cdpl_api_doc/c%2B%2B_api_doc/Pharm_8hpp_source.html

 /*

  * Pharm.hpp

  *

  * This file is part of the Chemical Data Processing Toolkit

  *

  * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>

  *

  * This library is free software; you can redistribute it and/or

  * modify it under the terms of the GNU Lesser General Public

  * License as published by the Free Software Foundation; either

  * version 2 of the License, or (at your option) any later version.

  *

  * This library is distributed in the hope that it will be useful,

  * but WITHOUT ANY WARRANTY; without even the implied warranty of

  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU

  * Lesser General Public License for more details.

  *

  * You should have received a copy of the GNU Lesser General Public License

  * along with this library; see the file COPYING. If not, write to

  * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,

  * Boston, MA 02111-1307, USA.

  */


 #ifndef CDPL_PHARM_HPP

 #define CDPL_PHARM_HPP


 #include "CDPL/Pharm/Feature.hpp"

 #include "CDPL/Pharm/BasicFeature.hpp"

 #include "CDPL/Pharm/FeatureContainer.hpp"

 #include "CDPL/Pharm/FeatureSet.hpp"

 #include "CDPL/Pharm/Pharmacophore.hpp"

 #include "CDPL/Pharm/BasicPharmacophore.hpp"

 #include "CDPL/Pharm/FeatureMapping.hpp"

 #include "CDPL/Pharm/FeatureTypeHistogram.hpp"

 #include "CDPL/Pharm/Feature3DCoordinatesFunction.hpp"

 #include "CDPL/Pharm/FeatureContainerProperty.hpp"

 #include "CDPL/Pharm/FeatureProperty.hpp"

 #include "CDPL/Pharm/FeatureContainerPropertyDefault.hpp"

 #include "CDPL/Pharm/FeaturePropertyDefault.hpp"

 #include "CDPL/Pharm/ControlParameter.hpp"

 #include "CDPL/Pharm/ControlParameterDefault.hpp"

 #include "CDPL/Pharm/DataFormat.hpp"

 #include "CDPL/Pharm/FeatureType.hpp"

 #include "CDPL/Pharm/FeatureGeometry.hpp"

 #include "CDPL/Pharm/FeatureGenerator.hpp"

 #include "CDPL/Pharm/PatternBasedFeatureGenerator.hpp"

 #include "CDPL/Pharm/AromaticFeatureGenerator.hpp"

 #include "CDPL/Pharm/HydrophobicFeatureGenerator.hpp"

 #include "CDPL/Pharm/HydrophobicAtomFeatureGenerator.hpp"

 #include "CDPL/Pharm/HBondAcceptorFeatureGenerator.hpp"

 #include "CDPL/Pharm/HBondDonorFeatureGenerator.hpp"

 #include "CDPL/Pharm/PosIonizableFeatureGenerator.hpp"

 #include "CDPL/Pharm/NegIonizableFeatureGenerator.hpp"

 #include "CDPL/Pharm/XBondAcceptorFeatureGenerator.hpp"

 #include "CDPL/Pharm/XBondDonorFeatureGenerator.hpp"

 #include "CDPL/Pharm/PharmacophoreGenerator.hpp"

 #include "CDPL/Pharm/DefaultPharmacophoreGenerator.hpp"

 #include "CDPL/Pharm/InteractionAnalyzer.hpp"

 #include "CDPL/Pharm/DefaultInteractionAnalyzer.hpp"

 #include "CDPL/Pharm/InteractionConstraintConnector.hpp"

 #include "CDPL/Pharm/FeatureDistanceConstraint.hpp"

 #include "CDPL/Pharm/HydrophobicInteractionConstraint.hpp"

 #include "CDPL/Pharm/IonicInteractionConstraint.hpp"

 #include "CDPL/Pharm/OrthogonalPiPiInteractionConstraint.hpp"

 #include "CDPL/Pharm/ParallelPiPiInteractionConstraint.hpp"

 #include "CDPL/Pharm/CationPiInteractionConstraint.hpp"

 #include "CDPL/Pharm/HBondingInteractionConstraint.hpp"

 #include "CDPL/Pharm/XBondingInteractionConstraint.hpp"

 #include "CDPL/Pharm/InteractionPharmacophoreGenerator.hpp"

 #include "CDPL/Pharm/FeatureInteractionScore.hpp"

 #include "CDPL/Pharm/FeatureInteractionScoreCombiner.hpp"

