Chemical Data Processing Library C++ API - Version 1.1.1
Pharm.hpp
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1 /*
2  * Pharm.hpp
3  *
4  * This file is part of the Chemical Data Processing Toolkit
5  *
6  * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
7  *
8  * This library is free software; you can redistribute it and/or
9  * modify it under the terms of the GNU Lesser General Public
10  * License as published by the Free Software Foundation; either
11  * version 2 of the License, or (at your option) any later version.
12  *
13  * This library is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16  * Lesser General Public License for more details.
17  *
18  * You should have received a copy of the GNU Lesser General Public License
19  * along with this library; see the file COPYING. If not, write to
20  * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
21  * Boston, MA 02111-1307, USA.
22  */
23 
29 #ifndef CDPL_PHARM_HPP
30 #define CDPL_PHARM_HPP
31 
32 #include "CDPL/Pharm/Feature.hpp"
33 #include "CDPL/Pharm/BasicFeature.hpp"
34 #include "CDPL/Pharm/FeatureContainer.hpp"
35 #include "CDPL/Pharm/FeatureSet.hpp"
36 #include "CDPL/Pharm/Pharmacophore.hpp"
37 #include "CDPL/Pharm/BasicPharmacophore.hpp"
38 #include "CDPL/Pharm/FeatureMapping.hpp"
39 #include "CDPL/Pharm/FeatureTypeHistogram.hpp"
40 #include "CDPL/Pharm/Feature3DCoordinatesFunction.hpp"
41 #include "CDPL/Pharm/FeatureContainerProperty.hpp"
42 #include "CDPL/Pharm/FeatureProperty.hpp"
43 #include "CDPL/Pharm/FeatureContainerPropertyDefault.hpp"
44 #include "CDPL/Pharm/FeaturePropertyDefault.hpp"
45 #include "CDPL/Pharm/ControlParameter.hpp"
46 #include "CDPL/Pharm/ControlParameterDefault.hpp"
47 #include "CDPL/Pharm/DataFormat.hpp"
48 #include "CDPL/Pharm/FeatureType.hpp"
49 #include "CDPL/Pharm/FeatureGeometry.hpp"
50 #include "CDPL/Pharm/FeatureGenerator.hpp"
51 #include "CDPL/Pharm/PatternBasedFeatureGenerator.hpp"
52 #include "CDPL/Pharm/AromaticFeatureGenerator.hpp"
53 #include "CDPL/Pharm/HydrophobicFeatureGenerator.hpp"
54 #include "CDPL/Pharm/HydrophobicAtomFeatureGenerator.hpp"
55 #include "CDPL/Pharm/HBondAcceptorFeatureGenerator.hpp"
56 #include "CDPL/Pharm/HBondDonorFeatureGenerator.hpp"
57 #include "CDPL/Pharm/PosIonizableFeatureGenerator.hpp"
58 #include "CDPL/Pharm/NegIonizableFeatureGenerator.hpp"
59 #include "CDPL/Pharm/XBondAcceptorFeatureGenerator.hpp"
60 #include "CDPL/Pharm/XBondDonorFeatureGenerator.hpp"
61 #include "CDPL/Pharm/PharmacophoreGenerator.hpp"
62 #include "CDPL/Pharm/DefaultPharmacophoreGenerator.hpp"
63 #include "CDPL/Pharm/InteractionAnalyzer.hpp"
64 #include "CDPL/Pharm/DefaultInteractionAnalyzer.hpp"
65 #include "CDPL/Pharm/InteractionConstraintConnector.hpp"
66 #include "CDPL/Pharm/FeatureDistanceConstraint.hpp"
67 #include "CDPL/Pharm/HydrophobicInteractionConstraint.hpp"
68 #include "CDPL/Pharm/IonicInteractionConstraint.hpp"
69 #include "CDPL/Pharm/OrthogonalPiPiInteractionConstraint.hpp"
70 #include "CDPL/Pharm/ParallelPiPiInteractionConstraint.hpp"
71 #include "CDPL/Pharm/CationPiInteractionConstraint.hpp"
72 #include "CDPL/Pharm/HBondingInteractionConstraint.hpp"
73 #include "CDPL/Pharm/XBondingInteractionConstraint.hpp"
74 #include "CDPL/Pharm/InteractionPharmacophoreGenerator.hpp"
