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protocols::constel Namespace Reference

Classes

class  ChainTerm
 
class  ExcludedFilter
 
class  FilterByAmphetamine
 Class to filter out constellations that cannot (putatively) be rescued by amphetamine. More...
 
class  FilterByHistamine
 Class to filter out constellations that cannot (putatively) be rescued by histamine. More...
 
class  FilterByIndoleCOO
 Class to filter out constellations that cannot (putatively) be rescued by compounds containing indole and a carboxylic group. More...
 
class  FilterByProxTerm
 
class  FilterBySASA
 
class  FilterByTryptamine
 Class to filter out constellations that cannot (putatively) be rescued by tryptamine. More...
 
class  HBondCommon
 A class to hold data structures and functions shared by filters that consider hydrogen bonding. More...
 
class  MasterFilter
 
class  NeighTeller
 
class  OrientCommon
 A class to hold data structures and functions common to filters that consider how groups of atoms within a constellation are oriented. More...
 
class  PresenceCommon
 A class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present. More...
 
class  ResidueMask
 
struct  ResMut
 A class to represent the mutation of a residue. More...
 
class  SingResCnlCrea
 

Typedefs

typedef
utility::pointer::shared_ptr
< ResidueMask
ResidueMaskOP
 

Functions

bool has_aromatic (Pose const &ps, utility::vector1< core::Size > const &cnl)
 : returns true if the given constellation contains at least one aromatic ring; returns false otherwise. More...
 
void get_chain_terms (core::pose::Pose const &ps, utility::vector1< ChainTerm > &chains)
 identifies each chain and its N- and C-terminal residues in a pose. More...
 
void print_chains (utility::vector1< ChainTerm > const &chains, basic::Tracer &t)
 Prints the N- and C-terminal residues of all chains. More...
 
xyzVector< Real > cnl_com (vector1< core::Size > const &cnl, Pose const &ps)
 returns the center of mass of a constellation More...
 
numeric::xyzVector< core::Realcnl_com (utility::vector1< core::Size > const &cnl, core::pose::Pose const &ps)
 returns the center of mass of a constellation More...
 
bool has_prox_termini (Pose const &ps, ChainTerm const &chain, core::Size NRES, Real DMAX2)
 Tells whether a chain has proximal N- and C-termini. More...
 
bool has_prox_termini (core::pose::Pose const &ps, ChainTerm const &chain, core::Size NRES, core::Real DMAX2)
 tells whether a chain has proximal termini More...
 
bool at_interface (Pose const &ps, utility::vector1< core::Size > const &cnl)
 Returns true if a constellation is shared by multiple chains; returns false otherwise. More...
 
static basic::Tracer TR ("protocols.constel.NeighTeller")
 
void mk_neigh_list (core::Size const tgtnum, utility::vector1< bool > &neighs, Pose &ps)
 Creates the list of residues that are neighbors of a given target residue. More...
 
void pair_constel_set_idx2 (core::Size const i, core::Size const j, Pose const &pose_init)
 Outputs all pair-constellations between a given pair of residues. More...
 
std::string create_constel_records_from_sfr (Pose const &ps, utility::vector1< core::Size > const &residues_to_print)
 concatenates into a string all the PDB ATOM records of a constellation More...
 
void out_pair_constel (ResMut const &mut1, ResMut const &mut2, Pose &ps)
 Outputs to file a constellation obtained from mutating a pair of residues. More...
 
void triple_constel_set_idx3 (core::Size const i, core::Size const j, core::Size const k, Pose const &pose_init)
 Outputs all triple-constellations among a given triple of residues. More...
 
void out_triple_constel (ResMut const &mut1, ResMut const &mut2, ResMut const &mut3, Pose &ps)
 Outputs to file a constellation obtained from mutating a triple of residues. More...
 
static basic::Tracer TR ("src.protocols.constel.SearchOptions")
 
void pair_constel_set (int const target_pdb_number, char const target_pdb_chain, Pose &pose_init)
 Searches pair-constellations by target residue. More...
 
void pair_constel_set (std::string const &tgtmuts, Pose &pose_init)
 Searches pair-constellations by pair of mutations. More...
 
void triple_constel_set (int const target_pdb_number, char const target_pdb_chain, Pose &pose_init)
 Searches for the triple-constellations of a target residue. More...
 
void target_constel (std::string &tgtcnl_fil, Pose &ps)
 Searches for a target constellation. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ResidueMask > protocols::constel::ResidueMaskOP

Function Documentation

bool protocols::constel::at_interface ( Pose const &  ps,
utility::vector1< core::Size > const &  cnl 
)

Returns true if a constellation is shared by multiple chains; returns false otherwise.

