File List

Here is a list of all files with brief descriptions:

[detail level 123456]

include
BALL
COMMON
constants.h
create.h
debug.h
exception.h
global.h
hash.h
init.h
logStream.h
macros.h
parserDefinitions.h
rtti.h
version.h
CONCEPT
autoDeletable.h
baseFunctor.h
baseIterator.h
benchmark.h
bidirectionalIterator.h
classTest.h
client.h
comparator.h
composite.h
embeddable.h
enumerator.h
factory.h
forwardIterator.h
molecularInformation.h
moleculeObjectCreator.h
object.h
objectCreator.h
persistenceManager.h
persistentObject.h
predicate.h
preferencesObject.h
processor.h
property.h
randomAccessIterator.h
selectable.h
stdIteratorWrapper.h
textPersistenceManager.h
timeStamp.h
visitor.h
XDRPersistenceManager.h
DATATYPE
GRAPH
graphAlgorithms.h
molecularGraph.h
treeWidth.h
bitVector.h
contour.h
contourLine.h
contourSurface.h
forEach.h
hashGrid.h
hashMap.h
hashSet.h
list.h
options.h
quadruple.h
regularData1D.h
regularData2D.h
regularData3D.h
regularExpression.h
string.h
stringHashMap.h
stringHashSet.h
triple.h
DOCKING
COMMON
conformation.h
conformationSet.h
constraints.h
dockingAlgorithm.h
dockResult.h
flexDefinition.h
flexibleMolecule.h
gridAnalysis.h
poseClustering.h
receptor.h
result.h
sideChainOptimizer.h
staticLigandFragment.h
structurePreparer.h
GENETICDOCK
dockProblem.h
evolutionaryDocking.h
genes.h
geneticAlgorithm.h
geneticIndividual.h
parameter.h
rotateBond.h
rotateBonds.h
IMGDOCK
IMGDock.h
geometricFit.h
ENERGY
atomicContactEnergy.h
composedEnergyProcessor.h
coulomb.h
distanceCoulomb.h
energyProcessor.h
FORMAT
amiraMeshFile.h
antechamberFile.h
bruker1DFile.h
bruker2DFile.h
CCP4File.h
CIFFile.h
commandlineParser.h
DCDFile.h
dockResultFile.h
DSN6File.h
GAMESSDatFile.h
GAMESSLogFile.h
genericMolFile.h
HINFile.h
HMOFile.h
INIFile.h
JCAMPFile.h
KCFFile.h
lineBasedFile.h
MOL2File.h
MOLFile.h
molFileFactory.h
MOPACInputFile.h
MOPACOutputFile.h
NMRStarFile.h
parameters.h
parameterSection.h
paramFile.h
PDBdefs.h
PDBFile.h
PDBInfo.h
PDBRecords.h
pubchemDownloader.h
resourceFile.h
SCWRLRotamerFile.h
SDFile.h
trajectoryFile.h
trajectoryFileFactory.h
TRRFile.h
XYZFile.h
KERNEL
atom.h
atomContainer.h
atomContainerIterator.h
atomIterator.h
bond.h
bondIterator.h
chain.h
chainIterator.h
expression.h
expressionParser.h
expressionPredicate.h
expressionTree.h
extractors.h
forEach.h
fragment.h
fragmentIterator.h
global.h
iterator.h
molecularInteractions.h
molecule.h
moleculeIterator.h
nucleicAcid.h
nucleicAcidIterator.h
nucleotide.h
nucleotideIterator.h
PDBAtom.h
PDBAtomIterator.h
predicate.h
protein.h
proteinIterator.h
PTE.h
residue.h
residueIterator.h
secondaryStructure.h
secondaryStructureIterator.h
selector.h
standardPredicates.h
system.h
MATHS
analyticalGeometry.h
angle.h
box3.h
circle3.h
common.h
complex.h
cubicSpline1D.h
cubicSpline2D.h
FFT1D.h
FFT2D.h
FFT3D.h
fftwCommon.h
function.h
line3.h
matrix44.h
numericalIntegrator.h
