00001 /********************************************************************** 00002 forcefield.h - Handle OBForceField class. 00003 00004 Copyright (C) 2006-2007 by Tim Vandermeersch <[email protected]> 00005 00006 This file is part of the Open Babel project. 00007 For more information, see <http://openbabel.sourceforge.net/> 00008 00009 This program is free software; you can redistribute it and/or modify 00010 it under the terms of the GNU General Public License as published by 00011 the Free Software Foundation version 2 of the License. 00012 00013 This program is distributed in the hope that it will be useful, 00014 but WITHOUT ANY WARRANTY; without even the implied warranty of 00015 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00016 GNU General Public License for more details. 00017 ***********************************************************************/ 00018 00019 #ifndef OB_FORCEFIELD_H 00020 #define OB_FORCEFIELD_H 00021 00022 #include <vector> 00023 #include <string> 00024 #include <map> 00025 00026 #include <list> 00027 #include <set> 00028 #include <openbabel/base.h> 00029 #include <openbabel/mol.h> 00030 #include <openbabel/pluginiter.h> 00031 00032 namespace OpenBabel 00033 { 00034 // log levels 00035 #define OBFF_LOGLVL_NONE 0 00036 #define OBFF_LOGLVL_LOW 1 00037 #define OBFF_LOGLVL_MEDIUM 2 00038 #define OBFF_LOGLVL_HIGH 3 00039 00040 // terms 00041 #define OBFF_ENERGY (1 << 0) 00042 #define OBFF_EBOND (1 << 1) 00043 #define OBFF_EANGLE (1 << 2) 00044 #define OBFF_ESTRBND (1 << 3) 00045 #define OBFF_ETORSION (1 << 4) 00046 #define OBFF_EOOP (1 << 5) 00047 #define OBFF_EVDW (1 << 6) 00048 #define OBFF_EELECTROSTATIC (1 << 7) 00049 00050 // mode arguments for SteepestDescent, ConjugateGradients, ... 00051 #define OBFF_NUMERICAL_GRADIENT (1 << 0) 00052 #define OBFF_ANALYTICAL_GRADIENT (1 << 1) 00053 00054 #define KCAL_TO_KJ 4.1868 00055 00056 // inline if statements for logging. 00057 #define IF_OBFF_LOGLVL_LOW if(loglvl >= OBFF_LOGLVL_LOW) 00058 #define IF_OBFF_LOGLVL_MEDIUM if(loglvl >= OBFF_LOGLVL_MEDIUM) 00059 #define IF_OBFF_LOGLVL_HIGH if(loglvl >= OBFF_LOGLVL_HIGH) 00060 00063 class OBFFParameter { 00064 public: 00066 int a, b, c, d; 00068 std::string _a, _b, _c, _d; 00069 00071 int ipar1, ipar2, ipar3, ipar4, ipar5; 00073 double dpar1, dpar2, dpar3, dpar4, dpar5; 00074 00076 OBFFParameter& operator=(const OBFFParameter &ai) 00077 { 00078 if (this != &ai) { 00079 a = ai.a; 00080 b = ai.b; 00081 c = ai.c; 00082 d = ai.d; 00083 _a = ai._a; 00084 _b = ai._b; 00085 _c = ai._c; 00086 _d = ai._d; 00087 ipar1 = ai.ipar1; 00088 ipar2 = ai.ipar2; 00089 ipar3 = ai.ipar3; 00090 ipar4 = ai.ipar4; 00091 ipar5 = ai.ipar5; 00092 dpar1 = ai.dpar1; 00093 dpar2 = ai.dpar2; 00094 dpar3 = ai.dpar3; 00095 dpar4 = ai.dpar4; 00096 dpar5 = ai.dpar5; 00097 } 00098 00099 return *this; 00100 } 00101 00103 void clear () 00104 { 00105 a = 0; 00106 b = 0; 00107 c = 0; 00108 d = 0; 00109 ipar1 = 0; 00110 ipar2 = 0; 00111 ipar3 = 0; 00112 ipar4 = 0; 00113 ipar5 = 0; 00114 dpar1 = 0.0f; 00115 dpar2 = 0.0f; 00116 dpar3 = 0.0f; 00117 dpar4 = 0.0f; 00118 dpar5 = 0.0f; 00119 } 