Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
core::pose Namespace Reference

Namespaces

 carbohydrates
 
 copydofs
 
 datacache
 
 full_model_info
 
 metrics
 
 ncbb
 
 rna
 
 signals
 
 symmetry
 

Classes

class  CrystInfo
 
class  MiniPose
 
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  Py_basic_datacache_DataCache_CacheableObserver
 
class  RemarkInfo
 
class  Remarks
 
class  UnrecognizedAtomRecord
 info about an atom in a unrecognized res (not in pose, but we want to remember it) More...
 

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 boost::shared_ptr< PosePoseSP
 
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

void parse_sequence (std::string const &sequence_in, utility::vector1< std::string > &fullname_list, std::vector< Size > &oneletter_to_fullname_index, std::string &one_letter_sequence)
 parse the annotated sequence. More...
 
Size get_sequence_len (std::string const &sequence_in)
 Get the length of the annotated sequence. More...
 
chemical::ResidueTypeCOPs residue_types_from_sequence (std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
 return a list of ResidueTypes corresponding to an annotated protein sequence More...
 
chemical::ResidueTypeCOPs residue_types_from_saccharide_sequence (std::string const &sequence, chemical::ResidueTypeSet const &residue_set)
 Return a list of carbohydrate ResidueTypes corresponding to an annotated polysaccharide sequence. More...
 
void make_pose_from_sequence (pose::Pose &pose, chemical::ResidueTypeCOPs requested_types, bool const auto_termini=true)
 Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose> More...
 
void make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini)
 
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> More...
 
void make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true)
 Create a Pose from an annotated polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>. More...
 
void make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true)
 Create a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name> and stores it in <pose>. More...
 
pose::PoseOP pose_from_saccharide_sequence (std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true)
 Return a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name>. More...
 
std::string annotated_to_oneletter_sequence (std::string const &annotated_seq)
 Returns the oneletter_sequence that corresponds to the given annotated sequence. More...
 
std::ostream & operator<< (std::ostream &os, PDBInfo const &info)
 
std::ostream & operator<< (std::ostream &os, Pose const &pose)
 Test IO operator for debug and Python bindings. More...
 
core::Size get_resnum (utility::tag::TagCOP tag_ptr, core::pose::Pose const &pose, std::string const &prefix)
 a convenience function to test whether the user has specified pdb numbering rather than rosetta numbering. More...
 
core::Size parse_resnum (std::string const &resnum, core::pose::Pose const &pose)
 Extracts a residue number from a string. More...
 
utility::vector1< core::Sizeparse_selection_block (std::string const &sele, core::pose::Pose const &pose)
 Extracts residue numbers from a 'selection'. More...
 
vector1< Sizeget_resnum_list (utility::tag::TagCOP tag_ptr, string const &tag, pose::Pose const &pose)
 Extracts a list of residue numbers from a tag. More...
 
set< Sizeget_resnum_list (std::string const str, core::pose::Pose const &pose)
 returns a resnum list directly from a string More...
 
utility::vector1< Sizeget_resnum_list_ordered (std::string const str, core::pose::Pose const &pose)
 returns a resnum list directly from a string, preserving order More...
 
void append_pose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, bool new_chain=true)
 Append residues of pose2 to pose1. More...
 
void append_subpose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, core::Size start_res, core::Size end_res, bool new_chain=true)
 Append specified residues of pose2 to pose1. More...
 
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. More...
 
void remove_virtual_residues (core::pose::Pose *pose)
 Removes all virtual residues from <pose> More...
 
void swap_transform (Size jump_num, const kinematics::RT &xform, Pose *pose)
 Updates the rigid-body transform of the specified jump in <pose> More...
 
bool is_position_conserved_residue (const Pose &pose, core::Size residue)
 Returns true if <residue> is positionally conserved, false otherwise. More...
 
void create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)
 Create a subpose of the src pose. PDBInfo is set as NULL. More...
 
void pdbslice (pose::Pose &new_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)
 Create a subpose of the src pose – figures out a reasonable fold tree. More...
 
void pdbslice (pose::Pose &pose, utility::vector1< Size > const &slice_res)
 Create a subpose of the src pose – figures out a reasonable fold tree. More...
 
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. More...
 
