Chemical Data Processing Library C++ API - Version 1.1.1
SurfaceAtomExtractor.hpp
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1 /*
2  * SurfaceAtomExtractor.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_SURFACEATOMEXTRACTOR_HPP
30 #define CDPL_CHEM_SURFACEATOMEXTRACTOR_HPP
31 
32 #include <vector>
33 #include <cstddef>
34 #include <memory>
35 
36 #include "CDPL/Chem/APIPrefix.hpp"
38 #include "CDPL/Math/Matrix.hpp"
39 #include "CDPL/Math/Vector.hpp"
40 
41 
42 namespace CDPL
43 {
44 
45  namespace Chem
46  {
47 
48  class MolecularGraph;
49  class AtomContainer;
50  class Fragment;
51 
56  {
57 
58  public:
59  static constexpr double DEF_PROBE_RADIUS = 1.2;
60  static constexpr double DEF_GRID_OVERSIZE = 5.0;
61  static constexpr double DEF_GRID_STEP_SIZE = 0.75;
62  static constexpr double DEF_MIN_SURFACE_ACC = 0.01;
63  static constexpr std::size_t DEF_NUM_TEST_POINTS = 250;
64 
69 
76  SurfaceAtomExtractor(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph, Fragment& frag);
77 
83  void setProbeRadius(double radius);
84 
85  /*
86  * \brief Returns the radius of the probe sphere that determines the accessibility of the surface atoms.
87  * \return The used probe sphere radius.
88  */
89  double getProbeRadius() const;
90 
96  void setGridStepSize(double size);
97 
102  double getGridStepSize() const;
103 
110  void setGridOversize(double size);
111 
117  double getGridOversize() const;
118 
125  void setMinSurfaceAccessibility(double min_acc);
126 
133 
139  void setNumTestPoints(std::size_t num_points);
140 
145  std::size_t getNumTestPoints() const;
146 
152 
158 
166  void extract(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph, Fragment& frag);
167 
168  private:
169  typedef std::vector<double> AtomRadiusTable;
170  typedef std::vector<std::size_t> AtomIndexList;
171  typedef std::shared_ptr<AtomIndexList> AtomIndexListPtr;
172  typedef std::vector<AtomIndexListPtr> GridAtomLookupTable;
173  typedef std::vector<Math::Vector3D> Vector3DArray;
174 
175  bool init(const AtomContainer& cntnr, const MolecularGraph& parent_molgraph);
176 
177  void transformCoordinates();
178  void calcBoundingBox();
179  void initGridAtomLookupTable();
180  void extractSurfaceAtoms(Fragment& frag);
181 
182  void initTestPoints();
183 
184  double probeRadius;
185  double gridOversize;
186  double gridStepSize;
187  double minSurfAcc;
188  std::size_t numTestPoints;
189  Atom3DCoordinatesFunction coordsFunc;
190  const AtomContainer* atomContainer;
191  const MolecularGraph* parentMolGraph;
192  AtomRadiusTable atomRadii;
193  AtomIndexList atomIndices;
195  Vector3DArray atomCoords;
196  Vector3DArray testPoints;
197  Math::Vector3D bBoxMin;
198  Math::Vector3D bBoxMax;
199  std::size_t gridXSize;
200  std::size_t gridYSize;
201  std::size_t gridZSize;
202  GridAtomLookupTable gridAtomLookup;
203  };
204  } // namespace Chem
205 } // namespace CDPL
206 
207 #endif // CDPL_CHEM_SURFACEATOMEXTRACTOR_HPP
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CHEM_API.
CDPL_CHEM_API
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::Chem::SurfaceAtomExtractor::setProbeRadius
void setProbeRadius(double radius)
Specifies the radius of the probe sphere that determines the accessibility of the surface atoms.
CDPL::Chem::SurfaceAtomExtractor::extract
void extract(const AtomContainer &cntnr, const MolecularGraph &parent_molgraph, Fragment &frag)
Perceives the surface accessible atoms of cntnr that are part of molgraph and adds them to the fragme...
