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...

void	addRemark (const std::vector< std::string > &v1)
	Add information to the remark. 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...

std::string	getResidueName (const unsigned &resnum, const std::string &chain) const
	get the name of the resnum'th residue of chain Chain=="*" matches any chain and makes it equivalent to getResidueName 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...

AtomNumber	getNamedAtomFromResidueAndChain (const std::string &aname, const unsigned &resnum, const std::string &chain) const
	Return the atom named aname from residue number resnum and chain. More...

std::vector< AtomNumber >	getAtomsInResidue (const unsigned &resnum, const std::string &chainid) const
	Access to the atoms of a residue. More...

std::vector< AtomNumber >	getAtomsInChain (const std::string &chainid) const
	Access to the atoms of a chain. 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...

void	setPositions (const std::vector< Vector > &v)
	Set the position array. More...

Vector	getPosition (AtomNumber a) const
	Access to the position array. More...

Private Attributes
std::vector< unsigned >	block_ends

std::vector< std::string >	atomsymb

std::vector< std::string >	chain

std::vector< unsigned >	residue

std::vector< Vector >	positions

std::vector< double >	occupancy

std::vector< double >	beta

std::vector< std::string >	remark

std::vector< AtomNumber >	numbers

std::map< AtomNumber, unsigned >	number2index

std::vector< std::string >	residuenames

Friends
Log &	operator<< (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

◆ addRemark()

void PLMD::PDB::addRemark ( const std::vector< std::string > & v1 )

Add information to the remark.

◆ checkForAtom()

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

Check if any of the atoms are named atom.

◆ checkForResidue()

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

Check if any of the residues are named name.

◆ getAtomBlockEnds()

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

Get the extents of the blocks containing the atoms.

◆ getAtomName()

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

return the name of a specific atom

◆ getAtomNumbers()

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

Access to the indexes.

◆ getAtomRange()

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.

◆ getAtomsInChain()

std::vector< AtomNumber > PLMD::PDB::getAtomsInChain ( const std::string & chainid ) const

Access to the atoms of a chain.

◆ getAtomsInResidue()

std::vector< AtomNumber > PLMD::PDB::getAtomsInResidue	(	const unsigned &	resnum,
		const std::string &	chainid
	)		const

Access to the atoms of a residue.

◆ getBeta()

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

Access to the beta array.

◆ getChainID()

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

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

◆ getChainNames()

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

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

◆ getNamedAtomFromResidue()

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

Return the atom named aname from residue number resnum.

◆ getNamedAtomFromResidueAndChain()

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

Return the atom named aname from residue number resnum and chain.

Chain=="*" matches any chain and makes it equivalent to getNamedAtomFromResidue.

◆ getNumberOfAtomBlocks()

unsigned PLMD::PDB::getNumberOfAtomBlocks ( ) const

Get the number of blocks of atoms in the pdb.

◆ getOccupancy()

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

Access to the occupancy array.

◆ getPosition()

Vector PLMD::PDB::getPosition ( AtomNumber a ) const

Access to the position array.

◆ getPositions()

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

Access to the position array.

◆ getRemark()

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

Access to the lines of REMARK.

◆ getResidueName() [1/3]

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

return the residue name for a specific atom

◆ getResidueName() [2/3]

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

get the name of the resnum'th residue

◆ getResidueName() [3/3]

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

get the name of the resnum'th residue of chain Chain=="*" matches any chain and makes it equivalent to getResidueName

◆ getResidueNumber()

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

return the residue number for a specific atom

◆ getResidueRange()

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.

◆ read()

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

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

◆ readFromFilepointer()

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

Read from a file pointer.

◆ setArgKeyword()

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

◆ setPositions()

void PLMD::PDB::setPositions ( const std::vector< Vector > & v )

Set the position array.

◆ size()

unsigned PLMD::PDB::size ( ) const

Returns the number of atoms.

Friends And Related Function Documentation

◆ operator<<

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

friend

use the log to dump information

Member Data Documentation

◆ atomsymb

std::vector<std::string> PLMD::PDB::atomsymb

private

◆ beta

std::vector<double> PLMD::PDB::beta

private

◆ block_ends

std::vector<unsigned> PLMD::PDB::block_ends

private

◆ chain

std::vector<std::string> PLMD::PDB::chain

private

◆ number2index

std::map<AtomNumber,unsigned> PLMD::PDB::number2index

private

◆ numbers

std::vector<AtomNumber> PLMD::PDB::numbers

private

◆ occupancy

std::vector<double> PLMD::PDB::occupancy

private

◆ positions

std::vector<Vector> PLMD::PDB::positions

private

◆ remark

std::vector<std::string> PLMD::PDB::remark

private

◆ residue

std::vector<unsigned> PLMD::PDB::residue

private

◆ residuenames

std::vector<std::string> PLMD::PDB::residuenames

private

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

tools/PDB.h
tools/PDB.cpp

Public Member Functions

Private Attributes

Friends

Detailed Description

Member Function Documentation

◆ addRemark()

◆ checkForAtom()

◆ checkForResidue()

◆ getAtomBlockEnds()

◆ getAtomName()

◆ getAtomNumbers()

◆ getAtomRange()

◆ getAtomsInChain()

◆ getAtomsInResidue()

◆ getBeta()

◆ getChainID()

◆ getChainNames()

◆ getNamedAtomFromResidue()

◆ getNamedAtomFromResidueAndChain()

◆ getNumberOfAtomBlocks()

◆ getOccupancy()

◆ getPosition()

◆ getPositions()

◆ getRemark()

◆ getResidueName() [1/3]

◆ getResidueName() [2/3]

◆ getResidueName() [3/3]

◆ getResidueNumber()

◆ getResidueRange()

◆ read()

◆ readFromFilepointer()

◆ setArgKeyword()

◆ setPositions()

◆ size()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ atomsymb

◆ beta

◆ block_ends

◆ chain

◆ number2index

◆ numbers

◆ occupancy

◆ positions

◆ remark

◆ residue

◆ residuenames