PDBRichPhantom Class Reference

#include <pdb.h>

Collaboration diagram for PDBRichPhantom:

Public Member Functions
void	addAtom (const RichAtom &atom)
	Add Atom. More...
size_t	getNumberOfAtoms () const
	Get number of atoms. More...
void	read (const FileName &fnPDB, const bool pseudoatoms=false, const double threshold=0.0)
	Read rich phantom from either a PDB of CIF file. More...
void	write (const FileName &fnPDB, const bool renumber=false)
	Write rich phantom to PDB or CIF file. More...

Public Attributes
std::vector< std::string >	remarks
	List of remarks. More...
std::vector< RichAtom >	atomList
	List of atoms. More...
std::vector< double >	intensities
cif::datablock	dataBlock

Detailed Description

Phantom description using atoms.

Definition at line 250 of file pdb.h.

Member Function Documentation

addAtom()

void PDBRichPhantom::addAtom ( const RichAtom &  atom )

inline

Add Atom.

Definition at line 264 of file pdb.h.

    {
        atomList.push_back(atom);
    }

getNumberOfAtoms()

size_t PDBRichPhantom::getNumberOfAtoms ( ) const

inline

Get number of atoms.

Definition at line 270 of file pdb.h.

    {
        return atomList.size();
    }

read()

void PDBRichPhantom::read	(	const FileName &	fnPDB,
		const bool	pseudoatoms = false,
		const double	threshold = 0.0
	)

Read rich phantom from either a PDB of CIF file.

This function reads the given PDB or CIF file and stores the found atoms, remarks, and intensities.

Parameters

fnPDB	PDB/CIF file.
pseudoatoms	Flag for returning intensities (stored in B-factors) instead of atoms. false (default) is used when there are no pseudoatoms or when using a threshold.
threshold	B factor threshold for filtering out for pdb_reduce_pseudoatoms.

Definition at line 704 of file pdb.cpp.

{
    // Checking if extension is .cif or .pdb
    if (checkExtension(fnPDB.getString(), {".cif"}, {".gz"})) {
        readRichCIF(fnPDB.getString(), bind(&PDBRichPhantom::addAtom, this, std::placeholders::_1), intensities, pseudoatoms, threshold, dataBlock);
    } else {
        readRichPDB(fnPDB, bind(&PDBRichPhantom::addAtom, this, std::placeholders::_1), intensities, remarks, pseudoatoms, threshold);
    }
}

write()

void PDBRichPhantom::write	(	const FileName &	fnPDB,
		const bool	renumber = false
	)

Write rich phantom to PDB or CIF file.

This function stores all the data of the rich phantom into a PDB or CIF file. Note: Conversion is not enabled yet, so if a file read from a PDB is written into a CIF file, results might not be great. Atoms should be properly translated, but remarks and intensities probably not.

Parameters

fnPDB	PDB/CIF file to write to.
renumber	Flag for determining if atom's serial numbers must be renumbered or not.

Definition at line 872 of file pdb.cpp.

{
    // Checking if extension is .cif or .pdb
    if (checkExtension(fnPDB.getString(), {".cif"}, {".gz"})) {
        writeCIF(fnPDB.getString(), atomList, dataBlock);
    } else {
        writePDB(fnPDB, renumber, remarks, atomList);
    }
}

Member Data Documentation

atomList

std::vector<RichAtom> PDBRichPhantom::atomList

List of atoms.

Definition at line 257 of file pdb.h.

dataBlock

cif::datablock PDBRichPhantom::dataBlock

Definition at line 261 of file pdb.h.

intensities

std::vector<double> PDBRichPhantom::intensities

Definition at line 258 of file pdb.h.

remarks

std::vector<std::string> PDBRichPhantom::remarks

List of remarks.

Definition at line 254 of file pdb.h.

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

• xmipp/libraries/data/pdb.h
• xmipp/libraries/data/pdb.cpp