75 #include "CDPL/Pharm/FeatureInteractionScore.hpp"
76 #include "CDPL/Pharm/FeatureInteractionScoreCombiner.hpp"
77 #include "CDPL/Pharm/FeatureDistanceScore.hpp"
78 #include "CDPL/Pharm/HydrophobicInteractionScore.hpp"
79 #include "CDPL/Pharm/IonicInteractionScore.hpp"
80 #include "CDPL/Pharm/HBondingInteractionScore.hpp"
81 #include "CDPL/Pharm/XBondingInteractionScore.hpp"
82 #include "CDPL/Pharm/OrthogonalPiPiInteractionScore.hpp"
83 #include "CDPL/Pharm/ParallelPiPiInteractionScore.hpp"
84 #include "CDPL/Pharm/CationPiInteractionScore.hpp"
85 #include "CDPL/Pharm/SpatialFeatureMapping.hpp"
86 #include "CDPL/Pharm/PharmacophoreAlignment.hpp"
87 #include "CDPL/Pharm/FeatureTypeMatchFunctor.hpp"
88 #include "CDPL/Pharm/FeaturePairDistanceMatchFunctor.hpp"
89 #include "CDPL/Pharm/FeaturePositionMatchFunctor.hpp"
90 #include "CDPL/Pharm/FeatureGeometryMatchFunctor.hpp"
91 #include "CDPL/Pharm/PharmacophoreFitScore.hpp"
92 #include "CDPL/Pharm/CDFPharmacophoreInputHandler.hpp"
93 #include "CDPL/Pharm/PMLPharmacophoreInputHandler.hpp"
94 #include "CDPL/Pharm/CDFFeatureContainerOutputHandler.hpp"
95 #include "CDPL/Pharm/PMLFeatureContainerOutputHandler.hpp"
96 #include "CDPL/Pharm/CDFPharmacophoreReader.hpp"
97 #include "CDPL/Pharm/PMLPharmacophoreReader.hpp"
98 #include "CDPL/Pharm/CDFFeatureContainerWriter.hpp"
99 #include "CDPL/Pharm/PMLFeatureContainerWriter.hpp"
100 #include "CDPL/Pharm/ScreeningDBCreator.hpp"
101 #include "CDPL/Pharm/ScreeningDBAccessor.hpp"
102 #include "CDPL/Pharm/ScreeningProcessor.hpp"
103 #include "CDPL/Pharm/PharmacophoreFitScreeningScore.hpp"
104 #include "CDPL/Pharm/MoleculeFunctions.hpp"
105 #include "CDPL/Pharm/PharmacophoreFunctions.hpp"
106 #include "CDPL/Pharm/FeatureFunctions.hpp"
107 #include "CDPL/Pharm/FeatureContainerFunctions.hpp"
108 #include "CDPL/Pharm/FeatureSetFunctions.hpp"
109 #include "CDPL/Pharm/ControlParameterFunctions.hpp"
110 #include "CDPL/Pharm/UtilityFunctions.hpp"
111 #include "CDPL/Pharm/FileScreeningHitCollector.hpp"
112 #include "CDPL/Pharm/CDFGZPharmacophoreInputHandler.hpp"
113 #include "CDPL/Pharm/CDFBZ2PharmacophoreInputHandler.hpp"
114 #include "CDPL/Pharm/CDFGZFeatureContainerOutputHandler.hpp"
115 #include "CDPL/Pharm/CDFBZ2FeatureContainerOutputHandler.hpp"
116 #include "CDPL/Pharm/CDFGZPharmacophoreReader.hpp"
117 #include "CDPL/Pharm/CDFBZ2PharmacophoreReader.hpp"
118 #include "CDPL/Pharm/CDFGZFeatureContainerWriter.hpp"
119 #include "CDPL/Pharm/CDFBZ2FeatureContainerWriter.hpp"
120 #include "CDPL/Pharm/PharmacophoreReader.hpp"
121 #include "CDPL/Pharm/FeatureContainerWriter.hpp"
122 # include "CDPL/Pharm/PSDPharmacophoreInputHandler.hpp"
123 # include "CDPL/Pharm/PSDMoleculeInputHandler.hpp"
124 # include "CDPL/Pharm/PSDMolecularGraphOutputHandler.hpp"
125 # include "CDPL/Pharm/PSDPharmacophoreReader.hpp"
126 # include "CDPL/Pharm/PSDMoleculeReader.hpp"
127 # include "CDPL/Pharm/PSDMolecularGraphWriter.hpp"
128 # include "CDPL/Pharm/PSDScreeningDBCreator.hpp"
129 # include "CDPL/Pharm/PSDScreeningDBAccessor.hpp"
130 
131 #endif // CDPL_PHARM_HPP
FeatureDistanceScore.hpp
Definition of the class CDPL::Pharm::FeatureDistanceScore.
PSDMolecularGraphWriter.hpp
Definition of the class CDPL::Pharm::PSDMolecularGraphWriter.
