AtomInterpolator Class Reference

#include <pdb.h>

Public Member Functions
void	setup (int m, double hights, bool computeProjection=false)
void	addAtom (const std::string &atomType, bool computeProjection=false)
	Add atom. More...
int	getAtomIndex (char atom) const
	Get atom index. More...
double	atomRadius (char atom) const
double	volumeAtDistance (char atom, double r) const
double	projectionAtDistance (char atom, double r) const

Public Attributes
std::vector< MultidimArray< double > >	volumeProfileCoefficients
std::vector< MultidimArray< double > >	projectionProfileCoefficients
std::vector< double >	radii
int	M
double	highTs

Detailed Description

Class for Atom interpolations.

Definition at line 342 of file pdb.h.

Member Function Documentation

addAtom()

void AtomInterpolator::addAtom	(	const std::string &	atomType,
		bool	computeProjection = false
	)

Add atom.

Definition at line 1422 of file pdb.cpp.

{
    MultidimArray<double> profile;
    MultidimArray<double> splineCoeffs;

    // Atomic profile
    atomRadialProfile(M, highTs, atom, profile);
    produceSplineCoefficients(xmipp_transformation::BSPLINE3,splineCoeffs,profile);
    volumeProfileCoefficients.push_back(splineCoeffs);

    // Radius
    radii.push_back((double)FINISHINGX(profile)/M);

    // Projection profile
    if (computeProjection)
    {
        atomProjectionRadialProfile(M, splineCoeffs, profile);
        produceSplineCoefficients(xmipp_transformation::BSPLINE3,splineCoeffs,profile);
        projectionProfileCoefficients.push_back(splineCoeffs);
    }
}

atomRadius()

double AtomInterpolator::atomRadius ( char  atom ) const

inline

Radius of an atom in the final sampling rate M*highTs.

Definition at line 414 of file pdb.h.

    {
        return radii[getAtomIndex(atom)];
    }

getAtomIndex()

int AtomInterpolator::getAtomIndex ( char  atom ) const

inline

Get atom index.

Definition at line 365 of file pdb.h.

    {
        int idx=-1;
        switch (atom)
        {
        case 'H':
            idx=0;
            break;
        case 'C':
            idx=1;
            break;
        case 'N':
            idx=2;
            break;
        case 'O':
            idx=3;
            break;
        case 'P':
            idx=4;
            break;
        case 'S':
            idx=5;
            break;
        case 'E': // Iron Fe
            idx=6;
            break;
        case 'K':
            idx=7;
            break;
        case 'F':
             idx=8;
             break;
        case 'G': // Magnesium Mg
             idx=9;
             break;
        case 'L': // Chlorine Cl
             idx=10;
             break;
        case 'A': // Calcium Ca
             idx=11;
             break;
        default:
            REPORT_ERROR(ERR_VALUE_INCORRECT,(std::string)
                         "AtomInterpolator::getAtomIndex: Atom "+atom+" unknown");
        }
        return idx;
    }

projectionAtDistance()

double AtomInterpolator::projectionAtDistance	(	char	atom,
		double	r
	)		const

Projection value at a distance r of the atom whose first letter is the one provided as atom.

Definition at line 111 of file pdb.cpp.

{
    int idx=getAtomIndex(atom);
    if (r>radii[idx])
        return 0;
    else
        return projectionProfileCoefficients[idx].
               interpolatedElementBSpline1D(r*M,3);
}

setup()

void AtomInterpolator::setup	(	int	m,
		double	hights,
		bool	computeProjection = false
	)

Setup. HighTs is a fine sampling rate, M is an integer number so that the final sampling rate is Ts=M*highTs;

Atom interpolations -------------------------------------------------—

Definition at line 1402 of file pdb.cpp.

{
    M=m;
    highTs=hights;
    if (volumeProfileCoefficients.size()==12)
        return;
    addAtom("H",computeProjection);
    addAtom("C",computeProjection);
    addAtom("N",computeProjection);
    addAtom("O",computeProjection);
    addAtom("P",computeProjection);
    addAtom("S",computeProjection);
    addAtom("Fe",computeProjection);
    addAtom("K",computeProjection);
    addAtom("F",computeProjection);
    addAtom("Mg",computeProjection);
    addAtom("Cl",computeProjection);
    addAtom("Ca",computeProjection);
}

volumeAtDistance()

double AtomInterpolator::volumeAtDistance	(	char	atom,
		double	r
	)		const

Volume value at a distance r of the atom whose first letter is the one provided as atom.

Definition at line 101 of file pdb.cpp.

{
    int idx=getAtomIndex(atom);
    if (r>radii[idx])
        return 0;
    else
        return volumeProfileCoefficients[idx].
               interpolatedElementBSpline1D(r*M,3);
}

Member Data Documentation

highTs

double AtomInterpolator::highTs

Definition at line 354 of file pdb.h.

M

int AtomInterpolator::M

Definition at line 352 of file pdb.h.

projectionProfileCoefficients

std::vector< MultidimArray<double> > AtomInterpolator::projectionProfileCoefficients

Definition at line 348 of file pdb.h.

radii

std::vector<double> AtomInterpolator::radii

Definition at line 350 of file pdb.h.

volumeProfileCoefficients

std::vector< MultidimArray<double> > AtomInterpolator::volumeProfileCoefficients

Definition at line 346 of file pdb.h.

---

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

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