PDBPhantom Class Reference

#include <pdb.h>

Collaboration diagram for PDBPhantom:

Public Member Functions
void	addAtom (const Atom &atom)
	Add Atom. More...
const Atom &	getAtom (int i) const
	Get Atom at position i. More...
size_t	getNumberOfAtoms () const
	Get number of atoms. More...
void	read (const FileName &fnPDB)
	Read phantom from either a PDB of CIF file. More...
void	shift (double x, double y, double z)
	Apply a shift to all atoms. More...
void	produceSideInfo ()

Public Attributes
std::vector< Atom >	atomList
	List of atoms. More...
cif::datablock	dataBlock

Detailed Description

Phantom description using atoms.

Definition at line 127 of file pdb.h.

Member Function Documentation

addAtom()

void PDBPhantom::addAtom ( const Atom &  atom )

inline

Add Atom.

Definition at line 137 of file pdb.h.

    {
        atomList.push_back(atom);
    }

getAtom()

const Atom& PDBPhantom::getAtom ( int  i ) const

inline

Get Atom at position i.

Definition at line 143 of file pdb.h.

    {
        return atomList[i];
    }

getNumberOfAtoms()

size_t PDBPhantom::getNumberOfAtoms ( ) const

inline

Get number of atoms.

Definition at line 149 of file pdb.h.

    {
        return atomList.size();
    }

produceSideInfo()

void PDBPhantom::produceSideInfo

(

)

Produce side info. The side info produces the radial profiles of each atom and its projections.

read()

void PDBPhantom::read

(

const FileName &

fnPDB

)

Read phantom from either a PDB of CIF file.

This function reads the given PDB or CIF file and inserts the found atoms inside in class's atom list.

Parameters

fnPDB

PDB/CIF file.

Definition at line 503 of file pdb.cpp.

{
    // Checking if extension is .cif or .pdb
    if (checkExtension(fnPDB.getString(), {".cif"}, {".gz"})) {
        readCIF(fnPDB.getString(), bind(&PDBPhantom::addAtom, this, std::placeholders::_1), dataBlock);
    } else {
        readPDB(fnPDB, bind(&PDBPhantom::addAtom, this, std::placeholders::_1));
    }
}

shift()

void PDBPhantom::shift	(	double	x,
		double	y,
		double	z
	)

Apply a shift to all atoms.

Definition at line 514 of file pdb.cpp.

{
    int imax=atomList.size();
    for (int i=0; i<imax; i++)
    {
        atomList[i].x+=x;
        atomList[i].y+=y;
        atomList[i].z+=z;
    }
}

Member Data Documentation

atomList

std::vector<Atom> PDBPhantom::atomList

List of atoms.

Definition at line 131 of file pdb.h.

dataBlock

cif::datablock PDBPhantom::dataBlock

Definition at line 134 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