Rosetta 3.4
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core::pose Namespace Reference

Namespaces

namespace  datacache
namespace  metrics
namespace  signals
namespace  symmetry

Classes

class  MiniPose
class  UnrecognizedAtomRecord
 info about an atom in a unrecognized res (not in pose, but we want to remember it) More...
class  PDBInfo
 maintains pdb residue & atom information inside a Pose More...
class  PDBPoseMap
 PDBPoseMap can be queried with PDB information (chain, sequence position) and returns a pose's resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map. More...
class  Pose
 A molecular system including residues, kinematics, and energies. More...
class  RemarkInfo
class  Remarks

Typedefs

typedef std::map< core::Size,
core::Size
ResMap
typedef
utility::pointer::owning_ptr
< MiniPose
MiniPoseOP
typedef
utility::pointer::owning_ptr
< MiniPose const > 
MiniPoseCOP
typedef
utility::pointer::access_ptr
< MiniPose
MiniPoseAP
typedef
utility::pointer::access_ptr
< MiniPose const > 
MiniPoseCAP
typedef
utility::pointer::owning_ptr
< PDBInfo
PDBInfoOP
typedef
utility::pointer::owning_ptr
< PDBInfo const > 
PDBInfoCOP
typedef
utility::pointer::owning_ptr
< PDBPoseMap
PDBPoseMapOP
typedef
utility::pointer::owning_ptr
< PDBPoseMap const > 
PDBPoseMapCOP
typedef
utility::pointer::owning_ptr
< Pose
PoseOP
typedef
utility::pointer::owning_ptr
< Pose const > 
PoseCOP
typedef
utility::pointer::access_ptr
< Pose
PoseAP
typedef
utility::pointer::access_ptr
< Pose const > 
PoseCAP
typedef utility::vector1< PoseOPPoseOPs
typedef utility::vector1< PoseCOPPoseCOPs
typedef
utility::pointer::owning_ptr
< Remarks
RemarksOP
typedef std::string String
typedef std::set< intJumps

