MTK++ Latest version: 0.2.0

Functions
prep2xml.cpp File Reference

Convert AMBER prep file to MTK++ xml library. More...

#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/bond.h"
#include "Molecule/ring.h"
#include "Molecule/connections.h"
#include "Molecule/stdLibrary.h"
#include "Molecule/stdGroup.h"
#include "Molecule/stdFrag.h"
#include "Molecule/functionalize.h"
#include "Molecule/hydrophobize.h"
#include "Utils/vector3d.h"
#include "Parsers/elementParser.h"
#include "Parsers/stdLibParser.h"
#include "Parsers/prepParser.h"
#include "Parsers/paramParser.h"
#include "Parsers/sdfParser.h"
#include "Parsers/commLineOptions.h"
#include "Log/errorHandler.h"
#include <iostream>
#include <stdlib.h>
#include <stdio.h>
#include <time.h>
#include <vector>
#include <map>
#include <algorithm>
Include dependency graph for prep2xml.cpp:

Functions

int main (int argc, char **argv)
 Convert AMBER prep file to MTK++ xml library.

Detailed Description

Convert AMBER prep file to MTK++ xml library.

Author:
Martin B. Peters
Date:
2010/04/22 22:19:54
Revision:
1.8

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

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

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

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


Function Documentation

int main ( int  argc,
char **  argv 
)

Convert AMBER prep file to MTK++ xml library.

References MTKpp::submolecule::addAtom(), MTKpp::molecule::addBond(), MTKpp::atom::addBondedAtom(), MTKpp::collection::addMolecule(), MTKpp::collection::addParameters(), MTKpp::stdFrag::addStdFeature(), MTKpp::stdGroup::addStdFrag(), MTKpp::stdFrag::addStdFuncGroup(), MTKpp::stdLibrary::addStdGroup(), MTKpp::collection::addStdLibrary(), MTKpp::stdFrag::addStdRing(), MTKpp::molecule::addSubMolecule(), commLineOptions::addUsage(), MTKpp::stdRing::aromatic, MTKpp::connections::assignAngles(), MTKpp::connections::assignImpropers(), MTKpp::connections::assignTorsions(), MTKpp::Bond::atom1, MTKpp::Bond::atom2, MTKpp::stdRing::atoms, MTKpp::stdFeature::atoms, MTKpp::stdFuncGroup::atoms, MTKpp::molecule::determineFunctionalGroups(), MTKpp::molecule::determineHybridizations(), MTKpp::molecule::determineHydrophobicGroups(), MTKpp::molecule::determineRings(), MTKpp::errorLogger, MTKpp::stdFuncGroup::fragName, MTKpp::stdLibrary::generateAdjMatrices(), MTKpp::molecule::generateAdjMatrix(), MTKpp::stdLibrary::generateAtomKinds(), MTKpp::stdFrag::generateCoordinates(), MTKpp::stdLibrary::generateSimpleFP(), MTKpp::molecule::generateSimpleFP(), MTKpp::molecule::getAtom(), MTKpp::molecule::getAtomList(), MTKpp::molecule::getBondMap(), MTKpp::stdFrag::getCoordinates(), MTKpp::elements::getElement(), MTKpp::atom::getElementSymbol(), commLineOptions::getFlag(), MTKpp::molecule::getFunctionalGroups(), MTKpp::molecule::getHydrophobicGroups(), MTKpp::collection::getNumberMolecules(), MTKpp::molecule::getNumSubMolecules(), MTKpp::collection::getParameters(), MTKpp::molecule::getRings(), MTKpp::atom::getStdAtom(), MTKpp::stdFrag::getStdAtomList(), MTKpp::stdFrag::getStdBond(), MTKpp::stdFrag::getStdBondList(), MTKpp::collection::getStdLibrary(), MTKpp::stdFrag::getStdLoop(), MTKpp::stdFrag::getStdLoopList(), commLineOptions::getValue(), MTKpp::stdFuncGroup::groupName, MTKpp::stdRing::hetero, MTKpp::INFO, MTKpp::Bond::kind, MTKpp::stdBond::kind, MTKpp::stdFeature::name, MTKpp::stdRing::nHetero, MTKpp::stdRing::nNitrogen, commLineOptions::noUsage(), MTKpp::stdRing::nOxygen, MTKpp::stdRing::nSulfur, MTKpp::collection::pElements, MTKpp::stdRing::planar, MTKpp::printHeader(), commLineOptions::printUsage(), commLineOptions::processCommandArgs(), MTKpp::elementParser::Read(), MTKpp::paramParser::Read(), MTKpp::stdLibParser::Read(), MTKpp::prepParser::Read(), MTKpp::stdFrag::setCode(), MTKpp::atom::setCoords(), MTKpp::atom::setElement(), MTKpp::atom::setFileID(), commLineOptions::setFlag(), MTKpp::molecule::setInSolution(), MTKpp::molecule::setMolId(), MTKpp::stdGroup::setName(), MTKpp::molecule::setName(), MTKpp::atom::setName(), MTKpp::submolecule::setName(), MTKpp::stdFrag::setName(), commLineOptions::setOption(), MTKpp::atom::setStdAtom(), MTKpp::errorHandler::setStream(), MTKpp::submolecule::setSubMolId(), MTKpp::stdFrag::setSymbol(), MTKpp::stdFrag::setType(), MTKpp::stdRing::size, MTKpp::Bond::stereo, MTKpp::stdBond::stereo, MTKpp::stdLoop::stereo, MTKpp::errorHandler::throwError(), MTKpp::Bond::topology, MTKpp::stdBond::topology, MTKpp::Bond::type, MTKpp::stdBond::type, MTKpp::stdLoop::type, commLineOptions::usageOn(), and MTKpp::stdLibParser::Write().

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