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. More...
 
numeric::xyzVector< core::Realget_center_of_mass (core::pose::Pose const &pose)
 Get center of mass of a pose. More...
 
void addVirtualResAsRoot (core::pose::Pose &pose)
 Adds a VRT res to the end of the pose at the center of mass. Reroots the structure on this res. More...
 
void read_comment_pdb (std::string const &file_name, core::pose::Pose &pose)
 Reads the comments from the pdb file and adds it into comments. More...
 
void dump_comment_pdb (std::string const &file_name, core::pose::Pose const &pose)
 dumps pose+ comments to pdb file More...
 
bool getPoseExtraScore (core::pose::Pose const &pose, std::string const name, core::Real &value)
 getters/setters for things in the Pose DataCache More...
 
bool getPoseExtraScore (core::pose::Pose const &pose, std::string const name, std::string &value)
 
void setPoseExtraScore (core::pose::Pose &pose, std::string name, core::Real value)
 
void setPoseExtraScore (core::pose::Pose &pose, std::string const name, std::string 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. More...
 
void add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Dumps a pdb with comments at end of file. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
utility::vector1< char > read_psipred_ss2_file (pose::Pose const &pose)
 
void conf2pdb_chain_default_map (core::pose::Pose const &pose, std::map< int, char > &chainmap)
 
std::map< int, char > conf2pdb_chain (core::pose::Pose const &pose)
 get Conformation chain -> PDBInfo chain mapping More...
 
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 More...
 
bool is_ideal_pose (core::pose::Pose const &pose)
 checks if the pose geometry is ideal More...
 
bool is_ideal_position (core::Size seqpos, core::pose::Pose const &pose)
 checks if the pose geometry is ideal in position seqpos More...
 
void remove_nonprotein_residues (core::pose::Pose &pose)
 this function removes all residues from the pose which are not protein residues. More...
 
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. More...
 
bool compare_atom_coordinates (Pose const &lhs, Pose const &rhs, 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. More...
 
bool compare_binary_protein_silent_struct (Pose const &lhs, Pose const &rhs)
 this function compares poses for equality up to the information stored in the binary protein silent struct format. More...
 
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 const &pose, core::scoring::ScoreType const &sc_type)
 
core::Real energy_from_pose (core::pose::Pose const &pose, std::string const &sc_type)
 
core::Real total_energy_from_pose (core::pose::Pose const &pose)
 
bool sort_pose_by_score (core::pose::PoseOP const &pose1, core::pose::PoseOP const &pose2)
 
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 More...
 
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 More...
 
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 More...
 
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 More...
 
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 More...
 
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) More...
 
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 More...
 
bool has_chain (std::string const &chain, core::pose::Pose const &pose)
 
bool has_chain (char const &chain, core::pose::Pose const &pose)
 
bool has_chain (core::Size chain_id, 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)
 
utility::vector1< core::Sizeget_jump_ids_from_chain (char const &chain, core::pose::Pose const &pose)
 
utility::vector1< core::Sizeget_jump_ids_from_chain (std::string 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)
 
core::Real mass (core::Size begin, core::Size const end, core::pose::Pose const &pose)
 
core::Size get_hash_from_chain (char const &chain, core::pose::Pose const &pose)
 
core::Size get_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)
 
std::string get_sha1_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)
 
void initialize_disulfide_bonds (Pose &pose)
 detect and fix disulfide bonds More...
 
std::string extract_tag_from_pose (core::pose::Pose &pose)
 Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise. More...
 
core::id::SequenceMapping sequence_map_from_pdbinfo (Pose const &first, Pose const &second)
 Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching. More...
 
core::Size canonical_residue_count (core::pose::Pose const &pose)
 count the number of canonical residues in the pose More...
 
core::Size noncanonical_residue_count (core::pose::Pose const &pose)
 count the number of non-canonical residues in the pose More...
 
core::Size canonical_atom_count (core::pose::Pose const &pose)
 count the number of canonical amino acid atoms in the pose More...
 
core::Size noncanonical_atom_count (core::pose::Pose const &pose)
 count the number of non-canonical amino acids in thepose More...
 
core::Size noncanonical_chi_count (core::pose::Pose const &pose)
 count the number of non-canonical chi angles in the pose More...
 
numeric::xyzVector< core::Realcenter_of_mass (pose::Pose const &pose, int const start, int const stop)
 calculates the center of mass of a pose More...
 
int residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
 calculates the center of mass of a pose More...
 