Functions

static basic::Tracer tr ("core.pose")
chemical::ResidueTypeCAPs residue_types_from_sequence (std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
 return of list of ResidueTypes corresponding to an annotated protein sequence
void make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
 Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>
void make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name,bool const auto_termini=true)
 Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose>
std::string annotated_to_oneletter_sequence (std::string const &annotated_seq)
 Returns the oneletter_sequence that corresponds to the given annotated sequence.
static basic::Tracer TR ("core.pose.PDBInfo")
std::ostream & operator<< (std::ostream &os, PDBInfo const &info)
static std::string const chr_chains (" ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz")
static basic::Tracer TR ("core.pose.PDBPoseMap")
std::ostream & operator<< (std::ostream &os, Pose const &pose)
 Test IO operator for debug and Python bindings.
static basic::Tracer TR ("core.pose.util")
void jumps_from_pose (const core::pose::Pose &pose, Jumps *jumps)
 Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id.
void remove_virtual_residues (core::pose::Pose *pose)
 Removes all virtual residues from <pose>
void swap_transform (int jump_num, const kinematics::RT &xform, Pose *pose)
 Updates the rigid-body transform of the specified jump in <pose>
bool is_position_conserved_residue (const Pose &pose, core::Size residue)
 Returns true if <residue> is positionally conserved, false otherwise.
void create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)
void partition_pose_by_jump (pose::Pose const &src, int const jump_number, pose::Pose &partner1, pose::Pose &partner2)
void set_ss_from_phipsi (pose::Pose &pose)
 Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that.
void addVirtualResAsRoot (const numeric::xyzVector< core::Real > &xyz, core::pose::Pose &pose)
 Adds a virtual residue to the end of the pose at the specified location. Roots the structure on this residue.
void addVirtualResAsRoot (core::pose::Pose &pose)
 Find residue closest to center-of-mass
bool getPoseExtraScores (core::pose::Pose &pose, std::string name, core::Real &value)
 getters/setters for things in the Pose DataCache
void setPoseExtraScores (core::pose::Pose &pose, std::string name, core::Real value)
void add_comment (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created.
void add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Sets a PDB-style REMARK entry in the Pose.
void clearPoseExtraScores (core::pose::Pose &pose)
void clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)
bool get_comment (core::pose::Pose const &pose, std::string const &key, std::string &val)
 Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified.
bool get_score_line_string (core::pose::Pose const &pose, std::string const &key, std::string &val)
void delete_comment (core::pose::Pose &pose, std::string const &key)
 Deletes the entry in the STRING_MAP associated with the given key.
std::map< std::string,
std::string > 
get_all_score_line_strings (core::pose::Pose const &pose)
 Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs.
std::map< std::string,
std::string > 
get_all_comments (core::pose::Pose const &pose)
 Gets a map< string, string > representing comments about the Pose in the form of key-value pairs.
utility::vector1< char > read_psipred_ss2_file (pose::Pose const &pose)
std::map< int, char > conf2pdb_chain (core::pose::Pose const &pose)
 get Conformation chain -> PDBInfo chain mapping
bool renumber_pdbinfo_based_on_conf_chains (core::pose::Pose &pose, bool fix_chains, bool const start_from_existing_numbering, bool const keep_insertion_codes, bool const rotate_chain_ids)
 renumber PDBInfo based on Conformation chains; each chain starts from 1
bool is_ideal_pose (core::pose::Pose const &pose)
 checks if the pose geometry is ideal
bool is_ideal_position (core::Size seqpos, core::pose::Pose const &pose)
 checks if the pose geometry is ideal in position seqpos
void remove_nonprotein_residues (core::pose::Pose &pose)
 this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).
void remove_ligand_canonical_residues (core::pose::Pose &pose)
 this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues.
bool compare_atom_coordinates (core::pose::Pose const &lhs, core::pose::Pose const &rhs, core::Size const n_dec_places=3)
 this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.
void copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, core::pose::ResMap const &res_map)
 A very useful function that copies degrees of freedom from one pose to another. res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.
void copy_dofs_match_atom_names (pose::Pose &pose, MiniPose const &chunk_pose, core::pose::ResMap const &res_map)
void copy_dofs (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map)
void copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map, bool const backbone_only, bool const ignore_virtual)
void copy_dofs (pose::Pose &pose, Pose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
void copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
bool check_domain_map (std::map< id::AtomID, Size > const &atom_id_domain_map, id::AtomID const &atom_id1, id::AtomID const &atom_id2)
bool check_domain_map (std::map< id::AtomID, Size > const &atom_id_domain_map, utility::vector1< id::AtomID > const &atom_ids1, utility::vector1< id::AtomID > const &atom_ids2)
void copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map, std::map< id::AtomID, Size > const &atom_id_domain_map)
bool get_scratch_atom_id (id::AtomID &other_scratch_atom_id, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::kinematics::tree::Atom const *other_atom)
void setup_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose)
void setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &reference_pose, bool const backbone_only, bool const ignore_virtual)
void setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, MiniPose const &chunk_pose)
id::NamedAtomID atom_id_to_named_atom_id (core::id::AtomID const &atom_id, Pose const &pose)
id::AtomID named_atom_id_to_atom_id (core::id::NamedAtomID const &named_atom_id, Pose const &pose, bool raise_exception)
id::NamedStubID stub_id_to_named_stub_id (id::StubID const &stub_id, core::pose::Pose const &pose)
id::StubID named_stub_id_to_stub_id (id::NamedStubID const &named_stub_id, core::pose::Pose const &pose)
std::string tag_from_pose (core::pose::Pose const &pose)
void tag_into_pose (core::pose::Pose &pose, std::string const &tag)
core::Real energy_from_pose (core::pose::Pose &pose, core::scoring::ScoreType const &sc_type)
void transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose, core::Size ir, core::Size jr)
void transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)
void transfer_jumps (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)
void replace_pose_residue_copying_existing_coordinates (pose::Pose &pose, Size const seqpos, core::chemical::ResidueType const &new_rsd_type)
core::conformation::ResidueOP remove_variant_type_from_residue (core::conformation::Residue const &old_rsd, core::chemical::VariantType const &variant_type, pose::Pose const &pose)
 removes variant from an existing residue
conformation::ResidueOP add_variant_type_to_residue (conformation::Residue const &old_rsd, chemical::VariantType const &variant_type, pose::Pose const &pose)
 construct a variant of an existing residue
void add_variant_type_to_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
 construct a variant of an existing pose residue
void remove_variant_type_from_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
 construct a non-variant of an existing pose residue
void add_lower_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void add_upper_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void remove_lower_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
void remove_upper_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
core::Real pose_max_nbr_radius (Pose const &pose)
 returns a Distance
void setup_dof_to_torsion_map (pose::Pose const &pose, id::DOF_ID_Map< id::TorsionID > &dof_map)
 set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID)
void setup_dof_mask_from_move_map (core::kinematics::MoveMap const &mm, pose::Pose const &pose, id::DOF_ID_Mask &dof_mask)
 convert from allow-bb,allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer
bool has_chain (std::string const &chain, core::pose::Pose const &pose)
bool has_chain (char const &chain, core::pose::Pose const &pose)
std::set< core::Sizeget_jump_ids_from_chain_ids (std::set< core::Size > const chain_ids, core::pose::Pose const &pose)
core::Size get_jump_id_from_chain_id (core::Size const &chain_id, const core::pose::Pose &pose)
core::Size get_chain_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
core::Size get_chain_id_from_chain (char const &chain, core::pose::Pose const &pose)
utility::vector1< core::Sizeget_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
utility::vector1< core::Sizeget_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)
core::Size get_jump_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
core::Size get_jump_id_from_chain (char const &chain, core::pose::Pose const &pose)
core::Size get_chain_id_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
char get_chain_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
core::conformation::ResidueCOPs get_chain_residues (core::pose::Pose const &pose, core::Size const chain_id)
char get_chain_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
core::Size num_heavy_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size num_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size num_hbond_acceptors (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size num_hbond_donors (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size num_chi_angles (core::Size begin, core::Size const end, core::pose::Pose const &pose)
void initialize_disulfide_bonds (Pose &pose)
 detect and fix disulfide bonds
template<typename T >
void initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose)
 Initialize a DOF_ID_Map for a given Pose using the DOF_ID_Map's current default fill values.
template<typename T >
void initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose, T const &value)
 Initialize a DOF_ID_Map for a given Pose using a specified fill value.
template<typename T >
void initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
 Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.
template<typename T >
void initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
 Initialize an AtomID_Map for a given Pose using a specified fill value.
template<typename T >
void initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
 Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.
template<typename T >
void initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
 Initialize an AtomID_Map for a given Conformation using a specified fill value.
template<typename T >
void initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
 Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.
template<typename T >
void initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
 Initialize an AtomID_Map for a given Pose using a specified fill value.
template<typename T >
void initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
 Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.
template<typename T >
void initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
 Initialize an AtomID_Map for a given Conformation using a specified fill value.