CDPL::Math::Vector3D
CVector< double, 3 > Vector3D
A bounded 3 element vector holding floating point values of type double.
Definition: Vector.hpp:1637
CDPL::Chem::SurfaceAtomExtractor
SurfaceAtomExtractor.
Definition: SurfaceAtomExtractor.hpp:56
CDPL::Chem::SurfaceAtomExtractor::getNumTestPoints
std::size_t getNumTestPoints() const
Returns the number of points on the atom surface at which a test for surface accessibility is carried...
CDPL::Chem::SurfaceAtomExtractor::SurfaceAtomExtractor
SurfaceAtomExtractor(const AtomContainer &cntnr, const MolecularGraph &parent_molgraph, Fragment &frag)
Perceives the surface accessible atoms of cntnr and adds them to the fragment frag.
CDPL::Chem::Fragment
Fragment.
Definition: Fragment.hpp:52
CDPL::Chem::SurfaceAtomExtractor::setAtom3DCoordinatesFunction
void setAtom3DCoordinatesFunction(const Atom3DCoordinatesFunction &func)
Specifies a function for the retrieval of atom 3D-coordinates.
CDPL::Chem::SurfaceAtomExtractor::setNumTestPoints
void setNumTestPoints(std::size_t num_points)
Specifies the number of points on the atom surface at which a test for surface accessibility is carri...
CDPL::Chem::MolecularGraph
MolecularGraph.
Definition: MolecularGraph.hpp:52
Atom3DCoordinatesFunction.hpp
Type definition of a generic wrapper class for storing user-defined Chem::Atom 3D-coordinates functio...
CDPL::Chem::AtomContainer
A common interface for data-structures that support a random access to stored Chem::Atom instances.
Definition: AtomContainer.hpp:55
CDPL::Chem::SurfaceAtomExtractor::getProbeRadius
double getProbeRadius() const
CDPL::Chem::SurfaceAtomExtractor::getMinSurfaceAccessibility
double getMinSurfaceAccessibility() const
Returns the minimum fraction of test points that have to be accessible by the probe sphere to conside...
CDPL::Math::Vector3DArray
VectorArray< Vector3D > Vector3DArray
An array of Math::Vector3D objects.
Definition: VectorArray.hpp:84
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::Matrix< double >
CDPL
The namespace of the Chemical Data Processing Library.
CDPL::Chem::SurfaceAtomExtractor::setGridOversize
void setGridOversize(double size)
Specifies the margin that gets added to each side of the molecular graph's bounding-box for the calcu...
CDPL::Chem::SurfaceAtomExtractor::setGridStepSize
void setGridStepSize(double size)
Specifies the distance between the grid-points in space which store lists of atoms with proximal posi...
Matrix.hpp
Definition of matrix data types.
CDPL::Chem::SurfaceAtomExtractor::setMinSurfaceAccessibility
void setMinSurfaceAccessibility(double min_acc)
Specifies the minimum fraction of test points that have to be accessible by the probe sphere to consi...
CDPL::Chem::calcBoundingBox
CDPL_CHEM_API void calcBoundingBox(const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true)
CDPL::Chem::SurfaceAtomExtractor::getAtom3DCoordinatesFunction
const Atom3DCoordinatesFunction & getAtom3DCoordinatesFunction() const
Returns the function that was registered for the retrieval of atom 3D-coordinates.
CDPL::Chem::SurfaceAtomExtractor::getGridOversize
double getGridOversize() const
Returns the margin that gets added to each side of the molecular graph's bounding-box for the calcula...
CDPL::Chem::SurfaceAtomExtractor::SurfaceAtomExtractor
SurfaceAtomExtractor()
Constructs the SurfaceAtomExtractor instance.
Vector.hpp
Definition of vector data types.
CDPL::Chem::SurfaceAtomExtractor::getGridStepSize
double getGridStepSize() const
Return the distance between the grid-points for proximal atom lookup.