
C++ signature :
double all_atom_rmsd(core::pose::Pose,core::pose::Pose)
- all_atom_rmsd_nosuper(...)
- all_atom_rmsd_nosuper( (Pose)pose1, (Pose)pose2) -> float :
core/scoring/rms_util.hh:349
C++ signature :
double all_atom_rmsd_nosuper(core::pose::Pose,core::pose::Pose)
- all_scatom_rmsd_nosuper(...)
- all_scatom_rmsd_nosuper( (Pose)pose1, (Pose)pose2) -> float :
core/scoring/rms_util.hh:343
C++ signature :
double all_scatom_rmsd_nosuper(core::pose::Pose,core::pose::Pose)
- annotated_atom_graph_from_conformation(...)
- annotated_atom_graph_from_conformation( (Conformation)conformation, (object)pg, (xyzVector_Real)additional_point) -> int :
create a pointgraph which consists of 1 node for every atom, plus 1 additional node which will be added as the last node. The index of the additional node is returned
C++ signature :
unsigned long annotated_atom_graph_from_conformation(core::conformation::Conformation,boost::shared_ptr<core::graph::UpperEdgeGraph<core::conformation::AtomGraphVertexData, core::conformation::AtomGraphEdgeData> >,numeric::xyzVector<double>)
- apply_adducts_to_residue(...)
- apply_adducts_to_residue( (ResidueType)rsd, (vector1_bool)add_mask) -> ResidueType :
Apply adducts to residue using a boolean mask
C++ signature :
boost::shared_ptr<core::chemical::ResidueType> apply_adducts_to_residue(core::chemical::ResidueType,utility::vector1<bool, std::allocator<bool> > {lvalue})
- apply_best_scoring_fragdata(...)
- apply_best_scoring_fragdata( (Pose)pose, (Frame)frame, (ScoreFunction)sfxn) -> None :
goes through all frag_data in the frame and puts the
best scoring one into the pose, i.e. quenches the frame
C++ signature :
void apply_best_scoring_fragdata(core::pose::Pose {lvalue},core::fragment::Frame,core::scoring::ScoreFunction)
- apply_sequence_mapping(...)
- apply_sequence_mapping( (Pose)pose, (str)target_seq, (SequenceMapping)start_mapping) -> None :
protocols/loops/loops_main.hh:325
C++ signature :
void apply_sequence_mapping(core::pose::Pose {lvalue},std::string,core::id::SequenceMapping)
- atom_graph_from_conformation(...)
- atom_graph_from_conformation( (Conformation)conformation, (object)pg) -> None :
core/conformation/AtomGraph.hh:31
C++ signature :
void atom_graph_from_conformation(core::conformation::Conformation,boost::shared_ptr<core::graph::UpperEdgeGraph<core::conformation::AtomGraphVertexData, core::conformation::AtomGraphEdgeData> >)
- atom_id_to_named_atom_id(...)
- atom_id_to_named_atom_id( (AtomID)atom_id, (Residue)rsd) -> NamedAtomID :
core/conformation/util.hh:350
C++ signature :
core::id::NamedAtomID atom_id_to_named_atom_id(core::id::AtomID,core::conformation::Residue)
- automorphic_rmsd(...)
- automorphic_rmsd( (Residue)rsd1, (Residue)rsd2, (bool)superimpose) -> float :
RMSD between residues, accounting for automorphisms
(symmetries). For example if you have something like a tyrosine,
you won't get a higher rmsd just because you flipped the ring 180 degrees (Rocco).
Does NOT include H atoms -- they add lots of extra symmetries.
C++ signature :
double automorphic_rmsd(core::conformation::Residue,core::conformation::Residue,bool)
- bb_rmsd(...)
- bb_rmsd( (Pose)pose1, (Pose)pose2) -> float :
Compute rmsd for only backbone residues (excluding carboxyl oxygen)
C++ signature :
double bb_rmsd(core::pose::Pose,core::pose::Pose)
- bb_rmsd_including_O(...)
- bb_rmsd_including_O( (Pose)pose1, (Pose)pose2) -> float :
Compute rmsd for only backbone residues (including carboxyl oxygen)
C++ signature :
double bb_rmsd_including_O(core::pose::Pose,core::pose::Pose)
- build_chemical_edge(...)
- build_chemical_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
build a sub atom-tree for a chemical edge and attach it to main atom-tree
C++ signature :
void build_chemical_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})
- build_jump_edge(...)
- build_jump_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
build a sub atom-tree for a jump edge and attach it to main atom-tree
C++ signature :
void build_jump_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})
- build_polymer_edge(...)
- build_polymer_edge( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
build a sub atom-tree for a polymer edge and attach it to main atom-tree
C++ signature :
void build_polymer_edge(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})
- build_residue_tree(...)
- build_residue_tree( (object)residues, (Residue)rsd, (FoldTree)fold_tree, (object)atom_ptr) -> None :
build_residue_tree function that uses the foldtree info
also used in build_tree to build the residue tree for the root residue
C++ signature :
void build_residue_tree(utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::kinematics::tree::Atom>, std::allocator<boost::shared_ptr<core::kinematics::tree::Atom> > > {lvalue})
build_residue_tree( (int)root_atomno, (Residue)rsd, (object)atom_ptr, (bool)root_atom_is_jump_atom) -> None :
build the tree of atoms for this residue, anchored at root_atomno
C++ signature :
void build_residue_tree(int,core::conformation::Residue,utility::vector1<boost::shared_ptr<core::kinematics::tree::Atom>, std::allocator<boost::shared_ptr<core::kinematics::tree::Atom> > > {lvalue},bool)
- build_tree(...)
- build_tree( (FoldTree)fold_tree, (object)residues, (object)atom_pointer) -> None :
core/conformation/util.hh:179
C++ signature :
void build_tree(core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> > {lvalue})
- calc_CA_Irmsd(...)
- calc_CA_Irmsd( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms
C++ signature :
double calc_CA_Irmsd(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)
- calc_Fnat(...)
- calc_Fnat( (Pose)pose, (str)list_file, (vector1_int)movable_jumps) -> float :
Calculates the fraction of native contacts from the given native contacts pair list
C++ signature :
double calc_Fnat(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> >)
calc_Fnat( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure
C++ signature :
double calc_Fnat(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)
- calc_Fnonnat(...)
- calc_Fnonnat( (Pose)pose, (str)list_file, (vector1_int)movable_jumps) -> float :
Calculates the fraction of non-native contacts from the given native contacts pari list
C++ signature :
double calc_Fnonnat(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> >)
calc_Fnonnat( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined
as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact
C++ signature :
double calc_Fnonnat(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)
- calc_Irmsd(...)
- calc_Irmsd( (Pose)pose, (Pose)native_pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
Calculates the all-atom RMSD of all residues within 5A of the interface at superposition along those same atoms
C++ signature :
double calc_Irmsd(core::pose::Pose,core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)
- calc_Lrmsd(...)
- calc_Lrmsd( (Pose)pose, (Pose)native_pose, (vector1_int)movable_jumps) -> float :
Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner
C++ signature :
double calc_Lrmsd(core::pose::Pose,core::pose::Pose,utility::vector1<int, std::allocator<int> >)
- calc_atom_masks(...)
- calc_atom_masks( (Residue)irsd, (Residue)jrsd, (float)probe_radius, (float)cutoff_distance, (vector1_Real)radii, (AtomID_Map_T_bool_T)atom_subset, (object)atom_mask) -> None :
core/scoring/sasa.hh:90
C++ signature :
void calc_atom_masks(core::conformation::Residue,core::conformation::Residue,double,double,utility::vector1<double, std::allocator<double> >,core::id::AtomID_Map<bool>,core::id::AtomID_Map<utility::vector1<ObjexxFCL::ubyte, std::allocator<ObjexxFCL::ubyte> > > {lvalue})
- calc_interaction_energy(...)
- calc_interaction_energy( (Pose)pose, (__CPP_ScoreFunction__)dock_scorefxn, (vector1_int)movable_jumps) -> float :
Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other
C++ signature :
double calc_interaction_energy(core::pose::Pose,boost::shared_ptr<core::scoring::ScoreFunction const>,utility::vector1<int, std::allocator<int> >)
- calc_per_atom_sasa(...)
- calc_per_atom_sasa( (Pose)pose, (AtomID_Map_T_double_T)atom_sasa, (vector1_Real)rsd_sasa, (float)probe_radius, (bool)use_big_polar_H, (AtomID_Map_T_bool_T)atom_subset [, (bool)use_naccess_sasa_radii=False [, (bool)expand_polar_radii=False [, (float)polar_expansion_radius=1.0 [, (bool)include_probe_radius_in_atom_radii=True [, (bool)use_lj_radii=False]]]]]) -> float :
core/scoring/sasa.hh:79
C++ signature :
double calc_per_atom_sasa(core::pose::Pose,core::id::AtomID_Map<double> {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},double,bool,core::id::AtomID_Map<bool> {lvalue} [,bool=False [,bool=False [,double=1.0 [,bool=True [,bool=False]]]]])
calc_per_atom_sasa( (Pose)pose, (AtomID_Map_T_double_T)atom_sasa, (vector1_Real)rsd_sasa, (float)probe_radius [, (bool)use_big_polar_H=False]) -> float :
Return total SASA
C++ signature :
double calc_per_atom_sasa(core::pose::Pose,core::id::AtomID_Map<double> {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},double [,bool=False])
- calc_per_atom_sasa_sc(...)
- calc_per_atom_sasa_sc( (Pose)pose, (vector1_Real)rsd_sasa, (bool)normalize) -> float :
core/scoring/sasa.hh:58
C++ signature :
double calc_per_atom_sasa_sc(core::pose::Pose,utility::vector1<double, std::allocator<double> > {lvalue},bool)
- calc_per_res_hydrophobic_sasa(...)
- calc_per_res_hydrophobic_sasa( (Pose)pose, (vector1_Real)rsd_sasa, (vector1_Real)rsd_hydrophobic_sasa, (float)probe_radius [, (bool)use_naccess_sasa_radii=False]) -> float :
core/scoring/sasa.hh:104
C++ signature :
double calc_per_res_hydrophobic_sasa(core::pose::Pose,utility::vector1<double, std::allocator<double> > {lvalue},utility::vector1<double, std::allocator<double> > {lvalue},double [,bool=False])
- calc_res_contact(...)
- calc_res_contact( (Residue)rsd1, (Residue)rsd2, (float)dist_cutoff) -> bool :
protocols/docking/metrics.hh:66
C++ signature :
bool calc_res_contact(boost::shared_ptr<core::conformation::Residue>,boost::shared_ptr<core::conformation::Residue>,double)
- calc_total_sasa(...)
- calc_total_sasa( (Pose)pose, (float)probe_radius) -> float :
returns total sasa
C++ signature :
double calc_total_sasa(core::pose::Pose,double)
- calculate_rigid_matrix(...)
- calculate_rigid_matrix( (ResidueType)res, (vec1_vec1_Real)distances) -> None :
Calculate the rigid matrix for neighbor atom finding
Assume that distances has been initialized to some really large value, and is square
C++ signature :
void calculate_rigid_matrix(core::chemical::ResidueType,utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > {lvalue})
- calpha_superimpose_pose(...)
- calpha_superimpose_pose( (Pose)mod_pose, (Pose)ref_pose) -> float :
Superimpose two poses by their calpha coordinates. Ignores residues
that do not have atoms named "CA."
C++ signature :
double calpha_superimpose_pose(core::pose::Pose {lvalue},core::pose::Pose)
- ccd_close_loops(...)
- ccd_close_loops( (Pose)pose, (Loops)loops, (MoveMap)mm) -> None :
close loops by the CCD mechanism
C++ signature :
void ccd_close_loops(core::pose::Pose {lvalue},protocols::loops::Loops,core::kinematics::MoveMap)
- change_cys_state(...)
- change_cys_state( (int)index, (str)cys_type_name3, (Conformation)conf) -> bool :
Replace a CYS with a CYD or vice-versa for changing disulfide bonds.
[in] index Position of the residue to replace.
[in] cys_type_name3 The 3-letter name of the cys type to use: either CYS
or CYD.
[inout] conf The conformation to modify
true if the replacement was successful, false otherwise.
C++ signature :
bool change_cys_state(unsigned long,std::string,core::conformation::Conformation {lvalue})
- char_valid_as_torsion_bin(...)
- char_valid_as_torsion_bin( (str)torbin) -> bool :
returns true if the input character represents a valid torsion bin
C++ signature :
bool char_valid_as_torsion_bin(char)
- chop_fragments(...)
- chop_fragments( (FragSet)source, (FragSet)dest) -> None :
Function for chopping the X-sized fragments in source into fragments that
go into N-sized fragments in dest. Sizes are encoded by the value of
max_frag_length() in both source and dest.
C++ signature :
void chop_fragments(core::fragment::FragSet {lvalue},core::fragment::FragSet {lvalue})
- cis_omega_torsion_bin(...)
- cis_omega_torsion_bin( (ppo_torsion_bin)torbin) -> bool :
core/conformation/ppo_torsion_bin.hh:43
C++ signature :
bool cis_omega_torsion_bin(core::conformation::ppo_torsion_bin)
- combine_sequence_mappings(...)
- combine_sequence_mappings( (SequenceMapping)smap, (SequenceMapping)smap_to_add) -> None :
combine the input sequence mappings into one
utility function added by flo, feb 2011
C++ signature :
void combine_sequence_mappings(core::id::SequenceMapping {lvalue},core::id::SequenceMapping)
combine_sequence_mappings( (object)smaps) -> SequenceMapping :
make one sequence mapping out of all input ones
utility function added by flo, feb 2011
C++ signature :
boost::shared_ptr<core::id::SequenceMapping> combine_sequence_mappings(utility::vector1<core::id::SequenceMapping, std::allocator<core::id::SequenceMapping> >)
- comment_begin(...)
- comment_begin( (vector1_string)tokens, (int)which_token) -> bool :
utility function for resfile reader (checks for a leading # signaling a comment)
C++ signature :
bool comment_begin(utility::vector1<std::string, std::allocator<std::string> >,unsigned long)
- compute_bb_centroid(...)
- compute_bb_centroid( (Residue)r1) -> xyzVector_Real :
Compute the average coordinate of the backbone heavy atoms
(aka center of mass).
C++ signature :
numeric::xyzVector<double> compute_bb_centroid(core::conformation::Residue)
- compute_bb_radius(...)
- compute_bb_radius( (Residue)r1, (xyzVector_Real)r1bb_centroid) -> float :
Given a representative point for the center of the backbone,
compute the largest distance of all backbone heavy atoms to that point.
C++ signature :
double compute_bb_radius(core::conformation::Residue,numeric::xyzVector<double>)
- compute_jump_rmsd(...)
- compute_jump_rmsd( (Pose)reference, (Pose)model, (object)rmsds) -> None :
Computes the RMSD of the jump residues between <model> and <native>,
storing the results in a map keyed by jump_id.
C++ signature :
void compute_jump_rmsd(core::pose::Pose,core::pose::Pose,boost::unordered::unordered_map<unsigned long, double, boost::hash<unsigned long>, std::equal_to<unsigned long>, std::allocator<std::pair<unsigned long const, double> > >*)
- compute_per_residue_coverage(...)
- compute_per_residue_coverage( (FragSet)frags, (vector1_Size)nr_frags) -> None :
core/fragment/util.hh:90
C++ signature :
void compute_per_residue_coverage(core::fragment::FragSet,utility::vector1<unsigned long, std::allocator<unsigned long> > {lvalue})
- compute_sc_centroid(...)
- compute_sc_centroid( (Residue)r1) -> xyzVector_Real :
Compute the average coordiante of the sidechain atoms, (aka center of mass)
or, if there are no side chain heavy atoms, compute the center of mass of the
backbone.
C++ signature :
numeric::xyzVector<double> compute_sc_centroid(core::conformation::Residue)
- compute_sc_radius(...)
- compute_sc_radius( (Residue)r1, (xyzVector_Real)r1sc_centroid) -> float :
Given a representative point for the center of the sidechain,
compute the largest distance of all sidechain heavy atoms to that point.
C++ signature :
double compute_sc_radius(core::conformation::Residue,numeric::xyzVector<double>)
- compute_ss_regions(...)