Typedef Documentation

typedef std::set<int> core::pose::Jumps
typedef std::string core::pose::String

Function Documentation

void core::pose::add_comment ( core::pose::Pose pose,
std::string const &  key,
std::string const &  val 
)
void core::pose::add_lower_terminus_type_to_pose_residue ( pose::Pose pose,
Size const  seqpos 
)
void core::pose::add_score_line_string ( core::pose::Pose pose,
std::string const &  key,
std::string const &  val 
)

Sets a PDB-style REMARK entry in the Pose.

Detailed: This is different from a comment in its interpretation by the
silent-file output machinery. A REMARK is written on its own separate line in the output silent-file, while a comment is written as part of the Pose SCORE: lines.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS.

Referenced by protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), core::io::silent::SilentStruct::energies_into_pose(), and protocols::frag_picker::FragmentPicker::nonlocal_pairs().

void core::pose::add_upper_terminus_type_to_pose_residue ( pose::Pose pose,
Size const  seqpos 
)
void core::pose::add_variant_type_to_pose_residue ( pose::Pose pose,
chemical::VariantType const &  variant_type,
Size const  seqpos 
)

construct a variant of an existing pose residue

eg make a terminus variant, and replace the orignal in pose.

Note:
this copies any atoms in common between old and new residues, rebuild the others

References replace_pose_residue_copying_existing_coordinates(), and core::pose::Pose::residue().

Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::loops::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), core::util::add_cutpoint_variants(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), add_lower_terminus_type_to_pose_residue(), protocols::loops::add_single_cutpoint_variant(), add_upper_terminus_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::idealize::basic_idealize(), core::io::pdb::build_pose_as_is1(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::abinitio::copy_side_chains(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::forge::methods::cyclize_pose(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::antibody2::CDRH3Modeler2::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::methods::make_star_foldtree(), protocols::swa::rna::minimize_all_sampled_floating_bases(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::revert_loops_to_original(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::antibody2::Ab_RelaxCDRs_Mover::setup_objects(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::swa::virtualize_o2star().

conformation::ResidueOP core::pose::add_variant_type_to_residue ( conformation::Residue const &  old_rsd,
chemical::VariantType const &  variant_type,
pose::Pose const &  pose 
)
void core::pose::addVirtualResAsRoot ( const numeric::xyzVector< core::Real > &  xyz,
core::pose::Pose pose 
)
void core::pose::addVirtualResAsRoot ( core::pose::Pose pose)

Find residue closest to center-of-mass

Adds a VRT res to the end of the pose at the center of mass. Reroots the structure on this res.

