Chemical Data Processing Library C++ API - Version 1.1.1
Hydrogen3DCoordinatesCalculator.hpp
Go to the documentation of this file.
1 /*
2  * Hydrogen3DCoordinatesCalculator.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_CHEM_HYDROGEN3DCOORDINATESCALCULATOR_HPP
30 #define CDPL_CHEM_HYDROGEN3DCOORDINATESCALCULATOR_HPP
31 
32 #include <cstddef>
33 #include <vector>
34 
35 #include "CDPL/Chem/APIPrefix.hpp"
39 #include "CDPL/Math/Matrix.hpp"
41 #include "CDPL/Util/BitSet.hpp"
42 
43 
44 namespace CDPL
45 {
46 
47  namespace Chem
48  {
49 
50  class MolecularGraph;
51  class Atom;
52 
57  {
58 
59  public:
64 
78  Hydrogen3DCoordinatesCalculator(const MolecularGraph& molgraph, Math::Vector3DArray& coords, bool undef_only = true);
79 
85  void undefinedOnly(bool undef_only);
86 
91  bool undefinedOnly() const;
92 
98 
104 
110 
116 
117  void setup(const MolecularGraph& molgraph);
118 
128  void calculate(const MolecularGraph& molgraph, Math::Vector3DArray& coords, bool init_coords = true);
129 
130  void calculate(Math::Vector3DArray& coords, bool init_coords = true);
131 
132  private:
133  typedef std::vector<std::size_t> AtomIndexList;
134 
135  void assignCoordinates(Math::Vector3DArray&, bool init_coords);
136  void assignDiatomicMolCoords(const Atom&, std::size_t, Math::Vector3DArray&);
137  void assignLinearCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
138  void assignTrigonalPlanarCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
139  void assignTetrahedralCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
140  void assignSquarePlanarCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
141  void assignTrigonalBipyramidalCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
142  void assignOctahedralCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
143  void assignPentagonalBipyramidalCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
144  void assignEvenlyDistributedCoords(const Atom&, std::size_t, std::size_t, Math::Vector3DArray&);
145 
146  void assignTemplateCoords(const Atom&, std::size_t, std::size_t,
147  std::size_t, const Math::Vector3D[], const std::size_t*,
149 
150  std::size_t getConnectedAtoms(const Atom&, AtomIndexList&);
151  bool getConnectedAtomWithCoords(std::size_t, const Atom&, std::size_t&) const;
152 
153  double getHydrogenBondLength(const Atom&) const;
154 
155  unsigned int getHybridizationState(const Atom&, std::size_t) const;
156 
157  void buildOrthogonalBasis(const Math::Vector3D&, const Math::Vector3D&,
158  Math::Matrix3D&, bool) const;
159  void getRotationReferenceVector(const Atom&, std::size_t, std::size_t, std::size_t,
161  void getPerpendicularVector(const Math::Vector3D&, Math::Vector3D&) const;
162 
163  typedef std::vector<Math::Vector3D> DynamicPointArray;
164 
165  const MolecularGraph* molGraph;
166  bool undefOnly;
167  Atom3DCoordinatesFunction coordsFunc;
168  AtomPredicate hasCoordsFunc;
169  Util::BitSet defCoordsMask;
170  Util::BitSet savedCoordsMask;
171  AtomIndexList centerAtoms;
172  AtomIndexList conctdAtoms;
173  Math::DMatrix refPoints;
174  Math::DMatrix tmpltPoints;
175  DynamicPointArray genPoints;
177  Util::BitSet usedPosMask;
178  };
179  } // namespace Chem
180 } // namespace CDPL
181 
182 #endif // CDPL_CHEM_HYDROGEN3DCOORDINATESCALCULATOR_HPP
CDPL::Chem::Hydrogen3DCoordinatesCalculator::Hydrogen3DCoordinatesCalculator
Hydrogen3DCoordinatesCalculator()
Constructs the Hydrogen3DCoordinatesCalculator instance.
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CHEM_API.
VectorArray.hpp
Definition of the class CDPL::Math::VectorArray.
CDPL_CHEM_API
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Math::Vector3D
CVector< double, 3 > Vector3D
A bounded 3 element vector holding floating point values of type double.
Definition: Vector.hpp:1637
CDPL::Util::BitSet
boost::dynamic_bitset BitSet
A dynamic bitset class.