- compute_ss_regions( (float)max_loop_frac, (int)min_length, (SecondaryStructure)ss) -> Loops :
protocols/loops/util.hh:64
C++ signature :
protocols::loops::Loops compute_ss_regions(double,unsigned long,core::fragment::SecondaryStructure)
- convert_residuetype_to_light_graph(...)
- convert_residuetype_to_light_graph( (ResidueType)res) -> object :
core/chemical/residue_support.hh:35
C++ signature :
boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_name_t, void*, boost::no_property>, boost::property<boost::edge_name_t, boost::detail::edge_desc_impl<boost::undirected_tag, void*>, boost::no_property>, boost::no_property, boost::listS> convert_residuetype_to_light_graph(core::chemical::ResidueType)
- convert_to_BondName(...)
- convert_to_BondName( (str)id) -> BondName :
core/chemical/Bond.hh:33
C++ signature :
core::chemical::BondName convert_to_BondName(std::string)
- coordinate_constrain_selection(...)
- coordinate_constrain_selection( (Pose)pose, (SequenceAlignment)aln, (float)coord_sdev) -> None :
protocols/relax/cst_util.hh:33
C++ signature :
void coordinate_constrain_selection(core::pose::Pose {lvalue},core::sequence::SequenceAlignment,double)
- copy_residue_coordinates_and_rebuild_missing_atoms(...)
- copy_residue_coordinates_and_rebuild_missing_atoms( (Residue)source_rsd, (Residue)target_rsd, (Conformation)conformation) -> None :
Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.
C++ signature :
void copy_residue_coordinates_and_rebuild_missing_atoms(core::conformation::Residue,core::conformation::Residue {lvalue},core::conformation::Conformation)
copy_residue_coordinates_and_rebuild_missing_atoms( (Residue)source_rsd, (Residue)target_rsd, (Conformation)conformation, (bool)preserve_only_sidechain_dihedrals) -> None :
Fills coords of target_rsd with coords from source_rsd of same atom_name, rebuilds others.
If preserve_only_sidechain_dihedrals is true, then this function only copies mainchain coordinates,
and rebuilds all sidechain coordinates from scratch, setting side-chain dihedrals based on the source residue.
Otherwise, if false, it copies all the atoms that it can from the source residue, then rebuilds the rest.
Vikram K. Mulligan (vmullig@uw.edu)
C++ signature :
void copy_residue_coordinates_and_rebuild_missing_atoms(core::conformation::Residue,core::conformation::Residue {lvalue},core::conformation::Conformation,bool)
- create_ClassicFragmentMover(...)
- create_ClassicFragmentMover( (FragSet)arg1, (MoveMap)arg2) -> ClassicFragmentMover :
C++ signature :
boost::shared_ptr<protocols::simple_moves::ClassicFragmentMover> create_ClassicFragmentMover(core::fragment::FragSet,core::kinematics::MoveMap)
create_ClassicFragmentMover( (ConstantLengthFragSet)arg1, (MoveMap)arg2) -> ClassicFragmentMover :
C++ signature :
boost::shared_ptr<protocols::simple_moves::ClassicFragmentMover> create_ClassicFragmentMover(core::fragment::ConstantLengthFragSet,core::kinematics::MoveMap)
- create_bond_length(...)
- create_bond_length( (GasteigerAtomTypeData)atom1, (GasteigerAtomTypeData)atom2, (BondName)bond_type) -> float :
core/chemical/bond_support.hh:34
C++ signature :
double create_bond_length(core::chemical::gasteiger::GasteigerAtomTypeData,core::chemical::gasteiger::GasteigerAtomTypeData,core::chemical::BondName)
- create_command_map(...)
- create_command_map() -> object :
utility for resfile reader, commands MUST be entered into this hard-coded map
C++ signature :
std::map<std::string, boost::shared_ptr<core::pack::task::ResfileCommand>, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<core::pack::task::ResfileCommand> > > > create_command_map()
- create_score_function(...)
- create_score_function( (str)arg1) -> ScoreFunction :
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> create_score_function(std::string)
- create_score_function_ws_patch(...)
- create_score_function_ws_patch( (str)arg1, (str)arg2) -> ScoreFunction :
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> create_score_function_ws_patch(std::string,std::string)
- create_shuffle_map_recursive_rms(...)
- create_shuffle_map_recursive_rms( (std_vector_int)sequence, (int)N, (object)map) -> None :
core/scoring/rms_util.hh:546
C++ signature :
void create_shuffle_map_recursive_rms(std::vector<int, std::allocator<int> >,int,std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > {lvalue})
- define_mainchain_atoms(...)
- define_mainchain_atoms( (ResidueType)rsd) -> vector1_Size :
If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER.
C++ signature :
utility::vector1<unsigned long, std::allocator<unsigned long> > define_mainchain_atoms(boost::shared_ptr<core::chemical::ResidueType>)
- define_scorable_core_from_secondary_structure(...)
- define_scorable_core_from_secondary_structure( (SecondaryStructure), (Loops)score_core) -> None :
protocols/loops/util.hh:81
C++ signature :
void define_scorable_core_from_secondary_structure(core::fragment::SecondaryStructure,protocols::loops::Loops {lvalue})
- delete_virtual_residues(...)
- delete_virtual_residues( (Pose)pose) -> None :
protocols/relax/cst_util.hh:56
C++ signature :
void delete_virtual_residues(core::pose::Pose {lvalue})
- derive_sc_sc_restraints(...)
- derive_sc_sc_restraints( (Pose)pose, (float)upper_dist_cutoff) -> None :
protocols/relax/cst_util.hh:61
C++ signature :
void derive_sc_sc_restraints(core::pose::Pose {lvalue},double)
- distance(...)
- distance( (Jump)a_in, (Jump)b_in) -> float :
RT root squared deviation
C++ signature :
double distance(core::kinematics::Jump,core::kinematics::Jump)
distance( (RT)a, (RT)b) -> float :
////////////////////////////////////////////////////////////////////////////
root squared devitation of two RTs
C++ signature :
double distance(core::kinematics::RT,core::kinematics::RT)
distance( (Stub)a, (Stub)b) -> float :
root squared deviation between two stubs
C++ signature :
double distance(core::kinematics::Stub,core::kinematics::Stub)
- disulfide_bonds(...)
- disulfide_bonds( (Conformation)conformation, (vector1_pair_Size_Size)disulfides) -> None :
Generate a list of all disulfide bonds in the conformation
C++ signature :
void disulfide_bonds(core::conformation::Conformation,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > > {lvalue})
- dump_frames_as_pdb(...)
- dump_frames_as_pdb( (Pose)pose, (vector1_FrameOP)frames, (str)filename [, (int)start_frag=1]) -> None :
writes FragData in multimodel pdb format
start_tag can be used to only write a subset
of the contained frag data
C++ signature :
void dump_frames_as_pdb(core::pose::Pose,utility::vector1<boost::shared_ptr<core::fragment::Frame>, std::allocator<boost::shared_ptr<core::fragment::Frame> > >,std::string [,unsigned long=1])
- dump_pdb(...)
- dump_pdb( (Pose)pose, (str)filename [, (str)tag='1']) -> None :
Writes the <pose> data to <filename>
example(s):
dump_pdb(pose,'my_pose.pdb')
See also:
Pose
Pose.dump_pdb
C++ signature :
void dump_pdb(core::pose::Pose,std::string [,std::string='1'])
dump_pdb( (Pose)pose, (OStream)out [, (str)tag='1']) -> None :
Writes <pose> data
C++ signature :
void dump_pdb(core::pose::Pose,std::ostream {lvalue} [,std::string='1'])
dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask [, (str)tag='1']) -> None :
Writes <pose> data
C++ signature :
void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool> [,std::string='1'])
dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask, (str)tag, (str)chain, (vector1_Size)resnums) -> None :
Writes <pose> data
C++ signature :
void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool>,std::string,char,utility::vector1<unsigned long, std::allocator<unsigned long> >)
dump_pdb( (Pose)pose, (OStream)out, (AtomID_Map_T_bool_T)mask, (int)atomno, (str)tag, (str)chain, (vector1_Size)resnums) -> None :
Writes <pose> data
C++ signature :
void dump_pdb(core::pose::Pose,std::ostream {lvalue},core::id::AtomID_Map<bool>,unsigned long {lvalue},std::string,char,utility::vector1<unsigned long, std::allocator<unsigned long> >)
- enlarge_h_lj_wdepth(...)
- enlarge_h_lj_wdepth( (AtomTypeSet)atom_type_set) -> None :
core/chemical/util.hh:73
C++ signature :
void enlarge_h_lj_wdepth(core::chemical::AtomTypeSet {lvalue})
enlarge_h_lj_wdepth( (vector1_Real)lj_wdepth, (AtomTypeSet)atom_type_set) -> None :
core/chemical/util.hh:70
C++ signature :
void enlarge_h_lj_wdepth(utility::vector1<double, std::allocator<double> > {lvalue},core::chemical::AtomTypeSet)
- error_check_requested_adducts(...)
- error_check_requested_adducts( (map_string_int)add_map, (object)rsd_types) -> None :
Make sure requested adducts exist in some residue
C++ signature :
void error_check_requested_adducts(std::map<std::string, int, std::less<std::string>, std::allocator<std::pair<std::string const, int> > >,utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > >)
- eval_atom_derivatives_for_minedge(...)
- eval_atom_derivatives_for_minedge( (MinimizationEdge)min_edge, (Residue)res1, (Residue)res2, (ResSingleMinimizationData)res1_min_data, (ResSingleMinimizationData)res2_min_data, (Pose)pose, (EMapVector)respair_weights, (object)r1atom_derivs, (object)r2atom_derivs) -> None :
core/scoring/MinimizationGraph.hh:526
C++ signature :
void eval_atom_derivatives_for_minedge(core::scoring::MinimizationEdge,core::conformation::Residue,core::conformation::Residue,core::scoring::ResSingleMinimizationData,core::scoring::ResSingleMinimizationData,core::pose::Pose,core::scoring::EMapVector,utility::vector1<core::scoring::DerivVectorPair, std::allocator<core::scoring::DerivVectorPair> > {lvalue},utility::vector1<core::scoring::DerivVectorPair, std::allocator<core::scoring::DerivVectorPair> > {lvalue})
- eval_atom_derivatives_for_minnode(...)
- eval_atom_derivatives_for_minnode( (MinimizationNode)min_node, (Residue)rsd, (Pose)pose, (EMapVector)res_weights, (object)atom_derivs) -> None :
Evaluate the derivatives for all atoms on the input residue
for the terms that apply to this residue (which are stored on the input
minimization node).
C++ signature :
void eval_atom_derivatives_for_minnode(core::scoring::MinimizationNode,core::conformation::Residue,core::pose::Pose,core::scoring::EMapVector,utility::vector1<core::scoring::DerivVectorPair, std::allocator<core::scoring::DerivVectorPair> > {lvalue})
- eval_bbbb_sr2b_energies(...)
- eval_bbbb_sr2b_energies( (Residue)r1, (Residue)r2, (xyzVector_Real)r1bb_centroid, (xyzVector_Real)r2bb_centroid, (float)r1bb_radius, (float)r2bb_radius, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap) -> None :
With two bounding spheres for a pair of backbones,
evaluate all the backbone/sidechain energies. This will
avoid a call to EnergyMethod E's backbone_backbone_energiy
method if either a) E's atomic_interaction_cutoff + r1bb_radius +
r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b)
E returns "false" in a call to its divides_backbone_and_-
sidechain_energetics() method. The reason the call is avoided if
"false" is returned is that, the entirety of a residue-pair-energy
evaluation should be returned in the sidechain_sidechain_energy
evaluation, if E does not implement its own versions of the bb/bb,
bb/sc and sc/sc energy evaluation methods. Both context-dependent and
context-independent 2-body energies are evaluated in this
function.
C++ signature :
void eval_bbbb_sr2b_energies(core::conformation::Residue,core::conformation::Residue,numeric::xyzVector<double>,numeric::xyzVector<double>,double,double,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue})
- eval_bbsc_sr2b_energies(...)
- eval_bbsc_sr2b_energies( (Residue)r1, (Residue)r2, (xyzVector_Real)r1bb_centroid, (xyzVector_Real)r2sc_centroid, (float)r1bb_radius, (float)r2sc_radius, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap) -> None :
With two bounding spheres for a backbone and a sidechain,
evaluate all the backbone/sidechain energies. This will
avoid a call to EnergyMethod E's backbone_sidechain_energiy
method if either a) E's atomic_interaction_cutoff + r1bb_radius +
r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b)
E returns "false" in a call to its divides_backbone_and_-
sidechain_energetics() method. The reason the call is avoided if
"false" is returned is that, the entirety of a residue-pair-energy
evaluation should be returned in the sidechain_sidechain_energy
evaluation, if E does not implement its own versions of the bb/bb,
bb/sc and sc/sc energy evaluation methods. Both context-dependent and
context-independent 2-body energies are evaluated in this
function.
C++ signature :
void eval_bbsc_sr2b_energies(core::conformation::Residue,core::conformation::Residue,numeric::xyzVector<double>,numeric::xyzVector<double>,double,double,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue})
- eval_dof_deriv_for_minnode(...)
- eval_dof_deriv_for_minnode( (MinimizationNode)min_node, (Residue)rsd, (Pose)pose, (DOF_ID)dof_id, (TorsionID)torsion_id, (ScoreFunction)sfxn, (EMapVector)weights) -> float :
core/scoring/MinimizationGraph.hh:577
C++ signature :
double eval_dof_deriv_for_minnode(core::scoring::MinimizationNode,core::conformation::Residue,core::pose::Pose,core::id::DOF_ID,core::id::TorsionID,core::scoring::ScoreFunction,core::scoring::EMapVector)
- eval_res_onebody_energies_for_minnode(...)
- eval_res_onebody_energies_for_minnode( (MinimizationNode)min_node, (Residue)rsd, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap) -> None :
core/scoring/MinimizationGraph.hh:513
C++ signature :
void eval_res_onebody_energies_for_minnode(core::scoring::MinimizationNode,core::conformation::Residue,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue})
- eval_res_pair_energy_for_minedge(...)
- eval_res_pair_energy_for_minedge( (MinimizationEdge)min_edge, (Residue)res1, (Residue)res2, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap) -> None :
core/scoring/MinimizationGraph.hh:566
C++ signature :
void eval_res_pair_energy_for_minedge(core::scoring::MinimizationEdge,core::conformation::Residue,core::conformation::Residue,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue})
- eval_scsc_sr2b_energies(...)
- eval_scsc_sr2b_energies( (Residue)r1, (Residue)r2, (xyzVector_Real)r1sc_centroid, (xyzVector_Real)r2sc_centroid, (float)r1sc_radius, (float)r2sc_radius, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap) -> None :
With two bounding spheres for a pair of sidechains,
evaluate all the sidechain/sidechain energies. This will
avoid a call to EnergyMethod E's sidechain_sidechain_energiy
method if a) E's atomic_interaction_cutoff + r1sc_radius +
r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b)
E returns "true" in a call to its divides_backbone_and_-
sidechain_energetics() method. Both context-dependent and
context-independent 2-body energies are evaluated in this
function.
C++ signature :
void eval_scsc_sr2b_energies(core::conformation::Residue,core::conformation::Residue,numeric::xyzVector<double>,numeric::xyzVector<double>,double,double,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue})
- eval_weighted_atom_derivatives_for_minedge(...)
- eval_weighted_atom_derivatives_for_minedge( (MinimizationEdge)min_edge, (Residue)res1, (Residue)res2, (ResSingleMinimizationData)res1_min_data, (ResSingleMinimizationData)res2_min_data, (Pose)pose, (EMapVector)respair_weights, (object)r1atom_derivs, (object)r2atom_derivs) -> None :
core/scoring/MinimizationGraph.hh:539
C++ signature :
void eval_weighted_atom_derivatives_for_minedge(core::scoring::MinimizationEdge,core::conformation::Residue,core::conformation::Residue,core::scoring::ResSingleMinimizationData,core::scoring::ResSingleMinimizationData,core::pose::Pose,core::scoring::EMapVector,utility::vector1<core::scoring::DerivVectorPair, std::allocator<core::scoring::DerivVectorPair> > {lvalue},utility::vector1<core::scoring::DerivVectorPair, std::allocator<core::scoring::DerivVectorPair> > {lvalue})
- eval_weighted_dof_deriv_for_minnode(...)