References core::chemical::aa_vrt, addVirtualResAsRoot(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

std::string core::pose::annotated_to_oneletter_sequence ( std::string const &  annotated_seq)
id::NamedAtomID core::pose::atom_id_to_named_atom_id ( core::id::AtomID const &  atom_id,
Pose const &  pose 
)
bool core::pose::check_domain_map ( std::map< id::AtomID, Size > const &  atom_id_domain_map,
id::AtomID const &  atom_id1,
id::AtomID const &  atom_id2 
)

Referenced by check_domain_map(), and copy_dofs().

bool core::pose::check_domain_map ( std::map< id::AtomID, Size > const &  atom_id_domain_map,
utility::vector1< id::AtomID > const &  atom_ids1,
utility::vector1< id::AtomID > const &  atom_ids2 
)

References check_domain_map().

static std::string const core::pose::chr_chains ( " ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz"  ) [static]
void core::pose::clearPoseExtraScore ( core::pose::Pose pose,
std::string const &  name 
)
void core::pose::clearPoseExtraScores ( core::pose::Pose pose)
bool core::pose::compare_atom_coordinates ( core::pose::Pose const &  lhs,
core::pose::Pose const &  rhs,
core::Size const  n_dec_places 
)

this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.

this function compares the 3-d coordinates of two poses. Along the way it is forced to check for certain other (in)equalities to prevent vector overrruns, etc. These include: pose length, ResidueType, and # atoms in residue. Inequalities other than 3-d coordinates result in a warning message (you shouldn't have been comparing those poses!) This is NOT a complete equality operator for a pose, but I think it does a good job with the coordinates. Note that it performs floating-point coordinate comparisons by floor(X*10^n_dec_places) - this may cause failures if your pose is a billion angstroms from 0,0,0. This comparison is preferred to an epsilon comparison std::abs( a.x - b.x ) < epsilon because it can run into situations where a == b and b == c, but a != c (thanks to APL for pointing this out). The last argument, n_dec_places, is the number of decimal places of precision when comparing.

Author:
Steven Lewis smlewi@gmail.com
Parameters:
[in]lhsone pose to compare
[in]rhsone pose to compare
[in]n_dec_placesnumber of decimal places to compare for the coordinates (remember == doesn't work for float); defaults to 3 which is PDB accuracy

References core::conformation::Residue::atoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), TR(), and protocols::kinmatch::xyz().

std::map< int, char > core::pose::conf2pdb_chain ( core::pose::Pose const &  pose)

get Conformation chain -> PDBInfo chain mapping

Remarks:
Any chains whose PDBInfo chain records are marked entirely as PDBInfo::empty_record() will be mapped to that character. Note that Conformation -> PDBInfo is always unique, but the reverse may not be true.
Returns:
the mapping if PDBInfo available and chains appear consistent, otherwise returns an empty mapping

References core::pose::Pose::chain(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), core::pose::Pose::n_residue(), core::conformation::Conformation::num_chains(), core::pose::Pose::pdb_info(), and TR().

Referenced by renumber_pdbinfo_based_on_conf_chains().

void core::pose::copy_dofs ( pose::Pose pose,
MiniPose const &  scratch_pose,
core::pose::ResMap const &  res_map 
)

A very useful function that copies degrees of freedom from one pose to another. res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.

-- rhiju, 2009.

Author:
rhiju, 2009.

References setup_atom_id_map().

Referenced by protocols::swa::protein::StepWiseProteinPoseSetup::apply(), copy_dofs(), copy_dofs_match_atom_names(), and protocols::rna::ChunkSet::insert_chunk_into_pose().

void core::pose::copy_dofs ( pose::Pose pose,
Pose const &  scratch_pose,
core::pose::ResMap const &  res_map 
)

References copy_dofs(), and setup_atom_id_map().

void core::pose::copy_dofs ( pose::Pose pose,
Pose const &  scratch_pose,
std::map< id::AtomID, id::AtomID > const &  atom_id_map 
)

References copy_dofs().

void core::pose::copy_dofs ( pose::Pose pose,
MiniPose const &  scratch_pose,
std::map< id::AtomID, id::AtomID > const &  atom_id_map 
)
void core::pose::copy_dofs ( pose::Pose pose,
MiniPose const &  scratch_pose,
std::map< id::AtomID, id::AtomID > const &  atom_id_map,
std::map< id::AtomID, Size > const &  atom_id_domain_map 
)
void core::pose::copy_dofs_match_atom_names ( pose::Pose pose,
MiniPose const &  chunk_pose,
core::pose::ResMap const &  res_map 
)
void core::pose::copy_dofs_match_atom_names ( pose::Pose pose,
Pose const &  scratch_pose,
core::pose::ResMap const &  res_map,
bool const  backbone_only,
bool const  ignore_virtual 
)
void core::pose::create_subpose ( Pose const &  src,
utility::vector1< Size > const &  positions,
kinematics::FoldTree const &  f,
Pose pose 
)
void core::pose::delete_comment ( core::pose::Pose pose,
std::string const &  key 
)

Deletes the entry in the STRING_MAP associated with the given key.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs().

core::Real core::pose::energy_from_pose ( core::pose::Pose pose,
core::scoring::ScoreType const &  sc_type 
)
std::map< std::string, std::string > core::pose::get_all_comments ( core::pose::Pose const &  pose)

Gets a map< string, string > representing comments about the Pose in the form of key-value pairs.