Definition: BitSet.hpp:46
CDPL::Chem::Atom
Atom.
Definition: Atom.hpp:52
CDPL::Chem::Hydrogen3DCoordinatesCalculator::setup
void setup(const MolecularGraph &molgraph)
CDPL::Chem::Hydrogen3DCoordinatesCalculator::getAtom3DCoordinatesFunction
const Atom3DCoordinatesFunction & getAtom3DCoordinatesFunction() const
Returns the function that was registered for the retrieval of atom 3D-coordinates.
CDPL::Chem::Hydrogen3DCoordinatesCalculator::calculate
void calculate(Math::Vector3DArray &coords, bool init_coords=true)
VectorArray< Vector3D >
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
BitSet.hpp
Definition of the type CDPL::Util::BitSet.
Atom3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom 3D-coordinates functio...
CDPL::Chem::AtomPredicate
std::function< bool(const Chem::Atom &)> AtomPredicate
A generic wrapper class used to store a user-defined atom predicate.
Definition: AtomPredicate.hpp:41
CDPL::Chem::Hydrogen3DCoordinatesCalculator::setAtom3DCoordinatesCheckFunction
void setAtom3DCoordinatesCheckFunction(const AtomPredicate &func)
Specifies a function that tells whether 3D coordinates are available for it's argument atom.
CDPL::Chem::getHybridizationState
CDPL_CHEM_API unsigned int getHybridizationState(const Atom &atom)
CDPL::Chem::getConnectedAtoms
std::size_t getConnectedAtoms(AtomType &atom, const MolecularGraph &molgraph, OutputIterator it, AtomType *excl_atom=0)
Definition: Chem/AtomFunctions.hpp:425
AtomPredicate.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom predicates.
CDPL::Math::KabschAlgorithm< double >
CDPL::Chem::Atom3DCoordinatesFunction
std::function< const Math::Vector3D &(const Chem::Atom &)> Atom3DCoordinatesFunction
A generic wrapper class used to store a user-defined Chem::Atom 3D-coordinates function.
Definition: Atom3DCoordinatesFunction.hpp:43
CDPL::Math::Matrix3D
CMatrix< double, 3, 3 > Matrix3D
A bounded 3x3 matrix holding floating point values of type double.
Definition: Matrix.hpp:1849
KabschAlgorithm.hpp
Implementation of the Kabsch algorithm.
CDPL::Chem::Hydrogen3DCoordinatesCalculator::Hydrogen3DCoordinatesCalculator
Hydrogen3DCoordinatesCalculator(const MolecularGraph &molgraph, Math::Vector3DArray &coords, bool undef_only=true)
Constructs the Hydrogen3DCoordinatesCalculator instance and calculates 3D-coordinates for the hydroge...
CDPL::Math::Matrix< double >
CDPL::Chem::Hydrogen3DCoordinatesCalculator::undefinedOnly
bool undefinedOnly() const
Tells whether already defined hydrogen atom coordinates are recalculated or left unchanged.
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Chem::Hydrogen3DCoordinatesCalculator::undefinedOnly
void undefinedOnly(bool undef_only)
Allows to specify whether already defined hydrogen atom coordinates have to be recalculated or are le...
Matrix.hpp
Definition of matrix data types.
CDPL::Chem::Hydrogen3DCoordinatesCalculator
Hydrogen3DCoordinatesCalculator.
Definition: Hydrogen3DCoordinatesCalculator.hpp:57
CDPL::Chem::Hydrogen3DCoordinatesCalculator::calculate
void calculate(const MolecularGraph &molgraph, Math::Vector3DArray &coords, bool init_coords=true)
Calculates 3D-coordinates for the hydrogen atoms of the molecular graph molgraph.
CDPL::Chem::Hydrogen3DCoordinatesCalculator::getAtom3DCoordinatesCheckFunction
const AtomPredicate & getAtom3DCoordinatesCheckFunction() const
Returns the function that was registered to determine whether for a given atom 3D coordinates are ava...
CDPL::Chem::Hydrogen3DCoordinatesCalculator::setAtom3DCoordinatesFunction
void setAtom3DCoordinatesFunction(const Atom3DCoordinatesFunction &func)
Specifies a function for the retrieval of atom 3D-coordinates.