MTK++ Latest version: 0.2.0

Typedefs | Functions
pdbSearcher.cpp File Reference

Search a local copy of the pdb for info, assuming that all file are *.Z. More...

#include "Utils/constants.h"
#include "Utils/printHeader.h"
#include "Molecule/collection.h"
#include "Molecule/molecule.h"
#include "Molecule/submolecule.h"
#include "Molecule/atom.h"
#include "Molecule/element.h"
#include "Molecule/connections.h"
#include "Molecule/stdLibrary.h"
#include "Molecule/metalCenter.h"
#include "Utils/vector3d.h"
#include "Utils/diagonalize.h"
#include "Statistics/sheet.h"
#include "Statistics/table.h"
#include "Parsers/elementParser.h"
#include "Parsers/pdbParser.h"
#include "Parsers/StringManip.h"
#include "Parsers/commLineOptions.h"
#include "Parsers/inputParser.h"
#include <iostream>
#include <stdlib.h>
#include <stdio.h>
#include <time.h>
#include <vector>
#include <map>
#include <algorithm>
#include <math.h>
#include <cmath>
Include dependency graph for pdbSearcher.cpp:

Typedefs

typedef std::map< std::string,
double >::iterator 
strDbMapIterator
 string - double map for
typedef std::map< std::string,
int >::iterator 
strIntMapIterator
 string - int map for
typedef std::map< std::string,
std::string >::iterator 
strStrMapIterator
 string - string map for
typedef std::vector< unsigned
int >::iterator 
intVectorIterator
 int vector for

Functions

int uncompressFile (std::string filename, std::string newFileName)
 Uncompress a .Z file using zcat.
int main (int argc, char **argv)
 Searches a local copy of the Protein Data Bank.

Detailed Description

Search a local copy of the pdb for info, assuming that all file are *.Z.

Author:
Martin B. Peters
Date:
2010/05/04 20:04:07
Revision:
1.14

----------------------------------------------------------------------------

MTK++ - C++ package of modeling libraries.

Copyright (C) 2005-2006 (see AUTHORS file for a list of contributors)

----------------------------------------------------------------------------


Typedef Documentation

typedef std::map<std::string, double>::iterator strDbMapIterator

string - double map for

typedef std::map<std::string, int>::iterator strIntMapIterator

string - int map for

typedef std::map<std::string, std::string>::iterator strStrMapIterator

string - string map for

typedef std::vector<unsigned int>::iterator intVectorIterator

int vector for


Function Documentation

int uncompressFile ( std::string  filename,
std::string  newFileName 
)

Uncompress a .Z file using zcat.

Referenced by main().

int main ( int  argc,
char **  argv 
)

Searches a local copy of the Protein Data Bank.

Parameters:
argc
argv
Returns:
success
            Function: quit

            Description: Exits program

            syntax: quit
            Function: expTechniques

            Description: 

            syntax: expTechniques X-RAY NMR
            Function: resolution

            Description:

            syntax: resolution 2.5
            Function: monoMetal

            Description:

            syntax: monoMetal 1
           Function: readPDBList

           Description: Read list of pdb files

           syntax: readPDBList list_name file_name
           Function: writePDBList

           Description: Write list of pdb files

           syntax: writePDBList list_name file_name
           Function: hasMetal

           Description: Does pdb file contain a metal

           syntax: hasMetal list_name new_list_name metal
           Function: getEnvironment

           Description: Determine ligating residues

           syntax: getEnvironment list_name output_file metal
            Function: writeMetalEnvironment

            Description: Turn on writing of metal environments

            syntax: writeMetalEnvironment 1

Unknown command

References MTKpp::collection::addParameters(), MTKpp::collection::addStdLibrary(), commLineOptions::addUsage(), MTKpp::baseName(), MTKpp::collection::clear(), MTKpp::collection::delAllMolecules(), MTKpp::collection::determineMetalEnvironments(), MTKpp::errorLogger, MTKpp::pdbInfo::expTechnique, MTKpp::extName(), MTKpp::collection::findMetals(), commLineOptions::getFlag(), MTKpp::collection::getMetalCenters(), MTKpp::collection::getNumAtoms(), commLineOptions::getValue(), MTKpp::collection::hasMetal(), MTKpp::pdbParser::itsPdbInfo, commLineOptions::noUsage(), MTKpp::collection::pElements, MTKpp::printHeader(), commLineOptions::printUsage(), commLineOptions::processCommandArgs(), MTKpp::elementParser::Read(), MTKpp::pdbParser::Read(), MTKpp::readInputFile(), MTKpp::readListFile(), MTKpp::pdbInfo::resolution, commLineOptions::setFlag(), commLineOptions::setOption(), MTKpp::errorHandler::setStream(), MTKpp::string2Int(), MTKpp::errorHandler::throwError(), MTKpp::toUpper(), uncompressFile(), commLineOptions::usageOn(), and MTKpp::pdbParser::Write().

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