parsedFunction.h
piecewiseFunction.h
piecewisePolynomial.h
plane3.h
quaternion.h
rombergIntegrator.h
simpleBox3.h
sphere3.h
surface.h
vector2.h
vector3.h
vector4.h
MOLMEC
AMBER
amber.h
amberBend.h
amberNonBonded.h
amberStretch.h
amberTorsion.h
GAFFCESParser.h
GAFFTypeProcessor.h
CHARMM
charmm.h
charmmBend.h
charmmImproperTorsion.h
charmmNonBonded.h
charmmStretch.h
charmmTorsion.h
COMMON
assignTypes.h
atomVector.h
bendComponent.h
chargeRuleProcessor.h
forceField.h
forceFieldComponent.h
gradient.h
periodicBoundary.h
radiusRuleProcessor.h
ruleEvaluator.h
ruleProcessor.h
snapShot.h
snapShotManager.h
stretchComponent.h
support.h
typenameRuleProcessor.h
typeRuleProcessor.h
MDSIMULATION
canonicalMD.h
microCanonicalMD.h
molecularDynamics.h
MINIMIZATION
conjugateGradient.h
energyMinimizer.h
lineSearch.h
shiftedLVMM.h
steepestDescent.h
strangLBFGS.h
MMFF94
MMFF94.h
MMFF94NonBonded.h
MMFF94OutOfPlaneBend.h
MMFF94Parameters.h
MMFF94Processors.h
MMFF94StretchBend.h
MMFF94Torsion.h
PARAMETER
atomTypes.h
charmmEEF1.h
cosineTorsion.h
forceFieldParameters.h
lennardJones.h
potential1210.h
quadraticAngleBend.h
quadraticBondStretch.h
quadraticImproperTorsion.h
residueTorsions.h
templates.h
NMR
anisotropyShiftProcessor.h
clearShiftProcessor.h
createSpectrumProcessor.h
EFShiftProcessor.h
empiricalHSShiftProcessor.h
experiment.h
haighMallionShiftProcessor.h
HBondShiftProcessor.h
johnsonBoveyShiftProcessor.h
peak.h
peakList.h
randomCoilShiftProcessor.h
shiftModel.h
shiftModel1D.h
shiftModel2D.h
shiftModule.h
spectrum.h
PLUGIN
BALLPlugin.h
pluginHandler.h
pluginManager.h
PYTHON
EXTENSIONS
pyBALLSipHelper.h
pyColorRGBAVector.h
pyCompositeList.h
pyConstant.h
pyDatasetVector.h
pyIndexList.h
pyListHelper.h
pyUnaryProcessors.h
pyCAPIKernel.h
pyInterpreter.h
pyKernel.h
pyServer.h
pyWrapper.h
QSAR
allModel.h
aromaticityProcessor.h
automaticModelCreator.h
bayesModel.h
classificationModel.h
classificationValidation.h
common.h
configIO.h
connectivityBase.h
connectivityDescriptors.h
descriptor.h
exception.h
featureSelection.h
gpModel.h
kernel.h
kernelModel.h
knnModel.h
kpcrModel.h
kplsModel.h
latentVariableModel.h
ldaModel.h
libsvmModel.h
linearModel.h
logitModel.h
mlrModel.h
Model.h
modelFactory.h
nBModel.h
NMRDescriptors.h
nonlinearModel.h
oplsModel.h
partialChargeBase.h
partialChargeDescriptors.h
partialChargeProcessor.h
pcrModel.h
plsModel.h
QSARData.h
registry.h
regressionModel.h
regressionValidation.h
ringPerceptionProcessor.h
rrModel.h
simpleBase.h
simpleDescriptors.h
snBModel.h
statistics.h
surfaceBase.h
surfaceDescriptors.h
svmModel.h
svrModel.h
validation.h
SCORING
COMMON
baseFunction.h
diffGridBasedScoring.h
diffScoringFunction.h
fermiBaseFunction.h
gridBasedScoring.h
linearBaseFunction.h
rescorer.h
scoreGridSet.h
scoringComponent.h
scoringFunction.h
scoringOptimizer.h
COMPONENTS
advElectrostatic.h
aromaticRingStacking.h
