Chemical Data Processing Library C++ API - Version 1.1.1
ConfGen/MolecularGraphFunctions.hpp
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1 /*
2  * MolecularGraphFunctions.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_MOLECULARGRAPHFUNCTIONS_HPP
30 #define CDPL_CONFGEN_MOLECULARGRAPHFUNCTIONS_HPP
31 
32 #include <cstddef>
33 
36 #include "CDPL/Util/BitSet.hpp"
37 
38 
39 namespace CDPL
40 {
41 
42  namespace Chem
43  {
44 
45  class MolecularGraph;
46  class Fragment;
47  class SubstructureSearch;
48  class CommonConnectedSubstructureSearch;
49  }
50 
51  namespace ForceField
52  {
53 
54  class MMFF94InteractionData;
55  class MMFF94InteractionParameterizer;
56  } // namespace ForceField
57 
58  namespace ConfGen
59  {
60 
61  CDPL_CONFGEN_API std::size_t createFragmentLinkBondMask(const Chem::MolecularGraph& molgraph, Util::BitSet& bond_mask, bool reset = true);
62 
64  bool het_h_rotors, bool reset = true);
65 
66  CDPL_CONFGEN_API std::size_t createRotatableBondMask(const Chem::MolecularGraph& molgraph, const Util::BitSet& excl_bond_mask,
67  Util::BitSet& bond_mask, bool het_h_rotors, bool reset = true);
68 
69  CDPL_CONFGEN_API std::size_t getRotatableBondCount(const Chem::MolecularGraph& molgraph, bool het_h_rotors);
70 
72 
75  ForceField::MMFF94InteractionData& param_data, unsigned int ff_type,
76  bool strict, double estat_de_const, double estat_dist_expo);
77 
79 
83  CDPL_CONFGEN_API std::size_t setupFixedSubstructureData(const Chem::SubstructureSearch& sub_search, std::size_t max_num_matches,
84  Chem::MolecularGraph& molgraph, Chem::Fragment& fixed_substr,
85  Math::Vector3DArray* fixed_substr_coords);
90  std::size_t max_num_matches, Chem::MolecularGraph& molgraph,
91  Chem::Fragment& fixed_substr, Math::Vector3DArray* fixed_substr_coords);
96 
101 
102  } // namespace ConfGen
103 } // namespace CDPL
104 
105 #endif // CDPL_CONFGEN_MOLECULARGRAPHFUNCTIONS_HPP
CDPL::ConfGen::createRotatableBondMask
CDPL_CONFGEN_API std::size_t createRotatableBondMask(const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool het_h_rotors, bool reset=true)
CDPL::ConfGen::setupFixedSubstructureData
CDPL_CONFGEN_API std::size_t setupFixedSubstructureData(const Chem::SubstructureSearch &sub_search, std::size_t max_num_matches, Chem::MolecularGraph &molgraph, Chem::Fragment &fixed_substr, Math::Vector3DArray *fixed_substr_coords)
CDPL::ConfGen::ConformerDataArray
std::vector< ConformerData::SharedPointer > ConformerDataArray
A data type for the storage of dyn. allocated ConfGen::ConformerData objects.
Definition: ConformerDataArray.hpp:46
CDPL::ForceField::MMFF94InteractionData
Definition: MMFF94InteractionData.hpp:51
CDPL::ConfGen::initFixedSubstructureTemplate
CDPL_CONFGEN_API void initFixedSubstructureTemplate(Chem::MolecularGraph &molgraph, bool init_match_expr)
CDPL::Chem::SubstructureSearch
SubstructureSearch.
Definition: SubstructureSearch.hpp:64
CDPL::ConfGen::setConformers
CDPL_CONFGEN_API void setConformers(Chem::MolecularGraph &molgraph, const ConformerDataArray &conf_array)
CDPL::Util::BitSet
boost::dynamic_bitset BitSet
A dynamic bitset class.
Definition: BitSet.hpp:46
CDPL::Chem::Fragment
Fragment.
Definition: Fragment.hpp:52
ConformerDataArray.hpp
Definition of the type CDPL::ConfGen::ConformerDataArray.
CDPL::Chem::CommonConnectedSubstructureSearch
CommonConnectedSubstructureSearch.
Definition: CommonConnectedSubstructureSearch.hpp:62
VectorArray< Vector3D >
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
BitSet.hpp
Definition of the type CDPL::Util::BitSet.
CDPL::ConfGen::initFixedSubstructurePattern
CDPL_CONFGEN_API bool initFixedSubstructurePattern(Chem::MolecularGraph &molgraph, const Chem::MolecularGraph *tmplt)
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CONFGEN_API.
CDPL_CONFGEN_API
#define CDPL_CONFGEN_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::ConfGen::perceiveFragmentType
CDPL_CONFGEN_API unsigned int perceiveFragmentType(const Chem::MolecularGraph &molgraph)
CDPL::ConfGen::getRotatableBondCount
CDPL_CONFGEN_API std::size_t getRotatableBondCount(const Chem::MolecularGraph &molgraph, bool het_h_rotors)
CDPL::ConfGen::parameterizeMMFF94Interactions
CDPL_CONFGEN_API unsigned int parameterizeMMFF94Interactions(const Chem::MolecularGraph &molgraph, ForceField::MMFF94InteractionParameterizer &parameterizer, ForceField::MMFF94InteractionData &param_data, unsigned int ff_type, bool strict, double estat_de_const, double estat_dist_expo)
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::ConfGen::createFragmentLinkBondMask
CDPL_CONFGEN_API std::size_t createFragmentLinkBondMask(const Chem::MolecularGraph &molgraph, Util::BitSet &bond_mask, bool reset=true)
CDPL::ForceField::MMFF94InteractionParameterizer
Definition: MMFF94InteractionParameterizer.hpp:88