References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::STRING_MAP.

Referenced by get_comment(), and protocols::cluster::ClusterBase::print_cluster_PDBs().

std::map< std::string, std::string > core::pose::get_all_score_line_strings ( core::pose::Pose const &  pose)
char core::pose::get_chain_from_chain_id ( core::Size const &  chain_id,
core::pose::Pose const &  pose 
)
char core::pose::get_chain_from_jump_id ( core::Size const &  jump_id,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_chain_id_from_chain ( std::string const &  chain,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_chain_id_from_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_chain_id_from_jump_id ( core::Size const &  jump_id,
core::pose::Pose const &  pose 
)
utility::vector1< core::Size > core::pose::get_chain_ids_from_chain ( std::string const &  chain,
core::pose::Pose const &  pose 
)
utility::vector1< core::Size > core::pose::get_chain_ids_from_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
core::conformation::ResidueCOPs core::pose::get_chain_residues ( core::pose::Pose const &  pose,
core::Size const  chain_id 
)
bool core::pose::get_comment ( core::pose::Pose const &  pose,
std::string const &  key,
std::string &  val 
)

Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified.

References get_all_comments().

Referenced by core::sequence::alignment_from_pose(), protocols::loophash::LoopHashSampler::build_structures(), protocols::jobdist::pose_matches_user_tag(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), and core::io::pdb::write_additional_pdb_data().

core::Size core::pose::get_jump_id_from_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_jump_id_from_chain ( std::string const &  chain,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_jump_id_from_chain_id ( core::Size const &  chain_id,
const core::pose::Pose pose 
)
std::set< core::Size > core::pose::get_jump_ids_from_chain_ids ( std::set< core::Size > const  chain_ids,
core::pose::Pose const &  pose 
)
bool core::pose::get_score_line_string ( core::pose::Pose const &  pose,
std::string const &  key,
std::string &  val 
)
bool core::pose::get_scratch_atom_id ( id::AtomID &  other_scratch_atom_id,
std::map< core::id::AtomID, core::id::AtomID > const &  atom_id_map,
core::kinematics::tree::Atom const *  other_atom 
)

References core::kinematics::tree::Atom::id().

Referenced by copy_dofs().

bool core::pose::getPoseExtraScores ( core::pose::Pose pose,
std::string  name,
core::Real value 
)
bool core::pose::has_chain ( std::string const &  chain,
core::pose::Pose const &  pose 
)
bool core::pose::has_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
conformation::Conformation const &  conformation 
)
template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
pose::Pose const &  pose 
)

Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.

References core::id::AtomID_Map< T >::clear(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID_Map< T >::resize().

Referenced by protocols::loops::addScoresForLoopParts(), protocols::antibody2::Ab_Info::align_to_native(), protocols::antibody::Antibody::align_to_native(), protocols::simple_moves::RepackSidechainsMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::antibody2::Ab_GraftOneCDR_Mover::apply(), protocols::antibody::GraftOneMover::apply(), core::io::pdb::build_pose_as_is1(), protocols::fldsgn::topology::calc_delta_sasa(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::scoring::packstat::compute_atom_packing_scores(), core::scoring::packing::compute_holes_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::packing::compute_rosettaholes_score(), protocols::swa::create_alignment_id_map(), protocols::swa::rna::create_alignment_id_map(), protocols::comparative_modeling::hybridize::InsertChunkMover::get_local_sequence_mapping(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::recompute(), core::optimization::MinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::docking::ConformerSwitchMover::switch_conformer(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
pose::Pose const &  pose,
T const &  value 
)
template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
conformation::Conformation const &  conformation,
T const &  value 
)
template<typename T >
void core::pose::initialize_atomid_map_heavy_only ( id::AtomID_Map< T > &  atom_map,
pose::Pose const &  pose 
)
template<typename T >
void core::pose::initialize_atomid_map_heavy_only ( id::AtomID_Map< T > &  atom_map,
pose::Pose const &  pose,
T const &  value 
)
template<typename T >
void core::pose::initialize_atomid_map_heavy_only ( id::AtomID_Map< T > &  atom_map,
conformation::Conformation const &  conformation 
)
template<typename T >
void core::pose::initialize_atomid_map_heavy_only ( id::AtomID_Map< T > &  atom_map,
conformation::Conformation const &  conformation,
T const &  value 
)
void core::pose::initialize_disulfide_bonds ( Pose pose)
template<typename T >
void core::pose::initialize_dof_id_map ( id::DOF_ID_Map< T > &  dof_map,
Pose const &  pose 
)
template<typename T >
void core::pose::initialize_dof_id_map ( id::DOF_ID_Map< T > &  dof_map,
Pose const &  pose,
T const &  value 
)
bool core::pose::is_ideal_pose ( core::pose::Pose const &  pose)

checks if the pose geometry is ideal

Returns true if the <pose> geometry is ideal.

