ProgPdbValueToVol Class Reference

#include <pdb_label_from_volume.h>

Inheritance diagram for ProgPdbValueToVol:

Collaboration diagram for ProgPdbValueToVol:

Public Member Functions
void	defineParams ()
void	readParams ()
void	produceSideInfo ()
void	show ()
void	run ()
void	computeProteinGeometry ()
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Public Attributes
double	Ts
double	radius
StringVector	origin
bool	defOrig
bool	withMask
FileName	fn_pdb
FileName	fnVol
FileName	fnMask
MultidimArray< double >	inputVol
MultidimArray< double >	inputMask
FileName	fn_out
FileName	fnMD
int	output_dim
int	M
Matrix1D< double >	centerOfMass
Matrix1D< double >	limit
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
Protected Attributes inherited from XmippProgram
int	errorCode
ProgramDef *	progDef
	Program definition and arguments parser. More...
std::map< String, CommentList >	defaultComments
int	argc
	Original command line arguments. More...
const char **	argv

Detailed Description

Parameter class for the PDB Phantom program

Definition at line 39 of file pdb_label_from_volume.h.

Member Function Documentation

computeProteinGeometry()

void ProgPdbValueToVol::computeProteinGeometry

(

)

Definition at line 125 of file pdb_label_from_volume.cpp.

{
    PDBRichPhantom pdbIn;
    PDBRichPhantom pdbOut;
    pdbIn.read(fn_pdb);

    MetaDataVec mdmean;
    size_t objId;
    objId = mdmean.addObject();

    double suma=0, sumaP=0;
    int numA=0;
    for (const auto& atomIn : pdbIn.atomList)
    {
        const auto& x = atomIn.x;
        const auto& y = atomIn.y;
        const auto& z = atomIn.z;

        // Correct position
        Matrix1D<double> r(3);
        VECTOR_R3(r, x, y, z);
        r *= 1/Ts;

        // Characterize atom
        double radius2=radius*radius;

        // Find the part of the volume that must be updated
        int k0 = XMIPP_MAX(FLOOR(ZZ(r) - radius), STARTINGZ(inputVol));
        int kF = XMIPP_MIN(CEIL(ZZ(r) + radius), FINISHINGZ(inputVol));
        int i0 = XMIPP_MAX(FLOOR(YY(r) - radius), STARTINGY(inputVol));
        int iF = XMIPP_MIN(CEIL(YY(r) + radius), FINISHINGY(inputVol));
        int j0 = XMIPP_MAX(FLOOR(XX(r) - radius), STARTINGX(inputVol));
        int jF = XMIPP_MIN(CEIL(XX(r) + radius), FINISHINGX(inputVol));

        int ka = XMIPP_MAX(FLOOR(ZZ(r)), STARTINGZ(inputVol));
        int ia = XMIPP_MAX(FLOOR(YY(r)), STARTINGZ(inputVol));
        int ja = XMIPP_MAX(FLOOR(XX(r)), STARTINGZ(inputVol));


        float atomS=0.0;
        float atomP=0.0;
        float value=0.0;
        int cont=0;
        for (int k = k0; k <= kF; k++)
        {
            double zdiff=ZZ(r) - k;
            double zdiff2=zdiff*zdiff;
            for (int i = i0; i <= iF; i++)
            {
                double ydiff=YY(r) - i;
                double zydiff2=zdiff2+ydiff*ydiff;
                for (int j = j0; j <= jF; j++)
                {
                    double xdiff=XX(r) - j;
                    double rdiffModule2=zydiff2+xdiff*xdiff;
                    if (withMask)
                    {
                        if ( (rdiffModule2<radius2 || (k==ka && i==ia && j==ja)) && (inputMask(k, i , j)>0.00001) )
                        {
                            atomS += A3D_ELEM(inputVol,k, i, j);
                            ++cont;

