Minimalistic pdb parser. More...

#include <PDB.h>

Public Member Functions
void	addBlockEnd (const unsigned &end)
	Check if the properties that are required are in this pdb this is used in PLMD::mapping::Mapping. More...

void	addRemark (std::vector< std::string > &v1)
	Add data to argnames map. More...

bool	allowedResidue (const std::string &type, const std::string &residuename) const
	Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins. More...

bool	checkForAtom (AtomNumber a) const
	Check if specific atom exists. More...

bool	checkForAtom (const std::string &name) const
	Check if any of the atoms are named atom. More...

bool	checkForResidue (const std::string &name) const
	Check if any of the residues are named name. More...

std::vector< std::string >	getArgumentNames () const

bool	getArgumentValue (const std::string &name, std::vector< double > &value) const
	Get the value of one of the arguments in the PDB file. More...

const std::vector< unsigned > &	getAtomBlockEnds () const
	Get the extents of the blocks containing the atoms. More...

std::string	getAtomName (AtomNumber a) const
	return the name of a specific atom More...

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

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

const std::vector< double > &	getBeta () const
	Access to the beta array. More...

const Vector &	getBoxAng () const
	Returns box axis angles. More...

const Vector &	getBoxAxs () const
	Returns box axis lengths. More...

const Tensor &	getBoxVec () const
	Returns box axis vectors. More...

std::string	getChainID (AtomNumber a) const
	Get the chain ID from atom number. More...

std::string	getChainID (const unsigned &resnumber) const
	Get the chain ID that a particular residue is a part of. More...

void	getChainNames (std::vector< std::string > &chains) const
	Get the names of all the chains in the pdb file. More...

std::string	getMtype () const
	Get the metric type. 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...

unsigned	getNumberOfAtomBlocks () const
	Get the number of blocks of atoms in the pdb. More...

const std::vector< double > &	getOccupancy () const
	Access to the occupancy array. More...

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

const std::vector< Vector > &	getPositions () const
	Access to the position array. 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...

unsigned	getResidueNumber (AtomNumber a) const
	return the residue number for a specific atom 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...

bool	hasFlag (const std::string &fname) const
	Does the PDB have this flag. More...

void	print (const double &lunits, GenericMolInfo *mymoldat, OFile &ofile, const std::string &fmt)
	Print out a PDB object. More...

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...

void	setArgumentNames (const std::vector< std::string > &argument_names)
	Set the argument names that you would like to use. More...

void	setArgumentValue (const std::string &argname, const double &val)
	This is used in PLMD::analysis::AnalysisWithDataCollection to set the argument values. More...

void	setAtomNumbers (const std::vector< AtomNumber > &atoms)
	This is used in PLMD::analysis::AnalysisWithDataCollection to add the numbers of the atoms. More...

void	setAtomPositions (const std::vector< Vector > &pos)
	This is used in PLMD::analysis::AnalysisWithDataCollection to set the atom positions. More...

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

unsigned	size () const
	Returns the number of atoms. More...

Private Attributes
std::map< std::string, std::vector< double > >	arg_data

std::vector< std::string >	argnames

std::vector< std::string >	atomsymb

std::vector< double >	beta

std::vector< unsigned >	block_ends

Tensor	Box

Vector	BoxABG

Vector	BoxXYZ

std::vector< std::string >	chain

std::vector< std::string >	flags

std::string	mtype

std::map< AtomNumber, unsigned >	number2index

std::vector< AtomNumber >	numbers

std::vector< double >	occupancy

std::vector< Vector >	positions

std::vector< unsigned >	residue

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

◆ addBlockEnd()

void PLMD::PDB::addBlockEnd ( const unsigned & end )

Check if the properties that are required are in this pdb this is used in PLMD::mapping::Mapping.

This is used in PLMD::analysis::AnalysisWithDataCollection to add the sizes of the domains for PLMD::MultiRMSD

◆ addRemark()

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

Add data to argnames map.

◆ allowedResidue()

bool PLMD::PDB::allowedResidue	(	const std::string &	type,
		const std::string &	residuename
	)		const

Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins.

◆ checkForAtom() [1/2]

bool PLMD::PDB::checkForAtom ( AtomNumber a ) const

Check if specific atom exists.

