ProgPdbSphDeform Class Reference

#include <pdb_sph_deform.h>

Inheritance diagram for ProgPdbSphDeform:

Collaboration diagram for ProgPdbSphDeform:

Public Member Functions
void	defineParams () override
void	readParams () override
void	show () const override
void	run () override
std::string	readNthLine (int N) const
std::vector< double >	string2vector (std::string const &s) const
void	fillVectorTerms ()
void	centerOfMass (PDBRichPhantom pdb, Matrix1D< double > &cm)
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	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 ()

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
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

Definition at line 33 of file pdb_sph_deform.h.

Member Function Documentation

centerOfMass()

void ProgPdbSphDeform::centerOfMass	(	PDBRichPhantom	pdb,
		Matrix1D< double > &	cm
	)

Compute center of mass of the PDB file

Definition at line 182 of file pdb_sph_deform.cpp.

{
    size_t numAtoms = pdb.getNumberOfAtoms();
    for (size_t a=0; a<numAtoms; a++)
    {
        RichAtom& atom_i=pdb.atomList[a];
        auto z = atom_i.z;
        auto y = atom_i.y;
        auto x = atom_i.x;
        VEC_ELEM(cm, 0) += x;
        VEC_ELEM(cm, 1) += y;
        VEC_ELEM(cm, 2) += z;

    }
    VEC_ELEM(cm, 0) /= numAtoms;
    VEC_ELEM(cm, 1) /= numAtoms;
    VEC_ELEM(cm, 2) /= numAtoms;
}

defineParams()

void ProgPdbSphDeform::defineParams ( )

overridevirtual

Params definitions

Reimplemented from XmippProgram.

Definition at line 30 of file pdb_sph_deform.cpp.

{
    addUsageLine("Deform a PDB according to a list of SPH deformation coefficients");
    addParamsLine("--pdb <file>            : PDB to deform");
    addParamsLine("--clnm <metadata_file>  : List of deformation coefficients");
    addParamsLine("-o <file>               : Deformed PDB");
    addParamsLine("[--center_mass]         : Center the PDB according with its center of mass");
    addParamsLine("[--boxsize <b=0> ]      : Box size of the volume where the PDB was fitted");
    addParamsLine("[--sr <s=1> ]           : Sampling rate of the volume where the PDB was fitted");
    addExampleLine("xmipp_pdb_sph_deform --pdb 2tbv.pdb -o 2tbv_deformed.pdb --clnm coefficients.txt");
}

fillVectorTerms()

void ProgPdbSphDeform::fillVectorTerms

(

)

Fill degree and order vectors

Definition at line 156 of file pdb_sph_deform.cpp.

{
    int idx = 0;
    auto vecSize = (int)(clnm.size()/3);
    vL1.initZeros(vecSize);
    vN.initZeros(vecSize);
    vL2.initZeros(vecSize);
    vM.initZeros(vecSize);
    for (int h=0; h<=basisParams[1]; h++)
    {
        int totalSPH = 2*h+1;
        auto aux = (int)(std::floor(totalSPH/2));
        for (int l=h; l<=basisParams[0]; l+=2)
        {
            for (int m=0; m<totalSPH; m++)
            {
                VEC_ELEM(vL1,idx) = l;
                VEC_ELEM(vN,idx) = h;
                VEC_ELEM(vL2,idx) = h;
                VEC_ELEM(vM,idx) = m-aux;
                idx++;
            }
        }
    }
}

readNthLine()

std::string ProgPdbSphDeform::readNthLine

(

int

N

)

const

Read Nth line of file

Definition at line 133 of file pdb_sph_deform.cpp.

{
    std::ifstream in(fn_sph.getString());
    std::string s;  

    //skip N lines
    for(int i = 0; i < N; ++i)
        std::getline(in, s);

    std::getline(in,s);
    return s;
}

readParams()

void ProgPdbSphDeform::readParams ( )

overridevirtual

Read from a command line.

Reimplemented from XmippProgram.

Definition at line 42 of file pdb_sph_deform.cpp.

{
    fn_pdb = getParam("--pdb");
    fn_sph = getParam("--clnm");
    fn_out = getParam("-o");
    center = checkParam("--center_mass");
    boxSize= 0.5 * getDoubleParam("--boxsize") * getDoubleParam("--sr");
}

run()

void ProgPdbSphDeform::run ( )

overridevirtual

Run.

Reimplemented from XmippProgram.

Definition at line 62 of file pdb_sph_deform.cpp.

{
    PDBRichPhantom pdb;
    pdb.read(fn_pdb);
    std::string line;
    line = readNthLine(0);
    basisParams = string2vector(line);
    line = readNthLine(1);
    clnm = string2vector(line);
    fillVectorTerms();
    size_t idxY0=clnm.size()/3;
    size_t idxZ0=2*idxY0;
    Matrix1D<double> cm;
    cm.initZeros(3);
    centerOfMass(pdb, cm);
    for (size_t a=0; a<pdb.getNumberOfAtoms(); a++)
    {
        double gx=0.0; 
        double gy=0.0; 
        double gz=0.0;
        RichAtom& atom_i=pdb.atomList[a];
        auto k = atom_i.z;
        auto i = atom_i.y;
        auto j = atom_i.x;
        if (center)
        {
            k -= VEC_ELEM(cm, 2);
            i -= VEC_ELEM(cm, 1);
            j -= VEC_ELEM(cm, 0);
        }
        else
        {
            k -= boxSize;
            i -= boxSize;
            j -= boxSize;
        }
        for (size_t idx=0; idx<idxY0; idx++)
        {
            double Rmax=basisParams[2];
            double Rmax2=Rmax*Rmax;
            double iRmax=1.0/Rmax;
            double k2=k*k;
            double kr=k*iRmax;
            double k2i2=k2+i*i;
            double ir=i*iRmax;
            double r2=k2i2+j*j;
            double jr=j*iRmax;
            double rr=std::sqrt(r2)*iRmax;
            double zsph=0.0;
            if (r2<Rmax2)
            {
                int l1 = VEC_ELEM(vL1,idx);
                int n = VEC_ELEM(vN,idx);
                int l2 = VEC_ELEM(vL2,idx);
                int m = VEC_ELEM(vM,idx);
                zsph=ZernikeSphericalHarmonics(l1,n,l2,m,jr,ir,kr,rr);
                if (rr>0 || l2==0)
                {
                    gx += clnm[idx]        *zsph;
                    gy += clnm[idx+idxY0]  *zsph;
                    gz += clnm[idx+idxZ0]  *zsph;
                }
            }
        }
        atom_i.x += gx;
        atom_i.y += gy;
        atom_i.z += gz;
    }
    pdb.write(fn_out);
}

show()

void ProgPdbSphDeform::show ( ) const

overridevirtual

Show parameters.

Reimplemented from XmippProgram.

Definition at line 51 of file pdb_sph_deform.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "PDB:                  " << fn_pdb << std::endl
    << "Coefficient list:     " << fn_sph << std::endl
    << "Output:               " << fn_out << std::endl
    ;
}

string2vector()

std::vector< double > ProgPdbSphDeform::string2vector

(

std::string const &

s

)

const

Convert String to Vector

Definition at line 146 of file pdb_sph_deform.cpp.

{
    std::stringstream iss(s);
    double number;
    std::vector<double> v;
    while (iss >> number)
        v.push_back(number);
    return v;
}

---

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

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