Parameters
[in]pspose containing the constellation
[in]cnlpose indexes of the residues forming the constellation

References core::chemical::element::N, and core::pose::Pose::pdb_info().

Referenced by core::select::util::calc_interacting_vector(), core::select::util::calc_interface_vector(), and protocols::stepwise::modeler::packer::figure_out_working_interface_res().

numeric::xyzVector<core::Real> protocols::constel::cnl_com ( vector1< core::Size > const &  cnl,
Pose const &  ps 
)

returns the center of mass of a constellation

Parameters
[in]cnlpose residue indexes of the residues forming the constellation.
[in]pspose to which all residues in the constellation belong.
Remarks
1. It is assumed that the residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation were previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".

References protocols::membrane::com(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::FilterByProxTerm::is_satisfied().

xyzVector<Real> protocols::constel::cnl_com ( vector1< core::Size > const &  cnl,
Pose const &  ps 
)

returns the center of mass of a constellation

Parameters
[in]cnlpose residue indexes of the residues forming the constellation.
[in]pspose to which all residues in the constellation belong.
Remarks
1. It is assumed that the residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation were previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".

References protocols::membrane::com(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::FilterByProxTerm::is_satisfied().

std::string protocols::constel::create_constel_records_from_sfr ( Pose const &  ps,
utility::vector1< core::Size > const &  residues_to_print 
)

concatenates into a string all the PDB ATOM records of a constellation

Parameters
[in]pspose containing the constellation
[in]residues_to_printpose indexes of the residues forming the constellation

References core::io::pdb::create_pdb_line_from_record(), core::io::pdb::create_records_from_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::init_from_pose(), and core::io::pose_to_sfr::PoseToStructFileRepConverter::sfr().

Referenced by out_pair_constel(), and out_triple_constel().

void protocols::constel::get_chain_terms ( core::pose::Pose const &  ps,
utility::vector1< ChainTerm > &  chains 
)

identifies each chain and its N- and C-terminal residues in a pose.

Parameters
[in]psthe pose.
[out]chainsvector to be filled with ChainTerm items for the chains in the pose.

chains[i] represents the ith chain in the pose built using only the protein residues of pose ps (i=1,...,N, where N is the number of such chains)

References core::pose::Pose::chain_begin(), core::pose::Pose::chain_end(), core::conformation::Residue::is_protein(), core::pose::Pose::num_chains(), core::pose::Pose::pdb_info(), core::io::pose_from_pose(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::constel::FilterByProxTerm::init().

bool protocols::constel::has_aromatic ( Pose const &  ps,
utility::vector1< core::Size > const &  cnl 
)

: returns true if the given constellation contains at least one aromatic ring; returns false otherwise.

Parameters
[in]pspose containing the constellation
[in]cnlpose indexes of the residues forming the constellation

Histidine is considered to be aromatic.

Remarks
It is assumed that:
  1. The residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation had their indexes previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".

References core::conformation::Residue::aa(), core::chemical::aa_his, core::conformation::Residue::atom_index(), core::conformation::Residue::is_aromatic(), core::chemical::element::N, core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

bool protocols::constel::has_prox_termini ( core::pose::Pose const &  ps,
ChainTerm const &  chain,
core::Size  NRES,
core::Real  DMAX2 
)

tells whether a chain has proximal termini

bool protocols::constel::has_prox_termini ( Pose const &  ps,
ChainTerm const &  chain,
core::Size  NRES,
Real  DMAX2 
)

Tells whether a chain has proximal N- and C-termini.

Parameters
[in]pspose to which the chain belongs.
[in]chainthe chain.
[in]NRESnumber of residues forming either terminus.
[in]DMAX2squared maximum distance for proximity.
Returns
true if the chain has proximal termini; false otherwise.

The termini are considered to be proximal if at least one residue on one terminus is within the maximum distance of a residue on the other terminus. Distance is computed on C-alpha atoms.

