Chemical Data Processing Library C++ API - Version 1.1.1
HydrophobicAtomFeatureGenerator.hpp
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1 /*
2  * HydrophobicAtomFeatureGenerator.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_HYDROPHOBICATOMFEATUREGENERATOR_HPP
30 #define CDPL_PHARM_HYDROPHOBICATOMFEATUREGENERATOR_HPP
31 
32 #include "CDPL/Pharm/APIPrefix.hpp"
36 #include "CDPL/Chem/Fragment.hpp"
37 #include "CDPL/Util/Array.hpp"
38 
39 
40 namespace CDPL
41 {
42 
43  namespace Pharm
44  {
45 
46  class Feature;
47 
53  {
54 
55  public:
56  static constexpr double DEF_HYD_THRESHOLD = 0.5;
57  static constexpr double DEF_FEATURE_TOL = 1.5;
58  static constexpr unsigned int DEF_FEATURE_TYPE = FeatureType::HYDROPHOBIC;
59  static constexpr unsigned int DEF_FEATURE_GEOM = FeatureGeometry::SPHERE;
60 
61  typedef std::shared_ptr<HydrophobicAtomFeatureGenerator> SharedPointer;
62 
67 
73 
81 
86 
93  void setFeatureType(unsigned int type);
94 
100  unsigned int getFeatureType() const;
101 
108  void setFeatureTolerance(double tol);
109 
115  double getFeatureTolerance() const;
116 
123  void setFeatureGeometry(unsigned int geom);
124 
130  unsigned int getFeatureGeometry() const;
131 
137  void setHydrophobicityThreshold(double thresh);
138 
144 
151 
153 
154  private:
155  void addNonPatternFeatures(const Chem::MolecularGraph& molgraph, Pharmacophore& pharm);
156 
157  void emitFeature(const Chem::Atom&, Pharmacophore&, const Chem::Fragment::SharedPointer&, double) const;
158 
159  void getAtomHydrophobicities();
160 
161  Chem::Fragment::SharedPointer makeFragment(const Chem::Atom&) const;
162 
163  unsigned int featureType;
164  double featureTol;
165  unsigned int featureGeom;
166  double hydThreshold;
167  Util::DArray atomHydTable;
168  };
169  } // namespace Pharm
170 } // namespace CDPL
171 
172 #endif // CDPL_PHARM_HYDROPHOBICATOMFEATUREGENERATOR_HPP
CDPL::Pharm::HydrophobicAtomFeatureGenerator
HydrophobicAtomFeatureGenerator.
Definition: HydrophobicAtomFeatureGenerator.hpp:53
APIPrefix.hpp
Definition of the preprocessor macro CDPL_PHARM_API.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::HydrophobicAtomFeatureGenerator
HydrophobicAtomFeatureGenerator()
Constructs the HydrophobicAtomFeatureGenerator instance.
CDPL_PHARM_API
#define CDPL_PHARM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::HydrophobicAtomFeatureGenerator
HydrophobicAtomFeatureGenerator(const Chem::MolecularGraph &molgraph, Pharmacophore &pharm)
Perceives hydrophobic group features of the molecular graph a\ molgraph and adds them to the pharmaco...
CDPL::Pharm::FeatureGeometry::SPHERE
const unsigned int SPHERE
Definition: FeatureGeometry.hpp:47
CDPL::Pharm::FeatureGenerator::SharedPointer
std::shared_ptr< FeatureGenerator > SharedPointer
Definition: FeatureGenerator.hpp:60
CDPL::Chem::Atom
Atom.
Definition: Atom.hpp:52
CDPL::Pharm::HydrophobicAtomFeatureGenerator::setFeatureType
void setFeatureType(unsigned int type)
Specifies the value of the feature type property that has to be set on newly generated features.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::getFeatureType
unsigned int getFeatureType() const
Returns the value of the feature type property that gets set on newly generated features.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::setFeatureGeometry
void setFeatureGeometry(unsigned int geom)
Specifies the value of the feature geometry property that has to be set on newly generated features.
CDPL::Pharm::PatternBasedFeatureGenerator
PatternBasedFeatureGenerator.
Definition: PatternBasedFeatureGenerator.hpp:58
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
Array.hpp
Definition of the class CDPL::Util::Array.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::HydrophobicAtomFeatureGenerator
HydrophobicAtomFeatureGenerator(const HydrophobicAtomFeatureGenerator &gen)
Constructs a copy of the HydrophobicAtomFeatureGenerator instance gen.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::getFeatureGeometry
unsigned int getFeatureGeometry() const
Returns the value of the feature geometry property that gets set on newly generated features.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::SharedPointer
std::shared_ptr< HydrophobicAtomFeatureGenerator > SharedPointer
Definition: HydrophobicAtomFeatureGenerator.hpp:61
FeatureGeometry.hpp
Definition of constants in namespace CDPL::Pharm::FeatureGeometry.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::setFeatureTolerance
void setFeatureTolerance(double tol)
Specifies the value of the feature tolerance property that has to be set on newly generated features.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::~HydrophobicAtomFeatureGenerator
~HydrophobicAtomFeatureGenerator()
CDPL::Chem::Fragment::SharedPointer
std::shared_ptr< Fragment > SharedPointer
A reference-counted smart pointer [SHPTR] for dynamically allocated Fragment instances.
Definition: Fragment.hpp:61
CDPL::Pharm::Pharmacophore
Pharmacophore.
Definition: Pharmacophore.hpp:48
Fragment.hpp
Definition of the class CDPL::Chem::Fragment.
CDPL
The namespace of the Chemical Data Processing Library.
PatternBasedFeatureGenerator.hpp
Definition of the class CDPL::Pharm::PatternBasedFeatureGenerator.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::setHydrophobicityThreshold
void setHydrophobicityThreshold(double thresh)
Specifies the minimum hydrophobicity of an atom that is required for the generation of a new feature.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::clone
FeatureGenerator::SharedPointer clone() const
CDPL::Util::DArray
Array< double > DArray
An array of double precision floating-point numbers.
Definition: Array.hpp:587
CDPL::Pharm::HydrophobicAtomFeatureGenerator::operator=
HydrophobicAtomFeatureGenerator & operator=(const HydrophobicAtomFeatureGenerator &gen)
Copies the HydrophobicAtomFeatureGenerator instance gen.
CDPL::Pharm::FeatureType::HYDROPHOBIC
const unsigned int HYDROPHOBIC
Definition: Pharm/FeatureType.hpp:47
CDPL::Pharm::HydrophobicAtomFeatureGenerator::getHydrophobicityThreshold
double getHydrophobicityThreshold() const
Returns the minimum hydrophobicity of an atom that is required for the generation of a new feature.
FeatureType.hpp
Definition of constants in namespace CDPL::Pharm::FeatureType.
CDPL::Pharm::HydrophobicAtomFeatureGenerator::getFeatureTolerance
double getFeatureTolerance() const
Returns the value of the feature tolerance property that gets set on newly generated features.