ConformerGeneratorSettings.hpp

Go to the documentation of this file.

/* 
 * ConformerGeneratorSettings.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_CONFGEN_CONFORMERGENERATORSETTINGS_HPP
#define CDPL_CONFGEN_CONFORMERGENERATORSETTINGS_HPP
 
#include <cstddef>
#include <vector>
#include <utility>
 
#include "CDPL/ConfGen/APIPrefix.hpp"
#include "CDPL/ConfGen/FragmentConformerGeneratorSettings.hpp"
 
 
namespace CDPL
{
 
    namespace ConfGen
    {
 
        class CDPL_CONFGEN_API ConformerGeneratorSettings
        {
 
          public:
            static const ConformerGeneratorSettings DEFAULT;
            static const ConformerGeneratorSettings SMALL_SET_DIVERSE;
            static const ConformerGeneratorSettings MEDIUM_SET_DIVERSE;
            static const ConformerGeneratorSettings LARGE_SET_DIVERSE;
            static const ConformerGeneratorSettings SMALL_SET_DENSE;
            static const ConformerGeneratorSettings MEDIUM_SET_DENSE;
            static const ConformerGeneratorSettings LARGE_SET_DENSE;
 
            ConformerGeneratorSettings();
 
            void setSamplingMode(unsigned int mode);
 
            unsigned int getSamplingMode() const;
 
            void sampleHeteroAtomHydrogens(bool sample);
 
            bool sampleHeteroAtomHydrogens() const;
 
            void sampleAngleToleranceRanges(bool sample);
 
            bool sampleAngleToleranceRanges() const;
 
            void enumerateRings(bool enumerate);
 
            bool enumerateRings() const;
 
            void setNitrogenEnumerationMode(unsigned int mode);
 
            unsigned int getNitrogenEnumerationMode() const;
 
            void generateCoordinatesFromScratch(bool generate);
 
            bool generateCoordinatesFromScratch() const;
 
            void includeInputCoordinates(bool include);
 
            bool includeInputCoordinates() const;
 
            void setEnergyWindow(double win_size);
 
            double getEnergyWindow() const;
 
            double getEnergyWindow(std::size_t num_rot_bonds) const;
 
            void clearEnergyWindowRanges();
 
            void addEnergyWindowRange(std::size_t num_rot_bonds, double win_size);
 
            void setMaxPoolSize(std::size_t max_size);
 
            std::size_t getMaxPoolSize() const;
 
            void setMaxRotatableBondCount(long max_count);
 
            long getMaxRotatableBondCount() const;
 
            void setTimeout(std::size_t mil_secs);
 
            std::size_t getTimeout() const;
 
            void setForceFieldTypeSystematic(unsigned int type);
 
            unsigned int getForceFieldTypeSystematic() const;
 
            void setForceFieldTypeStochastic(unsigned int type);
 
            unsigned int getForceFieldTypeStochastic() const;
 
            void strictForceFieldParameterization(bool strict);
 
            bool strictForceFieldParameterization() const;
 
            void setDielectricConstant(double de_const);
 
            double getDielectricConstant() const;
 
            void setDistanceExponent(double exponent);
 
            double getDistanceExponent() const;
 
            void setMaxNumOutputConformers(std::size_t max_num);
 
            std::size_t getMaxNumOutputConformers() const;
 
            std::size_t getMaxNumOutputConformers(std::size_t num_rot_bonds) const;
 
            void clearMaxNumOutputConformersRanges();
 
            void addMaxNumOutputConformersRange(std::size_t num_rot_bonds, std::size_t max_num);
 
            void setMinRMSD(double min_rmsd);
 
            double getMinRMSD() const;
 
            double getMinRMSD(std::size_t num_rot_bonds) const;
 
            void clearMinRMSDRanges();
 
            void addMinRMSDRange(std::size_t num_rot_bonds, double min_rmsd);
 
            void setMaxNumRefinementIterations(std::size_t max_iter);
 
            std::size_t getMaxNumRefinementIterations() const;
 
            void setRefinementTolerance(double tol);
 
            double getRefinementTolerance() const;
 
            void setMaxNumSampledConformers(std::size_t max_num);
 
            std::size_t getMaxNumSampledConformers() const;
 
            void setConvergenceCheckCycleSize(std::size_t size);
 
            std::size_t getConvergenceCheckCycleSize() const;
 
            void setMacrocycleRotorBondCountThreshold(std::size_t min_count);
 
            std::size_t getMacrocycleRotorBondCountThreshold() const;
 
            FragmentConformerGeneratorSettings& getFragmentBuildSettings();
 
            const FragmentConformerGeneratorSettings& getFragmentBuildSettings() const;
 
          private:
            typedef std::pair<std::size_t, std::size_t> STPair;
            typedef std::pair<std::size_t, double>      STDoublePair;
            typedef std::vector<STPair>                 STPairArray;
            typedef std::vector<STDoublePair>           STDoublePairArray;
 
            template <typename A>
            static typename A::value_type::second_type getValueForCount(const A& array, std::size_t num_rot_bonds);
            
            unsigned int                       samplingMode;
            bool                               sampleHetAtomHs;
            bool                               sampleTolRanges;
            bool                               enumRings;
            unsigned int                       nitrogenEnumMode;
            bool                               fromScratch;
            bool                               incInputCoords;
            double                             eWindow;
            STDoublePairArray                  eWindowRanges;
            std::size_t                        maxPoolSize;
            long                               maxRotorBondCount;
            std::size_t                        timeout;
            unsigned int                       forceFieldTypeSys;
            unsigned int                       forceFieldTypeStoch;
            bool                               strictParam;
            double                             dielectricConst;
            double                             distExponent;
            std::size_t                        maxNumOutputConfs;
            STPairArray                        maxNumOutputConfRanges;
            double                             minRMSD;
            STDoublePairArray                  minRMSDRanges;
            std::size_t                        maxNumRefIters;
            double                             refTolerance;
            std::size_t                        maxNumSampledConfs;
            std::size_t                        convCheckCycleSize;
            std::size_t                        mcRotorBondCountThresh;
            FragmentConformerGeneratorSettings fragBuildSettings;
        };
    }; // namespace ConfGen
} // namespace CDPL
 
#endif // CDPL_CONFGEN_CONFORMERGENERATORSETTINGS_HPP