MTK++ Latest version: 0.2.0

File List
Here is a list of all files with brief descriptions:
acParser.cppParses AMBER antechamber files
acParser.h [code]Parses AMBER antechamber files
amber.cppAMBER MM potential
amber.h [code]AMBER MM potential
amberAngle.cppAMBER angle energy and gradient
amberAngle.h [code]AMBER angle energy and gradient
amberBond.cppAMBER bond energy and gradient
amberBond.h [code]AMBER bond energy and gradient
amberImproper.cppAMBER improper energy and gradient
amberImproper.h [code]AMBER improper energy and gradient
amberNonBonded.cppAMBER non-bonded energy and gradient
amberNonBonded.h [code]AMBER non-bonded energy and gradient
amberParser.cppParses amber prmtop/crd files
amberParser.h [code]Parses amber prmtop/crd files
amberTorsion.cppAMBER torsion energy and gradient
amberTorsion.h [code]AMBER torsion energy and gradient
angle.h [code]Container for angle information
atom.cppContainer for atom information
atom.h [code]Container for atom information
atomType.cppContainer of atom types
atomType.h [code]Container of atom types
atomTypeParser.cppAtom type parser
atomTypeParser.h [code]Atom type parser
atomTyper.cppAtom Types molecules
atomTyper.h [code]Atom Types molecules
baseParser.cppBase parser class
baseParser.h [code]Base parser class
BaseStats.cppBase class for statistical routines
BaseStats.h [code]Base class for statistical routines
BaseStats_boost.cpp
BaseStats_boost.h [code]
bond.h [code]Container for bond information
capActiveSite.cppCaps active site using a cutoff with NME/ACE residues
collection.cppContainer for molecules
collection.h [code]Container for molecules
commLineOptions.cpp
commLineOptions.h [code]Command line class for c++ code
complex.cppDetermine the receptor, solvent and ligands
complex.h [code]Container for a receptor and ligand
config.h [code]
conformer.cppRotatable bond based conformer class
conformer.h [code]Rotatable bond based conformer class
connections.cppAssigns connectivity
connections.h [code]Assigns connectivity
constants.h [code]Container for constants
copyright.h [code]MTK++ copyright
dcParser.cppParses Divcon files
dcParser.h [code]Parses Divcon files
deleteItem.h [code]
diagonalize.h [code]Inferface function to boost/lapack syev function
diagonalize_eigen.h [code]Inferface functions to eigen library
DivConInterface.h [code]A bunch of routines to deal with DivCon
dMParser.cppMatrix xml parser
dMParser.h [code]Sheet/tables parser
domErrorHandler.h [code]Dom xml parser error handling
edge.h [code]Container for edge information
element.cppContainer for element information
element.h [code]Container for element information
elementParser.cppParses elements xml file using XERCES-C and Trolltech's Qt
elementParser.h [code]Parses elements xml file using XERCES-C or Trolltech's Qt
error.cppError object used in errorHandler
error.h [code]Error object used in errorHandler
errorHandler.cppError Handling within MTK++
errorHandler.h [code]Error Handling within MTK++
fileFormatsTest.cppTests file reading functionality in MTK++
fingerPrint.cppGenerates very simple molecular fingerprints
fingerPrint.h [code]Generates very simple molecular fingerprints
frcmod2xml.cppConvert AMBER frcmod file to MTK++ xml parameter file
frcmodParser.cppParses AMBER frcmod files
frcmodParser.h [code]Parses AMBER frcmod files
func.cppDetermines the functional groups in ligands
functionalize.cppBreaks a molecule into its functional group
functionalize.h [code]Breaks a molecule into its functional group
gaAverage.cppPerforms chromosome averaging
gaAverage.h [code]Performs chromosome averaging
gaChromosome.cppContainer for gaGenes
gaChromosome.h [code]Container for gaGenes
gaCrossOver.cppPerforms recombination of gaChromosomes
gaCrossOver.h [code]Performs recombination of gaChromosomes
