Chemical Data Processing Library C++ API - Version 1.1.1
ConformerGeneratorSettings.hpp
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1 /*
2  * ConformerGeneratorSettings.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_CONFORMERGENERATORSETTINGS_HPP
30 #define CDPL_CONFGEN_CONFORMERGENERATORSETTINGS_HPP
31 
32 #include <cstddef>
33 #include <vector>
34 #include <utility>
35 
38 
39 
40 namespace CDPL
41 {
42 
43  namespace ConfGen
44  {
45 
47  {
48 
49  public:
51 
55 
59 
61 
62  void setSamplingMode(unsigned int mode);
63 
64  unsigned int getSamplingMode() const;
65 
66  void sampleHeteroAtomHydrogens(bool sample);
67 
69 
70  void sampleAngleToleranceRanges(bool sample);
71 
73 
74  void enumerateRings(bool enumerate);
75 
76  bool enumerateRings() const;
77 
78  void setNitrogenEnumerationMode(unsigned int mode);
79 
80  unsigned int getNitrogenEnumerationMode() const;
81 
82  void generateCoordinatesFromScratch(bool generate);
83 
85 
86  void includeInputCoordinates(bool include);
87 
89 
90  void setEnergyWindow(double win_size);
91 
92  double getEnergyWindow() const;
93 
94  /*
95  * \since 1.1
96  */
97  double getEnergyWindow(std::size_t num_rot_bonds) const;
98 
99  /*
100  * \since 1.1
101  */
103 
104  /*
105  * \since 1.1
106  */
107  void addEnergyWindowRange(std::size_t num_rot_bonds, double win_size);
108 
109  void setMaxPoolSize(std::size_t max_size);
110 
111  std::size_t getMaxPoolSize() const;
112 
113  /*
114  * \since 1.1
115  */
116  void setMaxRotatableBondCount(long max_count);
117 
118  /*
119  * \since 1.1
120  */
122 
123  void setTimeout(std::size_t mil_secs);
124 
125  std::size_t getTimeout() const;
126 
127  void setForceFieldTypeSystematic(unsigned int type);
128 
129  unsigned int getForceFieldTypeSystematic() const;
130 
131  void setForceFieldTypeStochastic(unsigned int type);
132 
133  unsigned int getForceFieldTypeStochastic() const;
134 
136 
138 
139  void setDielectricConstant(double de_const);
140 
141  double getDielectricConstant() const;
142 
143  void setDistanceExponent(double exponent);
144 
145  double getDistanceExponent() const;
146 
147  void setMaxNumOutputConformers(std::size_t max_num);
148 
149  std::size_t getMaxNumOutputConformers() const;
150 
151  /*
152  * \since 1.1
153  */
154  std::size_t getMaxNumOutputConformers(std::size_t num_rot_bonds) const;
155 
156  /*
157  * \since 1.1
158  */
160 
161  /*
162  * \since 1.1
163  */
164  void addMaxNumOutputConformersRange(std::size_t num_rot_bonds, std::size_t max_num);
165 
166  void setMinRMSD(double min_rmsd);
167 
168  double getMinRMSD() const;
169 
170  /*
171  * \since 1.1
172  */
173  double getMinRMSD(std::size_t num_rot_bonds) const;
174 
175  /*
176  * \since 1.1
177  */
179 
180  /*
181  * \since 1.1
182  */
183  void addMinRMSDRange(std::size_t num_rot_bonds, double min_rmsd);
184 
185  void setMaxNumRefinementIterations(std::size_t max_iter);
186 
187  std::size_t getMaxNumRefinementIterations() const;
188 
189  void setRefinementTolerance(double tol);
190 
191  double getRefinementTolerance() const;
192 
193  void setMaxNumSampledConformers(std::size_t max_num);