int return_nearest_residue (pose::Pose const &pose, int const begin, int const end, Vector center)
 finds the residue nearest some position passed in (normally a center of mass) More...
 
id::AtomID_Map< id::AtomIDconvert_from_std_map (std::map< id::AtomID, id::AtomID > const &atom_map, core::pose::Pose const &pose)
 
void correctly_add_cutpoint_variants (core::pose::Pose &pose)
 Add cutpoint variants to all residues annotated as cutpoints in the pose. More...
 
void correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const cutpoint_res, bool const check_fold_tree)
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
void initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, pose::Pose const &pose)
 
void initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, pose::Pose const &pose, id::AtomID const &value)
 
void initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, conformation::Conformation const &conformation)
 
void initialize_atomid_map_AtomID (id::AtomID_Map< id::AtomID > &atom_map, conformation::Conformation const &conformation, id::AtomID const &value)
 

Variables

static basic::Tracer tr ("core.pose")
 
static basic::Tracer TR ("core.pose.PDBInfo")
 
static basic::Tracer TR ("core.pose.PDBPoseMap")
 
static basic::Tracer TR ("core.pose.util")
 

Typedef Documentation

typedef boost::shared_ptr< Pose > core::pose::PoseSP

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 
)

Dumps a pdb with comments at end of file.

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(), utility::pointer::owning_ptr< T >::get(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), runtime_assert, core::pose::datacache::CacheableDataType::SCORE_LINE_STRINGS, and basic::datacache::BasicDataCache::set().

Referenced by core::io::silent::SilentStruct::energies_into_pose().

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 
)
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)

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

Find residue closest to center-of-mass

References addVirtualResAsRoot(), get_center_of_mass(), nres, core::pose::Pose::total_residue(), and TR.

std::string core::pose::annotated_to_oneletter_sequence ( std::string const &  annotated_seq)

Returns the oneletter_sequence that corresponds to the given annotated sequence.

References add().

Referenced by make_pose_from_sequence().

void core::pose::append_pose_to_pose ( core::pose::Pose pose1,
core::pose::Pose const &  pose2,
bool  new_chain 
)

Append residues of pose2 to pose1.

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

void core::pose::append_subpose_to_pose ( core::pose::Pose pose1,
core::pose::Pose const &  pose2,
core::Size  start_res,
core::Size  end_res,
bool  new_chain 
)
id::NamedAtomID core::pose::atom_id_to_named_atom_id ( core::id::AtomID const &  atom_id,
Pose const &  pose 
)
core::Size core::pose::canonical_atom_count ( core::pose::Pose const &  pose)

count the number of canonical amino acid atoms in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::canonical_residue_count ( core::pose::Pose const &  pose)

count the number of canonical residues in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

numeric::xyzVector< core::Real > core::pose::center_of_mass ( pose::Pose const &  pose,
int const  start,
int const  stop 
)

calculates the center of mass of a pose

center_of_mass

Detailed:
the start and stop positions (or residues) within the pose are used to find the starting and finishing locations
Authors
Monica Berrondo June 14 2007
Last Modified: Javier Castellanos June 4 2012

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by residue_center_of_mass().

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 smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om
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 xyz.

bool core::pose::compare_binary_protein_silent_struct ( Pose const &  lhs,
Pose const &  rhs 
)

this function compares poses for equality up to the information stored in the binary protein silent struct format.

References core::io::silent::BinarySilentStruct::print_conformation().

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(), conf2pdb_chain_default_map(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), utility::pointer::owning_ptr< T >::get(), core::pose::Pose::n_residue(), core::conformation::Conformation::num_chains(), pdb, core::pose::Pose::pdb_info(), and TR.

Referenced by core::pose::symmetry::make_symmetric_pose(), and renumber_pdbinfo_based_on_conf_chains().

void core::pose::conf2pdb_chain_default_map ( core::pose::Pose const &  pose,
std::map< int, char > &  chainmap 
)
id::AtomID_Map< id::AtomID > core::pose::convert_from_std_map ( std::map< id::AtomID, id::AtomID > const &  atom_map,
core::pose::Pose const &  pose 
)
void core::pose::correctly_add_cutpoint_variants ( core::pose::Pose pose)

Add cutpoint variants to all residues annotated as cutpoints in the pose.