- eval_weighted_dof_deriv_for_minnode( (MinimizationNode)min_node, (Residue)rsd, (Pose)pose, (DOF_ID)dof_id, (TorsionID)torsion_id, (ScoreFunction)sfxn, (EMapVector)weights) -> float :
core/scoring/MinimizationGraph.hh:639
C++ signature :
double eval_weighted_dof_deriv_for_minnode(core::scoring::MinimizationNode,core::conformation::Residue,core::pose::Pose,core::id::DOF_ID,core::id::TorsionID,core::scoring::ScoreFunction,core::scoring::EMapVector)
- eval_weighted_res_onebody_energies_for_minnode(...)
- eval_weighted_res_onebody_energies_for_minnode( (MinimizationNode)min_node, (Residue)rsd, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap, (EMapVector)scratch_emap) -> None :
core/scoring/MinimizationGraph.hh:600
C++ signature :
void eval_weighted_res_onebody_energies_for_minnode(core::scoring::MinimizationNode,core::conformation::Residue,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue},core::scoring::EMapVector {lvalue})
- eval_weighted_res_pair_energy_for_minedge(...)
- eval_weighted_res_pair_energy_for_minedge( (MinimizationEdge)min_edge, (Residue)res1, (Residue)res2, (Pose)pose, (ScoreFunction)sfxn, (EMapVector)emap, (EMapVector)scratch_emap) -> None :
core/scoring/MinimizationGraph.hh:628
C++ signature :
void eval_weighted_res_pair_energy_for_minedge(core::scoring::MinimizationEdge,core::conformation::Residue,core::conformation::Residue,core::pose::Pose,core::scoring::ScoreFunction,core::scoring::EMapVector {lvalue},core::scoring::EMapVector {lvalue})
- extend_sequence_mapping(...)
- extend_sequence_mapping( (Pose)pose, (SequenceMapping)mapping, (str)source_seq, (str)target_seq) -> None :
protocols/loops/loops_main.hh:310
C++ signature :
void extend_sequence_mapping(core::pose::Pose,core::id::SequenceMapping {lvalue},std::string {lvalue},std::string {lvalue})
- extract_continuous_chunks(...)
- extract_continuous_chunks( (Pose)pose [, (int)minimum_size=3 [, (float)CA_CA_distance_cutoff=4]]) -> Loops :
protocols/loops/util.hh:128
C++ signature :
protocols::loops::Loops extract_continuous_chunks(core::pose::Pose [,unsigned long=3 [,double=4]])
- extract_secondary_structure_chunks(...)
- extract_secondary_structure_chunks( (Pose)pose, (str)extracted_ss_type) -> Loops :
Extract secondary structure chunks from the pose, using a given secondary structure type
C++ signature :
protocols::loops::Loops extract_secondary_structure_chunks(core::pose::Pose,char)
extract_secondary_structure_chunks( (Pose)pose [, (str)extracted_ss_types='HE' [, (int)gap_size=1 [, (int)minimum_length_of_chunk_helix=5 [, (int)minimum_length_of_chunk_strand=3 [, (float)CA_CA_distance_cutoff=4]]]]]) -> Loops :
Extract secondary structure chunks from the pose, using multiple secondary structure types
this function requires that the pose object already have secstruct information
to get this information from structure (DSSP), call
protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose );
or from secondary structure prediction (psipred_ss2 file), call
core::pose::read_psipred_ss2_file(pose);
C++ signature :
protocols::loops::Loops extract_secondary_structure_chunks(core::pose::Pose [,std::string='HE' [,unsigned long=1 [,unsigned long=5 [,unsigned long=3 [,double=4]]]]])
- fill_ideal_xyz_from_icoor(...)
- fill_ideal_xyz_from_icoor( (ResidueType)restype, (object)graph) -> None :
core/chemical/icoor_support.hh:44
C++ signature :
void fill_ideal_xyz_from_icoor(core::chemical::ResidueType {lvalue},boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>)
- fill_template_frames_from_pdb(...)
- fill_template_frames_from_pdb( (Pose)pose, (vector1_FrameOP)template_frames, (str)filename) -> bool :
filling a frameset from a multimodel pdb file
returns true if no error occured
C++ signature :
bool fill_template_frames_from_pdb(core::pose::Pose,utility::vector1<boost::shared_ptr<core::fragment::Frame>, std::allocator<boost::shared_ptr<core::fragment::Frame> > >,std::string)
- filter_loop_neighbors_by_distance(...)
- filter_loop_neighbors_by_distance( (Pose)pose, (vector1_bool)map, (Loops)loops, (float)dist_cutoff) -> None :
filter set of loop neighbors to a certain CB distance
C++ signature :
void filter_loop_neighbors_by_distance(core::pose::Pose,utility::vector1<bool, std::allocator<bool> > {lvalue},protocols::loops::Loops,double {lvalue})
- find_bonds_in_rings(...)
- find_bonds_in_rings( (ResidueType)res) -> None :
Determine which bonds are in rings, and set the BondRingness property of each
C++ signature :
void find_bonds_in_rings(core::chemical::ResidueType {lvalue})
- find_chi_bonds(...)
- find_chi_bonds( (ResidueType)restype) -> object :
Find which bonds are rotatatable (chi) bonds
Returns a list of four vds representing the chi
C++ signature :
utility::vector1<utility::vector1<void*, std::allocator<void*> >, std::allocator<utility::vector1<void*, std::allocator<void*> > > > find_chi_bonds(core::chemical::ResidueType)
- find_filter_or_die(...)
- find_filter_or_die( (str)filter_name, (Tag)tag, (object)filters) -> Filter :
Searches <filters> for the named filter, returning it if it exists,
otherwise halts execution with an error message.
C++ signature :
boost::shared_ptr<protocols::filters::Filter> find_filter_or_die(std::string,boost::shared_ptr<utility::tag::Tag const>,std::map<std::string const, boost::shared_ptr<protocols::filters::Filter>, std::less<std::string const>, std::allocator<std::pair<std::string const, boost::shared_ptr<protocols::filters::Filter> > > >)
- find_mover_or_die(...)
- find_mover_or_die( (str)mover_name, (Tag)tag, (object)movers) -> Mover :
Searches <movers> for the named mover, returning it if it exists,
otherwise halts execution with an error message.
C++ signature :
boost::shared_ptr<protocols::moves::Mover> find_mover_or_die(std::string,boost::shared_ptr<utility::tag::Tag const>,std::map<std::string const, boost::shared_ptr<protocols::moves::Mover>, std::less<std::string const>, std::allocator<std::pair<std::string const, boost::shared_ptr<protocols::moves::Mover> > > >)
- find_nbr_dist(...)
- find_nbr_dist( (ResidueType)res, (object)nbr_atom) -> float :
Find the neighbor distance to the given neighbor atom.
If nbr_atom is null_vertex, give the smallest neighbor distance,
and set nbr_atom to the atom for that distance.
The neighbor distance here is adjusted for rotatable bonds -
It should be at least as large as the maximum neighbor distance
in any torsional rotamer
If the neighbor atom is not provided, the atom chosen will be a
multiply-bonded heavy atom.
Assumes:
* All atoms and bond are present
* All ideal_xyz coordinates have been set
* All elements have been set
* All ring bonds have been annotated
C++ signature :
double find_nbr_dist(core::chemical::ResidueType,void* {lvalue})
- find_non_protein_chunks(...)
- find_non_protein_chunks( (Pose)pose) -> Loops :
protocols/loops/util.hh:108
C++ signature :
protocols::loops::Loops find_non_protein_chunks(core::pose::Pose)
- find_weights_file(...)
- find_weights_file( (str)name [, (str)extension='.wts']) -> str :
Utility function to locate a weights or patch file, either with a fully qualified path,
in the local directory, or in the database. Names may be passes either with or without the
optional extension.
C++ signature :
std::string find_weights_file(std::string [,std::string='.wts'])
- fix_with_coord_cst(...)
- fix_with_coord_cst( (Loops)rigid, (Pose)pose, (bool)bCstAllAtom, (vector1_Real)) -> None :
protocols/loops/util.hh:31
C++ signature :
void fix_with_coord_cst(protocols::loops::Loops,core::pose::Pose {lvalue},bool,utility::vector1<double, std::allocator<double> > {lvalue})
- fix_worst_bad_ramas(...)
- fix_worst_bad_ramas( (Pose)original_pose [, (int)how_many=1 [, (float)skip_prob=0.0 [, (float)limit_rms=0.5 [, (float)limit_rama=2.0]]]]) -> None :
protocols/relax/Ramady.hh:28
C++ signature :
void fix_worst_bad_ramas(core::pose::Pose {lvalue} [,unsigned long=1 [,double=0.0 [,double=0.5 [,double=2.0]]]])
- fixup_patches(...)
- fixup_patches( (str)string_in) -> str :
Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":".
C++ signature :
std::string fixup_patches(std::string)
- flatten_list(...)
- flatten_list( (FrameList)frames, (object)frag_ids) -> None :
core/fragment/util.hh:97
C++ signature :
void flatten_list(core::fragment::FrameList {lvalue},utility::vector1<core::fragment::FragID, std::allocator<core::fragment::FragID> > {lvalue})
- fold_tree_from_loops(...)
- fold_tree_from_loops( (Pose)pose, (Loops)loops, (FoldTree)f [, (bool)terminal_cutpoint=False]) -> None :
the main function for perform loop modeling
/voi/d
loops_main( core::pose::Pose & pose );
construct a fold tree from loop definition
C++ signature :
void fold_tree_from_loops(core::pose::Pose,protocols::loops::Loops,core::kinematics::FoldTree {lvalue} [,bool=False])
- form_disulfide(...)
- form_disulfide( (Conformation)conformation, (int)lower_res, (int)upper_res) -> None :
Introduce cysteines at the specified location and define a disulfide bond between them.
Does not do the repacking & minimization required to place the disulfide correctly.
C++ signature :
void form_disulfide(core::conformation::Conformation {lvalue},unsigned long,unsigned long)
- form_disulfide_helper(...)
- form_disulfide_helper( (Conformation)conformation, (int)lower_res, (ResidueTypeSet)restype_set) -> None :
Helper function for the form_disulfide function.
This function ensures that as a residue is mutated to a disulfide-bonding residue type,
all other variant types are preserved; it is used to avoid code duplication.
Vikram K. Mulligan, Baker laboratory (vmullig@uw.edu)
C++ signature :
void form_disulfide_helper(core::conformation::Conformation {lvalue},unsigned long,boost::shared_ptr<core::chemical::ResidueTypeSet const>)
- formatted_icoord_tree(...)
- formatted_icoord_tree( (ResidueType)restype) -> str :
Return a string representing the internal coordinates tree of this ResidueType.
C++ signature :
std::string formatted_icoord_tree(core::chemical::ResidueType)
- fragment_set_slice(...)
- fragment_set_slice( (ConstantLengthFragSet)fragset, (vector1_Size)slice_res) -> None :
core/fragment/util.hh:139
C++ signature :
void fragment_set_slice(boost::shared_ptr<core::fragment::ConstantLengthFragSet> {lvalue},utility::vector1<unsigned long, std::allocator<unsigned long> >)
fragment_set_slice( (ConstantLengthFragSet)fragset, (int)min_res, (int)max_res) -> None :
core/fragment/util.hh:135
C++ signature :
void fragment_set_slice(boost::shared_ptr<core::fragment::ConstantLengthFragSet> {lvalue},unsigned long,unsigned long)
- gdtha(...)
- gdtha( (Pose)ref, (Pose)model, (map_Size_Size)residues) -> float :
Returns the average fraction of residues superimposable under a
series of distance thresholds-- 0.5, 1.0, 2.0, and 4.0 Angstroms.
C++ signature :
double gdtha(core::pose::Pose,core::pose::Pose,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
- gdtsc(...)
- gdtsc( (Pose)ref, (Pose)model, (map_Size_Size)residues) -> float :
Returns a single, Global Distance Test-like value that measures the
extent to which the functional ends of a model's sidechains agree with their
counterparts in a given reference structure.
@detail Instead of comparing residue positions on the basis of CAs, gdtsc
uses a characteristic atom near the end of each sidechain type for the
evaluation of residue-residue distance deviations.
The traditional GDT score is a weighted sum of the fraction of residues
superimposed within limits of 1, 2, 4, and 8Å. For gdtsc, the backbone
superposition is used to calculate fractions of corresponding model-ref
sidechain atom pairs that fit under 10 distance-limit values from 0.5A
to 5A. Ambiguity in Asp or Glu terminal oxygen naming is not currently
considered.
Reference:
Keedy, DA. The other 90% of the protein. Proteins. 2009; 77 Suppl 9:29-49.
C++ signature :
double gdtsc(core::pose::Pose,core::pose::Pose,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
- generate_bb_coordinate_constraints(...)
- generate_bb_coordinate_constraints( (Pose)pose, (vector1_Real)coord_sdevs) -> ConstraintSet :
Generate a set of coordinate constraints to backbone atoms using the
given standard deviations, with one sd per-reside. If no constraint should
be applied to a given residue, give a -1 for the value of the sdev.
C++ signature :
boost::shared_ptr<core::scoring::constraints::ConstraintSet> generate_bb_coordinate_constraints(core::pose::Pose {lvalue},utility::vector1<double, std::allocator<double> >)
- generate_relax_from_cmd(...)
- generate_relax_from_cmd([ (bool)NULL_if_no_cmd=False]) -> RelaxProtocolBase :
protocols/relax/util.hh:44
C++ signature :
boost::shared_ptr<protocols::relax::RelaxProtocolBase> generate_relax_from_cmd([ bool=False])
- get_2way_orientation(...)
- get_2way_orientation( (xyzVector_Real)a_xyz, (xyzVector_Real)b_xyz, (int)phi_a2b_index, (int)theta_a2b_index, (int)phi_b2a_index, (int)theta_b2a_index, (float)distance_ijxyz) -> None :
core/scoring/sasa.hh:51
C++ signature :
void get_2way_orientation(numeric::xyzVector<double>,numeric::xyzVector<double>,int {lvalue},int {lvalue},int {lvalue},int {lvalue},double)
- get_D_equivalent(...)
- get_D_equivalent( (AA)aa) -> AA :
///////////////////////////////////////////////////////
Given an enum type for a L-amino acid with a
canonical side-chain, return the enum type for the
corresponding D-amino acid (or aa_unk if the
corresponding D-amino acid cannot be determined).
///////////////////////////////////////////////////////
C++ signature :
core::chemical::AA get_D_equivalent(core::chemical::AA)
- get_L_equivalent(...)
- get_L_equivalent( (AA)aa) -> AA :
///////////////////////////////////////////////////////
Given an enum type for a D-amino acid with a
canonical side-chain, return the enum type for the
corresponding L-amino acid (or aa_unk if the
corresponding L-amino acid cannot be determined).
///////////////////////////////////////////////////////
C++ signature :
core::chemical::AA get_L_equivalent(core::chemical::AA)
- get_anchor_and_root_atoms(...)
- get_anchor_and_root_atoms( (Residue)anchor_rsd, (Residue)root_rsd, (Edge)edge, (int)anchor_atomno, (int)root_atomno) -> None :
Use this routine to deduce atom indices of connect atoms in the tree
C++ signature :
void get_anchor_and_root_atoms(core::conformation::Residue,core::conformation::Residue,core::kinematics::Edge,unsigned long {lvalue},unsigned long {lvalue})
- get_anchor_atomno(...)
- get_anchor_atomno( (Residue)rsd, (int)dir) -> int :
get anchor atom to which the atom-tree of next residue in the edge is attached.
C++ signature :
int get_anchor_atomno(core::conformation::Residue,int)
get_anchor_atomno( (Residue)anchor_rsd, (int)seqpos, (FoldTree)fold_tree) -> int :
Get the atom-index of the atom to which the residue at position seqpos should be anchored.
C++ signature :
int get_anchor_atomno(core::conformation::Residue,unsigned long,core::kinematics::FoldTree)
- get_angles(...)
