MTK++ Latest version: 0.2.0

Functions
MCPB.cpp File Reference

Developes Metal Cluster Force Field Parameters. More...

#include "Utils/printHeader.h"
#include "Molecule/collection.h"
#include "Molecule/molecule.h"
#include "Molecule/submolecule.h"
#include "Molecule/selection.h"
#include "Molecule/atom.h"
#include "Molecule/bond.h"
#include "Molecule/angle.h"
#include "Molecule/torsion.h"
#include "Molecule/element.h"
#include "Molecule/connections.h"
#include "Molecule/atomTyper.h"
#include "Molecule/stdLibrary.h"
#include "Molecule/stdGroup.h"
#include "Molecule/stdFrag.h"
#include "Molecule/parameters.h"
#include "Molecule/protonate.h"
#include "Molecule/metalCenter.h"
#include "Utils/vector3d.h"
#include "Utils/constants.h"
#include "Utils/diagonalize.h"
#include "Statistics/sheet.h"
#include "Statistics/table.h"
#include "MM/amber.h"
#include "Parsers/baseParser.h"
#include "Parsers/elementParser.h"
#include "Parsers/pdbParser.h"
#include "Parsers/molParser.h"
#include "Parsers/sdfParser.h"
#include "Parsers/gaussianParser.h"
#include "Parsers/paramParser.h"
#include "Parsers/stdLibParser.h"
#include "Parsers/prepParser.h"
#include "Parsers/frcmodParser.h"
#include "Parsers/acParser.h"
#include "Parsers/amberParser.h"
#include "Parsers/inputParser.h"
#include "Parsers/mtkppParser.h"
#include "Parsers/dMParser.h"
#include "Parsers/commLineOptions.h"
#include "Parsers/StringManip.h"
#include "Log/errorHandler.h"
#include "config.h"
#include <math.h>
#include <cmath>
#include <fstream>
#include <iomanip>
#include <stdio.h>
#include <iostream>
#include <vector>

Functions

std::string getEnvVar (std::string const &key)
void printFunctionList ()
int main (int argc, char **argv)
 Developes metal cluster force field parameters.

Detailed Description

Developes Metal Cluster Force Field Parameters.

Author:
Martin B. Peters
Date:
2010/05/04 21:43:32
Revision:
1.1

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

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

Copyright (C) 2005-2009 (see AUTHORS file for a list of contributors)

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


Function Documentation

std::string getEnvVar ( std::string const &  key)

Referenced by main().

void printFunctionList ( )

Referenced by main().

int main ( int  argc,
char **  argv 
)

Developes metal cluster force field parameters.

Parameters:
argc
argv
Returns:
success
                                 Function: source

                                 Description: Source a global file

                                 syntax: source file_name
                         Function: quit

                         Description: Exits program

                         syntax: quit
                         Function: setLoggingLevel

                         Description: Set the verbosity of error/warning/info messages

                         syntax: setLoggingLevel 1

                         Values:
                         1 - Error
                         2 - Warning
                         3 - Debug
                         4 - Info
                         Function: set

                         Description: Set variable

                         syntax: set variable_name value
                         Function: loadParam

                         Description: Loads AMBER Parameters into MCPB

                         syntax: loadParam ~/MTKpp/data/parm94.xml
                         Function: loadLib

                         Description: Loads AMBER library files into MCPB

                         syntax: loadLib ~/MTKpp/data/amino94.xml
                         Function: printFrag

                         Description: Print fragment details

                         syntax: printGroupCharge Zn-CCCC
                         Function: printFrag

                         Description: Print fragment details

                         syntax: printFrag Zn-CCCC CY1
                         Function: readPdb

                         Description: Reads a PDB file

                         syntax: readPdb 1FEE 1FEE.pdb
                         Function: writeFrcmodFile

                         Description: Writes AMBER Parameters

                         syntax: writeFrcmodFile ZnCCCC.frcmod 1A5T
                         Function: writePrepFile

                         Description: Writes AMBER prep file

                         syntax: writePrepFile ZnCCCC.prep 1A5T
                         Function: printAtomTypes

                         Description: Print Available atom types

                         syntax: printAtomTypes
                         Function assignDisulfideBonds

                         Description: Assigns all disulfide bonds (Needs to be carried out before atomtyping)

                         syntax assignDisulfideBonds
                         Function: atomType

                         Description: Assigns atom types in the collection

                         syntax: atomType
                         Function: atomType ---- fix this in the future

                         Description: Assigns atom types in the collection

                         syntax: atomType
                         Function: optimizePolarHs

                         Description: Optimize polar hydrogens in a collection

                         syntax: optimizePolarHs
                         Function: assignConnectivity

                         Description: Assigns all bonds, angles, torsions and impropers

                         syntax: assignConnectivity
                         Function: assignParameters

                         Description: Assigns bond/angle/torsion/improper parameters

                         syntax: assignParameters /COL/MOL
                         Function: addBondAndAngleParameters

                         Description: Add bond and angle parameters if missing

                         syntax: addBondAndAngleParameters /col/mol groupName
                         Function: createStdGroup

                         Description: Create standard group in current directory

                         syntax: createStdGroup myLib
                         Function: copyStdResidue

                         Description: Copy residue named HIS to a residue named HS1

                         syntax: copyStdResidue aminoAcids94/HIS myLib/HS1
                         Function: copyAtomType

                         Description: Copy atom type named NB in parm94 to atom type named NX in 1CA2

                         syntax: copyAtomType parm94/NB 1CA2/NX
                         Function: setAtomType

                         Description: Set atom type named of HS1@NE2 to NX from 1CA2

                         syntax: setAtomType myLib/HS1/.NE2 1CA2/NX
                         Function: createMolecule

                         Description: Create molecule named cuCYM4

                         syntax: createMolecule cuCYM4
                         Function: setMaxFileID

                         Description:

                         syntax: setMaxFileID /1L6J/znCLR /1L6J/1
                         Function: createResidue

                         Description: Create residue named HS1 in molecule named MOL

                         syntax: createResidue HS1 in MOL
                         Function: addToResidue

                         Description: Add atoms in CYS-12 to CY1

                         bb_heavy  == backbone [ca, n, c, o]
                         bb  == backbone [ca, h, ha, n, nh, c, o]
                         bbb == backbone [ca, h, ha, n, nh, c, o, cb]

                         syntax: addToResidue 
                         syntax: addToResidue 
                         syntax: addToResidue 
                         ^            ^
                         |            +-- selection-expression
                         +-- residue name
                         Function: appendResidue

                         Description: Add CYS-12@CB of molecule to residue CY1 of cluster cuCYM4

                         syntax: appendResidue /1FEE/cuCYM4/CY1 /1FEE/1/CYS-12/.CB.
                         Function: addHs

                         Description: Add Hydrogens to the cluster cuCYM4

                         syntax: addHs
                         syntax: addHs /COL/MOL
                         Function: setResidueName

                         Description: Set residue name

                         syntax: setResidueName /1CA2/1/HIS-119 to HIE
                         Function: setMoleculeName

                         Description: Set molecule name

                         syntax: setResidueName /1AMP//HOH-935 to MOH
                         Function: setAtomName

                         Description: Set atom name

                         syntax: setAtomName /1CA2/znCLR/ACE-1/.CA. to .CH3
                         Function: createBond

                         Description: Create bond

                         syntax: createBond /1FEE/cuCYM4//CU.. /1FEE/cuCYM4//.SG.
                         Function: print

                         Description: Print to screen details of structure

                         syntax: print cuCYM4
                         Function: capResidue

                         Description: Cap residue R1 with NME and ACE

                         syntax: capResidue /1FEE/cuCYM4/CY1/.N.. ACE

                         syntax: capResidue /1FEE/cuCYM4/CY1/.C.. NME

                         syntax: capResidue /1FEE/cuCYM4/CY1/.SG. CH3
                         Function: setFormalCharge

                         Description: Set Formal Charge on atom

                         syntax: setFormalCharge /1FEE/cuCYM4//CU.. 1
                         Function: writePdb

                         Description: Write pdb file

                         syntax: writePdb /1ABC/clr cuCYS.pdb
                         Function: writeMol

                         Description: Write mol file

                         syntax: writeMol /1ABC/clr cuCYS.mol
                         Function: writeSdf

                         Description: Write sd file

                         syntax: writeSdf /1ABC/clr CLR.sdf
                         Function: readSdf

                         Description: Read sd file

                         syntax: readSdf 1ABC CLR.sdf
                         Function: levelOfTheory

                         Description: Set Gaussian Theory Level

                         syntax: levelOfTheory HF
                         Function: basisSet

                         Description: Set Gaussian Basis Set

                         syntax: basisSet 6-31G*

                         syntax: basisSet GEN bs.txt
                         syntax: basisSet GEN.6D.7F bs.txt
                         Function: pseudoPotentials

                         Description: Specify pseudopotentials

                         syntax: pseudoPotential pseudo.txt
                         Function: modRedundant

                         Description: Specify redundant coordinates

                         syntax: modRedundant modred.txt
                         Function: clusterCharge

                         Description: Set Gaussian Charge

                         syntax: clusterCharge cuCYM4 -3
                         Function: clusterSpin
                         
                         Description: Set Gaussian Spin
                         
                         syntax: clusterSpin 0
                         Function: gaussianMoldenFormat
                         
                         Description: Use Molden formatted output in log file. Print out
                         details of the basis set and the molecular orbitals.
                         
                         syntax: gaussianMoldenFormat (bare word)
                         Function: gaussianMem
                         
                         Description: Set amount of memory requested for Gaussian
                         
                         syntax: gaussianMem 3600MB
                         Function: gaussianNProc
                         
                         Description: Set number of processors requested for Gaussian
                         
                         syntax: gaussianNProc 2
                         Function: gaussianOptAndFC
                         
                         Description: Set Gaussian input name
                         
                         syntax: gaussianOptAndFC //cuCYM4 cuCYM4.com
                         Function: gaussianCharges
                         
                         Description: Set Gaussian input name
                         
                         syntax: gaussianCharges //cuCYM4 cuCYM4.com
                         Function: respgenAdditions
                         
                         Description: Add info to respgen files
                         
                         syntax: respgenAdditions groupName fileName bb
                         
                         bb Definitions:
                         - 0 No restraints
                         - 1 Heavy Atoms in Backbone (bb_heavy, [ca, n, c, o]) set to parm94 values
                         - 2 Atoms in Backbone (bb, [ca, h, ha, n, nh, c, o]) set to parm94 values
                         - 3 Atoms in Backbone plus CB (bbb, [ca, h, ha, n, nh, c, o, cb]) set to parm94 values
                         Function: setMKRadii
                         
                         Description: Set Merz-Kollman radii for element
                         
                         syntax: setMKRadii cu 0.91
                         Function: readGaussianOutput
                         
                         Description: Read Gaussian Output
                         
                         syntax: readGaussianOutput cuCYM4.log
                         Function: readMolZmatMapping
                         
                         Description: Read Molecule <--> Z-Matrix mapping file
                         
                         syntax: readMolZmatMapping file.map
                         Function: readFormattedChkPtFile
                         
                         Description:
                         
                         syntax: readFormattedChkPtFile file.fchk
                         Function: writeLib
                         
                         Description: Write standard library
                         
                         syntax: writeLib groupName fileName.xml
                         Function: writeParams
                         
                         Description: Write all new parameters
                         
                         syntax: writeParams groupName fileName.xml
                         Function: listFragments
                         
                         Description: List available fragments in a particular library
                         
                         syntax: listFragments terminal
                         Function: addFragment
                         
                         Description: Add Fragment to atom
                         
                         syntax: addFragment 6MemRings/6CH bd /col/Mol//34 ag /col/Mol//27 tr /col/Mol//9 180.0
                         Function: tmpWriteZMatrix
                         
                         Description:
                         
                         syntax: tmpWriteZMatrix /1A5T/1A5T file.zmat
                         Function: updateForceConstants
                         
                         Description:
                         
                         syntax: updateForceConstants /COL/MOL Group X Y
                         X Values:
                         - 0 Do not update bonds and angle equilibrium values
                         - 1 Do update bonds and angle equilibrium values (req)
                         Y Values:
                         - 0 Seminario Method
                         - 1 Z-matrix Method
                         Function: readRespCharges
                         
                         Description:
                         
                         syntax: readRespCharges /COL/MOL file.resp2.chg
                         Function: updateRespCharges
                         
                         Description:
                         
                         syntax: updateRespCharges /COL/MOL Group
                         Function: respgen

                         Description: Create resp1 and resp2 files (recreates functionality of respgen)

                         syntax: respgen /COL/MOL Group fileName
                         Function: addStdMol
                         
                         Description:
                         
                         syntax: addStdMol /COL/MOL Group
                         Function: assignStdFeatures
                         
                         Description: Assigns std features to molecule
                         
                         syntax: assignStdFeatures /col/mol
                         Function: findMetalCenters
                         
                         Description: Find all metal centers in the collection
                         
                         syntax: findMetalCenters
                         Function: writeLeap
                         
                         Description: Write the metal center bonding info for leap
                         
                         syntax: writeLeap name pdbFile
                         Function: writePrmtop
                         
                         Description: Write prmtop and coordinate files for sander
                         
                         syntax: writePrmtop inpcrd prmtop
                         Function: readNMode
                         
                         Description: Read frequencies from nmode
                         
                         syntax: readNMode /Col/mol file_nmd2.out
                         Function: readNModeVectors
                         
                         Description: Read eigenvalues and eigenvectors from nmode vecs file
                         
                         syntax: readNModeVectors /Col/mol file_nmd2.vecs file_nmd2.molden
                         Function: updateFrequencies
                         
                         Description:
                         
                         syntax: updateFrequencies /Col/mol 0.9806
                         Function: writeState
                         
                         Description: Write state xml file
                         
                         syntax: writeState file.mtk
                         Function: writeData
                         
                         Description: Write contents
                         
                         syntax: writeData f.xml
                         Function: nmodeMatch
                         
                         Description: Compare nMode and Gaussian Normal Modes
                         
                         syntax: nmodeMatch filename.xml
                         Function: renumber
                         
                         Description: Renumbers collection
                         
                         syntax: renumber

References MTKpp::parameters::addAngleParam(), MTKpp::submolecule::addAtom(), MTKpp::parameters::addAtomType(), MTKpp::molecule::addBond(), MTKpp::atom::addBondedAtom(), MTKpp::parameters::addBondParam(), MTKpp::gaussianParser::addCommandOption(), MTKpp::molecule::addHydrogens(), MTKpp::gaussianParser::addIop(), MTKpp::collection::addMolecule(), MTKpp::collection::addParameters(), MTKpp::molecule::addProperty(), MTKpp::stdGroup::addStdFrag(), MTKpp::stdLibrary::addStdGroup(), MTKpp::collection::addStdLibrary(), MTKpp::molecule::addSubMolecule(), MTKpp::parameters::addTorsionParam(), commLineOptions::addUsage(), MTKpp::connections::assignAngles(), MTKpp::connections::assignDisulfideBonds(), MTKpp::connections::assignImpropers(), MTKpp::connections::assignStd(), MTKpp::connections::assignStdBondsAngles(), MTKpp::atomTyper::assignStdProperties(), MTKpp::connections::assignTorsions(), MTKpp::stdAtom::atmCharge, MTKpp::Angle::atom1, MTKpp::Torsion::atom1, MTKpp::Bond::atom1, MTKpp::Angle::atom2, MTKpp::Torsion::atom2, MTKpp::Bond::atom2, MTKpp::Angle::atom3, MTKpp::Torsion::atom3, MTKpp::Torsion::atom4, MTKpp::bondParam::atomType1, MTKpp::angleParam::atomType1, MTKpp::torsionParam::atomType1, MTKpp::bondParam::atomType2, MTKpp::angleParam::atomType2, MTKpp::torsionParam::atomType2, MTKpp::angleParam::atomType3, MTKpp::torsionParam::atomType3, MTKpp::torsionParam::atomType4, MTKpp::atomTyper::atomTypeByLib(), MTKpp::baseName(), MTKpp::stdAtom::bondTorsion, MTKpp::gaussianParser::clearIop(), MTKpp::containsSubStr(), MTKpp::DEG2RAD, MTKpp::molecule::delProperty(), MTKpp::collection::determineMetalEnvironments(), MTKpp::molecule::determineRings(), MTKpp::vector3d::dist(), MTKpp::double2String(), MTKpp::errorLogger, MTKpp::fileExists(), MTKpp::collection::findMetals(), MTKpp::torsionParam::gamma, MTKpp::stdFrag::generateCoordinates(), MTKpp::gaussianParser::generateZMatrix(), MTKpp::molecule::getAngleMap(), MTKpp::parameters::getAngleParam(), MTKpp::selection::getAtom(), MTKpp::molecule::getAtom(), MTKpp::molecule::getAtomIndex(), MTKpp::submolecule::getAtomList(), MTKpp::molecule::getAtomList(), MTKpp::selection::getAtoms(), MTKpp::parameters::getAtomType(), MTKpp::molecule::getBond(), MTKpp::atom::getBondedAtoms(), MTKpp::molecule::getBondMap(), MTKpp::parameters::getBondParam(), MTKpp::stdGroup::getCharge(), MTKpp::stdFrag::getCharge(), MTKpp::stdFrag::getCode(), MTKpp::submolecule::getColIndex(), MTKpp::gaussianParser::getCommandOption(), MTKpp::stdFrag::getCoordinates(), MTKpp::atom::getCoords(), MTKpp::elements::getElement(), MTKpp::atom::getElementSymbol(), getEnvVar(), MTKpp::atom::getFileID(), commLineOptions::getFlag(), MTKpp::gaussianParser::getForceConstant(), MTKpp::gaussianParser::getForceConstantZMAT(), MTKpp::gaussianParser::getFrequencies(), MTKpp::table< T >::getMatrix(), MTKpp::molecule::getMaxFileID(), MTKpp::collection::getMetalCenters(), MTKpp::selection::getMol(), MTKpp::collection::getMolecule(), MTKpp::collection::getMoleculeList(), MTKpp::stdGroup::getName(), MTKpp::molecule::getName(), MTKpp::submolecule::getName(), MTKpp::atom::getName(), MTKpp::molecule::getNumAtoms(), MTKpp::collection::getNumberMolecules(), MTKpp::molecule::getNumSubMolecules(), MTKpp::collection::getParameters(), MTKpp::molecule::getParent(), MTKpp::submolecule::getParent(), MTKpp::atom::getParent(), MTKpp::stdFrag::getParent(), MTKpp::molecule::getProperties(), MTKpp::selection::getSelectionType(), MTKpp::selection::getSMol(), MTKpp::atom::getStdAtom(), MTKpp::stdFrag::getStdAtom(), MTKpp::stdFrag::getStdAtomList(), MTKpp::stdFrag::getStdBondList(), MTKpp::stdLibrary::getStdFrag(), MTKpp::stdGroup::getStdFrag(), MTKpp::stdGroup::getStdFragList(), MTKpp::stdLibrary::getStdGroup(), MTKpp::collection::getStdLibrary(), MTKpp::stdFrag::getStdLoopList(), MTKpp::stdGroup::getStdMolecule(), MTKpp::molecule::getSubMoleculeList(), MTKpp::submolecule::getSubMolId(), MTKpp::stdFrag::getSymbol(), MTKpp::sheet::getTable(), MTKpp::molecule::getTorsionMap(), MTKpp::parameters::getTorsionParamList(), commLineOptions::getValue(), MTKpp::atomType::groupName, MTKpp::bondParam::groupName, MTKpp::angleParam::groupName, MTKpp::torsionParam::groupName, MTKpp::molecule::hasBond(), MTKpp::collection::hasMetal(), MTKpp::stdGroup::hasStdFrag(), MTKpp::stdAtom::identity, MTKpp::stdAtom::index, MTKpp::INFO, MTKpp::int2String(), MTKpp::bondParam::keq, MTKpp::angleParam::keq, MTKpp::Bond::kind, MTKpp::MTK_ERROR, commLineOptions::noUsage(), MTKpp::torsionParam::npth, MTKpp::torsionParam::Nt, MTKpp::stdFrag::numStdAtoms(), MTKpp::baseParser::OpenFile(), MTKpp::bondParam::optimize, MTKpp::angleParam::optimize, MTKpp::protonate::optimizePolarHs(), MTKpp::Angle::pAngleParam, MTKpp::Torsion::parametersAssigned, MTKpp::selection::parse(), MTKpp::Bond::pBondParam, MTKpp::collection::pElements, MTKpp::parameters::printAtomTypes(), printFunctionList(), MTKpp::printHeader(), commLineOptions::printUsage(), commLineOptions::processCommandArgs(), MTKpp::gaussianParser::Read(), MTKpp::elementParser::Read(), MTKpp::dMParser::read(), MTKpp::pdbParser::Read(), MTKpp::paramParser::Read(), MTKpp::stdLibParser::Read(), MTKpp::sdfParser::Read(), MTKpp::gaussianParser::readFormattedChkPtFile(), MTKpp::readInputFile(), MTKpp::gaussianParser::readMappingFile(), MTKpp::gaussianParser::removeCommandOption(), MTKpp::collection::renumber(), MTKpp::replaceCharacter(), MTKpp::replaceSubStr(), MTKpp::bondParam::req, MTKpp::angleParam::req, MTKpp::protonate::run(), MTKpp::connections::run(), MTKpp::gaussianParser::setBasisSet(), MTKpp::gaussianParser::setBasisSetFile(), MTKpp::gaussianParser::setCartesian(), MTKpp::gaussianParser::setCharge(), MTKpp::gaussianParser::setChkPt(), MTKpp::stdFrag::setCode(), MTKpp::atom::setCoords(), MTKpp::atom::setElement(), MTKpp::atom::setFileID(), commLineOptions::setFlag(), MTKpp::errorHandler::setLevel(), MTKpp::molecule::setMaxFileID(), MTKpp::gaussianParser::setMem(), MTKpp::gaussianParser::setMKRadii(), MTKpp::gaussianParser::setModRedundantFile(), MTKpp::gaussianParser::setMultiplicity(), MTKpp::stdGroup::setName(), MTKpp::sheet::setName(), MTKpp::collection::setName(), MTKpp::molecule::setName(), MTKpp::atom::setName(), MTKpp::submolecule::setName(), MTKpp::gaussianParser::setNoCoords(), MTKpp::gaussianParser::setNProc(), commLineOptions::setOption(), MTKpp::gaussianParser::setPseudoPotentialFile(), MTKpp::stdGroup::setStdMolecule(), MTKpp::errorHandler::setStream(), MTKpp::submolecule::setSubMolId(), MTKpp::stdFrag::setSymbol(), MTKpp::gaussianParser::setTheory(), MTKpp::gaussianParser::setVerbosity(), MTKpp::gaussianParser::setWriteChargeAndMult(), MTKpp::gaussianParser::setWriteMoleculeName(), MTKpp::Angle::size, MTKpp::Bond::size, MTKpp::splitString(), MTKpp::Bond::stereo, MTKpp::string2Double(), MTKpp::string2Int(), MTKpp::stripString(), MTKpp::errorHandler::throwError(), MTKpp::Bond::topology, MTKpp::stdAtom::type, MTKpp::Bond::type, commLineOptions::usageOn(), MTKpp::torsionParam::Vn, MTKpp::amberParser::Write(), MTKpp::frcmodParser::Write(), MTKpp::acParser::Write(), MTKpp::gaussianParser::Write(), MTKpp::molParser::Write(), MTKpp::paramParser::Write(), MTKpp::stdLibParser::Write(), MTKpp::dMParser::write(), MTKpp::mtkppParser::Write(), MTKpp::pdbParser::Write(), MTKpp::prepParser::Write(), MTKpp::sdfParser::Write(), and MTKpp::gaussianParser::writeMappingFile().

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