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

Referenced by core::util::ChainbreakUtil::has_chainbreak().

void core::pose::correctly_add_cutpoint_variants ( core::pose::Pose pose,
Size const  cutpoint_res,
bool const  check_fold_tree 
)
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 
)
void core::pose::dump_comment_pdb ( std::string const &  file_name,
core::pose::Pose const &  pose 
)

dumps pose+ comments to pdb file

References core::pose::Pose::dump_pdb(), get_all_comments(), and out.

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

Get center of mass of a pose.

Get center of mass of a pose.

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

Referenced by addVirtualResAsRoot().

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(), core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring(), and core::io::pdb::write_additional_pdb_data().

core::Size core::pose::get_hash_excluding_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
core::Size core::pose::get_hash_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 ( char 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 
)
utility::vector1< core::Size > core::pose::get_jump_ids_from_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
utility::vector1< core::Size > core::pose::get_jump_ids_from_chain ( std::string const &  chain,
core::pose::Pose const &  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 
)
core::Size core::pose::get_resnum ( utility::tag::TagCOP  tag_ptr,
core::pose::Pose const &  pose,
std::string const &  prefix 
)

a convenience function to test whether the user has specified pdb numbering rather than rosetta numbering.

References chain, utility::pointer::owning_ptr< T >::get(), core::pose::Pose::pdb_info(), runtime_assert, ss, TR, and utility_exit_with_message.

utility::vector1< core::Size > core::pose::get_resnum_list ( utility::tag::TagCOP  tag_ptr,
string const &  tag,
pose::Pose const &  pose 
)

Extracts a list of residue numbers from a tag.

The tag should contain a comma-separated list of numbers, in either pdb or rosetta format (

See also
parse_resnum for details)

References TR, and utility_exit.

Referenced by core::pack::task::residue_selector::ResidueIndexSelector::apply(), core::pack::task::residue_selector::NeighborhoodResidueSelector::get_focus(), and core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector::set_from_residue_list_string().

std::set< core::Size > core::pose::get_resnum_list ( std::string const  str,
core::pose::Pose const &  pose 
)
utility::vector1< core::Size > core::pose::get_resnum_list_ordered ( std::string const  str,
core::pose::Pose const &  pose 
)
bool core::pose::get_score_line_string ( core::pose::Pose const &  pose,
std::string const &  key,
std::string &  val 
)
Size core::pose::get_sequence_len ( std::string const &  sequence_in)

Get the length of the annotated sequence.

Get the real length of a annotated sequence.

References parse_sequence().

std::string core::pose::get_sha1_hash_excluding_chain ( char const &  chain,
core::pose::Pose const &  pose 
)
bool core::pose::getPoseExtraScore ( core::pose::Pose const &  pose,
std::string const  name,
core::Real value 
)
bool core::pose::getPoseExtraScore ( core::pose::Pose const &  pose,
std::string const  name,
std::string &  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 
)
bool core::pose::has_chain ( core::Size  chain_id,
core::pose::Pose const &  pose 
)
template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
pose::Pose const &  pose 
)
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 
)
template<typename T >
void core::pose::initialize_atomid_map ( id::AtomID_Map< T > &  atom_map,
conformation::Conformation const &  conformation,
T const &  value 
)
void core::pose::initialize_atomid_map_AtomID ( id::AtomID_Map< id::AtomID > &  atom_map,
pose::Pose const &  pose 
)
inline
void core::pose::initialize_atomid_map_AtomID ( id::AtomID_Map< id::AtomID > &  atom_map,
pose::Pose const &  pose,
id::AtomID const &  value 
)
inline
void core::pose::initialize_atomid_map_AtomID ( id::AtomID_Map< id::AtomID > &  atom_map,
conformation::Conformation const &  conformation 
)
inline
void core::pose::initialize_atomid_map_AtomID ( id::AtomID_Map< id::AtomID > &  atom_map,
conformation::Conformation const &  conformation,
id::AtomID const &  value 
)
inline
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(), 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(), and core::conformation::is_ideal_position().

Referenced by 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_saccharide_sequence ( pose::Pose pose,
std::string const &  sequence,
chemical::ResidueTypeSet const &  residue_set,
bool const  auto_termini 
)

Create a Pose from an annotated polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose>.