- get_angles() -> object :
core/scoring/sasa.hh:97
C++ signature :
ObjexxFCL::FArray2D<int> get_angles()
- get_bond(...)
- get_bond( (ResidueType)res, (object)source, (object)target) -> object :
core/chemical/bond_support.hh:30
C++ signature :
boost::detail::edge_desc_impl<boost::undirected_tag, void*> get_bond(core::chemical::ResidueType,void*,void*)
- get_cen_scorefxn(...)
- get_cen_scorefxn() -> ScoreFunction :
protocols/loops/util.hh:69
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> get_cen_scorefxn()
- get_chemical_root_and_anchor_atomnos(...)
- get_chemical_root_and_anchor_atomnos( (Residue)rsd_anchor, (Residue)rsd_root, (int)anchor_atom_no, (int)root_atom_no) -> None :
core/conformation/util.hh:308
C++ signature :
void get_chemical_root_and_anchor_atomnos(core::conformation::Residue,core::conformation::Residue,unsigned long {lvalue},unsigned long {lvalue})
- get_connecting_atoms(...)
- get_connecting_atoms( (object)res, (object)edge) -> object :
core/chemical/bond_support.hh:29
C++ signature :
utility::vector1<void*, std::allocator<void*> > get_connecting_atoms(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)
get_connecting_atoms( (ResidueType)res, (object)edge) -> object :
core/chemical/bond_support.hh:28
C++ signature :
utility::vector1<void*, std::allocator<void*> > get_connecting_atoms(core::chemical::ResidueType,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)
- get_fa_scorefxn(...)
- get_fa_scorefxn() -> ScoreFunction :
protocols/loops/util.hh:67
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> get_fa_scorefxn()
- get_masks(...)
- get_masks() -> object :
core/scoring/sasa.hh:98
C++ signature :
ObjexxFCL::FArray2D<ObjexxFCL::ubyte> get_masks()
- get_num_bytes(...)
- get_num_bytes() -> int :
core/scoring/sasa.hh:96
C++ signature :
int get_num_bytes()
- get_orientation(...)
- get_orientation( (xyzVector_Real)a_xyz, (xyzVector_Real)b_xyz, (int)phi_index, (int)theta_index, (float)distance_ijxyz) -> None :
core/scoring/sasa.hh:43
C++ signature :
void get_orientation(numeric::xyzVector<double>,numeric::xyzVector<double>,int {lvalue},int {lvalue},double)
- get_overlap(...)
- get_overlap( (float)radius_a, (float)radius_b, (float)distance_ijxyz, (int)degree_of_overlap) -> None :
core/scoring/sasa.hh:42
C++ signature :
void get_overlap(double,double,double,int {lvalue})
- get_per_residue_scores(...)
- get_per_residue_scores( (Pose)pose, (ScoreType)scoretype) -> vector1_Real :
protocols/relax/cst_util.hh:48
C++ signature :
utility::vector1<double, std::allocator<double> > get_per_residue_scores(core::pose::Pose {lvalue},core::scoring::ScoreType)
- get_rb_number(...)
- get_rb_number( (DOF_Type)t) -> int :
//////////////////////////////////////////////////////////////////////////
C++ signature :
unsigned long get_rb_number(core::id::DOF_Type)
- get_rb_type(...)
- get_rb_type( (int)k) -> DOF_Type :
//////////////////////////////////////////////////////////////////////////
C++ signature :
core::id::DOF_Type get_rb_type(unsigned long)
- get_residue_path_distances(...)
- get_residue_path_distances( (ResidueType)res) -> object :
relies on class Graph to find all pairs shortest path information
C++ signature :
ObjexxFCL::FArray2D<int> get_residue_path_distances(core::chemical::ResidueType)
- get_root_atomno(...)
- get_root_atomno( (Residue)rsd, (int)dir) -> int :
core/conformation/util.hh:251
C++ signature :
int get_root_atomno(core::conformation::Residue,int)
- get_root_residue_root_atomno(...)
- get_root_residue_root_atomno( (Residue)rsd, (FoldTree)fold_tree) -> int :
core/conformation/util.hh:257
C++ signature :
unsigned long get_root_residue_root_atomno(core::conformation::Residue,core::kinematics::FoldTree)
- get_rpp_charge(...)
- get_rpp_charge( (str)type) -> float :
Get charge for atom type based on Rosetta++ aaproperties_pack.cc values
C++ signature :
double get_rpp_charge(std::string)
- get_score_function(...)
- get_score_function([ (bool)is_fullatom=True]) -> ScoreFunction :
A helper function which returns a scoring function owning pointer according to the
user's command line parameters -score:weights and -score:patch
By default it returns weights=talaris2013 for fullatom,
and weights=cen_std and patch="" for centroid
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> get_score_function([ bool=True])
- get_score_functionName(...)
- get_score_functionName([ (bool)is_fullatom=True]) -> str :
use the logic of get_score_function to get the name.
The name format is <weights_tag>[_<patch_tag> ... ]
C++ signature :
std::string get_score_functionName([ bool=True])
- get_score_function_legacy(...)
- get_score_function_legacy( (str)pre_talaris_2013_weight_set [, (str)pre_talaris_2013_patch_file='']) -> ScoreFunction :
A helper function that either returns a ScoreFunctionOP created by get_score_function() or
the one specified by the protocol which is activated by the -restore_pre_talaris_2013_behavior
flag. The purpose of this function is to preserve legacy behavior for the sake of reproducibility
and so that a record of the old behavior is still preserved in the code to ease the process of
reverting the change to get_score_function if that were the wrong behavior.
C++ signature :
boost::shared_ptr<core::scoring::ScoreFunction> get_score_function_legacy(std::string [,std::string=''])
- get_tenA_neighbor_residues(...)
- get_tenA_neighbor_residues( (Pose)pose, (vector1_bool)residue_positions) -> None :
get neighbor residues within 10 A CB distance cutoff
C++ signature :
void get_tenA_neighbor_residues(core::pose::Pose,utility::vector1<bool, std::allocator<bool> > {lvalue})
- get_token(...)
- get_token( (int)which_token, (vector1_string)tokens [, (bool)make_upper_case=True]) -> str :
////////end of other options//////////////////////////
////////utility functions for resfile reader//////////
utility function to increment next token to be parsed
C++ signature :
std::string get_token(unsigned long,utility::vector1<std::string, std::allocator<std::string> > [,bool=True])
- get_torsion_bin(...)
- get_torsion_bin( (float)phi, (float)psi [, (float)omega=180]) -> ppo_torsion_bin :
determine the torsion bin for a given phi/psi/omega combination, assuming that omega is 180 if not specified
Amelie Stein (amelie.stein@ucsf.edu)
@date Wed May 2 11:18:29 PDT 2012
C++ signature :
core::conformation::ppo_torsion_bin get_torsion_bin(double,double [,double=180])
- getxform(...)
- getxform( (xyzVector_Real)m1, (xyzVector_Real)m2, (xyzVector_Real)m3, (xyzVector_Real)f1, (xyzVector_Real)f2, (xyzVector_Real)f3) -> Stub :
core/fragment/util.hh:43
C++ signature :
core::kinematics::Stub getxform(numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>,numeric::xyzVector<double>)
- has(...)
- has( (object)graph, (object)ed) -> bool :
Does a ResidueGraph have a given edge descriptor?
C++ signature :
bool has(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,boost::detail::edge_desc_impl<boost::undirected_tag, void*>)
has( (object)graph, (object)vd) -> bool :
/////////////////////////////////////////////
//////// Convenience Functions //////////////
Does a ResidueGraph have a given vertex descriptor?
C++ signature :
bool has(boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,void*)
- has_severe_pep_bond_geom_issues(...)
- has_severe_pep_bond_geom_issues( (Pose)pose, (int)resnum [, (bool)check_bonds=True [, (bool)check_angles=True [, (float)max_c_n_dis=2.0 [, (float)allowed_ca_c_n_deviation=25.0 [, (float)allowed_c_n_ca_deviation=25.0]]]]]) -> object :
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
Stringent cutoffs are: 1.5, 15, 15
C++ signature :
std::pair<bool, unsigned long> has_severe_pep_bond_geom_issues(core::pose::Pose,unsigned long [,bool=True [,bool=True [,double=2.0 [,double=25.0 [,double=25.0]]]]])
has_severe_pep_bond_geom_issues( (Pose)pose, (Loop)loop [, (bool)check_bonds=True [, (bool)check_angles=True [, (float)max_c_n_dis=2.0 [, (float)allowed_ca_c_n_deviation=25.0 [, (float)allowed_c_n_ca_deviation=25.0]]]]]) -> object :
Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff.
Returns boolean and the position of found wonky peptide bond (0 if none found).
Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1
Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values
out of this range. -JAB
Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009)
Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325.
deviation is +/- from the min/max values of the CDL.
Stringent cutoffs are: 1.5, 15, 15
C++ signature :
std::pair<bool, unsigned long> has_severe_pep_bond_geom_issues(core::pose::Pose,protocols::loops::Loop [,bool=True [,bool=True [,double=2.0 [,double=25.0 [,double=25.0]]]]])
- hash_value(...)
- hash_value( (StrandPairing)val) -> int :
protocols/abinitio/PairingStatistics.hh:111
C++ signature :
unsigned long hash_value(core::scoring::dssp::StrandPairing)
hash_value( (PairingStatEntry)val) -> int :
protocols/abinitio/PairingStatistics.hh:108
C++ signature :
unsigned long hash_value(protocols::abinitio::PairingStatEntry)
- idealize_hydrogens(...)
- idealize_hydrogens( (Residue)res, (Conformation)conf) -> None :
core/conformation/Residue.functions.hh:27
C++ signature :
void idealize_hydrogens(core::conformation::Residue {lvalue},core::conformation::Conformation)
- idealize_loop(...)
- idealize_loop( (Pose)pose, (Loop)loop) -> None :
set ideal BB geometry; this must occur so that loops with missing density work.
C++ signature :
void idealize_loop(core::pose::Pose {lvalue},protocols::loops::Loop)
- idealize_position(...)
- idealize_position( (int)seqpos, (Conformation)conformation) -> None :
Idealize backbone and sidechain at seqpos
C++ signature :
void idealize_position(unsigned long,core::conformation::Conformation {lvalue})
- input_sasa_dats(...)
- input_sasa_dats() -> None :
core/scoring/sasa.hh:40
C++ signature :
void input_sasa_dats()
- insert_ideal_bonds_at_polymer_junction(...)
- insert_ideal_bonds_at_polymer_junction( (int)seqpos, (Conformation)conformation) -> None :
Sets the two bond angles and the bond length across the junction, rebuilds dependent atoms (eg O,H)
C++ signature :
void insert_ideal_bonds_at_polymer_junction(unsigned long,core::conformation::Conformation {lvalue})
- insert_ideal_mainchain_bonds(...)
- insert_ideal_mainchain_bonds( (int)seqpos, (Conformation)conformation) -> None :
core/conformation/util.hh:72
C++ signature :
void insert_ideal_mainchain_bonds(unsigned long,core::conformation::Conformation {lvalue})
- insert_residue_into_atom_tree(...)
- insert_residue_into_atom_tree( (Residue)new_rsd, (FoldTree)fold_tree, (object)residues, (AtomTree)atom_tree) -> None :
Inserts/ appends new residue subtree into an existing atomtree
The foldtree must already have been changed to reflect the new residue
The sequence position of the new residue is deduced from new_rsd.seqpos()
This function handles renumbering of the atomtree if necessary
C++ signature :
void insert_residue_into_atom_tree(core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})
- interpolate_value_and_deriv(...)
- interpolate_value_and_deriv( (object)potential, (float)bin_width, (float)r, (float)value, (float)deriv) -> None :
//////////////////////////////////////////////////////////////////////////////////////
C++ signature :
void interpolate_value_and_deriv(ObjexxFCL::FArray1D<double>,double,double,double {lvalue},double {lvalue})
- invert_exclude_residues(...)
- invert_exclude_residues( (int)nres, (vector1_int)exclude_list) -> object :
core/scoring/rms_util.hh:52
C++ signature :
std::list<unsigned long, std::allocator<unsigned long> > invert_exclude_residues(unsigned long,utility::vector1<int, std::allocator<int> >)
invert_exclude_residues( (int)nres, (vector1_int)exclude_list, (object)) -> None :
core/scoring/rms_util.hh:50
C++ signature :
void invert_exclude_residues(unsigned long,utility::vector1<int, std::allocator<int> >,std::list<unsigned long, std::allocator<unsigned long> > {lvalue})
- is_canonical_D_aa(...)
- is_canonical_D_aa( (AA)aa) -> bool :
///////////////////////////////////////////////////////
Give an enum type, return true if and only if
it is a D-amino acid that is the mirror image of a
canonical alpha-L-amino acid.
Vikram K. Mulligan (vmullig@uw.edu)
///////////////////////////////////////////////////////
C++ signature :
bool is_canonical_D_aa(core::chemical::AA)
- is_disulfide_bond(...)
- is_disulfide_bond( (Conformation)conformation, (int)residueA_pos, (int)residueB_pos) -> bool :
Find whether there is a disulfide defined between two residues
C++ signature :
bool is_disulfide_bond(core::conformation::Conformation,unsigned long,unsigned long)
- is_heavyatom(...)
- is_heavyatom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:191
C++ signature :
bool is_heavyatom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_ideal_position(...)
- is_ideal_position( (int)seqpos, (Conformation)conformation [, (float)theta_epsilon=0.005 [, (float)D_epsilon=0.02]]) -> bool :
Return true if position contains an ideal geometry up to some epsilon
s seqpos - sequence position
s conformation - conformation object
s theta_epsilon - permitted deviation from ideal bond angles, in Radians
s D_epsilon - permitted deviation from ideal bond length
@remarks conformation is needed for context of polymer nbrs
C++ signature :
bool is_ideal_position(unsigned long,core::conformation::Conformation [,double=0.005 [,double=0.02]])
- is_ligand_heavyatom(...)
- is_ligand_heavyatom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:169
C++ signature :
bool is_ligand_heavyatom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_ligand_heavyatom_residues(...)
- is_ligand_heavyatom_residues( (Residue)residue1, (Residue), (int)atomno) -> bool :
core/scoring/rms_util.hh:176
C++ signature :
bool is_ligand_heavyatom_residues(core::conformation::Residue,core::conformation::Residue,unsigned long)
- is_nbr_atom(...)
- is_nbr_atom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:207
C++ signature :
bool is_nbr_atom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_non_peptide_heavy_atom(...)
- is_non_peptide_heavy_atom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
Return true if the pose residues and atoms specified are non-peptide heavy atoms.
C++ signature :
bool is_non_peptide_heavy_atom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_polymer_heavyatom(...)
- is_polymer_heavyatom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:161
C++ signature :
bool is_polymer_heavyatom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_protein_CA(...)
- is_protein_CA( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
///////////////////////////////////////////////////////////////////////////
C++ signature :
bool is_protein_CA(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_protein_CA_or_CB(...)
- is_protein_CA_or_CB( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:129
C++ signature :
bool is_protein_CA_or_CB(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_protein_backbone(...)
- is_protein_backbone( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:137
C++ signature :
bool is_protein_backbone(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_protein_backbone_including_O(...)
- is_protein_backbone_including_O( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:145
C++ signature :
bool is_protein_backbone_including_O(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_protein_sidechain_heavyatom(...)
- is_protein_sidechain_heavyatom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:153
C++ signature :
bool is_protein_sidechain_heavyatom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_rot_sample_name(...)
- is_rot_sample_name( (str)name) -> bool :
core/pack/task/RotamerSampleOptions.hh:40
C++ signature :
bool is_rot_sample_name(std::string)
- is_scatom(...)
- is_scatom( (Pose)pose1, (Pose), (int)resno, (int)atomno) -> bool :
core/scoring/rms_util.hh:199
C++ signature :
bool is_scatom(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long)
- is_sp2_proton_chi(...)
- is_sp2_proton_chi( (int)chi, (ResidueType)restype) -> bool :
Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom?
The use case is to see if the proton chi should flat or staggered with rotamers
C++ signature :
bool is_sp2_proton_chi(unsigned long,core::chemical::ResidueType)
- jump_distance(...)