References protocols::constel::ChainTerm::get_cps(), protocols::constel::ChainTerm::get_nps(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::constel::FilterByProxTerm::init().

void protocols::constel::mk_neigh_list ( core::Size const  tgtnum,
utility::vector1< bool > &  neighs,
Pose ps 
)

Creates the list of residues that are neighbors of a given target residue.

Creates the list of residues that are neighbors of a given residue.

Parameters
[in]tgtnumresidue number of the target residue in its pose.
[out]neighsboolean mask filled in by this function to represent the list of neighbors. neighs[i] will be true if the ith residue in the pose is a neighbor of the target; otherwise neighs[i] will be false.
[in]pspose that the target and its potential neighbors belong to.

References protocols::constel::NeighTeller::isneigh(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by pair_constel_set(), and triple_constel_set().

void protocols::constel::out_pair_constel ( ResMut const &  mut1,
ResMut const &  mut2,
Pose ps 
)

Outputs to file a constellation obtained from mutating a pair of residues.

Parameters
[in]mut1representation of the mutation of the first residue.
[in]mut2representation of the mutation of the second residue.
[in]psRosetta pose that both residues belong to. In the pose, the occupancy of atoms in either residue is that AFTER the mutation.
Remarks
  1. The file name of the constellation has the following format, SIIIIEC_siiiiec.pdb, where:
  • S is the first residue's start amino acid type
  • IIII is a four-digit field indicating the first residue's number in the input PDB file
  • E is the first residue's end amino acid type
  • C is the first residue's chain in the input PDB file
  • s is the second residue's start amino acid type
  • iiii is a four-digit field indicating the second residue's number in the input PDB file
  • e is the second residue's end amino acid type
  • c is the second residue's chain in the input PDB file
  1. This function may set to zero the occupancy of additional atoms of the residues forming the constellation..

References protocols::constel::ResMut::cid, create_constel_records_from_sfr(), protocols::constel::ResMut::eaa, core::conformation::membrane::out, protocols::constel::ResMut::pdbn, protocols::constel::ResMut::psn, protocols::constel::ResMut::saa, protocols::constel::SingResCnlCrea::strip_atoms(), and protocols::constel::SingResCnlCrea::stripped().

Referenced by pair_constel_set(), pair_constel_set_idx2(), and target_constel().

void protocols::constel::out_triple_constel ( ResMut const &  mut1,
ResMut const &  mut2,
ResMut const &  mut3,
Pose ps 
)

Outputs to file a constellation obtained from mutating a triple of residues.

Parameters
[in]mut1representation of the mutation of the first residue.
[in]mut2representation of the mutation of the second residue.
[in]mut3representation of the mutation of the third residue.
[in]psRosetta pose that all three residues belong to. In the pose, the occupancy of atoms in each residue is that AFTER the mutation.
Remarks
  1. The file name of the constellation has the following format, SIIIIEC_siiiiec_tjjjjfd.pdb, where:
  • S is the first residue's start amino acid type
  • IIII is a four-digit field indicating the first residue's number in the input PDB file
  • E is the first residue's end amino acid type
  • C is the first residue's chain in the input PDB file
  • s is the second residue's start amino acid type
  • iiii is a four-digit field indicating the second residue's number in the input PDB file
  • e is the second residue's end amino acid type
  • c is the second residue's chain in the input PDB file
  • t is the third residue's start amino acid type
  • jjjj is a four-digit field indicating the third residue's number in the input PDB file
  • f is the third residue's end amino acid type
  • d is the third residue's chain in the input PDB file

References protocols::constel::ResMut::cid, create_constel_records_from_sfr(), protocols::constel::ResMut::eaa, core::conformation::membrane::out, protocols::constel::ResMut::pdbn, protocols::constel::ResMut::psn, protocols::constel::ResMut::saa, protocols::constel::SingResCnlCrea::strip_atoms(), and protocols::constel::SingResCnlCrea::stripped().

Referenced by target_constel(), and triple_constel_set_idx3().

void protocols::constel::pair_constel_set ( int const  target_pdb_number,
char const  target_pdb_chain,
Pose pose_init 
)

Searches pair-constellations by target residue.

Extracts all the constellations formed by a target residue. Each constellation involves a pair of residues: the target residue and one of its neighbors. Different constellations are printed to different files.

Parameters
[in]target_pdb_numberresidue number of the target residue in the input PDB file.
[in]target_pdb_chainchain to which the target belongs in the PDB file.
[in]pose_initpose to which the target belongs.