 #include "CDPL/Pharm/FeatureDistanceScore.hpp"

 #include "CDPL/Pharm/HydrophobicInteractionScore.hpp"

 #include "CDPL/Pharm/IonicInteractionScore.hpp"

 #include "CDPL/Pharm/HBondingInteractionScore.hpp"

 #include "CDPL/Pharm/XBondingInteractionScore.hpp"

 #include "CDPL/Pharm/OrthogonalPiPiInteractionScore.hpp"

 #include "CDPL/Pharm/ParallelPiPiInteractionScore.hpp"

 #include "CDPL/Pharm/CationPiInteractionScore.hpp"

 #include "CDPL/Pharm/SpatialFeatureMapping.hpp"

 #include "CDPL/Pharm/PharmacophoreAlignment.hpp"

 #include "CDPL/Pharm/FeatureTypeMatchFunctor.hpp"

 #include "CDPL/Pharm/FeaturePairDistanceMatchFunctor.hpp"

 #include "CDPL/Pharm/FeaturePositionMatchFunctor.hpp"

 #include "CDPL/Pharm/FeatureGeometryMatchFunctor.hpp"

 #include "CDPL/Pharm/PharmacophoreFitScore.hpp"

 #include "CDPL/Pharm/CDFPharmacophoreInputHandler.hpp"

 #include "CDPL/Pharm/PMLPharmacophoreInputHandler.hpp"

 #include "CDPL/Pharm/CDFFeatureContainerOutputHandler.hpp"

 #include "CDPL/Pharm/PMLFeatureContainerOutputHandler.hpp"

 #include "CDPL/Pharm/CDFPharmacophoreReader.hpp"

 #include "CDPL/Pharm/PMLPharmacophoreReader.hpp"

 #include "CDPL/Pharm/CDFFeatureContainerWriter.hpp"

 #include "CDPL/Pharm/PMLFeatureContainerWriter.hpp"

 #include "CDPL/Pharm/ScreeningDBCreator.hpp"

 #include "CDPL/Pharm/ScreeningDBAccessor.hpp"

 #include "CDPL/Pharm/ScreeningProcessor.hpp"

 #include "CDPL/Pharm/PharmacophoreFitScreeningScore.hpp"

 #include "CDPL/Pharm/MoleculeFunctions.hpp"

 #include "CDPL/Pharm/PharmacophoreFunctions.hpp"

 #include "CDPL/Pharm/FeatureFunctions.hpp"

 #include "CDPL/Pharm/FeatureContainerFunctions.hpp"

 #include "CDPL/Pharm/FeatureSetFunctions.hpp"

 #include "CDPL/Pharm/ControlParameterFunctions.hpp"

 #include "CDPL/Pharm/UtilityFunctions.hpp"

 #include "CDPL/Pharm/FileScreeningHitCollector.hpp"

 #include "CDPL/Pharm/CDFGZPharmacophoreInputHandler.hpp"

 #include "CDPL/Pharm/CDFBZ2PharmacophoreInputHandler.hpp"

 #include "CDPL/Pharm/CDFGZFeatureContainerOutputHandler.hpp"

 #include "CDPL/Pharm/CDFBZ2FeatureContainerOutputHandler.hpp"

 #include "CDPL/Pharm/CDFGZPharmacophoreReader.hpp"

 #include "CDPL/Pharm/CDFBZ2PharmacophoreReader.hpp"

 #include "CDPL/Pharm/CDFGZFeatureContainerWriter.hpp"

 #include "CDPL/Pharm/CDFBZ2FeatureContainerWriter.hpp"

 #include "CDPL/Pharm/PharmacophoreReader.hpp"

 #include "CDPL/Pharm/FeatureContainerWriter.hpp"

 # include "CDPL/Pharm/PSDPharmacophoreInputHandler.hpp"

 # include "CDPL/Pharm/PSDMoleculeInputHandler.hpp"

 # include "CDPL/Pharm/PSDMolecularGraphOutputHandler.hpp"

 # include "CDPL/Pharm/PSDPharmacophoreReader.hpp"

 # include "CDPL/Pharm/PSDMoleculeReader.hpp"

 # include "CDPL/Pharm/PSDMolecularGraphWriter.hpp"

 # include "CDPL/Pharm/PSDScreeningDBCreator.hpp"

 # include "CDPL/Pharm/PSDScreeningDBAccessor.hpp"


 #endif // CDPL_PHARM_HPP

AromaticFeatureGenerator.hpp
Definition of the class CDPL::Pharm::AromaticFeatureGenerator.

