Chemical Data Processing Library C++ API - Version 1.1.1
MMFF94AngleBendingInteractionParameterizer.hpp
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1 /*
2  * MMFF94AngleBendingInteractionParameterizer.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_FORCEFIELD_MMFF94ANGLEBENDINGINTERACTIONPARAMETERIZER_HPP
30 #define CDPL_FORCEFIELD_MMFF94ANGLEBENDINGINTERACTIONPARAMETERIZER_HPP
31 
32 #include <vector>
33 #include <cstddef>
34 #include <memory>
35 
46 
47 
48 namespace CDPL
49 {
50 
51  namespace Chem
52  {
53 
54  class MolecularGraph;
55  class Atom;
56  class Bond;
57  } // namespace Chem
58 
59  namespace ForceField
60  {
61 
63  {
64 
65  public:
66  typedef std::shared_ptr<MMFF94AngleBendingInteractionParameterizer> SharedPointer;
67 
69 
72  bool strict);
73 
75 
77 
79 
81 
83 
85 
87 
89 
91 
92  void parameterize(const Chem::MolecularGraph& molgraph, MMFF94AngleBendingInteractionList& ia_list, bool strict);
93 
94  private:
95  void getParameters(const Chem::MolecularGraph& molgraph, const Chem::Atom& term_atom1, const Chem::Atom& ctr_atom,
96  const Chem::Atom& term_atom2, const Chem::Bond& term_atom1_bnd, const Chem::Bond& term_atom2_bnd,
97  unsigned int& angle_type_idx, bool& linear, double& force_const, double& ref_angle, bool strict) const;
98 
99  void getParameters(const Chem::MolecularGraph& molgraph, const Chem::Atom& term_atom1, unsigned int term_atom1_type, const Chem::Atom& ctr_atom,
100  unsigned int ctr_atom_type, const Chem::Atom& term_atom2, unsigned int term_atom2_type, const Chem::Bond& term_atom1_bnd,
101  const Chem::Bond& term_atom2_bnd, unsigned int& angle_type_idx, bool& linear, double& force_const, double& ref_angle, bool strict) const;
102 
103  std::size_t getSizeOfContaining3Or4Ring(const Chem::MolecularGraph& molgraph, const Chem::Atom& term_atom1,
104  const Chem::Atom& ctr_atom, const Chem::Atom& term_atom2) const;
105 
129  unsigned int getAngleTypeIndex(const Chem::Bond& bond1, const Chem::Bond& bond2, std::size_t r_size) const;
130 
131  typedef std::vector<const Chem::Atom*> AtomList;
132  typedef std::vector<const Chem::Bond*> BondList;
133 
134  InteractionFilterFunction3 filterFunc;
135  MMFF94NumericAtomTypeFunction atomTypeFunc;
136  MMFF94BondTypeIndexFunction bondTypeIdxFunc;
141  AtomList nbrAtoms;
142  BondList nbrBonds;
143  };
144  } // namespace ForceField
145 } // namespace CDPL
146 
147 #endif // CDPL_FORCEFIELD_MMFF94ANGLEBENDINGINTERACTIONPARAMETERIZER_HPP
CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer
Definition: MMFF94BondStretchingInteractionParameterizer.hpp:57
CDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMap::SharedPointer
std::shared_ptr< MMFF94PrimaryToParameterAtomTypeMap > SharedPointer
Definition: MMFF94PrimaryToParameterAtomTypeMap.hpp:59
APIPrefix.hpp
Definition of the preprocessor macro CDPL_FORCEFIELD_API.
MMFF94BondStretchingRuleParameterTable.hpp
Definition of the class CDPL::ForceField::MMFF94BondStretchingRuleParameterTable.
CDPL::Chem::Bond
Bond.
Definition: Bond.hpp:50
InteractionFilterFunctions.hpp
Type definition of generic wrapper classes for storing user-defined interaction filtering functions.
CDPL::Util::Array< MMFF94AngleBendingInteraction >
CDPL::Chem::Atom
Atom.