194 
195  std::size_t getMaxNumSampledConformers() const;
196 
197  void setConvergenceCheckCycleSize(std::size_t size);
198 
199  std::size_t getConvergenceCheckCycleSize() const;
200 
201  void setMacrocycleRotorBondCountThreshold(std::size_t min_count);
202 
204 
206 
208 
209  private:
210  typedef std::pair<std::size_t, std::size_t> STPair;
211  typedef std::pair<std::size_t, double> STDoublePair;
212  typedef std::vector<STPair> STPairArray;
213  typedef std::vector<STDoublePair> STDoublePairArray;
214 
215  template <typename A>
216  static typename A::value_type::second_type getValueForCount(const A& array, std::size_t num_rot_bonds);
217 
218  unsigned int samplingMode;
219  bool sampleHetAtomHs;
220  bool sampleTolRanges;
221  bool enumRings;
222  unsigned int nitrogenEnumMode;
223  bool fromScratch;
224  bool incInputCoords;
225  double eWindow;
226  STDoublePairArray eWindowRanges;
227  std::size_t maxPoolSize;
228  long maxRotorBondCount;
229  std::size_t timeout;
230  unsigned int forceFieldTypeSys;
231  unsigned int forceFieldTypeStoch;
232  bool strictParam;
233  double dielectricConst;
234  double distExponent;
235  std::size_t maxNumOutputConfs;
236  STPairArray maxNumOutputConfRanges;
237  double minRMSD;
238  STDoublePairArray minRMSDRanges;
239  std::size_t maxNumRefIters;
240  double refTolerance;
241  std::size_t maxNumSampledConfs;
242  std::size_t convCheckCycleSize;
243  std::size_t mcRotorBondCountThresh;
244  FragmentConformerGeneratorSettings fragBuildSettings;
245  };
246  }; // namespace ConfGen
247 } // namespace CDPL
248 
249 #endif // CDPL_CONFGEN_CONFORMERGENERATORSETTINGS_HPP
CDPL::ConfGen::ConformerGeneratorSettings::setRefinementTolerance
void setRefinementTolerance(double tol)
CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumRefinementIterations
std::size_t getMaxNumRefinementIterations() const
CDPL::ConfGen::ConformerGeneratorSettings::addEnergyWindowRange
void addEnergyWindowRange(std::size_t num_rot_bonds, double win_size)
CDPL::ConfGen::ConformerGeneratorSettings::clearEnergyWindowRanges
void clearEnergyWindowRanges()
CDPL::ConfGen::ConformerGeneratorSettings::MEDIUM_SET_DENSE
static const ConformerGeneratorSettings MEDIUM_SET_DENSE
Definition: ConformerGeneratorSettings.hpp:57
CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumSampledConformers
std::size_t getMaxNumSampledConformers() const
CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumSampledConformers
void setMaxNumSampledConformers(std::size_t max_num)
CDPL::ConfGen::ConformerGeneratorSettings::getRefinementTolerance
double getRefinementTolerance() const
CDPL::ConfGen::ConformerGeneratorSettings::sampleAngleToleranceRanges
void sampleAngleToleranceRanges(bool sample)
CDPL::ConfGen::ConformerGeneratorSettings::SMALL_SET_DENSE
static const ConformerGeneratorSettings SMALL_SET_DENSE
Definition: ConformerGeneratorSettings.hpp:56
CDPL::ConfGen::ConformerGeneratorSettings::setSamplingMode
void setSamplingMode(unsigned int mode)
CDPL::ConfGen::ConformerGeneratorSettings::getMinRMSD
double getMinRMSD() const
CDPL::ConfGen::ConformerGeneratorSettings::ConformerGeneratorSettings