Parameters:
[in]poseThe Pose to check.
Returns:
true if all pose positions have ideal bond lengths and angles up to some very small epsilon

References is_ideal_position(), and core::pose::Pose::total_residue().

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), and core::io::pdb::write_additional_pdb_data().

bool core::pose::is_ideal_position ( core::Size  seqpos,
core::pose::Pose const &  pose 
)

checks if the pose geometry is ideal in position seqpos

Returns true if the <pose> geometry is ideal in position <seqpos>

Parameters:
[in]poseThe Pose to check.
Returns:
true if position seqpos has ideal bond lengths and angles up to some very small epsilon

References core::pose::Pose::conformation().

Referenced by protocols::topology_broker::fix_mainchain_connect(), and is_ideal_pose().

bool core::pose::is_position_conserved_residue ( const Pose pose,
core::Size  residue 
)

Returns true if <residue> is positionally conserved, false otherwise.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::POSITION_CONSERVED_RESIDUES, and core::pose::Pose::total_residue().

void core::pose::jumps_from_pose ( const core::pose::Pose pose,
Jumps jumps 
)

Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id.

References core::pose::Pose::num_jump().

void core::pose::make_pose_from_sequence ( pose::Pose pose,
std::string const &  sequence_in,
chemical::ResidueTypeSet const &  residue_set,
bool const  auto_termini 
)

Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>

Given a Pose, a protein sequence where each character represents an amino acid, and a ResidueTypeSet, give the Pose a conformation of covalently linked residues that match the sequence. NOTE: support making pose from a fully annotated sequence now, that is, for each residue variant or ligand which cannot be deduced from one letter code directly, a [] is added directly following the one letter code containig the residue's fullname, e.g. K[lys_p:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu_p:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distiguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

Note:
: 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

References core::chemical::aa_unk, core::chemical::aa_vrt, core::pose::Pose::annotated_sequence(), annotated_to_oneletter_sequence(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueType::has_variant_type(), core::chemical::LOWER_TERMINUS, core::chemical::N_ACETYLATION, core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), residue_types_from_sequence(), core::pose::Pose::sequence(), and core::chemical::UPPER_TERMINUS.

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::swa::protein::StepWiseProteinPoseSetup::apply(), protocols::simple_moves::ExtendedPoseMover::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::domain_assembly::CombineChainsMover::apply(), protocols::rna::assert_phosphate_nomenclature_matches_mini(), protocols::forge::build::BuildManager::dummy_modify(), protocols::rna::ensure_phosphate_nomenclature_matches_mini(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::import_pose::pose_stream::ExtendedPoseInputStream::fill_pose(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd(), protocols::swa::protein::generate_beta_database_test(), protocols::star::generate_extended_pose(), protocols::topology_broker::SequenceClaimer::initialize_residues(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::rna::make_extended_coarse_pose(), protocols::rna::make_phosphate_nomenclature_matches_mini(), core::fragment::make_pose_from_frags(), make_pose_from_sequence(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), protocols::abinitio::IterativeBase::reassign_noesy_data(), core::fragment::FragmentRmsd::rmsd(), protocols::abinitio::run_boinc_debug(), protocols::frag_picker::scores::RDCScore::score(), protocols::pack_daemon::DaemonSet::set_entity_resfile(), protocols::topology_broker::SequenceClaimer::set_sequence(), and protocols::frag_picker::VallProvider::vallChunksFromLibrary().

void core::pose::make_pose_from_sequence ( pose::Pose pose,
std::string const &  sequence_in,
std::string const &  type_set_name,
bool const  auto_termini 
)

Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose>

overloaded version of previous mak_pose_from_sequence, does the same function, but reads in a string of the residue type set instead of a ResidueTypeSet object. Made for PyRosetta. olange: DONT DUPLICATE CODE sid! --- I removed the duplication by calling the original "core::pose::make_pose_from_sequence"

Note:
: any existing data in <pose> is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

References core::chemical::ChemicalManager::get_instance(), and make_pose_from_sequence().