FeatureMapping.hpp
Definition of the type CDPL::Pharm::FeatureMapping.
FeatureGeometryMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeatureGeometryMatchFunctor.
FeatureInteractionScore.hpp
Definition of the class CDPL::Pharm::FeatureInteractionScore.
CDFGZFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFGZFeatureContainerOutputHandler.
FeatureFunctions.hpp
Declaration of functions that operate on Pharm::Feature instances.
Feature.hpp
Definition of the class CDPL::Pharm::Feature.
PosIonizableFeatureGenerator.hpp
Definition of the class CDPL::Pharm::PosIonizableFeatureGenerator.
ControlParameter.hpp
Definition of constants in namespace CDPL::Pharm::ControlParameter.
CDFBZ2FeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFBZ2FeatureContainerWriter.
OrthogonalPiPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::OrthogonalPiPiInteractionConstraint.
CDFPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFPharmacophoreInputHandler.
CDFGZPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFGZPharmacophoreReader.
XBondDonorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::XBondDonorFeatureGenerator.
CDFGZFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFGZFeatureContainerWriter.
XBondingInteractionScore.hpp
Definition of the class CDPL::Pharm::XBondingInteractionScore.
FeatureContainer.hpp
Definition of the class CDPL::Pharm::FeatureContainer.
PharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PharmacophoreReader.
ScreeningProcessor.hpp
Definition of the class CDPL::Pharm::ScreeningProcessor.
CationPiInteractionScore.hpp
Definition of the class CDPL::Pharm::CationPiInteractionScore.
OrthogonalPiPiInteractionScore.hpp
Definition of the class CDPL::Pharm::OrthogonalPiPiInteractionScore.
HBondAcceptorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HBondAcceptorFeatureGenerator.
BasicPharmacophore.hpp
Definition of the class CDPL::Pharm::BasicPharmacophore.
InteractionConstraintConnector.hpp
Definition of the class CDPL::Pharm::InteractionConstraintConnector.
ControlParameterDefault.hpp
Definition of constants in namespace CDPL::Pharm::ControlParameterDefault.
AromaticFeatureGenerator.hpp
Definition of the class CDPL::Pharm::AromaticFeatureGenerator.
XBondingInteractionConstraint.hpp
Definition of the class CDPL::Pharm::XBondingInteractionConstraint.
FeatureProperty.hpp
Definition of constants in namespace CDPL::Pharm::FeatureProperty.
FileScreeningHitCollector.hpp
Definition of the class CDPL::Pharm::FileScreeningHitCollector.
ScreeningDBCreator.hpp
Definition of the class CDPL::Pharm::ScreeningDBCreator.
HydrophobicInteractionScore.hpp
Definition of the class CDPL::Pharm::HydrophobicInteractionScore.
CDFGZPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFGZPharmacophoreInputHandler.
MoleculeFunctions.hpp
Declaration of functions that operate on Chem::Molecule instances.
FeatureGeometry.hpp
Definition of constants in namespace CDPL::Pharm::FeatureGeometry.
PharmacophoreFitScreeningScore.hpp
Definition of the class CDPL::Pharm::PharmacophoreFitScreeningScore.
HydrophobicAtomFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HydrophobicAtomFeatureGenerator.
IonicInteractionConstraint.hpp
Definition of the class CDPL::Pharm::IonicInteractionConstraint.
CDFFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFFeatureContainerOutputHandler.
ParallelPiPiInteractionScore.hpp
Definition of the class CDPL::Pharm::ParallelPiPiInteractionScore.
FeatureSetFunctions.hpp
Declaration of functions that operate on Pharm::FeatureSet instances.
PSDMoleculeInputHandler.hpp
Definition of the class CDPL::Pharm::PSDMoleculeInputHandler.
PMLPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::PMLPharmacophoreInputHandler.
FeatureContainerFunctions.hpp
Declaration of functions that operate on Pharm::FeatureContainer instances.
PharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::PharmacophoreGenerator.
IonicInteractionScore.hpp
Definition of the class CDPL::Pharm::IonicInteractionScore.
PSDScreeningDBAccessor.hpp
Definition of the class CDPL::Pharm::PSDScreeningDBAccessor.
PharmacophoreFunctions.hpp
Declaration of functions that operate on Pharm::Pharmacophore instances.
HBondingInteractionConstraint.hpp
Definition of the class CDPL::Pharm::HBondingInteractionConstraint.
PSDMolecularGraphOutputHandler.hpp
Definition of the class CDPL::Pharm::PSDMolecularGraphOutputHandler.
InteractionPharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::InteractionPharmacophoreGenerator.
PMLFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::PMLFeatureContainerWriter.
PSDPharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::PSDPharmacophoreInputHandler.
NegIonizableFeatureGenerator.hpp
Definition of the class CDPL::Pharm::NegIonizableFeatureGenerator.
FeatureTypeHistogram.hpp
Definition of the type CDPL::Pharm::FeatureTypeHistogram.
FeatureInteractionScoreCombiner.hpp
Definition of the class CDPL::Pharm::FeatureInteractionScoreCombiner.
DefaultInteractionAnalyzer.hpp
Definition of the class CDPL::Pharm::DefaultInteractionAnalyzer.
CDFFeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::CDFFeatureContainerWriter.
CationPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::CationPiInteractionConstraint.
CDFBZ2FeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::CDFBZ2FeatureContainerOutputHandler.
XBondAcceptorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::XBondAcceptorFeatureGenerator.
ControlParameterFunctions.hpp
Declaration of convenience functions for control-parameter handling.
CDFBZ2PharmacophoreInputHandler.hpp
Definition of the class CDPL::Pharm::CDFBZ2PharmacophoreInputHandler.
DefaultPharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::DefaultPharmacophoreGenerator.
PMLFeatureContainerOutputHandler.hpp
Definition of the class CDPL::Pharm::PMLFeatureContainerOutputHandler.
PMLPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PMLPharmacophoreReader.
FeatureSet.hpp
Definition of the class CDPL::Pharm::FeatureSet.
PSDPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::PSDPharmacophoreReader.
PharmacophoreFitScore.hpp
Definition of the class CDPL::Pharm::PharmacophoreFitScore.
InteractionAnalyzer.hpp
Definition of the class CDPL::Pharm::InteractionAnalyzer.
PSDScreeningDBCreator.hpp
Definition of the class CDPL::Pharm::PSDScreeningDBCreator.
Pharmacophore.hpp
Definition of the class CDPL::Pharm::Pharmacophore.
FeaturePairDistanceMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeaturePairDistanceMatchFunctor.
HydrophobicFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HydrophobicFeatureGenerator.
FeatureTypeMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeatureTypeMatchFunctor.
HydrophobicInteractionConstraint.hpp
Definition of the class CDPL::Pharm::HydrophobicInteractionConstraint.
PatternBasedFeatureGenerator.hpp
Definition of the class CDPL::Pharm::PatternBasedFeatureGenerator.
BasicFeature.hpp
Definition of the class CDPL::Pharm::BasicFeature.
FeatureContainerPropertyDefault.hpp
Definition of constants in namespace CDPL::Pharm::FeatureContainerPropertyDefault.
FeatureContainerWriter.hpp
Definition of the class CDPL::Pharm::FeatureContainerWriter.
PharmacophoreAlignment.hpp
Definition of the class CDPL::Pharm::PharmacophoreAlignment.
FeatureDistanceConstraint.hpp
Definition of the class CDPL::Pharm::FeatureDistanceConstraint.
ScreeningDBAccessor.hpp
Definition of the class CDPL::Pharm::ScreeningDBAccessor.
FeatureContainerProperty.hpp
Definition of constants in namespace CDPL::Pharm::FeatureContainerProperty.
FeatureGenerator.hpp
Definition of the class CDPL::Pharm::FeatureGenerator.
CDFBZ2PharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFBZ2PharmacophoreReader.
FeaturePositionMatchFunctor.hpp
Definition of the class CDPL::Pharm::FeaturePositionMatchFunctor.
DataFormat.hpp
Provides the contents of namespace CDPL::Pharm::DataFormat.
PSDMoleculeReader.hpp
Definition of the class CDPL::Pharm::PSDMoleculeReader.
UtilityFunctions.hpp
Declaration of miscellaneous utility functions.
HBondDonorFeatureGenerator.hpp
Definition of the class CDPL::Pharm::HBondDonorFeatureGenerator.
CDFPharmacophoreReader.hpp
Definition of the class CDPL::Pharm::CDFPharmacophoreReader.
FeatureType.hpp
Definition of constants in namespace CDPL::Pharm::FeatureType.
SpatialFeatureMapping.hpp
Definition of the class CDPL::Pharm::SpatialFeatureMapping.
Feature3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Pharm::Feature 3D-coordinates fun...
HBondingInteractionScore.hpp
Definition of the class CDPL::Pharm::HBondingInteractionScore.
FeaturePropertyDefault.hpp
Definition of constants in namespace CDPL::Pharm::FeaturePropertyDefault.
ParallelPiPiInteractionConstraint.hpp
Definition of the class CDPL::Pharm::ParallelPiPiInteractionConstraint.
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