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PLMD::PDB Class Reference

Minimalistic pdb parser. More...

#include <PDB.h>

Public Member Functions

bool read (const std::string &file, bool naturalUnits, double scale)
 Read the pdb from a file, scaling positions by a factor scale. More...
 
bool readFromFilepointer (FILE *fp, bool naturalUnits, double scale)
 Read from a file pointer. More...
 
const std::vector< Vector > & getPositions () const
 Access to the position array. More...
 
const std::vector< double > & getOccupancy () const
 Access to the occupancy array. More...
 
const std::vector< double > & getBeta () const
 Access to the beta array. More...
 
void setArgKeyword (const std::string &new_args)
 This is used to set the keyword ARG - this is so we we can use a1. More...
 
const std::vector< std::string > & getRemark () const
 Access to the lines of REMARK. More...
 
const std::vector< AtomNumber > & getAtomNumbers () const
 Access to the indexes. More...
 
unsigned size () const
 Returns the number of atoms. More...
 
void getChainNames (std::vector< std::string > &chains) const
 Get the names of all the chains in the pdb file. More...
 
void getResidueRange (const std::string &chainname, unsigned &res_start, unsigned &res_end, std::string &errmsg) const
 Get the residues in each of the chains. More...
 
void getAtomRange (const std::string &chainname, AtomNumber &a_start, AtomNumber &a_end, std::string &errmsg) const
 Get the atoms in each of the chains. More...
 
std::string getChainID (const unsigned &resnumber) const
 Get the chain ID that a particular residue is a part of. More...
 
std::string getAtomName (AtomNumber a) const
 return the name of a specific atom More...
 
unsigned getResidueNumber (AtomNumber a) const
 return the residue number for a specific atom More...
 
std::string getResidueName (AtomNumber a) const
 return the residue name for a specific atom More...
 
std::string getResidueName (const unsigned &resnum) const
 get the name of the resnum'th residue More...
 
bool checkForResidue (const std::string &name) const
 Check if any of the residues are named name. More...
 
bool checkForAtom (const std::string &name) const
 Check if any of the atoms are named atom. More...
 
AtomNumber getNamedAtomFromResidue (const std::string &aname, const unsigned &resnum) const
 Return the atom named aname from residue number resnum. More...
 
const std::vector< unsigned > & getAtomBlockEnds () const
 Get the extents of the blocks containing the atoms. More...
 
unsigned getNumberOfAtomBlocks () const
 Get the number of blocks of atoms in the pdb. More...
 

Private Attributes

std::vector< unsigned > block_ends
 
std::vector< std::string > atomsymb
 
std::vector< std::string > chain
 
std::vector< unsigned > residue
 
std::vector< Vectorpositions
 
std::vector< double > occupancy
 
std::vector< double > beta
 
std::vector< std::string > remark
 
std::vector< AtomNumbernumbers
 
std::map< AtomNumber, unsigned > number2index
 
std::vector< std::string > residuenames
 

Friends

Logoperator<< (Log &ostr, const PDB &pdb)
 use the log to dump information More...
 

Detailed Description

Minimalistic pdb parser.

Contain positions, atomic indexes, occupancy and beta. We should also add other info (e.g. residue name etc).

Member Function Documentation

bool PLMD::PDB::checkForAtom ( const std::string &  name) const

Check if any of the atoms are named atom.

bool PLMD::PDB::checkForResidue ( const std::string &  name) const

Check if any of the residues are named name.

const std::vector< unsigned > & PLMD::PDB::getAtomBlockEnds ( ) const

Get the extents of the blocks containing the atoms.

std::string PLMD::PDB::getAtomName ( AtomNumber  a) const

return the name of a specific atom

const std::vector< AtomNumber > & PLMD::PDB::getAtomNumbers ( ) const

Access to the indexes.

void PLMD::PDB::getAtomRange ( const std::string &  chainname,
AtomNumber a_start,
AtomNumber a_end,
std::string &  errmsg 
) const

Get the atoms in each of the chains.

const std::vector< double > & PLMD::PDB::getBeta ( ) const

Access to the beta array.

std::string PLMD::PDB::getChainID ( const unsigned &  resnumber) const

Get the chain ID that a particular residue is a part of.

void PLMD::PDB::getChainNames ( std::vector< std::string > &  chains) const

Get the names of all the chains in the pdb file.

AtomNumber PLMD::PDB::getNamedAtomFromResidue ( const std::string &  aname,
const unsigned &  resnum 
) const

Return the atom named aname from residue number resnum.

unsigned PLMD::PDB::getNumberOfAtomBlocks ( ) const

Get the number of blocks of atoms in the pdb.

const std::vector< double > & PLMD::PDB::getOccupancy ( ) const

Access to the occupancy array.

const std::vector< Vector > & PLMD::PDB::getPositions ( ) const

Access to the position array.

const std::vector< std::string > & PLMD::PDB::getRemark ( ) const

Access to the lines of REMARK.

std::string PLMD::PDB::getResidueName ( AtomNumber  a) const

return the residue name for a specific atom

std::string PLMD::PDB::getResidueName ( const unsigned &  resnum) const

get the name of the resnum'th residue

unsigned PLMD::PDB::getResidueNumber ( AtomNumber  a) const

return the residue number for a specific atom

void PLMD::PDB::getResidueRange ( const std::string &  chainname,
unsigned &  res_start,
unsigned &  res_end,
std::string &  errmsg 
) const

Get the residues in each of the chains.

bool PLMD::PDB::read ( const std::string &  file,
bool  naturalUnits,
double  scale 
)

Read the pdb from a file, scaling positions by a factor scale.

bool PLMD::PDB::readFromFilepointer ( FILE *  fp,
bool  naturalUnits,
double  scale 
)

Read from a file pointer.

void PLMD::PDB::setArgKeyword ( const std::string &  new_args)

This is used to set the keyword ARG - this is so we we can use a1.

  • in the input for reference configurations
unsigned PLMD::PDB::size ( ) const

Returns the number of atoms.

Friends And Related Function Documentation

Log& operator<< ( Log ostr,
const PDB pdb 
)
friend

use the log to dump information

Member Data Documentation

std::vector<std::string> PLMD::PDB::atomsymb
private
std::vector<double> PLMD::PDB::beta
private
std::vector<unsigned> PLMD::PDB::block_ends
private
std::vector<std::string> PLMD::PDB::chain
private
std::map<AtomNumber,unsigned> PLMD::PDB::number2index
private
std::vector<AtomNumber> PLMD::PDB::numbers
private
std::vector<double> PLMD::PDB::occupancy
private
std::vector<Vector> PLMD::PDB::positions
private
std::vector<std::string> PLMD::PDB::remark
private
std::vector<unsigned> PLMD::PDB::residue
private
std::vector<std::string> PLMD::PDB::residuenames
private

The documentation for this class was generated from the following files: