MTK++ Latest version: 0.2.0

Functions
sequenceAligner.cpp File Reference

Aligns two sequences. More...

#include "Utils/printHeader.h"
#include "Utils/vector3d.h"
#include "Utils/constants.h"
#include "Molecule/collection.h"
#include "Molecule/molecule.h"
#include "Molecule/submolecule.h"
#include "Molecule/atom.h"
#include "Molecule/torsion.h"
#include "Molecule/element.h"
#include "Molecule/superimpose.h"
#include "Molecule/seqAlign.h"
#include "Molecule/parameters.h"
#include "Molecule/stdLibrary.h"
#include "Molecule/atomTyper.h"
#include "Molecule/connections.h"
#include "Molecule/complex.h"
#include "Statistics/sheet.h"
#include "Statistics/table.h"
#include "Parsers/elementParser.h"
#include "Parsers/molParser.h"
#include "Parsers/pdbParser.h"
#include "Parsers/pamParser.h"
#include "Parsers/dMParser.h"
#include "Parsers/StringManip.h"
#include "Parsers/paramParser.h"
#include "Parsers/stdLibParser.h"
#include "Parsers/inputParser.h"
#include "Parsers/commLineOptions.h"
#include "time.h"
#include <iostream>
#include <stdlib.h>
#include <stdio.h>
#include <vector>
#include <map>
#include <algorithm>
Include dependency graph for sequenceAligner.cpp:

Functions

int main (int argc, char **argv)
 Aligns two sequences.

Detailed Description

Aligns two sequences.

Author:
Martin B. Peters
Date:
2010/04/22 22:19:54
Revision:
1.2

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

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

Copyright (C) 2005-2007 (see AUTHORS file for a list of contributors)

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


Function Documentation

int main ( int  argc,
char **  argv 
)

Aligns two sequences.

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: loadElements

           Description: Loads AMBER Parameters into sequenceAligner

           syntax: loadElements ~/MTKpp/data/elements.xml
           Function: loadParam

           Description: Loads AMBER Parameters into sequenceAligner

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

           Description: Loads AMBER library files into sequenceAligner

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

           Description: Loads PAM file

           syntax: loadPam ~/MTKpp/data/PAM/PAM250
           Function: readPdb

           Description: Opens a PDB file

           syntax: readPdb 1FEE.pdb
           Function: removeHs

           Description: 

           syntax: removeHs
           Function: print

           Description: Print to screen details of structure

           syntax: print
           syntax: print protein
           syntax: print ligand
           syntax: print solvent
           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: 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: systemSetup

           Description: Select Receptor, Solvent, and Ligand

           The receptor is defined as any molecule with a molecular weight of >1000 A.U.
           The receptor can also contain metal atoms.

           The function relies on the solvent molecule being named either HOH or WAT

           The ligand is what remains.

           syntax: systemSetup
           Function: setTemplate

           Description: set the template molecule

           syntax: setTemplate 1
           syntax: setTemplate 1@start
           Function: setQuery

           Description: set the query molecule

           syntax: setQuery 1
           syntax: setQuery 2@end
           Function: setLigand

           Description: 

           syntax: setLigand 3@start
           syntax: setLigand 3
           Function: runAlign

           Description: Run sequence alignment

           syntax: runAlign 1 1 10.0 0.5
           Function: superimpose

           Description: Superimpose

           syntax: superimpose alphaCarbons
           syntax: superimpose bb
           syntax: superimpose bbb
           Function: transform

           Description: transform

           syntax: transform 1 140 alphaCarbons
           syntax: transform 2@start 2@end alphaCarbons
           Function: writePdb

           Description: writePdb

           syntax: writePdb 140 340 file.pdb
           Function: writeTransformationFile

           Description: writeTransformationFile

           syntax: writeTransformationFile alphaCarbons t.xml
           Function: createActiveSite

           Description: Creates an active site in the template around the provided ligand

           syntax: createActiveSite
           Function: compareActiveSites

           Description: Compares the active site in the template to the query

           syntax: compareActiveSites alphaCarbons
           syntax: compareActiveSites bb
           syntax: compareActiveSites bbb

References MTKpp::collection::addParameters(), MTKpp::collection::addStdLibrary(), MTKpp::sheet::addTable(), commLineOptions::addUsage(), MTKpp::connections::assignDisulfideBonds(), MTKpp::connections::assignStd(), MTKpp::atomTyper::atomTypeByLib(), MTKpp::superimpose::center(), MTKpp::containsSubStr(), MTKpp::vector3d::dist(), MTKpp::double2String(), MTKpp::errorLogger, MTKpp::fileExists(), MTKpp::superimpose::fit(), MTKpp::submolecule::get1LName(), MTKpp::submolecule::getAtom(), MTKpp::submolecule::getAtomList(), MTKpp::molecule::getAtomList(), MTKpp::table< T >::getCellValue(), MTKpp::atom::getCoords(), MTKpp::seqAlign::getCorrMap(), MTKpp::atom::getElementSymbol(), MTKpp::baseParser::getError(), MTKpp::baseParser::getErrorMessage(), commLineOptions::getFlag(), MTKpp::collection::getMolecule(), MTKpp::collection::getMoleculeList(), MTKpp::molecule::getMolId(), MTKpp::submolecule::getName(), MTKpp::molecule::getNumAtoms(), MTKpp::collection::getNumberMolecules(), MTKpp::molecule::getNumSubMolecules(), MTKpp::collection::getParameters(), MTKpp::submolecule::getParent(), MTKpp::superimpose::getRotationMatrix(), MTKpp::seqAlign::getSimScore(), MTKpp::collection::getStdLibrary(), MTKpp::molecule::getSubMolecule(), MTKpp::molecule::getSubMoleculeList(), MTKpp::submolecule::getSubMolId(), MTKpp::sheet::getTable(), commLineOptions::getValue(), MTKpp::vector3d::getX(), MTKpp::vector3d::getY(), MTKpp::vector3d::getZ(), MTKpp::INFO, MTKpp::int2String(), MTKpp::submolecule::less(), MTKpp::MESSAGE, MTKpp::MTK_ERROR, commLineOptions::noUsage(), MTKpp::collection::pElements, MTKpp::printHeader(), commLineOptions::printUsage(), commLineOptions::processCommandArgs(), MTKpp::pamParser::Read(), MTKpp::elementParser::Read(), MTKpp::pdbParser::Read(), MTKpp::paramParser::Read(), MTKpp::stdLibParser::Read(), MTKpp::readInputFile(), MTKpp::replaceSubStr(), MTKpp::seqAlign::run(), MTKpp::connections::run(), MTKpp::vector3d::set(), MTKpp::seqAlign::setAlgorithmType(), MTKpp::table< T >::setCellValue(), MTKpp::table< T >::setColumnLabel(), commLineOptions::setFlag(), MTKpp::seqAlign::setGapExtend(), MTKpp::seqAlign::setGapOpen(), MTKpp::seqAlign::setGapPenaltyType(), MTKpp::errorHandler::setLevel(), MTKpp::table< T >::setName(), commLineOptions::setOption(), MTKpp::seqAlign::setQuery(), MTKpp::table< T >::setSizes(), MTKpp::errorHandler::setStream(), MTKpp::seqAlign::setTemplate(), MTKpp::splitString(), MTKpp::string2Double(), MTKpp::string2Int(), MTKpp::errorHandler::throwError(), MTKpp::superimpose::updateCoords(), commLineOptions::usageOn(), MTKpp::dMParser::write(), and MTKpp::pdbParser::Write().

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