References mk_neigh_list(), pair_constel_set_idx2(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

void protocols::constel::pair_constel_set ( std::string const &  tgtmuts,
Pose pose_init 
)

Searches pair-constellations by pair of mutations.

Searches pair-constellations by mutation pair.

Extracts from a pose all the constellations that correspond to a given pair of mutations of amino acid types.

Parameters
[in]tgtmutsan AB_CD string identifying the desired pair of mutations, (A->B, C->D), where A, B, C, and D are amino acid types expressed in one-letter code.
[in]pose_initpose from which constellations have to be extracted.

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::NeighTeller::isneigh(), core::chemical::oneletter_code_from_aa(), out_pair_constel(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

void protocols::constel::pair_constel_set_idx2 ( core::Size const  i,
core::Size const  j,
Pose const &  pose_init 
)

Outputs all pair-constellations between a given pair of residues.

Parameters
[in]ipose index of the 1st residue.
[in]jpose index of the 2nd residue.
[in]pose_initthe pose.
Remarks
Output files have the names and format specified in out_pair_constel()

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::SingResCnlCrea::list_allowable_mutations(), core::chemical::oneletter_code_from_aa(), out_pair_constel(), core::pose::Pose::pdb_info(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

Referenced by pair_constel_set().

void protocols::constel::print_chains ( utility::vector1< ChainTerm > const &  chains,
basic::Tracer &  t 
)

Prints the N- and C-terminal residues of all chains.

prints the N- and C-terminal residues of all chains.

Parameters
[in]chainsvector of ChainTerm items, each representing a different chain.
[out]toutput tracer

The ith output line represents the ith chain in 'chains', for i=1,...,N, where N is the size of 'chains'.

void protocols::constel::target_constel ( std::string &  tgtcnl_fil,
Pose ps 
)

Searches for a target constellation.

Searches a single, target constellation.

Parameters
[in]tgtcnl_filfile specifying the target constellation.
[in]psthe pose

The format of the input file is as follows:

CID{1} RNU{1} ICO{1} AASTA{1} AAEND{1} ... CID{N} RNU{N} ICO{N} AASTA{N} AAEND{N}

where N is the number of residues forming the constellation and CID{i}, RNU{i}, ICO{i}, AASTA{i}, and AAEND{i} are the chain id, residue number, insertion code, start amino acid type, and end amino acid type of the ith residue contributing to the constellation (i=1,...,N). A blank chain identifier in the PDB file is denoted by ',' (comma); a blank insertion code in the PDB file is denoted by '_' (underscore).

The function exits if any input lines cannot identify any residue.

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::NeighTeller::is_neigh_tree(), core::chemical::element::N, core::chemical::oneletter_code_from_aa(), out_pair_constel(), out_triple_constel(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), TR(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

static basic::Tracer protocols::constel::TR ( "protocols.constel.NeighTeller"  )
static
static basic::Tracer protocols::constel::TR ( "src.protocols.constel.SearchOptions"  )
static
void protocols::constel::triple_constel_set ( int const  target_pdb_number,
char const  target_pdb_chain,
Pose pose_init 
)

Searches for the triple-constellations of a target residue.

Searches triple-constellations by target residue.

Each constellation comprises a triple of spatially contiguous residues, among which is the target. Different constellations are printed to different files.

Parameters
[in]target_pdb_numberresidue number of the target residue in the input PDB file.
[in]target_pdb_chainchain to which the target belongs in the PDB file.
[in]pose_initpose to which the target belongs.

References protocols::constel::NeighTeller::isneigh(), mk_neigh_list(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and triple_constel_set_idx3().

void protocols::constel::triple_constel_set_idx3 ( core::Size const  i,
core::Size const  j,
core::Size const  k,
Pose const &  pose_init 
)

Outputs all triple-constellations among a given triple of residues.

Parameters
[in]ipose index of the 1st residue.
[in]jpose index of the 2nd residue.
[in]kpose index of the 3rd residue.
[in]pose_initthe pose.
Remarks
Output files have the names and format specified in out_triple_constel()

References core::pose::Pose::aa(), protocols::constel::MasterFilter::is_constel_valid(), protocols::constel::SingResCnlCrea::list_allowable_mutations(), core::chemical::oneletter_code_from_aa(), out_triple_constel(), core::pose::Pose::pdb_info(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

Referenced by triple_constel_set().