Parameters
[in]<pose>the Pose to fill
[in]<sequence>an annotated polysaccharide sequence, e.g., "alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-D-Glcp"
[in]<residue_set>the desired residue set
[in]<auto_termini>if true (default) creates termini variants of terminal residues

Format for <sequence>:
Prefixes apply to the residue to which they are attached, below indicated by residue n.
Residues are listed from N to 1, where N is the total number of residues in the saccharide.
The sequence is parsed by reading to the next hyphen, so hyphens are crucial.
Linkage indication: "(a->x)-" specifies the linkage of residue n, where a is the anomeric carbon number of residue (n+1) and x is the oxygen number of residue n. The first residue listed in the annotated sequence (residue N) need not have the linkage prefix. A ->4) ResidueType will automatically be assigned by default if not specified.
Anomer indication: The strings "alpha-" or "beta-" are supplied next, which determines the stereochemistry of the anomeric carbon of the residue to which it is prefixed. An alpha ResidueType will automatically be assigned by default.
Stereochemical indication: "L-" or "D-" specifies whether residue n is an L- or D-sugar. The default is "D-".
3-Letter code: A three letter code (in sentence case) MUST be supplied next. This specifies the "base sugar name", e.g., Glc is for glucose. (A list of all recognized 3-letter codes for sugars can be found in src/core/chemical/carbohydrates/CarbohydrateInfo.cc.)
1-Letter suffix: If no suffix follows, residue n will be linear. If a letter is present, it indicates the ring size, where "f" is furanose, "p" is puranose, and "s" is septanose.

Remarks
The order of residues in the created pose is in the opposite direction as the annotated sequence of saccharide residues, as sugars are named with the 1st residue as the "main chain", with all other residues named as substituents and written as prefixes. In other words, sugars are usually drawn and named with residue 1 to the right.
At present time, param files only exist for a limited number of sugars! ~ Labonte

References add_lower_terminus_type_to_pose_residue(), add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::chain_sequence(), chemical, core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::conformation::ResidueFactory::create_residue(), residue_types_from_saccharide_sequence(), core::pose::Pose::set_phi(), and core::pose::Pose::total_residue().

Referenced by make_pose_from_saccharide_sequence(), and pose_from_saccharide_sequence().

void core::pose::make_pose_from_saccharide_sequence ( pose::Pose pose,
std::string const &  sequence,
std::string const &  type_set_name,
bool const  auto_termini 
)

Create a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name> and stores it in <pose>.

Overloaded version of make_pose_from_saccharide_sequence() that takes the string name for a residue type set instead of a ResidueTypeSet object. A convenience method for PyRosetta.

References chemical, make_pose_from_saccharide_sequence(), and residue_type_set.

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

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 containing the residue's fullname, e.g. K[lys:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distinguished HIS tautomers, various chain termini and cutpoint variants etc. Currently not working with disulfide variant CYD, but this is on to-do list.

References annotated_to_oneletter_sequence(), length, make_pose_from_sequence(), and residue_types_from_sequence().

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 make_pose_from_sequence, does the same function, but reads in a string of the residue type set instead of a ResidueTypeSet object.

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(), make_pose_from_sequence(), and residue_type_set.

core::Real core::pose::mass ( core::Size  begin,
core::Size const  end,
core::pose::Pose const &  pose 
)
id::AtomID core::pose::named_atom_id_to_atom_id ( core::id::NamedAtomID const &  named_atom_id,
Pose const &  pose,
bool  raise_exception 
)

returns an AtomID corresponding to your NamedAtomID check for a valid AtomID after this. following conditions return invalid ID : rsd > total_residue atom not present in residue ( e.g., no CB in GLY )

References core::id::NamedAtomID::atom(), core::chemical::ResidueType::atom_index(), core::id::BOGUS_ATOM_ID, core::chemical::ResidueType::has(), core::pose::Pose::residue_type(), core::id::NamedAtomID::rsd(), core::pose::Pose::total_residue(), and core::id::NamedAtomID::valid().

Referenced by core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), core::scoring::constraints::Obsolet_NamedAtomPairConstraint::mapto(), named_stub_id_to_stub_id(), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), and core::pose::Pose::set_xyz().

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::noncanonical_atom_count ( core::pose::Pose const &  pose)

count the number of non-canonical amino acids in thepose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::noncanonical_chi_count ( core::pose::Pose const &  pose)

count the number of non-canonical chi angles in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

core::Size core::pose::noncanonical_residue_count ( core::pose::Pose const &  pose)

count the number of non-canonical residues in the pose

References core::chemical::num_canonical_aas, resi, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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 
)
core::Size core::pose::parse_resnum ( std::string const &  resnum,
core::pose::Pose const &  pose 
)

Extracts a residue number from a string.