ConformerGeneratorSettings()
CDPL::ConfGen::ConformerGeneratorSettings::addMaxNumOutputConformersRange
void addMaxNumOutputConformersRange(std::size_t num_rot_bonds, std::size_t max_num)
CDPL::ConfGen::ConformerGeneratorSettings::setForceFieldTypeSystematic
void setForceFieldTypeSystematic(unsigned int type)
CDPL::ConfGen::ConformerGeneratorSettings::getMaxPoolSize
std::size_t getMaxPoolSize() const
CDPL::ConfGen::ConformerGeneratorSettings::MEDIUM_SET_DIVERSE
static const ConformerGeneratorSettings MEDIUM_SET_DIVERSE
Definition: ConformerGeneratorSettings.hpp:53
CDPL::ConfGen::ConformerGeneratorSettings::getNitrogenEnumerationMode
unsigned int getNitrogenEnumerationMode() const
CDPL::ConfGen::ConformerGeneratorSettings::clearMinRMSDRanges
void clearMinRMSDRanges()
CDPL::ConfGen::ConformerGeneratorSettings::setEnergyWindow
void setEnergyWindow(double win_size)
CDPL::ConfGen::ConformerGeneratorSettings::setMaxPoolSize
void setMaxPoolSize(std::size_t max_size)
CDPL::ConfGen::ConformerGeneratorSettings::LARGE_SET_DIVERSE
static const ConformerGeneratorSettings LARGE_SET_DIVERSE
Definition: ConformerGeneratorSettings.hpp:54
CDPL::ConfGen::ConformerGeneratorSettings::sampleHeteroAtomHydrogens
void sampleHeteroAtomHydrogens(bool sample)
CDPL::ConfGen::ConformerGeneratorSettings::setDielectricConstant
void setDielectricConstant(double de_const)
CDPL::ConfGen::ConformerGeneratorSettings::enumerateRings
void enumerateRings(bool enumerate)
CDPL::ConfGen::ConformerGeneratorSettings::getFragmentBuildSettings
const FragmentConformerGeneratorSettings & getFragmentBuildSettings() const
CDPL::ConfGen::ConformerGeneratorSettings::getSamplingMode
unsigned int getSamplingMode() const
CDPL::ConfGen::ConformerGeneratorSettings::setMaxRotatableBondCount
void setMaxRotatableBondCount(long max_count)
CDPL::ConfGen::ConformerGeneratorSettings::enumerateRings
bool enumerateRings() const
CDPL::ConfGen::ConformerGeneratorSettings::includeInputCoordinates
bool includeInputCoordinates() const
CDPL::ConfGen::ConformerGeneratorSettings::SMALL_SET_DIVERSE
static const ConformerGeneratorSettings SMALL_SET_DIVERSE
Definition: ConformerGeneratorSettings.hpp:52
CDPL::ConfGen::ConformerGeneratorSettings::generateCoordinatesFromScratch
bool generateCoordinatesFromScratch() const
CDPL::ConfGen::ConformerGeneratorSettings::clearMaxNumOutputConformersRanges
void clearMaxNumOutputConformersRanges()
CDPL::ConfGen::ConformerGeneratorSettings::getDistanceExponent
double getDistanceExponent() const
CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumRefinementIterations
void setMaxNumRefinementIterations(std::size_t max_iter)
CDPL::ConfGen::ConformerGeneratorSettings
Definition: ConformerGeneratorSettings.hpp:47
CDPL::ConfGen::ConformerGeneratorSettings::getDielectricConstant
double getDielectricConstant() const
APIPrefix.hpp
Definition of the preprocessor macro CDPL_CONFGEN_API.
CDPL::ConfGen::ConformerGeneratorSettings::sampleHeteroAtomHydrogens
bool sampleHeteroAtomHydrogens() const
CDPL::Util::STPairArray
Array< STPair > STPairArray
An array of pairs of unsigned integers of type std::size_t.
