Chemical Data Processing Library C++ API - Version 1.1.1
BuriednessGridCalculator.hpp
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1 /*
2  * BuriednessGridCalculator.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_GRAIL_BURIEDNESSGRIDCALCULATOR_HPP
30 #define CDPL_GRAIL_BURIEDNESSGRIDCALCULATOR_HPP
31 
32 #include <vector>
33 #include <cstddef>
34 #include <memory>
35 
36 #include "CDPL/GRAIL/APIPrefix.hpp"
38 #include "CDPL/Chem/Fragment.hpp"
40 #include "CDPL/Math/Vector.hpp"
42 
43 
44 namespace CDPL
45 {
46 
47  namespace Internal
48  {
49 
50  template <typename PT, typename CT, typename ST>
51  class Octree;
52  }
53 
54  namespace GRAIL
55  {
56 
61  {
62 
63  public:
64  typedef std::shared_ptr<BuriednessGridCalculator> SharedPointer;
65 
67 
69 
70  void setProbeRadius(double radius);
71 
72  double getProbeRadius() const;
73 
74  void setMinVdWSurfaceDistance(double dist);
75 
76  double getMinVdWSurfaceDistance() const;
77 
78  void setNumTestRays(std::size_t num_rays);
79 
80  std::size_t getNumTestRays() const;
81 
87 
89 
91 
93 
94  private:
95  typedef Internal::Octree<Math::Vector3D, Math::Vector3DArray, double> Octree;
96  typedef std::shared_ptr<Octree> OctreePtr;
97  typedef std::vector<std::size_t> AtomIndexList;
98 
99  BuriednessScore buriednessScore;
100  OctreePtr octree;
101  Math::Vector3DArray atomCoords;
102  AtomIndexList atomIndices;
103  Chem::Fragment atomSubset;
104  };
105  } // namespace GRAIL
106 } // namespace CDPL
107 
108 #endif // CDPL_GRAIL_BURIEDNESSGRIDCALCULATOR_HPP
CDPL::GRAIL::BuriednessGridCalculator::operator=
BuriednessGridCalculator & operator=(const BuriednessGridCalculator &calc)
VectorArray.hpp
Definition of the class CDPL::Math::VectorArray.
CDPL::Chem::Fragment
Fragment.
Definition: Fragment.hpp:52
CDPL::GRAIL::BuriednessGridCalculator::setNumTestRays
void setNumTestRays(std::size_t num_rays)
CDPL::GRAIL::BuriednessGridCalculator::SharedPointer
std::shared_ptr< BuriednessGridCalculator > SharedPointer
Definition: BuriednessGridCalculator.hpp:64
SpatialGrid.hpp
Definition of a spatial grid data type.
BuriednessScore.hpp
Definition of the class CDPL::GRAIL::BuriednessScore.
VectorArray< Vector3D >
CDPL::GRAIL::BuriednessGridCalculator::getProbeRadius
double getProbeRadius() const
CDPL::GRAIL::BuriednessGridCalculator::setMinVdWSurfaceDistance
void setMinVdWSurfaceDistance(double dist)
CDPL::Chem::AtomContainer
A common interface for data-structures that support a random access to stored Chem::Atom instances.
Definition: AtomContainer.hpp:55
CDPL::GRAIL::BuriednessGridCalculator
BuriednessGridCalculator.
Definition: BuriednessGridCalculator.hpp:61
CDPL::GRAIL::BuriednessGridCalculator::getAtom3DCoordinatesFunction
const Chem::Atom3DCoordinatesFunction & getAtom3DCoordinatesFunction() const
CDPL::GRAIL::BuriednessGridCalculator::setProbeRadius
void setProbeRadius(double radius)
CDPL::GRAIL::BuriednessGridCalculator::calculate
void calculate(const Chem::AtomContainer &atoms, Grid::DSpatialGrid &grid)
CDPL::Grid::SpatialGrid
SpatialGrid.
Definition: SpatialGrid.hpp:47
CDPL::GRAIL::BuriednessGridCalculator::BuriednessGridCalculator
BuriednessGridCalculator()
APIPrefix.hpp
Definition of the preprocessor macro CDPL_GRAIL_API.
Fragment.hpp
Definition of the class CDPL::Chem::Fragment.
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::GRAIL::BuriednessGridCalculator::getMinVdWSurfaceDistance
double getMinVdWSurfaceDistance() const
CDPL::GRAIL::BuriednessScore
BuriednessScore.
Definition: BuriednessScore.hpp:57
CDPL::GRAIL::BuriednessGridCalculator::getNumTestRays
std::size_t getNumTestRays() const
CDPL
The namespace of the Chemical Data Processing Library.
CDPL_GRAIL_API
#define CDPL_GRAIL_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::GRAIL::BuriednessGridCalculator::BuriednessGridCalculator
BuriednessGridCalculator(const BuriednessGridCalculator &calc)
Vector.hpp
Definition of vector data types.
CDPL::GRAIL::BuriednessGridCalculator::setAtom3DCoordinatesFunction
void setAtom3DCoordinatesFunction(const Chem::Atom3DCoordinatesFunction &func)
Specifies a function for the retrieval of atom 3D-coordinates for grid calculation.