id::AtomID core::pose::named_atom_id_to_atom_id ( core::id::NamedAtomID const &  named_atom_id,
Pose const &  pose,
bool  raise_exception 
)
id::StubID core::pose::named_stub_id_to_stub_id ( id::NamedStubID const &  named_stub_id,
core::pose::Pose const &  pose 
)
core::Size core::pose::num_atoms ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
core::Size core::pose::num_chi_angles ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
core::Size core::pose::num_hbond_acceptors ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
core::Size core::pose::num_hbond_donors ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
core::Size core::pose::num_heavy_atoms ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
std::ostream & core::pose::operator<< ( std::ostream &  os,
PDBInfo const &  info 
)
std::ostream & core::pose::operator<< ( std::ostream &  os,
Pose const &  pose 
)
void core::pose::partition_pose_by_jump ( pose::Pose const &  src,
int const  jump_number,
pose::Pose partner1,
pose::Pose partner2 
)
core::Real core::pose::pose_max_nbr_radius ( Pose const &  pose)
utility::vector1< char > core::pose::read_psipred_ss2_file ( pose::Pose const &  pose)
void core::pose::remove_ligand_canonical_residues ( core::pose::Pose pose)

this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues.

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::pose::remove_lower_terminus_type_from_pose_residue ( pose::Pose pose,
Size const  seqpos 
)
void core::pose::remove_nonprotein_residues ( core::pose::Pose pose)

this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

void core::pose::remove_upper_terminus_type_from_pose_residue ( pose::Pose pose,
Size const  seqpos 
)
void core::pose::remove_variant_type_from_pose_residue ( pose::Pose pose,
chemical::VariantType const &  variant_type,
Size const  seqpos 
)

construct a non-variant of an existing pose residue

eg remove a terminus variant, and replace the orignal in pose.

Note:
this copies any atoms in common between old and new residues, rebuild the others

References replace_pose_residue_copying_existing_coordinates(), and core::pose::Pose::residue().

Referenced by protocols::swa::rna::StepWiseRNA_Minimizer::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::swa::rna::copy_bulge_res_and_ribose_torsion(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::forge::methods::cyclize_pose(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::swa::protein::generate_beta_database_test(), protocols::toolbox::pose_manipulation::insert_pose_into_pose(), protocols::swa::rna::minimize_all_sampled_floating_bases(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::swa::rna::remove_all_variant_types(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), protocols::loops::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), core::util::remove_cutpoint_variants(), protocols::swa::protein::remove_end_variants(), remove_lower_terminus_type_from_pose_residue(), remove_upper_terminus_type_from_pose_residue(), protocols::swa::rna::Remove_virtual_O2Star_hydrogen(), protocols::swa::rna::remove_virtual_rna_residue_variant_type(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and protocols::loops::set_loop_cutpoint_in_pose_fold_tree().

conformation::ResidueOP core::pose::remove_variant_type_from_residue ( core::conformation::Residue const &  old_rsd,
core::chemical::VariantType const &  variant_type,
pose::Pose const &  pose 
)
void core::pose::remove_virtual_residues ( core::pose::Pose pose)
bool core::pose::renumber_pdbinfo_based_on_conf_chains ( core::pose::Pose pose,
bool  fix_chains,
bool const  start_from_existing_numbering,
bool const  keep_insertion_codes,
bool const  rotate_chain_ids 
)

renumber PDBInfo based on Conformation chains; each chain starts from 1

Parameters:
[in,out]poseThe Pose to modify.
[in]fix_chainsIf true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)
[in]start_from_existing_numberingIf true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)
[in]keep_insertion_codesIf true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)
[in]rotate_chain_idsIf true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)
Remarks:
If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.
Returns:
true if renumbering successful, false otherwise

References core::pose::Pose::chain(), core::pose::PDBInfo::chain(), core::conformation::Conformation::chain_endings(), conf2pdb_chain(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), core::pose::PDBInfo::icode(), core::pose::Pose::n_residue(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), core::pose::PDBInfo::set_resinfo(), and TR().

Referenced by protocols::forge::remodel::RemodelMover::apply().

void core::pose::replace_pose_residue_copying_existing_coordinates ( pose::Pose pose,
Size const  seqpos,
core::chemical::ResidueType const &  new_rsd_type 
)
chemical::ResidueTypeCAPs core::pose::residue_types_from_sequence ( std::string const &  sequence_in,
chemical::ResidueTypeSet const &  residue_set,
bool const  auto_termini 
)

return of list of ResidueTypes corresponding to an annotated protein sequence

Given a protein sequence where each character represents an amino acid, and a ResidueTypeSet, return the residue types that match the sequence. NOTE: support making residue types from a fully annotated sequence now, that is, for each residue variant or ligand which cannot be deduced from one letter code directly, a [] is added directly following the one letter code containig the residue's fullname, for example K[lys_p:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu_p:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distiguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

Parameters:
[in]sequence_inan annotated sequence
[in]residue_setthe desired residue set
[in]auto_terminimark position 1, last_residue with lower, upper termini; default true

References core::chemical::aa_from_oneletter_code(), core::chemical::ResidueTypeSet::aa_map(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_polymer(), core::chemical::LOWER_TERMINUS, core::chemical::ResidueTypeSet::name_map(), core::chemical::UPPER_TERMINUS, and core::chemical::ResidueType::variant_types().