gaGaussian.cppContains gaussian information used by gaSelection
gaGaussian.h [code]Contains gaussian information used by gaSelection
gaGene.cppClass to handle genes
gaGene.h [code]Class to handle genes
gaIndividual.cppContainer for gaChromosomes
gaIndividual.h [code]Container for gaChromosomes
gaMutate.cppPerforms mutation of gaChromosomes
gaMutate.h [code]Performs mutation of gaChromosomes
gaOperators.cppThis class performs the GA operations including crossover mutation, averaging, etc
gaOperators.h [code]This class performs the GA operations including crossover mutation, averaging, etc
gaOutput.cppClass to handle the GA output
gaOutput.h [code]Class to handle the GA output
gaParser.cppParses GA xml files using xercesc
gaParser.h [code]Parses GA xml files using Qt & xercesc
gaPopulation.cppContainer for gaIndividuals
gaPopulation.h [code]Container for gaIndividuals
gaRanNumGen.cpp
gaRanNumGen.h [code]Inline functions for random number generation
gaRegion.cppContainer for gaPopulations
gaRegion.h [code]Container for gaPopulations
gaSelection.cppSelects gaIndividuals from gaPopulation based on fitness
gaSelection.h [code]Selects gaIndividuals from gaPopulation based on fitness
gaussianParser.cppParses gaussian files
gaussianParser.h [code]Parses gaussian files
gaVersion.h [code]Contains version, author information for the GA
gaWorld.cppContainer for gaRegions
gaWorld.h [code]Container for gaRegions
graph.cppContainer for graph
graph.h [code]Container for graph
hybrid.cppDetermines the hybridizations of a molecule in a pdb file
hybridize.cppDetermines hybridizations of atoms in a molecule
hybridize.h [code]Determines hybridizations of atoms in a molecule
hybridizeTest.cppTests the preception to atomic hybridization of ligands from the PDB
hydrophobize.cppDetermines the hydrophobic groups in a molecule
hydrophobize.h [code]Determines the hydrophobic groups in a molecule
idObject.h [code]
improper.h [code]Container for improper information
index.h [code]Contains indexing functions for pairs, triplets and quadruples
inputParser.h [code]Parser an input file
inverseMatrix.h [code]
lbfgs.cppThis class contains code for the limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm for large-scale multidimensional unconstrained minimization problems. This file is a translation of Fortran code written by Jorge Nocedal. It is distributed as part of the RISO project
lbfgs.h [code]This class contains code for the limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm for large-scale multidimensional unconstrained minimization problems. This file is a translation of Fortran code written by Jorge Nocedal. It is distributed as part of the RISO project
ligProtonate.cppProtonates small molecule
ligProtonate.h [code]Protonates small molecule
linearAlgebraTest.cppTests the eigen functionality in MTK++
linearAlgebraTest_boost.cpp
logger.h [code]
MCPB.cppDevelopes Metal Cluster Force Field Parameters
metalCenter.cppContainer for metaloprotein information
metalCenter.h [code]Container for metaloprotein information
mmE.cppDetermines the MM energy of a pdb file
mmPotential.cppBase class for MM potentials
mmPotential.h [code]Base class for MM potentials
mmTest.cppTests the MM functionality in MTK++
mol2Parser.cppParsers mol2 files
mol2Parser.h [code]Parsers mol2 files
molecule.cppContainer for submolecules, bonds, angles, torsions, and impropers
molecule.h [code]Container for submolecules, bonds, angles, torsions, and impropers
molParser.cppParses mol files
molParser.h [code]Parses mol files
MTKException.cpp
MTKException.h [code]
MTKppConstants.cppProgram for printing the definitions and constants used in MTK++
mtkppParser.cppParses MTK++ State xml files using xercesc
mtkppParser.h [code]Parses MTK++ State files