- jump_distance( (Jump)a_in, (Jump)b_in, (float)dist, (float)theta) -> None :
compare the difference of two jumps in term of the translation (dist) and rotational angle(theta)
C++ signature :
void jump_distance(core::kinematics::Jump,core::kinematics::Jump,double {lvalue},double {lvalue})
- linearize_fold_tree(...)
- linearize_fold_tree( (FoldTree)tree) -> FoldTree :
linearizes (or defoliates, if you prefer) a FoldTree. "default" FoldTrees produced by the PDB reader have all chains (peptide edges) starting from jumps relative to residue 1. This code modifies the tree to instead have all the jumps be relative to the preceding edge. It is not tested with ligands and will not work with "functional" jumps. From A to B:
A:FOLD_TREE EDGE 1 78 -1 EDGE 1 79 1 EDGE 79 454 -1 EDGE 1 455 2 EDGE 455 540 -1 EDGE 1 541 3 EDGE 541 697 -1
B:FOLD_TREE EDGE 1 78 -1 EDGE 78 79 1 EDGE 79 454 -1 EDGE 454 455 2 EDGE 455 540 -1 EDGE 540 541 3 EDGE 541 697 -1
C++ signature :
core::kinematics::FoldTree linearize_fold_tree(core::kinematics::FoldTree)
- loop_local_rmsd(...)
- loop_local_rmsd( (Pose)pose1, (Pose)pose2, (Loops)loops) -> float :
calculate rmsd of loop residues with repect to native (loop fit)
C++ signature :
double loop_local_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops)
- loop_rmsd(...)
- loop_rmsd( (Pose)pose1, (Pose)pose2, (Loops)loops [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
calculate rmsd of loop residues with repect to native (template aligned)
C++ signature :
double loop_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops [,bool=False [,bool=True]])
- loop_rmsd_with_superimpose(...)
- loop_rmsd_with_superimpose( (Pose)pose1, (Pose)pose2, (Loops)loops [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
As above but actuall superimposes the non-loop part
C++ signature :
double loop_rmsd_with_superimpose(core::pose::Pose,core::pose::Pose,protocols::loops::Loops [,bool=False [,bool=True]])
- loop_rmsd_with_superimpose_core(...)
- loop_rmsd_with_superimpose_core( (Pose)pose1, (Pose)pose2, (Loops)loops, (Loops)core [, (bool)CA_only=False [, (bool)bb_only=True]]) -> float :
As above but actually superimposes only the core part (in case there are multiple loops...)
C++ signature :
double loop_rmsd_with_superimpose_core(core::pose::Pose,core::pose::Pose,protocols::loops::Loops,protocols::loops::Loops [,bool=False [,bool=True]])
- loopfinder(...)
- loopfinder( (Pose)pose, (Loops)loops) -> None :
protocols/loops/loopfinder.hh:29
C++ signature :
void loopfinder(core::pose::Pose {lvalue},protocols::loops::Loops {lvalue})
- loops_around_residues(...)
- loops_around_residues( (Loops)loops, (Pose)pose, (vector1_Size)residue_indices [, (int)gapsize=6 [, (int)extend=2]]) -> None :
protocols/loops/make_loops.hh:35
C++ signature :
void loops_around_residues(protocols::loops::Loops {lvalue},core::pose::Pose,utility::vector1<unsigned long, std::allocator<unsigned long> > [,unsigned long=6 [,unsigned long=2]])
- loops_from_string(...)
- loops_from_string( (str)loop_str, (Pose)pose) -> Loops :
loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop
C++ signature :
boost::shared_ptr<protocols::loops::Loops> loops_from_string(std::string,core::pose::Pose)
- loops_set_move_map(...)
- loops_set_move_map( (Loops)loops, (vector1_bool)allow_sc_move, (MoveMap)mm, (bool)allow_omega_move, (bool)allow_takeoff_torsion_move) -> None :
protocols/loops/loops_main.hh:110
C++ signature :
void loops_set_move_map(protocols::loops::Loops,utility::vector1<bool, std::allocator<bool> >,core::kinematics::MoveMap {lvalue},bool,bool)
loops_set_move_map( (Loops)loops, (vector1_bool)allow_sc_move, (MoveMap)mm) -> None :
create a MoveMap for use of minimization based on loop definition
C++ signature :
void loops_set_move_map(protocols::loops::Loops,utility::vector1<bool, std::allocator<bool> >,core::kinematics::MoveMap {lvalue})
loops_set_move_map( (Pose)pose, (Loops)loops, (bool)fix_template_sc, (MoveMap)mm [, (float)neighbor_dist=10.0]) -> None :
protocols/loops/loops_main.hh:93
C++ signature :
void loops_set_move_map(core::pose::Pose {lvalue},protocols::loops::Loops,bool,core::kinematics::MoveMap {lvalue} [,double=10.0])
loops_set_move_map( (Pose)pose, (Loops)loops, (bool)fix_template_sc, (MoveMap)mm, (float)neighbor_dist, (bool)allow_omega_move, (bool)allow_takeoff_torsion_move) -> None :
create a MoveMap for use of minimization based on loop definition (wrapper)
C++ signature :
void loops_set_move_map(core::pose::Pose {lvalue},protocols::loops::Loops,bool,core::kinematics::MoveMap {lvalue},double,bool,bool)
- make_dna_rigid(...)
- make_dna_rigid( (Pose)pose, (MoveMap)mm) -> None :
Make DNA Rigid in movemap if found in pose
C++ signature :
void make_dna_rigid(core::pose::Pose {lvalue},core::kinematics::MoveMap {lvalue})
- make_pose_from_frags(...)
- make_pose_from_frags( (Pose)pose, (str)sequence, (object)frags [, (bool)chains=False]) -> None :
core/fragment/util.hh:142
C++ signature :
void make_pose_from_frags(core::pose::Pose {lvalue},std::string,utility::vector1<boost::shared_ptr<core::fragment::FragData const>, std::allocator<boost::shared_ptr<core::fragment::FragData const> > > [,bool=False])
- make_pose_from_sequence(...)
- make_pose_from_sequence( (Pose)pose, (str)sequence, (str)type_set_name [, (bool)auto_termini=True]) -> None :
Creates a Pose from the annotated protein sequence <sequence>
with the desired <type_set_name> and stores it in <pose>
: any existing data in <pose> is cleared, auto_termini
mark position 1, last_residue with lower, upper termini; default true
C++ signature :
void make_pose_from_sequence(core::pose::Pose {lvalue},std::string,std::string [,bool=True])
make_pose_from_sequence( (Pose)pose, (str)sequence, (ResidueTypeSet)residue_set [, (bool)auto_termini=True]) -> None :
core/pose/annotated_sequence.hh:85
C++ signature :
void make_pose_from_sequence(core::pose::Pose {lvalue},std::string,core::chemical::ResidueTypeSet [,bool=True])
make_pose_from_sequence( (Pose)pose, (object)requested_types [, (bool)auto_termini=True]) -> None :
Creates a Pose from the annotated protein sequence <sequence>
with ResidueTypeSet <residue_set> and stores it in <pose>
: any existing data in <pose> is cleared, auto_termini
mark position 1, last_residue with lower, upper termini; default true
example(s):
make_pose_from_sequence(pose,"THANKSEVAN","fa_standard")
See also:
Pose
PDBInfo
pose_from_pdb
pose_from_rcsb
pose_from_sequence
C++ signature :
void make_pose_from_sequence(core::pose::Pose {lvalue},utility::vector1<boost::shared_ptr<core::chemical::ResidueType const>, std::allocator<boost::shared_ptr<core::chemical::ResidueType const> > > [,bool=True])
- make_simple_fold_tree_from_jump_frame(...)
- make_simple_fold_tree_from_jump_frame( (Frame), (int)total_residue, (FoldTree)new_fold_tree) -> None :
given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the
Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments
later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to
fit the FRAME ... if not it returns failure...
C++ signature :
void make_simple_fold_tree_from_jump_frame(core::fragment::Frame,unsigned long,core::kinematics::FoldTree {lvalue})
- map_char_to_torsion_bin(...)
- map_char_to_torsion_bin( (str)torbin) -> ppo_torsion_bin :
returns the torsion bin that the input character represents
C++ signature :
core::conformation::ppo_torsion_bin map_char_to_torsion_bin(char)
- map_string_to_torsion_bin_string(...)
- map_string_to_torsion_bin_string( (str)torstring) -> object :
convert a string of characters into a vector of the internally recognized ppo_torsion_bin enumeration
@throws utility::excn::EXCN_MsgException if any of the input characters in this string are invalid
C++ signature :
utility::vector0<core::conformation::ppo_torsion_bin, std::allocator<core::conformation::ppo_torsion_bin> > map_string_to_torsion_bin_string(std::string)
- map_torsion_bin_to_char(...)
- map_torsion_bin_to_char( (ppo_torsion_bin)torbin) -> str :
convert a torsion bin to a character s.t. that character can be converted back to a torsion bin
C++ signature :
char map_torsion_bin_to_char(core::conformation::ppo_torsion_bin)
- merge_frags(...)
- merge_frags( (FragSet)good_frags, (FragSet)filling, (int)min_nr_frags [, (bool)bRandom=True]) -> FragSet :
core/fragment/util.hh:95
C++ signature :
boost::shared_ptr<core::fragment::FragSet> merge_frags(core::fragment::FragSet,core::fragment::FragSet,unsigned long [,bool=True])
- modify_ResId_based_object(...)
- modify_ResId_based_object( (object)obj, (int)resid) -> None :
Checks whether a referencecount object is a derived from ResId and if so, sets its resid
C++ signature :
void modify_ResId_based_object(boost::shared_ptr<utility::pointer::ReferenceCount>,unsigned long)
- modify_atom_properties_from_command_line(...)
- modify_atom_properties_from_command_line( (str)atom_type_set_tag, (AtomTypeSet)atom_type_set) -> None :
Modify atom_type properties from the command line.
C++ signature :
void modify_atom_properties_from_command_line(std::string,core::chemical::AtomTypeSet {lvalue})
- move_map_from_loop(...)
- move_map_from_loop( (Pose)pose, (Loop)loop, (bool)fix_template_sc [, (float)neighbor_dist=10.0 [, (bool)flanking_residues=False]]) -> MoveMap :
Create a new MoveMapOP for use in minimizing the given loop.
C++ signature :
boost::shared_ptr<core::kinematics::MoveMap> move_map_from_loop(core::pose::Pose {lvalue},protocols::loops::Loop,bool [,double=10.0 [,bool=False]])
- move_map_from_loops(...)
- move_map_from_loops( (Pose)pose, (Loops)loops, (bool)fix_template_sc [, (float)neighbor_dist=10.0 [, (bool)flanking_residues=False]]) -> MoveMap :
Create a new MoveMapOP for use in minimizing the given loop.
C++ signature :
boost::shared_ptr<core::kinematics::MoveMap> move_map_from_loops(core::pose::Pose {lvalue},protocols::loops::Loops,bool [,double=10.0 [,bool=False]])
- mstype_from_name(...)
- mstype_from_name( (str)name) -> MoverStatus :
protocols/moves/MoverStatus.hh:35
C++ signature :
protocols::moves::MoverStatus mstype_from_name(std::string)
- name_from_aa(...)
- name_from_aa( (AA)aa) -> str :
////////////////////////////////////////////////////
give a enum type and return the string name
////////////////////////////////////////////////////
C++ signature :
std::string name_from_aa(core::chemical::AA)
- name_from_score_type(...)
- name_from_score_type( (ScoreType)score_type) -> str :
Returns the name of the ScoreType <score_type>
example(s):
name_from_score_type(fa_sol)
See also:
ScoreFunction
ScoreType
Energies
Energies.residue_total_energies
score_type_from_name
C++ signature :
std::string name_from_score_type(core::scoring::ScoreType)
- named_atom_id_to_atom_id(...)
- named_atom_id_to_atom_id( (NamedAtomID)atom_id, (Residue)rsd) -> AtomID :
core/conformation/util.hh:364
C++ signature :
core::id::AtomID named_atom_id_to_atom_id(core::id::NamedAtomID,core::conformation::Residue)
- native_CA_gdtmm(...)
- native_CA_gdtmm( (Pose)native_pose, (Pose)pose) -> float :
core/scoring/rms_util.hh:56
C++ signature :
double native_CA_gdtmm(core::pose::Pose,core::pose::Pose)
- native_CA_rmsd(...)
- native_CA_rmsd( (Pose)native_pose, (Pose)pose) -> float :
core/scoring/rms_util.hh:54
C++ signature :
double native_CA_rmsd(core::pose::Pose,core::pose::Pose)
- native_loop_core_CA_rmsd(...)
- native_loop_core_CA_rmsd( (Pose)native_pose, (Pose)pose, (Loops)loops, (int)corelength) -> float :
protocols/loops/loops_main.hh:251
C++ signature :
double native_loop_core_CA_rmsd(core::pose::Pose,core::pose::Pose,protocols::loops::Loops,int {lvalue})
- nbr_atom_rmsd(...)
- nbr_atom_rmsd( (Pose)pose1, (Pose)pose2) -> float :
core/scoring/rms_util.hh:362
C++ signature :
double nbr_atom_rmsd(core::pose::Pose,core::pose::Pose)
- non_peptide_heavy_atom_RMSD(...)
- non_peptide_heavy_atom_RMSD( (Pose)pose1, (Pose)pose2) -> float :
///////////////////////////////////////////////////////////////////////////
Return the RMSD of the non-peptide heavy atoms of two poses.
C++ signature :
double non_peptide_heavy_atom_RMSD(core::pose::Pose,core::pose::Pose)
- nonadduct_variants_match(...)
- nonadduct_variants_match( (ResidueType)res1, (ResidueType)res2) -> bool :
Similar to variants_match(), but allows different adduct-modified states.
C++ signature :
bool nonadduct_variants_match(core::chemical::ResidueType,core::chemical::ResidueType)
- nonconst_MembraneEmbed_from_pose(...)
- nonconst_MembraneEmbed_from_pose( (Pose)pose) -> MembraneEmbed :
Add Non Const Membrane Embedding to the pose cache
C++ signature :
core::scoring::MembraneEmbed {lvalue} nonconst_MembraneEmbed_from_pose(core::pose::Pose {lvalue})
- nonconst_MembraneTopology_from_pose(...)
- nonconst_MembraneTopology_from_pose( (Pose)pose) -> MembraneTopology :
core/scoring/MembraneTopology.hh:263
C++ signature :
core::scoring::MembraneTopology {lvalue} nonconst_MembraneTopology_from_pose(core::pose::Pose {lvalue})
- nonconst_Membrane_FAEmbed_from_pose(...)
- nonconst_Membrane_FAEmbed_from_pose( (Pose)) -> Membrane_FAEmbed :
Grab Const MP Fa embedding data from the pose cache
C++ signature :
core::scoring::Membrane_FAEmbed {lvalue} nonconst_Membrane_FAEmbed_from_pose(core::pose::Pose {lvalue})
- normalizing_area(...)
- normalizing_area( (str)res) -> float :
core/scoring/sasa.hh:59
C++ signature :
double normalizing_area(char)
- onError(...)
- onError( (str)message) -> None :
core/pack/task/ResfileReader.hh:756
C++ signature :
void onError(std::string)
- oneletter_code_from_aa(...)
- oneletter_code_from_aa( (AA)aa) -> str :
////////////////////////////////////////////////////
give a enum type and return the string name
////////////////////////////////////////////////////
C++ signature :
char oneletter_code_from_aa(core::chemical::AA)
- oneletter_code_specifies_aa(...)
- oneletter_code_specifies_aa( (str)onelettercode) -> bool :
core/chemical/AA.hh:194
C++ signature :
bool oneletter_code_specifies_aa(char)
- orient_residue_for_ideal_bond(...)
- orient_residue_for_ideal_bond( (Residue)moving_rsd, (ResidueConnection)moving_connection, (Residue)fixed_rsd, (ResidueConnection)fixed_connection, (Conformation)conformation [, (bool)lookup_bond_length=False]) -> None :
core/conformation/util.hh:59
C++ signature :
void orient_residue_for_ideal_bond(core::conformation::Residue {lvalue},core::chemical::ResidueConnection,core::conformation::Residue,core::chemical::ResidueConnection,core::conformation::Conformation [,bool=False])
- parse_adduct_string(...)
