Chemical Data Processing Library C++ API - Version 1.1.1
InteractionPharmacophoreGenerator.hpp
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1 /*
2  * InteractionPharmacophoreGenerator.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_INTERACTIONPHARMACOPHOREGENERATOR_HPP
30 #define CDPL_PHARM_INTERACTIONPHARMACOPHOREGENERATOR_HPP
31 
32 #include "CDPL/Pharm/APIPrefix.hpp"
38 #include "CDPL/Chem/Fragment.hpp"
39 
40 
41 namespace CDPL
42 {
43 
44  namespace Pharm
45  {
46 
51  {
52 
53  public:
59 
60  void setCoreEnvironmentRadius(double radius);
61 
62  double getCoreEnvironmentRadius() const;
63 
64  void addExclusionVolumes(bool add);
65 
66  bool exclusionVolumesAdded() const;
67 
69 
71 
73 
75 
77 
79 
81 
83 
85 
87 
88  void generate(const Chem::MolecularGraph& core, const Chem::MolecularGraph& tgt, Pharmacophore& ia_pharm,
89  bool extract_core_env, bool append = false);
90 
91  private:
92  DefaultPharmacophoreGenerator corePharmGen;
94  BasicPharmacophore corePharm;
95  BasicPharmacophore envPharm;
96  DefaultInteractionAnalyzer iaAnalyzer;
97  FeatureMapping iaMapping;
98  Chem::Fragment coreEnv;
99  Chem::Fragment iaEnvFeatureResAtoms;
100  Chem::Fragment iaEnvFeatureAtoms;
101  FeatureSet iaEnvFeatures;
102  double coreEnvRadius;
103  bool addXVolumes;
104  };
105  } // namespace Pharm
106 } // namespace CDPL
107 
108 #endif // CDPL_PHARM_INTERACTIONPHARMACOPHOREGENERATOR_HPP
APIPrefix.hpp
Definition of the preprocessor macro CDPL_PHARM_API.
FeatureMapping.hpp
Definition of the type CDPL::Pharm::FeatureMapping.
CDPL::Pharm::InteractionPharmacophoreGenerator::addExclusionVolumes
void addExclusionVolumes(bool add)
CDPL_PHARM_API
#define CDPL_PHARM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Pharm::FeatureMapping
A data type for the storage and lookup of arbitrary feature to feature mappings.
Definition: FeatureMapping.hpp:54
CDPL::Pharm::InteractionPharmacophoreGenerator::getCoreEnvironment
const Chem::Fragment & getCoreEnvironment() const
CDPL::Pharm::InteractionPharmacophoreGenerator::exclusionVolumesAdded
bool exclusionVolumesAdded() const
CDPL::Pharm::InteractionPharmacophoreGenerator
InteractionPharmacophoreGenerator.
Definition: InteractionPharmacophoreGenerator.hpp:51
CDPL::Pharm::InteractionPharmacophoreGenerator::getCorePharmacophoreGenerator
const PharmacophoreGenerator & getCorePharmacophoreGenerator() const
CDPL::Pharm::InteractionAnalyzer
InteractionAnalyzer.
Definition: InteractionAnalyzer.hpp:53
CDPL::Pharm::DefaultPharmacophoreGenerator::DEFAULT_CONFIG
@ DEFAULT_CONFIG
Default configuration.
Definition: DefaultPharmacophoreGenerator.hpp:71
CDPL::Chem::Fragment
Fragment.
Definition: Fragment.hpp:52
BasicPharmacophore.hpp
Definition of the class CDPL::Pharm::BasicPharmacophore.
CDPL::Pharm::DefaultInteractionAnalyzer
DefaultInteractionAnalyzer.
Definition: DefaultInteractionAnalyzer.hpp:46
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
CDPL::Pharm::InteractionPharmacophoreGenerator::InteractionPharmacophoreGenerator
InteractionPharmacophoreGenerator(DefaultPharmacophoreGenerator::Configuration core_ph4_gen_cfg=DefaultPharmacophoreGenerator::DEFAULT_CONFIG, DefaultPharmacophoreGenerator::Configuration env_ph4_gen_cfg=DefaultPharmacophoreGenerator::DEFAULT_CONFIG)
Constructs the InteractionPharmacophoreGenerator instance.
CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionAnalyzer
const InteractionAnalyzer & getInteractionAnalyzer() const
CDPL::Pharm::Pharmacophore
Pharmacophore.
Definition: Pharmacophore.hpp:48
Fragment.hpp
Definition of the class CDPL::Chem::Fragment.
CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophore
const Pharmacophore & getEnvironmentPharmacophore() const
DefaultInteractionAnalyzer.hpp
Definition of the class CDPL::Pharm::DefaultInteractionAnalyzer.
CDPL::Pharm::BasicPharmacophore
BasicPharmacophore.
Definition: BasicPharmacophore.hpp:52
CDPL::Pharm::FeatureSet
FeatureSet.
Definition: FeatureSet.hpp:52
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Pharm::InteractionPharmacophoreGenerator::getCoreEnvironmentRadius
double getCoreEnvironmentRadius() const
CDPL::Pharm::PharmacophoreGenerator
PharmacophoreGenerator.
Definition: PharmacophoreGenerator.hpp:49
DefaultPharmacophoreGenerator.hpp
Definition of the class CDPL::Pharm::DefaultPharmacophoreGenerator.
FeatureSet.hpp
Definition of the class CDPL::Pharm::FeatureSet.
CDPL::Pharm::InteractionPharmacophoreGenerator::generate
void generate(const Chem::MolecularGraph &core, const Chem::MolecularGraph &tgt, Pharmacophore &ia_pharm, bool extract_core_env, bool append=false)
CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophoreGenerator
const PharmacophoreGenerator & getEnvironmentPharmacophoreGenerator() const
CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionAnalyzer
InteractionAnalyzer & getInteractionAnalyzer()
CDPL::Pharm::DefaultPharmacophoreGenerator
DefaultPharmacophoreGenerator.
Definition: DefaultPharmacophoreGenerator.hpp:48
CDPL::Pharm::InteractionPharmacophoreGenerator::setCoreEnvironmentRadius
void setCoreEnvironmentRadius(double radius)
CDPL::Pharm::InteractionPharmacophoreGenerator::getInteractionMapping
const FeatureMapping & getInteractionMapping() const
CDPL::Pharm::InteractionPharmacophoreGenerator::getEnvironmentPharmacophoreGenerator
PharmacophoreGenerator & getEnvironmentPharmacophoreGenerator()
CDPL::Pharm::InteractionPharmacophoreGenerator::getCorePharmacophoreGenerator
PharmacophoreGenerator & getCorePharmacophoreGenerator()
CDPL::Pharm::DefaultPharmacophoreGenerator::Configuration
Configuration
Flags controlling feature generation.
Definition: DefaultPharmacophoreGenerator.hpp:55
CDPL::Pharm::InteractionPharmacophoreGenerator::getCorePharmacophore
const Pharmacophore & getCorePharmacophore() const