object.h [code]Base object
ols.cppOrdinary Least Squares
ols.h [code]Ordinary Least Squares
pamParser.cppParses pam files
pamParser.h [code]Parses pam files
parameters.cppContainer for parameter information
parameters.h [code]Container for parameter information
paramParser.cppParses parameter xml files using XERCES-C and Trolltech's Qt
paramParser.h [code]Parses parameter xml files using xercesc
parsingException.cpp
parsingException.h [code]Parses mol files
pca.cppPrincipal Component Analysis
pca.h [code]Principal Component Analysis
pdbParser.cppParses pdb files
pdbParser.h [code]Parses pdb files
pdbSearcher.cppSearch a local copy of the pdb for info, assuming that all file are *.Z
pharmacophore.cppDetermines the Maximum Common Pharmacophore (MCP) between two molecules
pharmacophore.h [code]Determines the Maximum Common Pharmacophore (MCP) between two molecules
pls.cppPartial Least Squares
pls.h [code]Partial Least Squares
prep2xml.cppConvert AMBER prep file to MTK++ xml library
prepParser.cppParses AMBER prep files
prepParser.h [code]Parses AMBER prep files
printHeader.h [code]Print header
proProtonate.cppProtonates proteins
proProtonate.h [code]Protonates proteins
protonate.cppProtonates a molecule
protonate.h [code]Protonates a molecule
protonator.cppProtonates mol/sdf/pdb files
randomNumbers.h [code]Inline functions for random number generation
ring.cppDetermines rings in a molecule
ring.h [code]Determines rings in a molecule
ringTest.cppTests the ring detection functionality in MTK++
sdfParser.cppParses sd files
sdfParser.h [code]Parses sd files
selection.cppAllows for the selection of certain parts of the collection
selection.h [code]Allows for the selection of certain parts of the collection
seqAlign.cppSequence Alignment
seqAlign.h [code]Sequence Alignment
sequenceAligner.cppAligns two sequences
sheet.cpp
sheet.h [code]
stats.cppSimple stats program
statsTest.cppTests the stats functionality in MTK++
stdFrag.cppContainer for standard atoms, bonds, angles, torsions and impropers
stdFrag.h [code]Container for standard atoms, bonds, angles, torsions and impropers
stdGroup.cppContainer for standard fragments
stdGroup.h [code]Container for standard fragments
stdLib2Sdf.cppConverts an xml library file into a sd file
stdLibParser.cppParses standard library xml files using XERCES-C and Trolltech's Qt
stdLibParser.h [code]Parses standard library xml files using xercesc
stdLibrary.cppContainer for standard groups
stdLibrary.h [code]Container for standard groups
StringManip.cppMiscellaneous string manipulation functions
StringManip.h [code]Miscellaneous string manipulation functions
submolecule.cppContainer for atoms and bonds
submolecule.h [code]Container for atoms and bonds
superimpose.cppSuperimposes molecules
superimpose.h [code]Superimposes molecules
superimposer.cppSuperimpose functions
table.h [code]Extension of ublas::matrix to store labels
table_boost.h [code]
tester.cppA source file used for testing new code
tinystr.cpp
tinystr.h [code]
tinyxml.cpp
tinyxml.h [code]
tinyxmlerror.cpp
tinyxmlparser.cpp
torsion.h [code]Container for Torsion info
utility.h [code]Contains string functions
vector3d.h [code]A 3-dimensional vector with many common functions needed for the manipulation of 3d vectors. Everything is inline so as to speed things up
version.h [code]Version information
vertex.cppContainer for vertex information
vertex.h [code]Container for vertex information
watProtonate.cppProtonates water molecule
watProtonate.h [code]Protonates water molecule
xmlConvertors.h [code]Xml handler
xyzParser.cppParses XYZ files
xyzParser.h [code]Parses XYZ files
zmatParser.cppParses Z-Matrix files
zmatParser.h [code]Parses Z-Matrix files

Generated on Fri Dec 23 2011 09:28:58 for MTK++ by Doxygen 1.7.5.1