BasicFeature.hpp
Definition of the class CDPL::Pharm::BasicFeature.

BasicPharmacophore.hpp
Definition of the class CDPL::Pharm::BasicPharmacophore.

CDFBZ2FeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFBZ2FeatureContainerOutputHandler.

CDFBZ2FeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFBZ2FeatureContainerWriter.

CDFBZ2PharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFBZ2PharmacophoreInputHandler.

CDFBZ2PharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFBZ2PharmacophoreReader.

CDFFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFFeatureContainerOutputHandler.

CDFFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFFeatureContainerWriter.

CDFGZFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFGZFeatureContainerOutputHandler.

CDFGZFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFGZFeatureContainerWriter.

CDFGZPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFGZPharmacophoreInputHandler.

CDFGZPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFGZPharmacophoreReader.

CDFPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFPharmacophoreInputHandler.

CDFPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFPharmacophoreReader.

CationPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::CationPiInteractionConstraint.

CationPiInteractionScore.hpp
Definition of the class CDPL::Pharm::CationPiInteractionScore.

DefaultInteractionAnalyzer.hpp
Definition of the class CDPL::Pharm::DefaultInteractionAnalyzer.

DefaultPharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::DefaultPharmacophoreGenerator.

Feature3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Pharm::Feature 3D-coordinates fun...

FeatureContainerFunctions.hpp
Declaration of functions that operate on Pharm::FeatureContainer instances.

FeatureContainerPropertyDefault.hpp
Definition of constants in namespace CDPL::Pharm::FeatureContainerPropertyDefault.

FeatureContainerProperty.hpp
Definition of constants in namespace CDPL::Pharm::FeatureContainerProperty.

FeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::FeatureContainerWriter.

FeatureContainer.hpp
Definition of the class CDPL::Pharm::FeatureContainer.

FeatureDistanceConstraint.hpp
Definition of the class CDPL::Pharm::FeatureDistanceConstraint.

FeatureDistanceScore.hpp
Definition of the class CDPL::Pharm::FeatureDistanceScore.

FeatureGenerator.hpp
Definition of the class CDPL::Pharm::FeatureGenerator.

FeatureGeometryMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeatureGeometryMatchFunctor.

FeatureGeometry.hpp
Definition of constants in namespace CDPL::Pharm::FeatureGeometry.

FeatureInteractionScoreCombiner.hpp
Definition of the class CDPL::Pharm::FeatureInteractionScoreCombiner.

FeatureInteractionScore.hpp
Definition of the class CDPL::Pharm::FeatureInteractionScore.

FeatureMapping.hpp
Definition of the type CDPL::Pharm::FeatureMapping.

FeaturePairDistanceMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeaturePairDistanceMatchFunctor.

FeaturePositionMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeaturePositionMatchFunctor.

FeaturePropertyDefault.hpp
Definition of constants in namespace CDPL::Pharm::FeaturePropertyDefault.

FeatureProperty.hpp
Definition of constants in namespace CDPL::Pharm::FeatureProperty.

FeatureSetFunctions.hpp
Declaration of functions that operate on Pharm::FeatureSet instances.

FeatureSet.hpp
Definition of the class CDPL::Pharm::FeatureSet.

FeatureTypeHistogram.hpp
Definition of the type CDPL::Pharm::FeatureTypeHistogram.

FeatureTypeMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeatureTypeMatchFunctor.

Feature.hpp
Definition of the class CDPL::Pharm::Feature.

FileScreeningHitCollector.hpp
Definition of the class CDPL::Pharm::FileScreeningHitCollector.

HBondAcceptorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HBondAcceptorFeatureGenerator.

HBondDonorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HBondDonorFeatureGenerator.

HBondingInteractionConstraint.hpp
Definition of the class CDPL::Pharm::HBondingInteractionConstraint.

HBondingInteractionScore.hpp
Definition of the class CDPL::Pharm::HBondingInteractionScore.

HydrophobicAtomFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HydrophobicAtomFeatureGenerator.

HydrophobicFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HydrophobicFeatureGenerator.

HydrophobicInteractionConstraint.hpp
Definition of the class CDPL::Pharm::HydrophobicInteractionConstraint.

HydrophobicInteractionScore.hpp
Definition of the class CDPL::Pharm::HydrophobicInteractionScore.

InteractionAnalyzer.hpp
Definition of the class CDPL::Pharm::InteractionAnalyzer.

