pdb_sph_deform.cpp

Go to the documentation of this file.

/***************************************************************************
 *
 * Authors:     David Herreros Calero (dherreros@cnb.csic.es)
 * 
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

#include "pdb_sph_deform.h"
#include <data/numerical_tools.h>
#include <fstream>

void ProgPdbSphDeform::defineParams()
{
    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");
}

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

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

void ProgPdbSphDeform::run()
{
    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);
}

std::string ProgPdbSphDeform::readNthLine(int N) const
{
    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;
}

std::vector<double> ProgPdbSphDeform::string2vector(std::string const &s) const
{
    std::stringstream iss(s);
    double number;
    std::vector<double> v;
    while (iss >> number)
        v.push_back(number);
    return v;
}

void ProgPdbSphDeform::fillVectorTerms()
{
    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++;
            }
        }
    }
}

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