Definition: Array.hpp:582
CDPL::ConfGen::ConformerGeneratorSettings::setNitrogenEnumerationMode
void setNitrogenEnumerationMode(unsigned int mode)
CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumOutputConformers
std::size_t getMaxNumOutputConformers() const
CDPL::ConfGen::ConformerGeneratorSettings::sampleAngleToleranceRanges
bool sampleAngleToleranceRanges() const
CDPL::ConfGen::ConformerGeneratorSettings::getEnergyWindow
double getEnergyWindow(std::size_t num_rot_bonds) const
CDPL::ConfGen::ConformerGeneratorSettings::getForceFieldTypeSystematic
unsigned int getForceFieldTypeSystematic() const
CDPL::ConfGen::ConformerGeneratorSettings::setMacrocycleRotorBondCountThreshold
void setMacrocycleRotorBondCountThreshold(std::size_t min_count)
CDPL::ConfGen::ConformerGeneratorSettings::includeInputCoordinates
void includeInputCoordinates(bool include)
CDPL_CONFGEN_API
#define CDPL_CONFGEN_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
CDPL::ConfGen::ConformerGeneratorSettings::getConvergenceCheckCycleSize
std::size_t getConvergenceCheckCycleSize() const
CDPL::ConfGen::ConformerGeneratorSettings::getMinRMSD
double getMinRMSD(std::size_t num_rot_bonds) const
CDPL::ConfGen::ConformerGeneratorSettings::setTimeout
void setTimeout(std::size_t mil_secs)
CDPL::ConfGen::ConformerGeneratorSettings::getMaxNumOutputConformers
std::size_t getMaxNumOutputConformers(std::size_t num_rot_bonds) const
CDPL
The namespace of the Chemical Data Processing Library.
FragmentConformerGeneratorSettings.hpp
Definition of the class CDPL::ConfGen::FragmentConformerGeneratorSettings.
CDPL::ConfGen::ConformerGeneratorSettings::setForceFieldTypeStochastic
void setForceFieldTypeStochastic(unsigned int type)
CDPL::ConfGen::ConformerGeneratorSettings::getFragmentBuildSettings
FragmentConformerGeneratorSettings & getFragmentBuildSettings()
CDPL::ConfGen::ConformerGeneratorSettings::LARGE_SET_DENSE
static const ConformerGeneratorSettings LARGE_SET_DENSE
Definition: ConformerGeneratorSettings.hpp:58
CDPL::ConfGen::ConformerGeneratorSettings::strictForceFieldParameterization
void strictForceFieldParameterization(bool strict)
CDPL::ConfGen::ConformerGeneratorSettings::setDistanceExponent
void setDistanceExponent(double exponent)
CDPL::ConfGen::ConformerGeneratorSettings::setMinRMSD
void setMinRMSD(double min_rmsd)
CDPL::ConfGen::ConformerGeneratorSettings::generateCoordinatesFromScratch
void generateCoordinatesFromScratch(bool generate)
CDPL::ConfGen::ConformerGeneratorSettings::getMacrocycleRotorBondCountThreshold
std::size_t getMacrocycleRotorBondCountThreshold() const
CDPL::ConfGen::ConformerGeneratorSettings::getForceFieldTypeStochastic
unsigned int getForceFieldTypeStochastic() const
CDPL::ConfGen::ConformerGeneratorSettings::strictForceFieldParameterization
bool strictForceFieldParameterization() const
CDPL::ConfGen::ConformerGeneratorSettings::getTimeout
std::size_t getTimeout() const
CDPL::ConfGen::ConformerGeneratorSettings::setMaxNumOutputConformers
void setMaxNumOutputConformers(std::size_t max_num)
CDPL::ConfGen::ConformerGeneratorSettings::DEFAULT
static const ConformerGeneratorSettings DEFAULT
Definition: ConformerGeneratorSettings.hpp:50
CDPL::ConfGen::ConformerGeneratorSettings::addMinRMSDRange
void addMinRMSDRange(std::size_t num_rot_bonds, double min_rmsd)
CDPL::Util::STPair
std::pair< std::size_t, std::size_t > STPair
A pair of unsigned integers of type std::size_t.
Definition: Array.hpp:577
CDPL::Chem::AtomType::A
const unsigned int A
A generic type that covers any element except hydrogen.
Definition: AtomType.hpp:617
CDPL::ConfGen::FragmentConformerGeneratorSettings
Definition: FragmentConformerGeneratorSettings.hpp:44
CDPL::ConfGen::ConformerGeneratorSettings::getEnergyWindow
double getEnergyWindow() const
CDPL::ConfGen::ConformerGeneratorSettings::setConvergenceCheckCycleSize
void setConvergenceCheckCycleSize(std::size_t size)
CDPL::ConfGen::ConformerGeneratorSettings::getMaxRotatableBondCount
long getMaxRotatableBondCount() const