burialDepth.h
buriedPolar.h
CHPI.h
CHPISlick.h
electrostatic.h
fragmentationalSolvation.h
fresnoTypes.h
hydrogenBond.h
hydrogenBondSlick.h
lipophilic.h
nonpolarSolvation.h
PB.h
PLP.h
polarity.h
polarSolvation.h
rotationalEntropy.h
solvation.h
vanDerWaals.h
vanDerWaalsSlick.h
FUNCTIONS
amberEvaluation.h
energeticEvaluation.h
forceFieldEvaluation.h
gridedMM.h
gridedPLP.h
MMScoring.h
PBScoring.h
PLPScoring.h
randomEvaluation.h
rescoring.h
rescoring1D.h
rescoring3D.h
rescoring4D.h
slickEnergy.h
slickScore.h
SOLVATION
claverieParameter.h
electrostaticPotentialCalculator.h
generalizedBornCase.h
molecularSurfaceGrid.h
ooiEnergy.h
pair6_12InteractionEnergyProcessor.h
pair6_12RDFIntegrator.h
pairExpInteractionEnergyProcessor.h
pairExpRDFIntegrator.h
PCMCavFreeEnergyProcessor.h
pierottiCavFreeEnergyProcessor.h
poissonBoltzmann.h
reissCavFreeEnergyProcessor.h
solventDescriptor.h
solventParameter.h
uhligCavFreeEnergyProcessor.h
STRUCTURE
BONDORDERS
AStarBondOrderStrategy.h
bondOrderAssignment.h
bondOrderAssignmentStrategy.h
branchAndBoundBondOrderStrategy.h
FPTBondOrderStrategy.h
ILPBondOrderStrategy.h
KGreedyBondOrderStrategy.h
partialBondOrderAssignment.h
addHydrogenProcessor.h
analyticalSES.h
assignBondOrderProcessor.h
atomBijection.h
atomTyper.h
binaryFingerprintMethods.h
bindingPocketProcessor.h
buildBondsProcessor.h
connectedComponentsProcessor.h
defaultProcessors.h
disulfidBondProcessor.h
DNAMutator.h
fragmentDB.h
geometricProperties.h
geometricTransformations.h
graphEdge.h
graphFace.h
graphVertex.h
HBondProcessor.h
hybridisationProcessor.h
kekulizer.h
logP.h
molecularSimilarity.h
mutator.h
nucleotideMapping.h
numericalSAS.h
peptideBuilder.h
peptideCapProcessor.h
peptides.h
radialDistributionFunction.h
RDFIntegrator.h
RDFParameter.h
RDFSection.h
reconstructFragmentProcessor.h
reducedSurface.h
residueChecker.h
residueRotamerSet.h
rGroupAssembler.h
ringAnalyser.h
RMSDMinimizer.h
rotamerLibrary.h
RSEdge.h
RSFace.h
RSVertex.h
SASEdge.h
SASFace.h
SASVertex.h
sdGenerator.h
secondaryStructureProcessor.h
SESEdge.h
SESFace.h
SESVertex.h
sideChainPlacementProcessor.h
simpleMolecularGraph.h
smartsMatcher.h
smartsParser.h
smilesParser.h
solventAccessibleSurface.h
solventExcludedSurface.h
structureMapper.h
surfaceProcessor.h
triangle.h
triangleEdge.h
trianglePoint.h
triangulatedSAS.h
triangulatedSES.h
triangulatedSurface.h
UCK.h
SYSTEM
binaryFileAdaptor.h
directory.h
file.h
fileSystem.h
MPISupport.h
mutex.h
networking.h
path.h
simpleDownloader.h
sysinfo.h
timer.h
VIEW
DATATYPE
colorExtensions.h
colorHSV.h
colorMap.h
colorRGBA.h
colorUnit.h
colorUnitHue.h
dataset.h
raytraceableGrid.h
standardDatasets.h
vertex1.h
vertex2.h
DIALOGS
amberConfigurationDialog.h
assignBondOrderConfigurationDialog.h
assignBondOrderResultsDialog.h
atomOverview.h
bondProperties.h
charmmConfigurationDialog.h
clippingDialog.h
coloringSettingsDialog.h