                            //Absolute
                            if (A3D_ELEM(inputVol,k, i, j) < 0)
                            {
                                value = -A3D_ELEM(inputVol,k, i, j);
                                atomP += value;
                            }
                            else
                                atomP += A3D_ELEM(inputVol,k, i, j);

                        }
                    }
                    else
                    {
                        if ( (rdiffModule2<radius2) || (k==ka && i==ia && j==ja))
                        {
                            atomS+=A3D_ELEM(inputVol,k, i, j);
                            ++cont;

                            //Absolute
                            if (A3D_ELEM(inputVol,k, i, j) < 0)
                            {
                                value = -A3D_ELEM(inputVol,k, i, j);
                                atomP += value;
                            }
                            else
                                atomP += A3D_ELEM(inputVol,k, i, j);

                        }
                    }

                }
            }
        }

        if (atomS>=0)
            atomS = atomP;
        else
            atomS = -atomP;

        if (atomS != 0)
            atomS=atomS/cont;
        else
            atomS=0.00;

        if (atomP != 0)
            atomP=atomP/cont;
        else
            atomP=0.00;


        ++numA;
        suma+=atomS;
        sumaP+=atomP;

        auto atomOut = atomIn;
        atomOut.occupancy = atomS;
        pdbOut.addAtom(atomOut);
    }

    double mean = suma/numA;
    double meanA = sumaP/numA;
    std::cout << "mean value: = " << mean << std::endl;
    std::cout << "absolute mean value: = " << meanA << std::endl;

    mdmean.setValue(MDL_VOLUME_SCORE1, mean, objId);
    mdmean.setValue(MDL_VOLUME_SCORE2, meanA, objId);
    mdmean.write(fnMD);

    pdbOut.write(fn_out);
}

defineParams()

void ProgPdbValueToVol::defineParams ( )

virtual

Params definitions

Reimplemented from XmippProgram.

Definition at line 38 of file pdb_label_from_volume.cpp.

{
    addUsageLine("Put a volume value to PDB file.");
    addExampleLine("   xmipp_pdb_label_from_volume --pdb 1o7d.pdb --vol volume.vol -o pdb_label.pdb --sampling 1.6");

    addParamsLine("  --pdb <pdb_file>                   : File to process");
    addParamsLine("  --vol <vol_file=\"\">              : Input volume");
    addParamsLine("  [--mask <vol_file=\"\">]           : Input mask (to calculate inside mask)");
    addParamsLine("  -o  <file>                         : Modified output PDB");
    addParamsLine("   --sampling <Ts=1>                 : Sampling rate (Angstroms/pixel)");
    addParamsLine("   [--origin <...>]                  : Origin of the volume --origin x y z");
    addParamsLine("   [--radius <radius=0.8>]           : Considered as radius of the atom (Angstroms)");
    addParamsLine("   [--md <output=\"params.xmd\">]    : Save mean and absolute mean output");
}

produceSideInfo()

void ProgPdbValueToVol::produceSideInfo

(

)

Produce side information. Produce the atomic profiles.

Definition at line 84 of file pdb_label_from_volume.cpp.

{
    Image<double> V, M;
    V.read(fnVol);
    V().setXmippOrigin();
    inputVol = V();
    inputVol.setXmippOrigin();

    if (withMask)
    {
        M.read(fnMask);
        inputMask = M();
        inputMask.setXmippOrigin();
    }

    //Origin of the volume
    if (defOrig)
    {
        STARTINGZ(inputVol) = -textToInteger(origin[2]);
        STARTINGY(inputVol) = -textToInteger(origin[1]);
        STARTINGX(inputVol) = -textToInteger(origin[0]);

        STARTINGZ(inputMask) = -textToInteger(origin[2]);
        STARTINGY(inputMask) = -textToInteger(origin[1]);
        STARTINGX(inputMask) = -textToInteger(origin[0]);
    }

    else
    {
        STARTINGZ(inputVol) = 0;
        STARTINGY(inputVol) = 0;
        STARTINGX(inputVol) = 0;

        STARTINGZ(inputMask) = 0;
        STARTINGY(inputMask) = 0;
        STARTINGX(inputMask) = 0;
    }

}

readParams()

void ProgPdbValueToVol::readParams ( )

virtual

Read from a command line. An exception might be thrown by any of the internal conversions, this would mean that there is an error in the command line and you might show a usage message.

