ProgPdbReduce Class Reference

#include <pdb_reduce_pseudoatoms.h>

Inheritance diagram for ProgPdbReduce:

Collaboration diagram for ProgPdbReduce:

Public Member Functions
	ProgPdbReduce ()
void	defineParams ()
void	readParams ()
void	show ()
void	run ()
void	reduceNumberPseudoatoms ()
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 ()

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 35 of file pdb_reduce_pseudoatoms.h.

Constructor & Destructor Documentation

ProgPdbReduce()

ProgPdbReduce::ProgPdbReduce

(

)

Definition at line 32 of file pdb_reduce_pseudoatoms.cpp.

{
    thresh = 0.0;
    num = -1.0;
}

Member Function Documentation

defineParams()

void ProgPdbReduce::defineParams ( )

virtual

Params definitions

Reimplemented from XmippProgram.

Definition at line 38 of file pdb_reduce_pseudoatoms.cpp.

{
    addUsageLine("Reduce the number of pseudoatoms in a volume.");
    addExampleLine("   xmipp_pdb_reduce_pseudoatoms -i 1o7d.vol -o 1o7dreduced.vol --threshold 0.15");

    addParamsLine("   -i <pdb_file>                          : File to process");
    addParamsLine("  [-o <fn_root>]                          : Root name for output");
    addParamsLine("  [--number <num=-1.0>]                   : Number of pseudoatoms to keep based on intensity");
    addParamsLine("  [--threshold <thresh=0.0>]              : Intensity threshold for removing pseudoatoms");
}

readParams()

void ProgPdbReduce::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 49 of file pdb_reduce_pseudoatoms.cpp.

{
    fn_volume = getParam("-i");
    fn_out = checkParam("-o") ? getParam("-o") : fn_volume.withoutExtension();
    num = getDoubleParam("--number");
    thresh = getDoubleParam("--threshold");

}

reduceNumberPseudoatoms()

void ProgPdbReduce::reduceNumberPseudoatoms

(

)

Definition at line 66 of file pdb_reduce_pseudoatoms.cpp.

{
    PDBRichPhantom pdb;
    if(thresh != 0.0)
        pdb.read(fn_volume, false, thresh);
    else
    {
        pdb.read(fn_volume, true);
        std::sort(pdb.intensities.rbegin(), pdb.intensities.rend());
        thresh = pdb.intensities.at(num);
        pdb.atomList.clear();
        pdb.remarks.clear();
        pdb.read(fn_volume, false, thresh);
    }
    pdb.write(fn_out, true); // keep renumbering
}

run()

void ProgPdbReduce::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 83 of file pdb_reduce_pseudoatoms.cpp.

{
    reduceNumberPseudoatoms();
}

show()

void ProgPdbReduce::show

(

)

Show parameters.

Definition at line 59 of file pdb_reduce_pseudoatoms.cpp.

{
    std::cout << "PDB file:           " << fn_volume           << std::endl
              << "Number:             " << num                 << std::endl
              << "Threshold:          " << thresh              << std::endl;
}

---

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

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