compositeProperties.h
contourSurfaceDialog.h
displayProperties.h
dockDialog.h
dockProgressDialog.h
dockResultDialog.h
downloadElectronDensity.h
downloadPDBFile.h
editSettings.h
editSingleShortcut.h
exportGeometryDialog.h
FDPBDialog.h
fieldLinesDialog.h
generateCrystalDialog.h
geometricFitDialog.h
gridVisualizationDialog.h
labelDialog.h
lightSettings.h
mainControlPreferences.h
materialSettings.h
minimizationDialog.h
MMFF94ConfigurationDialog.h
modelSettingsDialog.h
modifyRepresentationDialog.h
molecularDynamicsDialog.h
molecularFileDialog.h
networkPreferences.h
openSavePreferences.h
parsedFunctionDialog.h
peptideDialog.h
pluginDialog.h
preferences.h
PTEDialog.h
pubchemDialog.h
pythonSettings.h
raytraceableContourSurfaceDialog.h
serverPreferences.h
setCamera.h
setClippingPlane.h
shortcutDialog.h
snapShotVisualisation.h
stageSettings.h
stereoSettingsDialog.h
undoManagerDialog.h
INPUT
buttonEvent.h
deviceEvent.h
fakeDriver.h
headTrackingEvent.h
inputDeviceDriver.h
inputPlugin.h
motionTrackingEvent.h
notificationEvent.h
transformationEvent6D.h
KERNEL
MODES
editMode.h
interactionMode.h
interactionModeManager.h
moveMode.h
pickingMode.h
rotateMode.h
clippingPlane.h
common.h
compositeManager.h
connectionObject.h
editOperation.h
geometricObject.h
iconLoader.h
mainControl.h
message.h
modelInformation.h
modularWidget.h
preferencesEntry.h
representation.h
representationManager.h
serverWidget.h
shortcutRegistry.h
snapshotManagerInterface.h
stage.h
threads.h
UIOperationMode.h
MODELS
atomBondModelBaseProcessor.h
backboneModel.h
ballAndStickModel.h
cartoonModel.h
colorByGridProcessor.h
colorProcessor.h
fieldLineCreator.h
forceModel.h
HBondModel.h
labelModel.h
lineModel.h
modelProcessor.h
standardColorProcessor.h
surfaceModel.h
vanDerWaalsModel.h
PLUGIN
inputDevPluginHandler.h
modularWidgetPlugin.h
modularWidgetPluginHandler.h
VIEWPlugin.h
PRIMITIVES
box.h
disc.h
gridVisualisation.h
label.h
line.h
mesh.h
multiLine.h
point.h
quadMesh.h
simpleBox.h
sphere.h
tube.h
twoColoredLine.h
twoColoredTube.h
RENDERING
RENDERERS
bufferedRenderer.h
cudaVolumeRenderer.h
glRenderer.h
POVRenderer.h
raytracingRenderer.h
renderer.h
rtfactRenderer.h
STLRenderer.h
tilingRenderer.h
VRMLRenderer.h
XML3DRenderer.h
camera.h
glDisplayList.h
glOffscreenTarget.h
glRenderWindow.h
pixelFormat.h
renderSetup.h
renderTarget.h
renderWindow.h
vertexBuffer.h
WIDGETS
colorButton.h
colorTable.h
datasetControl.h
dockingController.h
dockWidget.h
fileObserver.h
genericControl.h
geometricControl.h
gridColorWidget.h
helpViewer.h
hotkeyTable.h
HTMLPage.h
HTMLView.h
logView.h
molecularControl.h
molecularStructure.h
propertyEditor.h
pyWidget.h
scene.h
SDWidget.h
shortcutTableView.h
testFramework.h
textEditorWidget.h
XRAY
crystalGenerator.h
crystalInfo.h
spaceGroupParameters.h
common.h
concept.h
datatype.h
energy.h
format.h
kernel.h
maths.h
molmec.h
solvation.h
structure.h
system.h