spectrophore.h
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00001 /********************************************************************** 00002 Spectrophore.h - Spectrophore(TM) calculator. 00003 Declarations of OBSpectrophore 00004 00005 Copyright (C) 2005-2010 by Silicos NV 00006 00007 This file is part of the Open Babel project. 00008 For more information, see <http://openbabel.org/> 00009 00010 This program is free software; you can redistribute it and/or modify 00011 it under the terms of the GNU General Public License as published by 00012 the Free Software Foundation version 2 of the License. 00013 00014 The algorithm in this software has been covered by patent WO2009146735. 00015 However, Silicos NV and the inventors of the above mentioned patent assure 00016 that no patent infringment claims will be issued against individuals or 00017 institutions that use this software under the GNU General Public License. 00018 00019 This program is distributed in the hope that it will be useful, 00020 but WITHOUT ANY WARRANTY; without even the implied warranty of 00021 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00022 GNU General Public License for more details. 00023 ***********************************************************************/ 00024 00025 00026 #ifndef OB_SPECTROPHORE_H 00027 #define OB_SPECTROPHORE_H 00028 00029 00040 #include <set> 00041 #include <openbabel/mol.h> 00042 00043 00044 #define MIN(x, y) (((x) < (y)) ? (x) : (y)) 00045 #define MAX(x, y) (((x) > (y)) ? (x) : (y)) 00046 #define N_PROPERTIES 4 00047 00048 00049 00050 namespace OpenBabel 00051 { 00052 00302 class OBAPI OBSpectrophore 00303 { 00304 public: 00305 00308 enum AccuracyOption {AngStepSize1, 00309 AngStepSize2, 00310 AngStepSize5, 00311 AngStepSize10, 00312 AngStepSize15, 00313 AngStepSize20, 00314 AngStepSize30, 00315 AngStepSize36, 00316 AngStepSize45, 00317 AngStepSize60}; 00318 00321 enum NormalizationOption {NoNormalization, 00322 NormalizationTowardsZeroMean, 00323 NormalizationTowardsUnitStd, 00324 NormalizationTowardsZeroMeanAndUnitStd}; 00325 00328 enum StereoOption {NoStereoSpecificProbes, 00329 UniqueStereoSpecificProbes, 00330 MirrorStereoSpecificProbes, 00331 AllStereoSpecificProbes}; 00332 00334 00339 OBSpectrophore(void); 00340 00346 OBSpectrophore(const OBSpectrophore& sphore); 00347 00350 virtual ~OBSpectrophore(void); 00352 00361 OBSpectrophore& operator=(const OBSpectrophore& sphore); 00363 00382 void SetResolution(const double r = 3.0); 00383 00412 void SetAccuracy(const AccuracyOption a = AngStepSize20); 00413 00436 void SetStereo(const StereoOption s = NoStereoSpecificProbes); 00437 00455 void SetNormalization(const NormalizationOption n = NoNormalization); 00457 00468 AccuracyOption GetAccuracy(void) const; 00469 00474 double GetResolution(void) const; 00475 00486 StereoOption GetStereo(void) const; 00487 00498 NormalizationOption GetNormalization(void) const; 00499 00547 std::vector<double> GetSpectrophore(OpenBabel::OBMol* mol); 00549 00550 00551 protected: 00552 00554 double _resolution; 00555 AccuracyOption _accuracy; 00556 StereoOption _stereoFlag; 00557 NormalizationOption _normalization; 00558 std::vector<int> _rotationStepList; 00559 unsigned int _nAtoms; 00560 double** _property; 00561 double* _radii; 00562 double** _oricoor; 00563 double** _coor; 00564 unsigned int _beginProbe; 00565 unsigned int _endProbe; 00566 unsigned int _numberOfProbes; 00567 std::vector<double> _spectro; 00568 struct 00569 { 00570 int value[12]; 00571 } _probe[48]; 00572 struct 00573 { 00574 double x; 00575 double y; 00576 double z; 00577 double v[N_PROPERTIES]; 00578 } _boxPoint[12]; 00580 00582 void _getMoleculeData(OpenBabel::OBMol*); 00583 void _orient(void); 00584 void _getBox(double**); 00585 void _setBox(void); 00586 void _getEnergies(double**, double*); 00587 void _initiateSpectrophore(double*, double*); 00588 void _rotateX(double**, double**, const double, const double); 00589 void _rotateY(double**, double**, const double, const double); 00590 void _rotateZ(double**, double**, const double, const double); 00591 void _updateSpectrophore(double*, double*); 00592 void _calculateProperties(OpenBabel::OBMol*); 00593 void _solveMatrix(double**, double*, unsigned int); 00594 void _luDecompose(double**, std::vector<int>&, unsigned int); 00595 void _luSolve(double**, std::vector<int>&, double*, unsigned int); 00596 void _swapRows(double*, unsigned int, unsigned int); 00597 void _swapRows(double**, unsigned int, unsigned int, unsigned int); 00599 00600 }; 00601 00602 } // end namespace OpenBabel 00603 00604 00605 #endif //OB_SPECTROPHORE_H