- parse_adduct_string( (object)add_vec) -> map_string_int :
Convert input string to map of adducts->max usage
C++ signature :
std::map<std::string, int, std::less<std::string>, std::allocator<std::pair<std::string const, int> > > parse_adduct_string(utility::options::StringVectorOption {lvalue})
- parse_resfile(...)
- parse_resfile( (Pose)pose, (PackerTask)the_task, (str)filename) -> None :
changes the state of the given PackerTask according to the commands in the resfile at filename
C++ signature :
void parse_resfile(core::pose::Pose,core::pack::task::PackerTask {lvalue},std::string)
parse_resfile( (Pose)pose, (PackerTask)the_task) -> None :
changes the state of the given PackerTask according to the commands in the resfile at read in from the -pack:resfile option system.
C++ signature :
void parse_resfile(core::pose::Pose,core::pack::task::PackerTask {lvalue})
- parse_resfile_string(...)
- parse_resfile_string( (Pose)pose, (PackerTask)the_task, (str)resfile_string) -> None :
changes the state of the given PackerTask according to the commands in the resfile.
C++ signature :
void parse_resfile_string(core::pose::Pose,core::pack::task::PackerTask {lvalue},std::string)
- patch_operation_from_patch_file_line(...)
- patch_operation_from_patch_file_line( (str)line) -> PatchOperation :
Virtual constructor, returns 0 if no match
C++ signature :
boost::shared_ptr<core::chemical::PatchOperation> patch_operation_from_patch_file_line(std::string)
- pick_loopy_cutpoint(...)
- pick_loopy_cutpoint( (int)n_res, (object)cut_bias_sum) -> int :
core/kinematics/util.hh:54
C++ signature :
int pick_loopy_cutpoint(unsigned long,ObjexxFCL::FArray1D<float>)
- pose_from_pdb(...)
- pose_from_pdb( (vector1_Pose)poses, (str)filename [, (bool)read_fold_tree=False]) -> None :
Reads data from an input PDB containing multiple models named
<filename> and stores it in a vector of Pose objects named <poses>
using the FA_STANDARD ResidueTypeSet (fullatom)
C++ signature :
void pose_from_pdb(utility::vector1<core::pose::Pose, std::allocator<core::pose::Pose> > {lvalue},std::string [,bool=False])
pose_from_pdb( (vector1_Pose)poses, (ResidueTypeSet)residue_set, (str)filename, (ImportPoseOptions)options [, (bool)read_fold_tree=False]) -> None :
core/import_pose/import_pose.hh:158
C++ signature :
void pose_from_pdb(utility::vector1<core::pose::Pose, std::allocator<core::pose::Pose> > {lvalue},core::chemical::ResidueTypeSet,std::string,core::import_pose::ImportPoseOptions [,bool=False])
pose_from_pdb( (vector1_Pose)poses, (ResidueTypeSet)residue_set, (str)filename [, (bool)read_fold_tree=False]) -> None :
Reads data from an input PDB containing multiple models named
<filename> and stores it in a vector of Pose objects named <poses> using
ResidueTypeSet <residue_set>
C++ signature :
void pose_from_pdb(utility::vector1<core::pose::Pose, std::allocator<core::pose::Pose> > {lvalue},core::chemical::ResidueTypeSet,std::string [,bool=False])
pose_from_pdb( (Pose)pose, (str)filename, (ImportPoseOptions)options [, (bool)read_fold_tree=False]) -> None :
core/import_pose/import_pose.hh:138
C++ signature :
void pose_from_pdb(core::pose::Pose {lvalue},std::string,core::import_pose::ImportPoseOptions [,bool=False])
pose_from_pdb( (Pose)pose, (str)filename [, (bool)read_fold_tree=False]) -> None :
Reads in data from input PDB <filename> and stores it in the Pose
<pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default
: will use centroid if in::file::centroid_input is true
example(s):
pose_from_pdb(pose,"YFP.pdb")
See also:
Pose
PDBInfo
C++ signature :
void pose_from_pdb(core::pose::Pose {lvalue},std::string [,bool=False])
pose_from_pdb( (Pose)pose, (ResidueTypeSet)residue_set, (str)filename [, (bool)read_fold_tree=False]) -> None :
Reads in data from input PDB <filename> and stores it in the Pose
<pose>, this constructor allows for a non-default ResidueTypeSet
<residue_set>
C++ signature :
void pose_from_pdb(core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,std::string [,bool=False])
pose_from_pdb( (Pose)pose, (ResidueTypeSet)residue_set, (str)filename, (ImportPoseOptions)options [, (bool)read_fold_tree=False]) -> None :
core/import_pose/import_pose.hh:103
C++ signature :
void pose_from_pdb(core::pose::Pose {lvalue},core::chemical::ResidueTypeSet,std::string,core::import_pose::ImportPoseOptions [,bool=False])
pose_from_pdb( (ResidueTypeSet)residue_set, (str)filename [, (bool)read_fold_tree=False]) -> Pose :
Returns a PoseOP object from the Pose created by reading the input
PDB <filename>, this constructor allows for a non-default ResidueTypeSet
<residue_set>
C++ signature :
boost::shared_ptr<core::pose::Pose> pose_from_pdb(core::chemical::ResidueTypeSet,std::string [,bool=False])
pose_from_pdb( (str)filename [, (bool)read_fold_tree=False]) -> Pose :
Returns a PoseOP object from the Pose created from input
PDB <filename>
: in PyRosetta, this will return a Pose object
example(s):
pose = pose_from_pdb("YFP.pdb")
See also:
Pose
PDBInfo
make_pose_from_sequence
pose_from_rcsb
pose_from_sequence
C++ signature :
boost::shared_ptr<core::pose::Pose> pose_from_pdb(std::string [,bool=False])
- pretty_print_atomicoor(...)
- pretty_print_atomicoor( (OStream)out, (AtomICoor)start, (ResidueType)rsd_type [, (int)indent=0]) -> None :
core/chemical/AtomICoor.hh:385
C++ signature :
void pretty_print_atomicoor(std::ostream {lvalue},core::chemical::AtomICoor,core::chemical::ResidueType [,unsigned long=0])
- print_chis(...)
- print_chis( (OStream)out, (ResidueType)res) -> None :
Utility to examine chi output.
C++ signature :
void print_chis(std::ostream {lvalue},core::chemical::ResidueType)
- promote_sameresidue_child_of_jump_atom(...)
- promote_sameresidue_child_of_jump_atom( (Edge)edge, (object)residues, (AtomTree)atom_tree) -> None :
Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list
C++ signature :
void promote_sameresidue_child_of_jump_atom(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})
promote_sameresidue_child_of_jump_atom( (Edge)edge, (object)residues, (object)atom_pointer) -> None :
Moves the first same-residue child of the jump atom corresponding to edge into first place in the child list
C++ signature :
void promote_sameresidue_child_of_jump_atom(core::kinematics::Edge,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> >)
- read_conformers_from_database_file_for_ring_size(...)
- read_conformers_from_database_file_for_ring_size( (str)filename, (int)ring_size) -> object :
Return a list of ring conformers, read from a database file.
C++ signature :
utility::vector1<core::chemical::RingConformer, std::allocator<core::chemical::RingConformer> > read_conformers_from_database_file_for_ring_size(std::string,unsigned long)
- read_loop_fragments(...)
- read_loop_fragments( (object)frag_libs) -> None :
protocols/loops/loops_main.hh:236
C++ signature :
void read_loop_fragments(utility::vector1<boost::shared_ptr<core::fragment::FragSet>, std::allocator<boost::shared_ptr<core::fragment::FragSet> > > {lvalue})
read_loop_fragments( (object)frag_libs) -> None :
protocols/loops/loops_main.hh:232
C++ signature :
void read_loop_fragments(std::vector<boost::shared_ptr<core::fragment::FragSet>, std::allocator<boost::shared_ptr<core::fragment::FragSet> > > {lvalue})
- read_std_frags_from_cmd(...)
- read_std_frags_from_cmd( (FragSet)fragset_large, (FragSet)fragset_small) -> None :
core/fragment/util.hh:126
C++ signature :
void read_std_frags_from_cmd(boost::shared_ptr<core::fragment::FragSet> {lvalue},boost::shared_ptr<core::fragment::FragSet> {lvalue})
- read_topology_file(...)
- read_topology_file( (object)istream, (AtomTypeSetCAP)atom_types, (ElementSetCAP)elements, (MMAtomTypeSetCAP)mm_atom_types, (OrbitalTypeSetCAP)orbital_atom_types, (ResidueTypeSetCAP)rsd_type_set) -> ResidueType :
core/chemical/residue_io.hh:57
C++ signature :
boost::shared_ptr<core::chemical::ResidueType> read_topology_file(utility::io::izstream {lvalue},boost::weak_ptr<core::chemical::AtomTypeSet const>,boost::weak_ptr<core::chemical::ElementSet const>,boost::weak_ptr<core::chemical::MMAtomTypeSet const>,boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>,boost::weak_ptr<core::chemical::ResidueTypeSet const>)
read_topology_file( (str)filename, (AtomTypeSetCAP)atom_types, (ElementSetCAP)elements, (MMAtomTypeSetCAP)mm_atom_types, (OrbitalTypeSetCAP)orbital_atom_types, (ResidueTypeSetCAP)rsd_type_set) -> ResidueType :
virtual constructor for ResidueType objects
C++ signature :
boost::shared_ptr<core::chemical::ResidueType> read_topology_file(std::string,boost::weak_ptr<core::chemical::AtomTypeSet const>,boost::weak_ptr<core::chemical::ElementSet const>,boost::weak_ptr<core::chemical::MMAtomTypeSet const>,boost::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>,boost::weak_ptr<core::chemical::ResidueTypeSet const>)
- register_options_broker(...)
- register_options_broker() -> None :
Registers options that are relevant to the application. This function
must be called prior to Broker_main() or Loopbuild_Threading_main().
C++ signature :
void register_options_broker()
- relax_pose(...)
- relax_pose( (Pose)pose, (__CPP_ScoreFunction__)scorefxn, (str)tag) -> None :
protocols/relax/util.hh:42
C++ signature :
void relax_pose(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction>,std::string)
- remap_cis_omega_torsion_bins_to_trans(...)
- remap_cis_omega_torsion_bins_to_trans( (ppo_torsion_bin)torbin) -> ppo_torsion_bin :
core/conformation/ppo_torsion_bin.hh:40
C++ signature :
core::conformation::ppo_torsion_bin remap_cis_omega_torsion_bins_to_trans(core::conformation::ppo_torsion_bin)
- remodel_fold_tree_to_account_for_insertion(...)
- remodel_fold_tree_to_account_for_insertion( (FoldTree)input_tree, (int)insert_after, (int)insert_size) -> FoldTree :
remodel a fold tree to account for a large insertion by adding the size of the insert to upstream positions
Steven Lewis smlewi@gmail.com as a favor for Jared
C++ signature :
core::kinematics::FoldTree remodel_fold_tree_to_account_for_insertion(core::kinematics::FoldTree,unsigned long,unsigned long)
- remove_cutpoint_variants(...)
- remove_cutpoint_variants( (Pose)pose [, (bool)force=False]) -> None :
Remove cutpoint variants
C++ signature :
void remove_cutpoint_variants(core::pose::Pose {lvalue} [,bool=False])
- remove_lower_terminus_type_from_conformation_residue(...)
- remove_lower_terminus_type_from_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
core/conformation/util.hh:165
C++ signature :
void remove_lower_terminus_type_from_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)
- remove_missing_density(...)
- remove_missing_density( (Pose)pose, (Loop)loop) -> None :
///////////////////////////////////////////////////////////////////////////////
Rebuild a loop via fragment insertion + ccd closure + minimization
C++ signature :
void remove_missing_density(core::pose::Pose {lvalue},protocols::loops::Loop)
- remove_short_chunks(...)
- remove_short_chunks( (Loops)input_chunks [, (int)min_length=3]) -> Loops :
Remove small chunks
C++ signature :
protocols::loops::Loops remove_short_chunks(protocols::loops::Loops [,unsigned long=3])
- remove_small_gaps(...)
- remove_small_gaps( (Loops)input_chunks [, (int)gap_size=1]) -> Loops :
If two chunks are separated by a small gap of size <= <gap_size>, combine them
C++ signature :
protocols::loops::Loops remove_small_gaps(protocols::loops::Loops [,unsigned long=1])
- remove_upper_terminus_type_from_conformation_residue(...)
- remove_upper_terminus_type_from_conformation_residue( (Conformation)conformation, (int)seqpos) -> None :
core/conformation/util.hh:172
C++ signature :
void remove_upper_terminus_type_from_conformation_residue(core::conformation::Conformation {lvalue},unsigned long)
- remove_variant_type_from_conformation_residue(...)
- remove_variant_type_from_conformation_residue( (Conformation)conformation, (VariantType)variant_type, (int)seqpos) -> None :
Construct a non-variant of an existing conformation residue.
C++ signature :
void remove_variant_type_from_conformation_residue(core::conformation::Conformation {lvalue},core::chemical::VariantType,unsigned long)
- rename_atoms(...)
- rename_atoms( (ResidueType)res [, (bool)preserve=True]) -> None :
Rename atoms in the residue type such that their names are unique.
If preserve is true, only rename those which have no names or who have
name conflicts. (Both of the conflicting atoms will be renamed.)
C++ signature :
void rename_atoms(core::chemical::ResidueType {lvalue} [,bool=True])
- replace_conformation_residue_copying_existing_coordinates(...)
- replace_conformation_residue_copying_existing_coordinates( (Conformation)conformation, (int)seqpos, (ResidueType)new_rsd_type) -> None :
core/conformation/util.hh:132
C++ signature :
void replace_conformation_residue_copying_existing_coordinates(core::conformation::Conformation {lvalue},unsigned long,core::chemical::ResidueType)
- replace_residue_in_atom_tree(...)
- replace_residue_in_atom_tree( (Residue)new_rsd, (FoldTree)fold_tree, (object)residues, (AtomTree)atom_tree) -> None :
Helper function for conformation routines
C++ signature :
void replace_residue_in_atom_tree(core::conformation::Residue,core::kinematics::FoldTree,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::kinematics::AtomTree {lvalue})
- reroot_restype(...)
- reroot_restype( (ResidueType)restype, (object)graph, (object)root) -> None :
core/chemical/icoor_support.hh:39
C++ signature :
void reroot_restype(core::chemical::ResidueType {lvalue},boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>,void*)
- residue_point_graph_from_conformation(...)
- residue_point_graph_from_conformation( (Conformation)conformation, (UpperEdgeGraph_T_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_T)pg) -> None :
core/conformation/PointGraph.hh:43
C++ signature :
void residue_point_graph_from_conformation(core::conformation::Conformation,core::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> {lvalue})
- residue_sc_rmsd_no_super(...)
- residue_sc_rmsd_no_super( (Residue)res1, (Residue)res2 [, (bool)fxnal_group_only=False]) -> float :
utility function to calculate per-residue sidechain rmsd without superposition
C++ signature :
double residue_sc_rmsd_no_super(boost::shared_ptr<core::conformation::Residue const>,boost::shared_ptr<core::conformation::Residue const> [,bool=False])
- residue_selector_single_from_line(...)
- residue_selector_single_from_line( (str)line) -> ResidueSelectorSingle :
/////////////////////////////////////////////////////////////////////////////////////
create a singe ResidueSelector from an input line.
C++ signature :
boost::shared_ptr<core::chemical::ResidueSelectorSingle> residue_selector_single_from_line(std::string)
- residue_type_all_patches_name(...)
- residue_type_all_patches_name( (ResidueType)rsd_type) -> str :
helper function, returns the name of all added patches
C++ signature :
std::string residue_type_all_patches_name(core::chemical::ResidueType)
- residue_type_base_name(...)
- residue_type_base_name( (ResidueType)rsd_type) -> str :
helper function, returns the base residue name prior to any patching
C++ signature :
std::string residue_type_base_name(core::chemical::ResidueType)
- retain_top(...)
- retain_top( (int)k, (FragSet)fragments) -> None :
Removes all but the top <k> fragments from <fragments>
C++ signature :
void retain_top(unsigned long,boost::shared_ptr<core::fragment::FragSet>)
- retrieve_CSA_from_pose(...)
