ProgPdbNmaDeform Class Reference

#include <pdb_nma_deform.h>

Inheritance diagram for ProgPdbNmaDeform:

Collaboration diagram for ProgPdbNmaDeform:

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
void	run ()
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
FileName	fn_pdb
FileName	fn_nma
FileName	fn_out
MultidimArray< double >	deformations
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 37 of file pdb_nma_deform.h.

Member Function Documentation

defineParams()

void ProgPdbNmaDeform::defineParams ( )

virtual

Params definitions

Reimplemented from XmippProgram.

Definition at line 32 of file pdb_nma_deform.cpp.

{
    addUsageLine("Deform a PDB according to a list of NMA modes");
    addUsageLine("+It is assumed that there is a deformation value per mode, and that the number of vectors in the mode is the same as the number of atoms in the PDB");
    addParamsLine("--pdb <file>    : PDB to deform");
    addParamsLine("--nma <metadata_file>  : List of modes, the metadata must use the label NMAModefile");
    addParamsLine("--deformations <...> : Deformation amplitudes in each direction");
    addParamsLine("-o <file>       : Deformed PDB");
    addExampleLine("xmipp_pdb_nma_deform --pdb 2tbv.pdb -o 2tbv_deformed.pdb --nma modelist.xmd --deformations 15");
}

readParams()

void ProgPdbNmaDeform::readParams ( )

virtual

Read from a command line.

Reimplemented from XmippProgram.

Definition at line 43 of file pdb_nma_deform.cpp.

{
    fn_pdb=getParam("--pdb");
    fn_nma=getParam("--nma");
    fn_out=getParam("-o");
    StringVector listDeformations;
    getListParam("--deformations",listDeformations);
    deformations.resizeNoCopy(listDeformations.size());
    FOR_ALL_ELEMENTS_IN_ARRAY1D(deformations)
    deformations(i)=textToFloat(listDeformations[i]);
}

run()

void ProgPdbNmaDeform::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 70 of file pdb_nma_deform.cpp.

{
    PDBRichPhantom pdb;
    MetaDataVec modes;
    pdb.read(fn_pdb);
    modes.read(fn_nma);
    modes.removeDisabled();
    int j=0;
    FileName fnMode;
    MultidimArray<double> mode;
    mode.resizeNoCopy(pdb.getNumberOfAtoms(),3);

    for (size_t objId : modes.ids())
    {
        // Read mode
        modes.getValue(MDL_NMA_MODEFILE,fnMode,objId);
        std::ifstream fhMode;
        fhMode.open(fnMode.c_str());
        if (!fhMode)
            REPORT_ERROR(ERR_IO_NOREAD,fnMode);
        fhMode >> mode;
        fhMode.close();

        // Apply mode
        double lambda=A1D_ELEM(deformations,j);
        for (size_t i=0; i<YSIZE(mode); ++i)
        {
            RichAtom& atom_i=pdb.atomList[i];
            atom_i.x+=lambda*DIRECT_A2D_ELEM(mode,i,0);
            atom_i.y+=lambda*DIRECT_A2D_ELEM(mode,i,1);
            atom_i.z+=lambda*DIRECT_A2D_ELEM(mode,i,2);
        }
        j++;
    }
    pdb.write(fn_out);
}

show()

void ProgPdbNmaDeform::show

(

)

Show parameters.

Definition at line 55 of file pdb_nma_deform.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "PDB:          " << fn_pdb << std::endl
    << "NMA list:     " << fn_nma << std::endl
    << "Output:       " << fn_out << std::endl
    << "Deformations: "
    ;
    FOR_ALL_ELEMENTS_IN_ARRAY1D(deformations)
        std::cout << deformations(i) << " ";
    std::cout << std::endl;
}

Member Data Documentation

deformations

MultidimArray<double> ProgPdbNmaDeform::deformations

Set of deformations

Definition at line 50 of file pdb_nma_deform.h.

fn_nma

FileName ProgPdbNmaDeform::fn_nma

NMA mode list

Definition at line 44 of file pdb_nma_deform.h.

fn_out

FileName ProgPdbNmaDeform::fn_out

Output fileroot

Definition at line 47 of file pdb_nma_deform.h.

fn_pdb

FileName ProgPdbNmaDeform::fn_pdb

PDB file

Definition at line 41 of file pdb_nma_deform.h.

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

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