Recognizes two forms of numbering:

  • Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
  • PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID.
    Returns
    the rosetta residue number for the string, or 0 upon an error

References chain, core::pose::Pose::pdb_info(), runtime_assert, ss, and TR.

Referenced by get_resnum_list(), get_resnum_list_ordered(), and parse_selection_block().

utility::vector1<core::Size> core::pose::parse_selection_block ( std::string const &  sele,
core::pose::Pose const &  pose 
)

Extracts residue numbers from a 'selection'.

Recognizes two forms of numbering:

  • Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+
  • PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID.
  • name3=ALA selects all alanines
    Returns
    the rosetta residue numbers for the string, or 0 upon an error

References core::pose::Pose::n_residue(), core::conformation::Residue::name3(), parse_resnum(), and core::pose::Pose::residue().

Referenced by get_resnum_list(), and get_resnum_list_ordered().

void core::pose::parse_sequence ( std::string const &  sequence_in,
utility::vector1< std::string > &  fullname_list,
std::vector< Size > &  oneletter_to_fullname_index,
std::string &  one_letter_sequence 
)

parse the annotated sequence.

Parse the input annotated sequence.

Referenced by get_sequence_len(), residue_types_from_sequence(), and core::io::silent::SilentFileData::setup_include_patches().

void core::pose::partition_pose_by_jump ( pose::Pose const &  src,
int const  jump_number,
pose::Pose &  partner1,
pose::Pose &  partner2 
)
void core::pose::pdbslice ( core::pose::Pose new_pose,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  slice_res 
)
void core::pose::pdbslice ( core::pose::Pose pose,
utility::vector1< core::Size > const &  slice_res 
)

Create a subpose of the src pose – figures out a reasonable fold tree.

References pdbslice().

pose::PoseOP core::pose::pose_from_saccharide_sequence ( std::string const &  sequence,
std::string const &  type_set_name,
bool const  auto_termini 
)

Return a Pose from an annotated polysaccharide sequence <sequence> with residue type set name <type_set_name>.

A convenience method for PyRosetta.

References make_pose_from_saccharide_sequence().

core::Real core::pose::pose_max_nbr_radius ( Pose const &  pose)
void core::pose::read_comment_pdb ( std::string const &  file_name,
core::pose::Pose pose 
)

Reads the comments from the pdb file and adds it into comments.

References add_comment(), getline(), key, utility::string_split(), TR, and utility_exit.

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 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).

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 
)
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 chain, core::pose::Pose::chain(), core::pose::PDBInfo::chain(), core::conformation::Conformation::chain_endings(), conf2pdb_chain(), core::pose::Pose::conformation(), core::pose::PDBInfo::empty_record(), utility::pointer::owning_ptr< T >::get(), core::pose::PDBInfo::icode(), core::pose::Pose::n_residue(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), runtime_assert, core::pose::PDBInfo::set_resinfo(), and TR.

void core::pose::replace_pose_residue_copying_existing_coordinates ( pose::Pose &  pose,
Size const  seqpos,
core::chemical::ResidueType const &  new_rsd_type 
)

helper function for residue replacement/residuetype switching these functions should probably move to pose/util.cc

Note
Will call new_rsd->fill_missing_atoms if the new residue has atoms that the old one doesn't

References core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::replace_residue(), and core::pose::Pose::residue().

Referenced by add_variant_type_to_pose_residue(), and remove_variant_type_from_pose_residue().

int core::pose::residue_center_of_mass ( pose::Pose const &  pose,
int const  start,
int const  stop 
)

calculates the center of mass of a pose

residue_center_of_mass

Detailed:
the start and stop positions (or residues) within the pose are used to find the starting and finishing locations
Authors
Monica Berrondo June 14 2007
Last Modified: Javier Castellanos June 4 2012

References core::conformation::membrane::center, center_of_mass(), and return_nearest_residue().

chemical::ResidueTypeCOPs core::pose::residue_types_from_saccharide_sequence ( std::string const &  sequence,
chemical::ResidueTypeSet const &  residue_set 
)

Return a list of carbohydrate ResidueTypes corresponding to an annotated polysaccharide sequence.