- retrieve_CSA_from_pose( (Pose)) -> ChemicalShiftAnisotropy :
core/scoring/ChemicalShiftAnisotropy.hh:34
C++ signature :
boost::shared_ptr<core::scoring::ChemicalShiftAnisotropy const> retrieve_CSA_from_pose(core::pose::Pose)
retrieve_CSA_from_pose( (Pose)) -> ChemicalShiftAnisotropy :
core/scoring/ChemicalShiftAnisotropy.hh:33
C++ signature :
boost::shared_ptr<core::scoring::ChemicalShiftAnisotropy> retrieve_CSA_from_pose(core::pose::Pose {lvalue})
- retrieve_DC_from_pose(...)
- retrieve_DC_from_pose( (Pose)) -> DipolarCoupling :
core/scoring/DipolarCoupling.hh:34
C++ signature :
boost::shared_ptr<core::scoring::DipolarCoupling const> retrieve_DC_from_pose(core::pose::Pose)
retrieve_DC_from_pose( (Pose)) -> DipolarCoupling :
core/scoring/DipolarCoupling.hh:33
C++ signature :
boost::shared_ptr<core::scoring::DipolarCoupling> retrieve_DC_from_pose(core::pose::Pose {lvalue})
- retrieve_RDC_ROHL_from_pose(...)
- retrieve_RDC_ROHL_from_pose( (Pose)) -> ResidualDipolarCoupling_Rohl :
core/scoring/ResidualDipolarCoupling_Rohl.hh:32
C++ signature :
boost::shared_ptr<core::scoring::ResidualDipolarCoupling_Rohl const> retrieve_RDC_ROHL_from_pose(core::pose::Pose)
retrieve_RDC_ROHL_from_pose( (Pose)) -> ResidualDipolarCoupling_Rohl :
core/scoring/ResidualDipolarCoupling_Rohl.hh:31
C++ signature :
boost::shared_ptr<core::scoring::ResidualDipolarCoupling_Rohl> retrieve_RDC_ROHL_from_pose(core::pose::Pose {lvalue})
- retrieve_RDC_from_pose(...)
- retrieve_RDC_from_pose( (Pose)) -> ResidualDipolarCoupling :
core/scoring/ResidualDipolarCoupling.hh:32
C++ signature :
boost::shared_ptr<core::scoring::ResidualDipolarCoupling const> retrieve_RDC_from_pose(core::pose::Pose)
retrieve_RDC_from_pose( (Pose)) -> ResidualDipolarCoupling :
core/scoring/ResidualDipolarCoupling.hh:31
C++ signature :
boost::shared_ptr<core::scoring::ResidualDipolarCoupling> retrieve_RDC_from_pose(core::pose::Pose {lvalue})
- retype_is_aromatic(...)
- retype_is_aromatic( (object)atom, (object)graph) -> bool :
core/chemical/atomtype_support.hh:24
C++ signature :
bool retype_is_aromatic(void*,boost::undirected_graph<core::chemical::Atom, core::chemical::Bond, boost::no_property>)
- rms_at_all_corresponding_atoms(...)
- rms_at_all_corresponding_atoms( (Pose)mod_pose, (Pose)ref_pose, (object)atom_id_map) -> float :
core/scoring/rms_util.hh:560
C++ signature :
double rms_at_all_corresponding_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >)
- rms_at_corresponding_atoms(...)
- rms_at_corresponding_atoms( (Pose)mod_pose, (Pose)ref_pose, (object)atom_id_map, (vector1_Size)calc_rms_res) -> float :
core/scoring/rms_util.hh:568
C++ signature :
double rms_at_corresponding_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >,utility::vector1<unsigned long, std::allocator<unsigned long> >)
rms_at_corresponding_atoms( (Pose)mod_pose, (Pose)ref_pose, (object)atom_id_map) -> float :
core/scoring/rms_util.hh:553
C++ signature :
double rms_at_corresponding_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >)
- rms_at_corresponding_atoms_no_super(...)
- rms_at_corresponding_atoms_no_super( (Pose)mod_pose, (Pose)ref_pose, (object)atom_id_map, (vector1_Size)calc_rms_res) -> float :
core/scoring/rms_util.hh:582
C++ signature :
double rms_at_corresponding_atoms_no_super(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >,utility::vector1<unsigned long, std::allocator<unsigned long> >)
rms_at_corresponding_atoms_no_super( (Pose)mod_pose, (Pose)ref_pose, (object)atom_id_map) -> float :
core/scoring/rms_util.hh:574
C++ signature :
double rms_at_corresponding_atoms_no_super(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >)
- rms_at_corresponding_heavy_atoms(...)
- rms_at_corresponding_heavy_atoms( (Pose)mod_pose, (Pose)ref_pose) -> float :
core/scoring/rms_util.hh:590
C++ signature :
double rms_at_corresponding_heavy_atoms(core::pose::Pose,core::pose::Pose)
- rosetta_recharge_fullatom(...)
- rosetta_recharge_fullatom( (ResidueType)res) -> None :
Apply molfile_to_params style partial charges to the ResidueType.
These partial charges are based off of the Rosetta atom type,
adjusted such that the net partial charge is equal to the net formal charge.
These charges are almost certainly dodgy. If you have any other source of
partial charges that are at all reasonable, you probably want to consider those instead.
Assumes:
* All atoms and bond are present.
* All atom types have been set.
* Formal charges (if any) have been set.
C++ signature :
void rosetta_recharge_fullatom(core::chemical::ResidueType {lvalue})
- rosetta_retype_fullatom(...)
- rosetta_retype_fullatom( (ResidueType)restype [, (bool)preserve=False]) -> None :
Reassign Rosetta atom types based on the current fullatom heuristics.
If preserve is true, only retype those atoms which have an atom_type_index of zero.
C++ signature :
void rosetta_retype_fullatom(core::chemical::ResidueType {lvalue} [,bool=False])
- rot_sample_from_name(...)
- rot_sample_from_name( (str)name) -> ExtraRotSample :
core/pack/task/RotamerSampleOptions.hh:37
C++ signature :
core::pack::task::ExtraRotSample rot_sample_from_name(std::string)
- rsd_set_from_cmd_line(...)
- rsd_set_from_cmd_line() -> ResidueTypeSetCAP :
Return a constant access pointer to the ResidueTypeSet specified by the command-line options.
C++ signature :
boost::weak_ptr<core::chemical::ResidueTypeSet const> rsd_set_from_cmd_line()
- run_boinc_debug(...)
- run_boinc_debug() -> int :
protocols/abinitio/vs_test.hh:19
C++ signature :
int run_boinc_debug()
- safe_set_extended_torsions_and_idealize_loops(...)
- safe_set_extended_torsions_and_idealize_loops( (Loops)loops, (Pose)pose) -> None :
Identical to set_extended_torsions_and_idealize_loops() without the irrational
behavior surrounding empty loops.
C++ signature :
void safe_set_extended_torsions_and_idealize_loops(protocols::loops::Loops,core::pose::Pose*)
- score_type_from_name(...)
- score_type_from_name( (str)name) -> ScoreType :
Returns the ScoreType titled <name>
example(s):
score_type_from_name("fa_sol")
See also:
ScoreFunction
ScoreType
Energies
Energies.residue_total_energies
name_from_score_type
C++ signature :
core::scoring::ScoreType score_type_from_name(std::string)
- select_loop_frags(...)
- select_loop_frags( (Loops)loops, (FragSet)source, (FragSet)loop_frags [, (int)min_size=1]) -> None :
get frags that are fully within the Loop --- shorten(=true/false) frags that are close to the end of loops.
C++ signature :
void select_loop_frags(protocols::loops::Loops,core::fragment::FragSet {lvalue},core::fragment::FragSet {lvalue} [,unsigned long=1])
- select_loop_residues(...)
- select_loop_residues( (Pose)pose, (Loop)loop, (bool)include_neighbors [, (float)neighbor_dist=10.0]) -> vector1_bool :
protocols/loops/loops_main.hh:192
C++ signature :
utility::vector1<bool, std::allocator<bool> > select_loop_residues(core::pose::Pose,protocols::loops::Loop,bool [,double=10.0])
select_loop_residues( (Pose)pose, (Loop)loop, (bool)include_neighbors, (vector1_bool)map [, (float)neighbor_dist=10.0]) -> None :
protocols/loops/loops_main.hh:184
C++ signature :
void select_loop_residues(core::pose::Pose,protocols::loops::Loop,bool,utility::vector1<bool, std::allocator<bool> > {lvalue} [,double=10.0])
select_loop_residues( (Pose)pose, (Loops)loops, (bool)include_neighbors [, (float)neighbor_dist=10.0]) -> vector1_bool :
mark loop residues and its neighbors as necessary in a sequence map.
C++ signature :
utility::vector1<bool, std::allocator<bool> > select_loop_residues(core::pose::Pose,protocols::loops::Loops,bool [,double=10.0])
select_loop_residues( (Pose)pose, (Loops)loops, (bool)include_neighbors, (vector1_bool)map [, (float)neighbor_dist=10.0]) -> None :
mark loop residues and its neighbors as necessary in a sequence map.
C++ signature :
void select_loop_residues(core::pose::Pose,protocols::loops::Loops,bool,utility::vector1<bool, std::allocator<bool> > {lvalue} [,double=10.0])
- set_chi_according_to_coordinates(...)
- set_chi_according_to_coordinates( (Residue)rotamer) -> None :
rotamer chi-update from coords useful for building rotamers from coordinates
C++ signature :
void set_chi_according_to_coordinates(core::conformation::Residue {lvalue})
- set_extended_torsions(...)
- set_extended_torsions( (Pose)pose, (Loop)loop) -> None :
Set a loop to extended torsion angles.
C++ signature :
void set_extended_torsions(core::pose::Pose {lvalue},protocols::loops::Loop)
- set_extended_torsions_and_idealize_loops(...)
- set_extended_torsions_and_idealize_loops( (Pose)pose, (Loops)loops) -> None :
protocols/loops/util.hh:43
C++ signature :
void set_extended_torsions_and_idealize_loops(core::pose::Pose {lvalue},protocols::loops::Loops)
- set_loop_cutpoint_in_pose_fold_tree(...)
- set_loop_cutpoint_in_pose_fold_tree( (int)new_cutpoint, (Pose)pose, (int)loop_begin, (int)loop_end) -> None :
protocols/loops/loops_main.hh:318
C++ signature :
void set_loop_cutpoint_in_pose_fold_tree(unsigned long,core::pose::Pose {lvalue},unsigned long,unsigned long)
- set_move_map_for_centroid_loop(...)
- set_move_map_for_centroid_loop( (Loop)loop, (MoveMap)mm) -> None :
protocols/loops/loops_main.hh:136
C++ signature :
void set_move_map_for_centroid_loop(protocols::loops::Loop,core::kinematics::MoveMap {lvalue})
- set_secstruct_from_dssp(...)
- set_secstruct_from_dssp( (Pose)pose, (str)filename) -> bool :
another helper function to set secondary structure of a Pose from an external file.
C++ signature :
bool set_secstruct_from_dssp(core::pose::Pose {lvalue},std::string)
- set_secstruct_from_psipred_ss2(...)
- set_secstruct_from_psipred_ss2( (Pose)pose) -> bool :
helper function to set secondary structure of a Pose from an external
file.
C++ signature :
bool set_secstruct_from_psipred_ss2(core::pose::Pose {lvalue})
- set_single_loop_fold_tree(...)
- set_single_loop_fold_tree( (Pose)pose, (Loop)loop) -> None :
///////////////////////////////////////////////////////////////////////////////
Set the fold tree to contain a single chain break at the loops' position
C++ signature :
void set_single_loop_fold_tree(core::pose::Pose {lvalue},protocols::loops::Loop)
- setup_atom_type_reassignments_from_commandline(...)
- setup_atom_type_reassignments_from_commandline( (str)rsd_type_name, (str)rsd_type_set_name, (map_string_string)atom_type_reassignments) -> None :
core/chemical/residue_io.hh:71
C++ signature :
void setup_atom_type_reassignments_from_commandline(std::string,std::string,std::map<std::string, std::string, std::less<std::string>, std::allocator<std::pair<std::string const, std::string> > > {lvalue})
- setup_backrub_atom_tree(...)
- setup_backrub_atom_tree( (vector1_AtomID)mainchain, (AtomID)downstream_id, (object)old_atom_pointer, (vector1_pair_Size_Size)edges, (int)first_new_pseudo_residue) -> Atom :
core/kinematics/util.hh:63
C++ signature :
boost::shared_ptr<core::kinematics::tree::Atom> setup_backrub_atom_tree(utility::vector1<core::id::AtomID, std::allocator<core::id::AtomID> >,core::id::AtomID,core::id::AtomID_Map<boost::shared_ptr<core::kinematics::tree::Atom> >,utility::vector1<std::pair<unsigned long, unsigned long>, std::allocator<std::pair<unsigned long, unsigned long> > >,unsigned long)
- setup_corresponding_atoms(...)
- setup_corresponding_atoms( (AtomID_Map_T_core_id_AtomID_T)atom_map, (Residue)rsd1, (Residue)rsd2) -> None :
set up a map to match mainchain atoms from residue1 to residue2
C++ signature :
void setup_corresponding_atoms(core::id::AtomID_Map<core::id::AtomID> {lvalue},core::conformation::Residue,core::conformation::Residue)
- setup_foldtree(...)
- setup_foldtree( (Pose)pose, (int)cutpoint, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
protocols/docking/util.hh:96
C++ signature :
void setup_foldtree(core::pose::Pose,unsigned long,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})
setup_foldtree( (Pose)pose, (int)cutpoint, (vector1_int)movable_jumps) -> None :
Sets up a docking fold tree based on user-specified chains for the first and second partner
C++ signature :
void setup_foldtree(core::pose::Pose {lvalue},unsigned long,utility::vector1<int, std::allocator<int> > {lvalue})
setup_foldtree( (Pose)pose, (object)partner_to_chains, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
protocols/docking/util.hh:81
C++ signature :
void setup_foldtree(core::pose::Pose,std::map<unsigned long, utility::vector1<unsigned long, std::allocator<unsigned long> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, utility::vector1<unsigned long, std::allocator<unsigned long> > > > >,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})
setup_foldtree( (Pose)pose, (object)partner_to_chains, (vector1_int)movable_jumps) -> None :
Sets up a docking fold tree based on a map of which chains
are part of which partner
C++ signature :
void setup_foldtree(core::pose::Pose {lvalue},std::map<unsigned long, utility::vector1<unsigned long, std::allocator<unsigned long> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, utility::vector1<unsigned long, std::allocator<unsigned long> > > > >,utility::vector1<int, std::allocator<int> > {lvalue})
setup_foldtree( (Pose)pose, (int)interface_id, (object)db_session, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
protocols/docking/util.hh:65
C++ signature :
void setup_foldtree(core::pose::Pose,unsigned long,boost::shared_ptr<utility::sql_database::session>,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})
setup_foldtree( (Pose)pose, (int)interface_id, (object)db_session, (vector1_int)movable_jumps) -> None :
Sets up a docking fold tree based on looking up the
interface in a database
C++ signature :
void setup_foldtree(core::pose::Pose {lvalue},unsigned long,boost::shared_ptr<utility::sql_database::session>,utility::vector1<int, std::allocator<int> > {lvalue})
setup_foldtree( (Pose)pose, (str)partner_chainID, (vector1_int)movable_jumps, (FoldTree)ft) -> None :
protocols/docking/util.hh:47
C++ signature :
void setup_foldtree(core::pose::Pose,std::string,utility::vector1<int, std::allocator<int> > {lvalue},core::kinematics::FoldTree {lvalue})
setup_foldtree( (Pose)pose, (str)partner_chainID, (vector1_int)movable_jumps) -> None :
Sets up a docking fold tree based on user-specified chains for the first and second partner
C++ signature :
void setup_foldtree(core::pose::Pose {lvalue},std::string,utility::vector1<int, std::allocator<int> > {lvalue})
- setup_for_dna(...)
- setup_for_dna( (ScoreFunction)scorefxn) -> None :
Set energy method options for DNA-DNA. Any other optimization for DNA relax should go here.
