ProgPdbAnalysis Class Reference

#include <pdb_analysis.h>

Inheritance diagram for ProgPdbAnalysis:

Collaboration diagram for ProgPdbAnalysis:

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
String	op
FileName	fn_hist
int	Nnearest
double	maxDistance
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 Analysis program

Definition at line 36 of file pdb_analysis.h.

Member Function Documentation

defineParams()

void ProgPdbAnalysis::defineParams ( )

virtual

Params definitions

Reimplemented from XmippProgram.

Definition at line 31 of file pdb_analysis.cpp.

{
    addUsageLine("Analyze a PDB file and produce different statistics");
    addParamsLine("-i <file>    : PDB to study");
    addParamsLine("--operation <op>  : Operation to perform");
    addParamsLine("    where <op>");
    addParamsLine("          distance_histogram <fileOut> <Nnearest=3> <MaxDistance=-1>: Compute the distance histogram between");
    addParamsLine("                                                                    : an atom and its N nearest neighbours");
    addParamsLine("                                                                    : The maximum distance of the neighbours may be limited (in Angstroms)");
    addExampleLine("Compute the histogram of interatomic distances",false);
    addExampleLine("xmipp_pdb_analysis -i mypdb.pdb --operation distance_histogram distance.hist");
}

readParams()

void ProgPdbAnalysis::readParams ( )

virtual

Read from a command line.

Reimplemented from XmippProgram.

Definition at line 44 of file pdb_analysis.cpp.

{
    fn_pdb=getParam("-i");
    op=getParam("--operation");
    if (op=="distance_histogram")
    {
        fn_hist=getParam("--operation",1);
        Nnearest=getIntParam("--operation",2);
        maxDistance=getDoubleParam("--operation",3);
    }
}

run()

void ProgPdbAnalysis::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 69 of file pdb_analysis.cpp.

{
    if (op=="distance_histogram")
    {
        PDBPhantom pdb; // It cannot be a PDBRichPhantom because it also has to work with pseudoatomic structures
        pdb.read(fn_pdb);
        Histogram1D hist;
        distanceHistogramPDB(pdb,Nnearest,maxDistance,200,hist);
        hist.write(fn_hist);
    }
}

show()

void ProgPdbAnalysis::show

(

)

Show parameters.

Definition at line 56 of file pdb_analysis.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "PDB:          " << fn_pdb << std::endl
    << "Operation:    " << op << std::endl;
    if (op=="distance_histogram")
        std::cout << "Output histogram: " << fn_hist << std::endl
                  << "Nnearest:         " << Nnearest << std::endl
                  << "MaxDistance:      " << maxDistance << std::endl;
}

Member Data Documentation

fn_hist

FileName ProgPdbAnalysis::fn_hist

Output distance histogram

Definition at line 46 of file pdb_analysis.h.

fn_pdb

FileName ProgPdbAnalysis::fn_pdb

PDB file

Definition at line 40 of file pdb_analysis.h.

maxDistance

double ProgPdbAnalysis::maxDistance

MaxDistance

Definition at line 52 of file pdb_analysis.h.

Nnearest

int ProgPdbAnalysis::Nnearest

Nearest neighbours to explore

Definition at line 49 of file pdb_analysis.h.

op

String ProgPdbAnalysis::op

Operation

Definition at line 43 of file pdb_analysis.h.

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

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