Chemical Data Processing Library C++ API - Version 1.1.1
DGStructureGenerator.hpp
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1 /*
2  * DGStructureGenerator.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_CONFGEN_DGSTRUCTUREGENERATOR_HPP
30 #define CDPL_CONFGEN_DGSTRUCTUREGENERATOR_HPP
31 
32 #include <cstddef>
33 
34 #include <boost/random/mersenne_twister.hpp>
35 
40 
41 
42 namespace CDPL
43 {
44 
45  namespace Chem
46  {
47 
48  class FragmentList;
49  }
50 
51  namespace ConfGen
52  {
53 
55  {
56 
57  public:
59 
61 
63 
65 
66  void setup(const Chem::MolecularGraph& molgraph);
67 
68  void setup(const Chem::MolecularGraph& molgraph, const ForceField::MMFF94InteractionData& ia_data);
69 
70  /*
71  * \since 1.1
72  */
73  void setup(const Chem::MolecularGraph& molgraph, const Chem::FragmentList& fixed_substr_frags,
74  const Math::Vector3DArray& fixed_substr_coords);
75 
76  /*
77  * \since 1.1
78  */
79  void setup(const Chem::MolecularGraph& molgraph, const ForceField::MMFF94InteractionData& ia_data,
80  const Chem::FragmentList& fixed_substr_frags, const Math::Vector3DArray& fixed_substr_coords);
81 
83 
86 
87  std::size_t getNumAtomStereoCenters() const;
88  std::size_t getNumBondStereoCenters() const;
89 
91 
92  private:
93  void setup(const Chem::MolecularGraph& molgraph, const ForceField::MMFF94InteractionData* ia_data,
94  const Chem::FragmentList* fixed_substr_frags, const Math::Vector3DArray* fixed_substr_coords);
95 
96  typedef boost::random::mt11213b RandNumEngine;
97 
98  const Chem::MolecularGraph* molGraph;
99  const Chem::FragmentList* fixedSubstructFrags;
100  const Math::Vector3DArray* fixedSubstructCoords;
101  Math::Vector3DArray fixedSubstructFragCtrs;
102  DGConstraintGenerator dgConstraintsGen;
103  Util::DG3DCoordinatesGenerator phase1CoordsGen;
104  Util::DG3DCoordinatesGenerator phase2CoordsGen;
105  RandNumEngine randomEngine;
107  };
108  } // namespace ConfGen
109 } // namespace CDPL
110 
111 #endif // CDPL_CONFGEN_DGSTRUCTUREGENERATOR_HPP
DGConstraintGenerator.hpp
Definition of the class CDPL::ConfGen::DGConstraintGenerator.
CDPL::ConfGen::DGStructureGenerator::getExcludedHydrogenMask
const Util::BitSet & getExcludedHydrogenMask() const
CDPL::ForceField::MMFF94InteractionData
Definition: MMFF94InteractionData.hpp:51
CDPL::Util::DG3DCoordinatesGenerator
DGCoordinatesGenerator< 3, double > DG3DCoordinatesGenerator
Definition: DGCoordinatesGenerator.hpp:296
CDPL::ConfGen::DGStructureGenerator::generate
bool generate(Math::Vector3DArray &coords)
CDPL::Util::BitSet
boost::dynamic_bitset BitSet
A dynamic bitset class.
Definition: BitSet.hpp:46
CDPL::ConfGen::DGStructureGenerator::getSettings
DGStructureGeneratorSettings & getSettings()
CDPL::ConfGen::DGStructureGenerator::getNumBondStereoCenters
std::size_t getNumBondStereoCenters() const
VectorArray< Vector3D >
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
DGStructureGeneratorSettings.hpp
Definition of the class CDPL::ConfGen::DGStructureGeneratorSettings.
CDPL::ConfGen::DGStructureGenerator::checkBondConfigurations
bool checkBondConfigurations(Math::Vector3DArray &coords) const
CDPL::ConfGen::DGStructureGenerator::setup
void setup(const Chem::MolecularGraph &molgraph)
CDPL::ConfGen::DGStructureGeneratorSettings
Definition: DGStructureGeneratorSettings.hpp:43
CDPL::ConfGen::DGStructureGenerator::checkAtomConfigurations
bool checkAtomConfigurations(Math::Vector3DArray &coords) const
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CONFGEN_API.
CDPL::ConfGen::DGStructureGenerator::DGStructureGenerator
DGStructureGenerator()
CDPL_CONFGEN_API
#define CDPL_CONFGEN_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Chem::FragmentList
A data type for the storage of Chem::Fragment objects.
Definition: FragmentList.hpp:49
CDPL::ConfGen::DGStructureGenerator::setup
void setup(const Chem::MolecularGraph &molgraph, const Chem::FragmentList &fixed_substr_frags, const Math::Vector3DArray &fixed_substr_coords)
CDPL::ConfGen::DGConstraintGenerator
Definition: DGConstraintGenerator.hpp:68
CDPL::ConfGen::DGStructureGenerator::getNumAtomStereoCenters
std::size_t getNumAtomStereoCenters() const
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::ConfGen::DGStructureGenerator::setup
void setup(const Chem::MolecularGraph &molgraph, const ForceField::MMFF94InteractionData &ia_data)
CDPL::ConfGen::DGStructureGenerator::setup
void setup(const Chem::MolecularGraph &molgraph, const ForceField::MMFF94InteractionData &ia_data, const Chem::FragmentList &fixed_substr_frags, const Math::Vector3DArray &fixed_substr_coords)
CDPL::ConfGen::DGStructureGenerator
Definition: DGStructureGenerator.hpp:55
DGCoordinatesGenerator.hpp
Implementation of a distance geometry based coordinates generator.
CDPL::ConfGen::DGStructureGenerator::getConstraintGenerator
const DGConstraintGenerator & getConstraintGenerator() const
CDPL::ConfGen::DGStructureGenerator::getSettings
const DGStructureGeneratorSettings & getSettings() const