C++ signature :
void setup_for_dna(core::scoring::ScoreFunction {lvalue})
- setup_icoor_reassignments_from_commandline(...)
- setup_icoor_reassignments_from_commandline( (str)rsd_type_name, (str)rsd_type_set_name, (object)icoor_reassignments) -> None :
core/chemical/residue_io.hh:79
C++ signature :
void setup_icoor_reassignments_from_commandline(std::string,std::string,std::map<std::string, utility::vector1<std::string, std::allocator<std::string> >, std::less<std::string>, std::allocator<std::pair<std::string const, utility::vector1<std::string, std::allocator<std::string> > > > > {lvalue})
- setup_matching_CA_atoms(...)
- setup_matching_CA_atoms( (Pose)pose1, (Pose)pose2, (object)atom_id_map) -> None :
core/scoring/rms_util.hh:600
C++ signature :
void setup_matching_CA_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > > {lvalue})
- setup_matching_atoms_with_given_names(...)
- setup_matching_atoms_with_given_names( (Pose)pose1, (Pose)pose2, (vector1_string)atom_names_to_find, (object)atom_id_map) -> None :
core/scoring/rms_util.hh:609
C++ signature :
void setup_matching_atoms_with_given_names(core::pose::Pose,core::pose::Pose,utility::vector1<std::string, std::allocator<std::string> >,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > > {lvalue})
- setup_matching_heavy_atoms(...)
- setup_matching_heavy_atoms( (Pose)pose1, (Pose)pose2, (object)atom_id_map) -> None :
core/scoring/rms_util.hh:585
C++ signature :
void setup_matching_heavy_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > > {lvalue})
- setup_matching_protein_backbone_heavy_atoms(...)
- setup_matching_protein_backbone_heavy_atoms( (Pose)pose1, (Pose)pose2, (object)atom_id_map) -> None :
core/scoring/rms_util.hh:604
C++ signature :
void setup_matching_protein_backbone_heavy_atoms(core::pose::Pose,core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > > {lvalue})
- setup_membrane_topology(...)
- setup_membrane_topology( (Pose)pose, (str)spanfile) -> None :
(pba) read in membrane topology
C++ signature :
void setup_membrane_topology(core::pose::Pose {lvalue},std::string)
- setup_vary_polar_hydrogen_geometry(...)
- setup_vary_polar_hydrogen_geometry( (MoveMap)mm, (Pose)pose, (__CPP_AllowInsert__)allow_insert) -> None :
protocols/simple_moves/ConstrainToIdealMover.hh:182
C++ signature :
void setup_vary_polar_hydrogen_geometry(core::kinematics::MoveMap {lvalue},core::pose::Pose {lvalue},boost::shared_ptr<protocols::toolbox::AllowInsert const>)
- setup_vary_rna_bond_geometry(...)
- setup_vary_rna_bond_geometry( (MoveMap)mm, (Pose)pose, (__CPP_AllowInsert__)allow_insert [, (ScoreType)score_type=rosetta.core.scoring.ScoreType.rna_bond_geometry]) -> None :
protocols/simple_moves/ConstrainToIdealMover.hh:178
C++ signature :
void setup_vary_rna_bond_geometry(core::kinematics::MoveMap {lvalue},core::pose::Pose {lvalue},boost::shared_ptr<protocols::toolbox::AllowInsert const> [,core::scoring::ScoreType=rosetta.core.scoring.ScoreType.rna_bond_geometry])
- show_atom_tree(...)
- show_atom_tree( (Atom)atom, (Conformation)conf, (OStream)os) -> None :
core/conformation/util.hh:125
C++ signature :
void show_atom_tree(core::kinematics::tree::Atom,core::conformation::Conformation,std::ostream {lvalue})
- simple_visualize_fold_tree(...)
- simple_visualize_fold_tree( (FoldTree)fold_tree, (OStream)out) -> None :
prints something like this ***1***C***1*********2***C********3****C****2********3*****
C++ signature :
void simple_visualize_fold_tree(core::kinematics::FoldTree,std::ostream {lvalue})
- simple_visualize_fold_tree_and_movemap(...)
- simple_visualize_fold_tree_and_movemap( (FoldTree)fold_tree, (MoveMap)mm, (OStream)out) -> None :
prints something like this ***1***C***1*********2***C********3****C****2********3*****
**********xxxxxxxxxxxxx************************************
C++ signature :
void simple_visualize_fold_tree_and_movemap(core::kinematics::FoldTree,core::kinematics::MoveMap,std::ostream {lvalue})
- simple_visualize_fold_tree_and_movemap_bb_chi(...)
- simple_visualize_fold_tree_and_movemap_bb_chi( (FoldTree)fold_tree, (MoveMap)mm, (OStream)out) -> None :
prints something like this ***1***C***1*********2***C********3****C****2********3*****
**********xxxxxxxxxxxxx************************************
C++ signature :
void simple_visualize_fold_tree_and_movemap_bb_chi(core::kinematics::FoldTree,core::kinematics::MoveMap,std::ostream {lvalue})
- split_by_ca_ca_dist(...)
- split_by_ca_ca_dist( (Pose)pose, (Loops)input_chunks [, (float)CA_CA_distance_cutoff=4]) -> Loops :
Split into separate chunks if CA-CA distance is over the cutoff
C++ signature :
protocols::loops::Loops split_by_ca_ca_dist(core::pose::Pose,protocols::loops::Loops [,double=4])
- split_by_resSeq(...)
- split_by_resSeq( (Pose)pose, (Loops)input_chunks) -> Loops :
protocols/loops/util.hh:105
C++ signature :
protocols::loops::Loops split_by_resSeq(core::pose::Pose,protocols::loops::Loops)
split_by_resSeq( (Pose)pose) -> Loops :
protocols/loops/util.hh:103
C++ signature :
protocols::loops::Loops split_by_resSeq(core::pose::Pose)
- steal_constant_length_frag_set_from_pose(...)
- steal_constant_length_frag_set_from_pose( (Pose)pose, (ConstantLengthFragSet)fragset) -> None :
core/fragment/util.hh:55
C++ signature :
void steal_constant_length_frag_set_from_pose(core::pose::Pose,core::fragment::ConstantLengthFragSet {lvalue})
- steal_frag_set_from_pose(...)
- steal_frag_set_from_pose( (Pose)pose_in, (FragSet)fragset, (__CPP_FragData__)frag_type, (set_Size)active_residues) -> None :
core/fragment/util.hh:76
C++ signature :
void steal_frag_set_from_pose(core::pose::Pose,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>,std::set<unsigned long, std::less<unsigned long>, std::allocator<unsigned long> >)
steal_frag_set_from_pose( (Pose)pose_in, (int)begin, (int)end, (FragSet)fragset, (__CPP_FragData__)frag_type) -> None :
core/fragment/util.hh:69
C++ signature :
void steal_frag_set_from_pose(core::pose::Pose,unsigned long,unsigned long,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>)
steal_frag_set_from_pose( (Pose)pose_in, (FragSet)fragset, (__CPP_FragData__)frag_type) -> None :
core/fragment/util.hh:61
C++ signature :
void steal_frag_set_from_pose(core::pose::Pose,core::fragment::FragSet {lvalue},boost::shared_ptr<core::fragment::FragData const>)
- store_CSA_in_pose(...)
- store_CSA_in_pose( (__CPP_ChemicalShiftAnisotropy__), (Pose)) -> None :
core/scoring/ChemicalShiftAnisotropy.hh:32
C++ signature :
void store_CSA_in_pose(boost::shared_ptr<core::scoring::ChemicalShiftAnisotropy>,core::pose::Pose {lvalue})
- store_DC_in_pose(...)
- store_DC_in_pose( (__CPP_DipolarCoupling__), (Pose)) -> None :
core/scoring/DipolarCoupling.hh:32
C++ signature :
void store_DC_in_pose(boost::shared_ptr<core::scoring::DipolarCoupling>,core::pose::Pose {lvalue})
- store_RDC_ROHL_in_pose(...)
- store_RDC_ROHL_in_pose( (__CPP_ResidualDipolarCoupling_Rohl__), (Pose)) -> None :
core/scoring/ResidualDipolarCoupling_Rohl.hh:30
C++ signature :
void store_RDC_ROHL_in_pose(boost::shared_ptr<core::scoring::ResidualDipolarCoupling_Rohl>,core::pose::Pose {lvalue})
- store_RDC_in_pose(...)
- store_RDC_in_pose( (__CPP_ResidualDipolarCoupling__), (Pose)) -> None :
core/scoring/ResidualDipolarCoupling.hh:30
C++ signature :
void store_RDC_in_pose(boost::shared_ptr<core::scoring::ResidualDipolarCoupling>,core::pose::Pose {lvalue})
- stub_id_to_named_stub_id(...)
- stub_id_to_named_stub_id( (StubID)stub_id, (Residue)rsd) -> NamedStubID :
core/conformation/util.hh:370
C++ signature :
core::id::NamedStubID stub_id_to_named_stub_id(core::id::StubID,core::conformation::Residue)
- superimpose_pose(...)
- superimpose_pose( (Pose)mod_pose, (MiniPose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map) -> float :
Superimpose mod_pose onto ref_pose using the mapping of atoms from
mod_pose to ref_pose given by atom_map
C++ signature :
double superimpose_pose(core::pose::Pose {lvalue},core::pose::MiniPose,core::id::AtomID_Map<core::id::AtomID>)
superimpose_pose( (Pose)mod_pose, (Pose)ref_pose, (AtomID_Map_T_core_id_AtomID_T)atom_map) -> float :
Superimpose mod_pose onto ref_pose using the mapping of atoms from
mod_pose to ref_pose given by atom_map
C++ signature :
double superimpose_pose(core::pose::Pose {lvalue},core::pose::Pose,core::id::AtomID_Map<core::id::AtomID>)
superimpose_pose( (Pose)mod_pose, (Pose)ref_pose, (object)atom_map) -> float :
Superimpose mod_pose onto ref_pose using the mapping of atoms from
mod_pose to ref_pose given by map< AtomID, AtomID >
C++ signature :
double superimpose_pose(core::pose::Pose {lvalue},core::pose::Pose,std::map<core::id::AtomID, core::id::AtomID, std::less<core::id::AtomID>, std::allocator<std::pair<core::id::AtomID const, core::id::AtomID> > >)
- to_string(...)
- to_string( (MCA)mc_accepted) -> str :
protocols/moves/MonteCarloStatus.hh:34
C++ signature :
std::string to_string(protocols::moves::MCA)
- tokenize_line(...)
- tokenize_line( (std_istream)inputstream) -> vector1_string :
utility function for resfile reader
C++ signature :
utility::vector1<std::string, std::allocator<std::string> > tokenize_line(std::istream {lvalue})
- trim_back_sequence_mapping(...)
- trim_back_sequence_mapping( (SequenceMapping)mapping, (str)source_seq, (str)target_seq, (int)min_loop_size) -> None :
Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.
C++ signature :
void trim_back_sequence_mapping(core::id::SequenceMapping {lvalue},std::string,std::string,unsigned long)
- turn_off_hbonds_to_ester_oxygens(...)
- turn_off_hbonds_to_ester_oxygens( (AtomTypeSet)atom_type_set) -> None :
core/chemical/util.hh:77
C++ signature :
void turn_off_hbonds_to_ester_oxygens(core::chemical::AtomTypeSet {lvalue})
- uniform_dof_distribution(...)
- uniform_dof_distribution( (DOF_Type)dof_type, (int)num_bins, (float)min, (float)max) -> vector1_Real :
protocols/simple_moves/DOFHistogramRecorder.hh:173
C++ signature :
utility::vector1<double, std::allocator<double> > uniform_dof_distribution(core::id::DOF_Type,unsigned long,double,double)
- v = is_string_numeric(...)
- is_string_numeric( (str)input) -> bool :
utility/string_util.hh:142
C++ signature :
bool is_string_numeric(std::string)
- validate_loop_start_stop(...)
- validate_loop_start_stop( (bool)prohibit_single_residue_loops, (int)start, (int)stop, (str)filename, (int)linecount) -> None :
Checks if there is a problem with the beginning and ending residues defined
in a loops file.
C++ signature :
void validate_loop_start_stop(bool,unsigned long,unsigned long,std::string,unsigned long)
- variants_match(...)
- variants_match( (ResidueType)res1, (ResidueType)res2) -> bool :
Are these two residues patched in exactly the same way?
C++ signature :
bool variants_match(core::chemical::ResidueType,core::chemical::ResidueType)
- variants_match_with_exceptions(...)
- variants_match_with_exceptions( (ResidueType)res1, (ResidueType)res2, (object)list_of_variants_to_ignore) -> bool :
Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions?
C++ signature :
bool variants_match_with_exceptions(core::chemical::ResidueType,core::chemical::ResidueType,utility::vector1<core::chemical::VariantType, std::allocator<core::chemical::VariantType> >)
- visualize_fold_tree(...)
- visualize_fold_tree( (FoldTree)fold_tree, (map_Size_string)node_labels_partial, (object)mark_jump_to_res, (map_Size_Size)jump_follows) -> str :
core/kinematics/util.hh:109
C++ signature :
std::string visualize_fold_tree(core::kinematics::FoldTree,std::map<unsigned long, std::string, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::string> > >,std::map<unsigned long, char, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, char> > >,std::map<unsigned long, unsigned long, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, unsigned long> > >)
visualize_fold_tree( (FoldTree)fold_tree, (object)mark_jump_to_res) -> str :
core/kinematics/util.hh:101
C++ signature :
std::string visualize_fold_tree(core::kinematics::FoldTree,std::map<unsigned long, char, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, char> > >)
visualize_fold_tree( (FoldTree)fold_tree, (map_Size_string)node_labels_partial) -> str :
core/kinematics/util.hh:95
C++ signature :
std::string visualize_fold_tree(core::kinematics::FoldTree,std::map<unsigned long, std::string, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::string> > >)
visualize_fold_tree( (FoldTree)fold_tree) -> str :
sheffler
C++ signature :
std::string visualize_fold_tree(core::kinematics::FoldTree)
- write_kinemage_header(...)
- write_kinemage_header( (OStream)ostr, (int)kin_number, (str)title, (xyzVector_Real)ctr) -> None :
core/conformation/ResidueKinWriter.hh:41
C++ signature :
void write_kinemage_header(std::ostream {lvalue},unsigned long,std::string,numeric::xyzVector<double>)
- write_topology_file(...)
- write_topology_file( (ResidueType)rsd [, (str)filename='']) -> None :
writes a .params file from a given ResidueType object
C++ signature :
void write_topology_file(core::chemical::ResidueType [,std::string=''])
- xform_pose(...)
- xform_pose( (Pose)pose, (Stub)s [, (int)sres=1 [, (int)eres=0]]) -> None :
core/fragment/util.hh:48
C++ signature :
void xform_pose(core::pose::Pose {lvalue},core::kinematics::Stub [,unsigned long=1 [,unsigned long=0]])
- xyz_gdtmm(...)
- xyz_gdtmm( (object)p1a, (object)p2a) -> float :
Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.
C++ signature :
double xyz_gdtmm(ObjexxFCL::FArray2D<double>,ObjexxFCL::FArray2D<double>)
xyz_gdtmm( (object)p1a, (object)p2a, (float)m_1_1, (float)m_2_2, (float)m_3_3, (float)m_4_3, (float)m_7_4) -> float :
Calculate gdtmm based on the given sets of xyz coordinates in p1a and p2a.
C++ signature :
double xyz_gdtmm(ObjexxFCL::FArray2D<double>,ObjexxFCL::FArray2D<double>,double {lvalue},double {lvalue},double {lvalue},double {lvalue},double {lvalue})
- xyz_gdttm(...)
- xyz_gdttm( (object)p1a, (object)p2a, (float)gdttm_score, (float)gdtha_score) -> None :
core/scoring/rms_util.hh:502
C++ signature :
void xyz_gdttm(ObjexxFCL::FArray2D<double>,ObjexxFCL::FArray2D<double>,double {lvalue},double {lvalue})
- xyz_maxsub(...)
- xyz_maxsub( (object)p1a, (object)p2a, (int)natoms) -> int :
core/scoring/rms_util.hh:400
C++ signature :
int xyz_maxsub(ObjexxFCL::FArray2D<double>,ObjexxFCL::FArray2D<double>,int)
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