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...

bool	getBackbone (const unsigned &resnumber, const std::vector< std::string > &backnames, std::vector< AtomNumber > &backnumbers) const
	Get the atoms in the backbone of a particular residue. More...

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

void	renameAtoms (const std::string &old_name, const std::string &new_name)
	This allows you to give atoms a new name - this is used to rename the HB1 atoms in GLY residues CB so that alpharmsd works. 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...

Private Attributes
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).

Definition at line 38 of file PDB.h.

Member Function Documentation

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

return the name of a specific atom

Definition at line 51 of file PDB.cpp.

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

Access to the indexes.

Definition at line 47 of file PDB.cpp.

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.

Definition at line 177 of file PDB.cpp.

bool PLMD::PDB::getBackbone	(	const unsigned &	resnumber,
		const std::vector< std::string > &	backnames,
		std::vector< AtomNumber > &	backnumbers
	)		const

Get the atoms in the backbone of a particular residue.

Definition at line 194 of file PDB.cpp.

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

Access to the beta array.

Definition at line 39 of file PDB.cpp.

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

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

Definition at line 212 of file PDB.cpp.

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

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

Definition at line 152 of file PDB.cpp.

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

Access to the occupancy array.

Definition at line 35 of file PDB.cpp.

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

Access to the position array.

Definition at line 31 of file PDB.cpp.

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

Access to the lines of REMARK.

Definition at line 43 of file PDB.cpp.

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

return the residue name for a specific atom

Definition at line 65 of file PDB.cpp.

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

return the residue number for a specific atom

Definition at line 58 of file PDB.cpp.

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.

Definition at line 160 of file PDB.cpp.

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

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

Definition at line 144 of file PDB.cpp.

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

Read from a file pointer.

Definition at line 76 of file PDB.cpp.

void PLMD::PDB::renameAtoms	(	const std::string &	old_name,
		const std::string &	new_name
	)

This allows you to give atoms a new name - this is used to rename the HB1 atoms in GLY residues CB so that alpharmsd works.

Definition at line 219 of file PDB.cpp.

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

Definition at line 134 of file PDB.cpp.

unsigned PLMD::PDB::size ( ) const

Returns the number of atoms.

Definition at line 72 of file PDB.cpp.

Friends And Related Function Documentation

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

friend

use the log to dump information

Definition at line 225 of file PDB.cpp.

Member Data Documentation

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

private

Definition at line 39 of file PDB.h.

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

private

Definition at line 43 of file PDB.h.

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

private

Definition at line 39 of file PDB.h.

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

private

Definition at line 46 of file PDB.h.

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

private

Definition at line 45 of file PDB.h.

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

private

Definition at line 42 of file PDB.h.

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

private

Definition at line 41 of file PDB.h.

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

private

Definition at line 44 of file PDB.h.

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

private

Definition at line 40 of file PDB.h.

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

private

Definition at line 47 of file PDB.h.

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

Friends And Related Function Documentation

Member Data Documentation