Parameters
[in]<sequence>an annotated polysaccharide sequence, e.g., "alpha-D-Glcp-(1->4)-alpha-D-Glcp-(1->4)-D-Glcp"
[in]<residue_set>the desired residue set
Returns
a 1-indexed vector of ResidueType owning pointers, from left-to-right, as indicated by the sequence

Format for <sequence>:
Prefixes apply to the residue to which they are attached, below indicated by residue n.
Residues are listed from N to 1, where N is the total number of residues in the saccharide.
The sequence is parsed by reading to the next hyphen, so hyphens are crucial.
Linkage indication: "(a->x)-" specifies the linkage of residue n, where a is the anomeric carbon number of residue (n+1) and x is the oxygen number of residue n. The first residue listed in the annotated sequence (residue N) need not have the linkage prefix. A ->4) ResidueType will automatically be assigned by default if not specified.
Anomer indication: The strings "alpha-" or "beta-" are supplied next, which determines the stereochemistry of the anomeric carbon of the residue to which it is prefixed. An alpha ResidueType will automatically be assigned by default.
Stereochemical indication: "L-" or "D-" specifies whether residue n is an L- or D-sugar. The default is "D-".
3-Letter code: A three letter code (in sentence case) MUST be supplied next. This specifies the "base sugar name", e.g., Glc is for glucose. (A list of all recognized 3-letter codes for sugars can be found in the database.)
1-Letter suffix: If no suffix follows, residue n will be linear. If a letter is present, it indicates the ring size, where "f" is furanose, "p" is pyranose, and "s" is septanose.

Remarks
At present time, param files only exist for a few saccharide residues! ~ Labonte

References carbohydrates, chemical, core::chemical::ResidueTypeSet::name_map(), suffix, and utility_exit_with_message.

Referenced by make_pose_from_saccharide_sequence().

chemical::ResidueTypeCOPs core::pose::residue_types_from_sequence ( std::string const &  sequence_in,
chemical::ResidueTypeSet const &  residue_set,
bool const  auto_termini 
)

return a 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 containing the residue's fullname, for example K[lys:NtermProteinFull]ADFGCH[HIS_D]QNVE[glu:CtermProteinFull]Z[ZN]. This allows a pose to be constructed with full features from a silent output file, such as with distinguished 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_VARIANT, core::chemical::ResidueTypeSet::name_map(), parse_sequence(), core::chemical::UPPER_TERMINUS_VARIANT, utility_exit_with_message, and core::chemical::ResidueType::variant_types().

Referenced by make_pose_from_sequence().

int core::pose::return_nearest_residue ( pose::Pose const &  pose,
int const  begin,
int const  end,
Vector  center 
)

finds the residue nearest some position passed in (normally a center of mass)

core::pose::return_nearest_residue

Detailed:
the start and stop positions (or residues) within the pose are used to find the starting and finishing locations
Authors
Monica Berrondo June 14 2007
Last Modified: June 29 2007

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::sequence::end, core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by core::membrane::geometry::residue_center_of_mass(), and residue_center_of_mass().

core::id::SequenceMapping core::pose::sequence_map_from_pdbinfo ( Pose const &  first,
Pose const &  second 
)

Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching.

References core::sequence::map_seq1_seq2(), core::pose::Pose::pdb_info(), core::pose::Pose::total_residue(), and TR.

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(), ss, and core::pose::Pose::total_residue().

Referenced by core::import_pose::pose_from_pdb(), core::fragment::read_std_frags_from_cmd(), core::io::sequence_comparation::DesignContrast::setSecStruct(), core::fragment::steal_constant_length_frag_set_from_pose(), and core::fragment::steal_frag_set_from_pose().

void core::pose::setPoseExtraScore ( core::pose::Pose pose,
std::string  name,
core::Real  value 
)
void core::pose::setPoseExtraScore ( core::pose::Pose pose,
std::string const  name,
std::string  value 
)
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 
)
bool core::pose::sort_pose_by_score ( core::pose::PoseOP const &  pose1,
core::pose::PoseOP const &  pose2 
)
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 ( Size  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 
)
core::Real core::pose::total_energy_from_pose ( core::pose::Pose const &  pose)
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 
)

Variable Documentation

basic::Tracer core::pose::TR("core.pose.PDBPoseMap")
static
basic::Tracer core::pose::tr("core.pose")
static
basic::Tracer core::pose::TR("core.pose.PDBInfo")
static
basic::Tracer core::pose::TR("core.pose.util")
static