Reimplemented from XmippProgram.

Definition at line 53 of file pdb_label_from_volume.cpp.

{
    fn_pdb = getParam("--pdb");
    fnVol = getParam("--vol");
    fnMask = getParam("--mask");
    fn_out=getParam("-o");
    fnMD = getParam("--md");
    Ts = getDoubleParam("--sampling");
    radius = getDoubleParam("--radius");
    withMask = checkParam("--mask");
    defOrig = checkParam("--origin");
    getListParam("--origin", origin);

}

run()

void ProgPdbValueToVol::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 260 of file pdb_label_from_volume.cpp.

{
    produceSideInfo();
    show();
    computeProteinGeometry();
}

show()

void ProgPdbValueToVol::show

(

)

Show parameters.

Definition at line 69 of file pdb_label_from_volume.cpp.

{
    if (verbose==0)
        return;
    std::cout << "PDB file:           " << fn_pdb           << std::endl
    << "Output:       " << fn_out << std::endl
    << "Sampling rate:        " << Ts          << std::endl
    << "Origin:               ";
    for (size_t i=0; i<origin.size(); ++i)
        std::cout << origin[i] << " ";
    std::cout << std::endl
    << "Radius:               " << radius      << std::endl;
}

Member Data Documentation

centerOfMass

Matrix1D<double> ProgPdbValueToVol::centerOfMass

Definition at line 96 of file pdb_label_from_volume.h.

defOrig

bool ProgPdbValueToVol::defOrig

Origin by user

Definition at line 52 of file pdb_label_from_volume.h.

fn_out

FileName ProgPdbValueToVol::fn_out

Output fileroot

Definition at line 65 of file pdb_label_from_volume.h.

fn_pdb

FileName ProgPdbValueToVol::fn_pdb

PDB file

Definition at line 58 of file pdb_label_from_volume.h.

fnMask

FileName ProgPdbValueToVol::fnMask

Definition at line 61 of file pdb_label_from_volume.h.

fnMD

FileName ProgPdbValueToVol::fnMD

Definition at line 65 of file pdb_label_from_volume.h.

fnVol

FileName ProgPdbValueToVol::fnVol

Volume file

Definition at line 61 of file pdb_label_from_volume.h.

inputMask

MultidimArray<double> ProgPdbValueToVol::inputMask

Definition at line 62 of file pdb_label_from_volume.h.

inputVol

MultidimArray<double> ProgPdbValueToVol::inputVol

Definition at line 62 of file pdb_label_from_volume.h.

limit

Matrix1D<double> ProgPdbValueToVol::limit

Definition at line 96 of file pdb_label_from_volume.h.

M

int ProgPdbValueToVol::M

Definition at line 93 of file pdb_label_from_volume.h.

origin

StringVector ProgPdbValueToVol::origin

Definition at line 49 of file pdb_label_from_volume.h.

output_dim

int ProgPdbValueToVol::output_dim

Final size in pixels

Definition at line 69 of file pdb_label_from_volume.h.

radius

double ProgPdbValueToVol::radius

Radius

Definition at line 46 of file pdb_label_from_volume.h.

Ts

double ProgPdbValueToVol::Ts

Sampling rate

Definition at line 43 of file pdb_label_from_volume.h.

withMask

bool ProgPdbValueToVol::withMask

Use Mask

Definition at line 55 of file pdb_label_from_volume.h.

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

• xmipp/libraries/reconstruction/pdb_label_from_volume.h
• xmipp/libraries/reconstruction/pdb_label_from_volume.cpp