◆ checkForAtom() [2/2]

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.

◆ getArgumentNames()

std::vector< std::string > PLMD::PDB::getArgumentNames ( ) const

◆ getArgumentValue()

bool PLMD::PDB::getArgumentValue	(	const std::string &	name,
		std::vector< double > &	value
	)		const

Get the value of one of the arguments in the PDB file.

◆ 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.

◆ getBoxAng()

const Vector & PLMD::PDB::getBoxAng ( ) const

Returns box axis angles.

◆ getBoxAxs()

const Vector & PLMD::PDB::getBoxAxs ( ) const

Returns box axis lengths.

◆ getBoxVec()

const Tensor & PLMD::PDB::getBoxVec ( ) const

Returns box axis vectors.

◆ getChainID() [1/2]

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

Get the chain ID from atom number.

◆ getChainID() [2/2]

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.

◆ getMtype()

std::string PLMD::PDB::getMtype ( ) const

Get the metric type.

◆ 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.

◆ 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.

◆ hasFlag()

bool PLMD::PDB::hasFlag ( const std::string & fname ) const

Does the PDB have this flag.

◆ print()

void PLMD::PDB::print	(	const double &	lunits,
		GenericMolInfo *	mymoldat,
		OFile &	ofile,
		const std::string &	fmt
	)

Print out a PDB object.

◆ 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.

◆ setArgumentNames()

void PLMD::PDB::setArgumentNames ( const std::vector< std::string > & argument_names )

Set the argument names that you would like to use.

◆ setArgumentValue()

void PLMD::PDB::setArgumentValue	(	const std::string &	argname,
		const double &	val
	)

This is used in PLMD::analysis::AnalysisWithDataCollection to set the argument values.

◆ setAtomNumbers()

void PLMD::PDB::setAtomNumbers ( const std::vector< AtomNumber > & atoms )

This is used in PLMD::analysis::AnalysisWithDataCollection to add the numbers of the atoms.

◆ setAtomPositions()

void PLMD::PDB::setAtomPositions ( const std::vector< Vector > & pos )

This is used in PLMD::analysis::AnalysisWithDataCollection to set the atom positions.

◆ 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

◆ arg_data

std::map<std::string,std::vector<double> > PLMD::PDB::arg_data

private

◆ argnames

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

private

◆ 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

◆ Box

Tensor PLMD::PDB::Box

private

◆ BoxABG

Vector PLMD::PDB::BoxABG

private

◆ BoxXYZ

Vector PLMD::PDB::BoxXYZ

private

◆ chain

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

private

◆ flags

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

private

◆ mtype

std::string PLMD::PDB::mtype

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

◆ 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

◆ addBlockEnd()

◆ addRemark()

◆ allowedResidue()

◆ checkForAtom() [1/2]

◆ checkForAtom() [2/2]

◆ checkForResidue()

◆ getArgumentNames()

◆ getArgumentValue()

◆ getAtomBlockEnds()

◆ getAtomName()

◆ getAtomNumbers()

◆ getAtomRange()

◆ getAtomsInChain()

◆ getAtomsInResidue()

◆ getBeta()

◆ getBoxAng()

◆ getBoxAxs()

◆ getBoxVec()

◆ getChainID() [1/2]

◆ getChainID() [2/2]

◆ getChainNames()

◆ getMtype()

◆ getNamedAtomFromResidue()

◆ getNamedAtomFromResidueAndChain()

◆ getNumberOfAtomBlocks()

◆ getOccupancy()

◆ getPosition()

◆ getPositions()

◆ getResidueName() [1/3]

◆ getResidueName() [2/3]

◆ getResidueName() [3/3]

◆ getResidueNumber()

◆ getResidueRange()

◆ hasFlag()

◆ print()

◆ read()

◆ readFromFilepointer()

◆ setArgumentNames()

◆ setArgumentValue()

◆ setAtomNumbers()

◆ setAtomPositions()

◆ setPositions()

◆ size()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ arg_data

◆ argnames

◆ atomsymb

◆ beta

◆ block_ends

◆ Box

◆ BoxABG

◆ BoxXYZ

◆ chain

◆ flags

◆ mtype

◆ number2index

◆ numbers

◆ occupancy

◆ positions

◆ residue

◆ residuenames