Referenced by make_pose_from_sequence(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::GrowRight::modify_impl(), and protocols::forge::build::GrowLeft::modify_impl().

void core::pose::set_ss_from_phipsi ( pose::Pose pose)

Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that.

Crude way to guess secondary structure given a pose. This function sets the sec_struct array of pose.conformation_ to the result of the guesswork. This has been ported directly from rosetta++.

References core::chemical::ResidueType::is_protein(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::pose::Pose::set_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::abinitio::StructureStore::add(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::antibody2::Ab_ModelCDRH3::apply(), protocols::antibody2::Ab_Assemble_Templates::apply(), protocols::antibody::AntibodyModeler::apply(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::antibody::AntibodyModeler::init_on_new_input(), protocols::comparative_modeling::initialize_ss(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::loop_build::LoopBuild_main(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), core::import_pose::pose_from_pdb(), protocols::RBSegmentRelax_main(), core::fragment::read_std_frags_from_cmd(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::loops::set_secstruct_from_psipred_ss2(), core::io::sequence_comparation::DesignContrast::setSecStruct(), protocols::abinitio::AbrelaxApplication::setup(), core::fragment::steal_constant_length_frag_set_from_pose(), and core::fragment::steal_frag_set_from_pose().

void core::pose::setPoseExtraScores ( core::pose::Pose pose,
std::string  name,
core::Real  value 
)

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), and make_table_of_pilot_apps::name.

Referenced by protocols::loops::addScoresForLoopParts(), protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::simple_moves::TailsScoreMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::relax::FastRelax::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::relax::FastRelax::batch_apply(), protocols::abinitio::AbrelaxApplication::check_filters(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), protocols::abinitio::AbrelaxApplication::fold(), protocols::jobdist::main_plain_pdb_mover(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_include_cut(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), core::scoring::DockingScoreFunction::operator()(), and protocols::jobdist::universal_main().

void core::pose::setup_atom_id_map ( std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map,
ResMap const &  res_map,
core::pose::Pose const &  pose 
)

References core::pose::Pose::residue_type().

Referenced by copy_dofs().

void core::pose::setup_atom_id_map_match_atom_names ( std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map,
ResMap const &  res_map,
core::pose::Pose const &  pose,
core::pose::Pose const &  reference_pose,
bool const  backbone_only,
bool const  ignore_virtual 
)
void core::pose::setup_atom_id_map_match_atom_names ( std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map,
ResMap const &  res_map,
core::pose::Pose const &  pose,
MiniPose const &  chunk_pose 
)
void core::pose::setup_dof_mask_from_move_map ( kinematics::MoveMap const &  mm,
pose::Pose const &  pose,
id::DOF_ID_Mask &  dof_mask 
)
void core::pose::setup_dof_to_torsion_map ( pose::Pose const &  pose,
id::DOF_ID_Map< id::TorsionID > &  dof_map 
)
id::NamedStubID core::pose::stub_id_to_named_stub_id ( id::StubID const &  stub_id,
core::pose::Pose const &  pose 
)
void core::pose::swap_transform ( int  jump_num,
const kinematics::RT &  xform,
Pose pose 
)
std::string core::pose::tag_from_pose ( core::pose::Pose const &  pose)
void core::pose::tag_into_pose ( core::pose::Pose pose,
std::string const &  tag 
)
static basic::Tracer core::pose::TR ( "core.pose.PDBPoseMap"  ) [static]
static basic::Tracer core::pose::tr ( "core.pose"  ) [static]
static basic::Tracer core::pose::TR ( "core.pose.util"  ) [static]
static basic::Tracer core::pose::TR ( "core.pose.PDBInfo"  ) [static]
void core::pose::transfer_jumps ( const core::pose::Pose srcpose,
core::pose::Pose tgtpose 
)
void core::pose::transfer_phi_psi ( const core::pose::Pose srcpose,
core::pose::Pose tgtpose,
core::Size  ir,
core::Size  jr 
)
void core::pose::transfer_phi_psi ( const core::pose::Pose srcpose,
core::pose::Pose tgtpose 
)
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