Definition: Atom.hpp:52
CDPL::ForceField::MMFF94BondStretchingParameterTable::SharedPointer
std::shared_ptr< MMFF94BondStretchingParameterTable > SharedPointer
Definition: MMFF94BondStretchingParameterTable.hpp:60
CDPL::ForceField::MMFF94AtomTypePropertyTable::SharedPointer
std::shared_ptr< MMFF94AtomTypePropertyTable > SharedPointer
Definition: MMFF94AtomTypePropertyTable.hpp:59
CDPL::ForceField::MMFF94AngleBendingParameterTable::SharedPointer
std::shared_ptr< MMFF94AngleBendingParameterTable > SharedPointer
Definition: MMFF94AngleBendingParameterTable.hpp:60
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::MMFF94AngleBendingInteractionParameterizer
MMFF94AngleBendingInteractionParameterizer()
CDPL::ForceField::MMFF94BondTypeIndexFunction
std::function< unsigned int(const Chem::Bond &)> MMFF94BondTypeIndexFunction
A generic wrapper class used to store a user-defined MMFF94 bond type index function.
Definition: MMFF94PropertyFunctions.hpp:71
MMFF94BondStretchingInteractionParameterizer.hpp
Definition of the class CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer.
MMFF94PrimaryToParameterAtomTypeMap.hpp
Definition of the class CDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMap.
MMFF94AngleBendingParameterTable.hpp
Definition of the class CDPL::ForceField::MMFF94AngleBendingParameterTable.
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setBondStretchingRuleParameterTable
void setBondStretchingRuleParameterTable(const MMFF94BondStretchingRuleParameterTable::SharedPointer &table)
MMFF94BondStretchingParameterTable.hpp
Definition of the class CDPL::ForceField::MMFF94BondStretchingParameterTable.
CDPL::ForceField::MMFF94BondStretchingRuleParameterTable::SharedPointer
std::shared_ptr< MMFF94BondStretchingRuleParameterTable > SharedPointer
Definition: MMFF94BondStretchingRuleParameterTable.hpp:60
CDPL::ForceField::MMFF94NumericAtomTypeFunction
std::function< unsigned int(const Chem::Atom &)> MMFF94NumericAtomTypeFunction
A generic wrapper class used to store a user-defined numeric MMFF94 atom type function.
Definition: MMFF94PropertyFunctions.hpp:56
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAtomTypeFunction
void setAtomTypeFunction(const MMFF94NumericAtomTypeFunction &func)
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAngleBendingParameterTable
void setAngleBendingParameterTable(const MMFF94AngleBendingParameterTable::SharedPointer &table)
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::MMFF94AngleBendingInteractionParameterizer
MMFF94AngleBendingInteractionParameterizer(const Chem::MolecularGraph &molgraph, MMFF94AngleBendingInteractionList &ia_list, bool strict)
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setBondStretchingParameterTable
void setBondStretchingParameterTable(const MMFF94BondStretchingParameterTable::SharedPointer &table)
MMFF94AtomTypePropertyTable.hpp
Definition of the class CDPL::ForceField::MMFF94AtomTypePropertyTable.
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::parameterize
void parameterize(const Chem::MolecularGraph &molgraph, MMFF94AngleBendingInteractionList &ia_list, bool strict)
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAtomTypePropertyTable
void setAtomTypePropertyTable(const MMFF94AtomTypePropertyTable::SharedPointer &table)
CDPL_FORCEFIELD_API
#define CDPL_FORCEFIELD_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer
Definition: MMFF94AngleBendingInteractionParameterizer.hpp:63
CDPL::ForceField::MMFF94RingSetFunction
std::function< const Chem::FragmentList::SharedPointer &(const Chem::MolecularGraph &)> MMFF94RingSetFunction
A generic wrapper class used to store a user-defined MMFF94 ring set function.
Definition: MMFF94PropertyFunctions.hpp:76
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setBondTypeIndexFunction
void setBondTypeIndexFunction(const MMFF94BondTypeIndexFunction &func)
CDPL::ForceField::InteractionFilterFunction3
std::function< bool(const Chem::Atom &, const Chem::Atom &, const Chem::Atom &)> InteractionFilterFunction3
Definition: InteractionFilterFunctions.hpp:50
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAromaticRingSetFunction
void setAromaticRingSetFunction(const MMFF94RingSetFunction &func)
MMFF94AngleBendingInteractionList.hpp
Definition of the class CDPL::ForceField::MMFF94AngleBendingInteractionList.
MMFF94PropertyFunctions.hpp
Type definition of generic wrapper classes for storing user-defined functions for the retrieval of MM...
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setParameterAtomTypeMap
void setParameterAtomTypeMap(const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer &map)
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::SharedPointer
std::shared_ptr< MMFF94AngleBendingInteractionParameterizer > SharedPointer
Definition: MMFF94AngleBendingInteractionParameterizer.hpp:66
CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setFilterFunction
void setFilterFunction(const InteractionFilterFunction3 &func)