InteractionConstraintConnector.hpp
Definition of the class CDPL::Pharm::InteractionConstraintConnector.

InteractionPharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::InteractionPharmacophoreGenerator.

IonicInteractionConstraint.hpp
Definition of the class CDPL::Pharm::IonicInteractionConstraint.

IonicInteractionScore.hpp
Definition of the class CDPL::Pharm::IonicInteractionScore.

NegIonizableFeatureGenerator.hpp
Definition of the class CDPL::Pharm::NegIonizableFeatureGenerator.

OrthogonalPiPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::OrthogonalPiPiInteractionConstraint.

OrthogonalPiPiInteractionScore.hpp
Definition of the class CDPL::Pharm::OrthogonalPiPiInteractionScore.

PMLFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::PMLFeatureContainerOutputHandler.

PMLFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::PMLFeatureContainerWriter.

PMLPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::PMLPharmacophoreInputHandler.

PMLPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PMLPharmacophoreReader.

PSDMolecularGraphOutputHandler.hpp
Definition of the class CDPL::Pharm::PSDMolecularGraphOutputHandler.

PSDMolecularGraphWriter.hpp
Definition of the class CDPL::Pharm::PSDMolecularGraphWriter.

PSDMoleculeInputHandler.hpp
Definition of the class CDPL::Pharm::PSDMoleculeInputHandler.

PSDMoleculeReader.hpp
Definition of the class CDPL::Pharm::PSDMoleculeReader.

PSDPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::PSDPharmacophoreInputHandler.

PSDPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PSDPharmacophoreReader.

PSDScreeningDBAccessor.hpp
Definition of the class CDPL::Pharm::PSDScreeningDBAccessor.

PSDScreeningDBCreator.hpp
Definition of the class CDPL::Pharm::PSDScreeningDBCreator.

ParallelPiPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::ParallelPiPiInteractionConstraint.

ParallelPiPiInteractionScore.hpp
Definition of the class CDPL::Pharm::ParallelPiPiInteractionScore.

PatternBasedFeatureGenerator.hpp
Definition of the class CDPL::Pharm::PatternBasedFeatureGenerator.

ControlParameterDefault.hpp
Definition of constants in namespace CDPL::Pharm::ControlParameterDefault.

ControlParameterFunctions.hpp
Declaration of convenience functions for control-parameter handling.

ControlParameter.hpp
Definition of constants in namespace CDPL::Pharm::ControlParameter.

DataFormat.hpp
Provides the contents of namespace CDPL::Pharm::DataFormat.

FeatureFunctions.hpp
Declaration of functions that operate on Pharm::Feature instances.

FeatureType.hpp
Definition of constants in namespace CDPL::Pharm::FeatureType.

MoleculeFunctions.hpp
Declaration of functions that operate on Chem::Molecule instances.

ScreeningProcessor.hpp
Definition of the class CDPL::Pharm::ScreeningProcessor.

UtilityFunctions.hpp
Declaration of miscellaneous utility functions.

PharmacophoreAlignment.hpp
Definition of the class CDPL::Pharm::PharmacophoreAlignment.

PharmacophoreFitScore.hpp
Definition of the class CDPL::Pharm::PharmacophoreFitScore.

PharmacophoreFitScreeningScore.hpp
Definition of the class CDPL::Pharm::PharmacophoreFitScreeningScore.

PharmacophoreFunctions.hpp
Declaration of functions that operate on Pharm::Pharmacophore instances.

PharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::PharmacophoreGenerator.

PharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PharmacophoreReader.

Pharmacophore.hpp
Definition of the class CDPL::Pharm::Pharmacophore.

PosIonizableFeatureGenerator.hpp
Definition of the class CDPL::Pharm::PosIonizableFeatureGenerator.

ScreeningDBAccessor.hpp
Definition of the class CDPL::Pharm::ScreeningDBAccessor.

ScreeningDBCreator.hpp
Definition of the class CDPL::Pharm::ScreeningDBCreator.

SpatialFeatureMapping.hpp
Definition of the class CDPL::Pharm::SpatialFeatureMapping.

XBondAcceptorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::XBondAcceptorFeatureGenerator.

XBondDonorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::XBondDonorFeatureGenerator.

XBondingInteractionConstraint.hpp
Definition of the class CDPL::Pharm::XBondingInteractionConstraint.

XBondingInteractionScore.hpp
Definition of the class CDPL::Pharm::XBondingInteractionScore.