00120 }; // class OBFFParameter 00121 00122 // specific class introductions in forcefieldYYYY.cpp (for YYYY calculations) 00125 class OBFFCalculation 00126 { 00127 public: 00129 double energy; 00131 vector3 grada, gradb, gradc, gradd; 00133 OBAtom *a, *b, *c, *d; 00134 00136 OBFFCalculation() 00137 { 00138 a = NULL; 00139 b = NULL; 00140 c = NULL; 00141 d = NULL; 00142 energy = 0.0f; 00143 grada = VZero; 00144 gradb = VZero; 00145 gradc = VZero; 00146 gradd = VZero; 00147 } 00149 virtual ~OBFFCalculation() 00150 { 00151 } 00152 00154 virtual void Compute(bool gradients = true) 00155 { 00156 } 00158 virtual double GetEnergy() 00159 { 00160 if (!energy) 00161 Compute(false); 00162 00163 return energy; 00164 } 00166 virtual vector3 GetGradient(OBAtom *atom) 00167 { 00168 if (atom == a) 00169 return grada; 00170 else if (atom == b) 00171 return gradb; 00172 else if (atom == c) 00173 return gradc; 00174 else if (atom == d) 00175 return gradd; 00176 else 00177 return VZero; 00178 } 00179 }; 00180 00181 // Class OBForceField 00182 // class introduction in forcefield.cpp 00183 class OBAPI OBForceField 00184 { 00185 00186 MAKE_PLUGIN(OBForceField) 00187 00188 protected: 00230 OBFFParameter* GetParameter(int a, int b, int c, int d, std::vector<OBFFParameter> ¶meter); 00232 OBFFParameter* GetParameter(const char* a, const char* b, const char* c, const char* d, std::vector<OBFFParameter> ¶meter); 00233 00235 00240 vector3 NumericalDerivative(OBAtom *a, int terms = OBFF_ENERGY); 00242 vector3 NumericalSecondDerivative(OBAtom *a, int terms = OBFF_ENERGY); 00252 virtual vector3 GetGradient(OBAtom *a, int terms = OBFF_ENERGY) 00253 { 00254 return -NumericalDerivative(a, terms); 00255 } 00261 bool IsInSameRing(OBAtom* a, OBAtom* b); 00262 00263 OBMol _mol; 00264 00266 std::ostream* logos; 00267 char logbuf[200]; 00268 int loglvl; 00269 00271 int current_conformer; 00272 00274 double _econv, _e_n1; 00275 int _method, _cstep, _nsteps; 00276 std::vector<vector3> _grad1, _dir1; 00277 00278 public: 00280 virtual ~OBForceField() 00281 { 00282 } 00284 //virtual std::string Description()=0; 00288 static OBForceField* FindForceField(const std::string& ID) 00289 { 00290 return Iter().FindType(ID); 00291 } 00295 static OBForceField* FindForceField(const char *ID) 00296 { 00297 std::string ffname(ID); 00298 return FindForceField(ffname); 00299 } 00301 virtual std::string GetUnit() { return std::string("au"); } 00306 virtual bool Setup(OBMol &mol) { return false; } 00311 bool UpdateCoordinates(OBMol &mol); 00316 bool UpdateConformers(OBMol &mol); 00320 void OBFFLog(std::string msg) 00321 { 00322 if (!logos) 00323 return; 00324 00325 *logos << msg; 00326 } 00330 void OBFFLog(const char *msg) 00331 { 00332 if (!logos) 00333 return; 00334 00335 *logos << msg; 00336 } 00337 00339 // Energy Evaluation // 00341 00343 00344 00352 virtual double Energy(bool gradients = true) { return 0.0f; } 00358 virtual double E_Bond(bool gradients = true) { return 0.0f; } 00364 virtual double E_Angle(bool gradients = true) { return 0.0f; } 00370 virtual double E_StrBnd(bool gradients = true) { return 0.0f; } 00376 virtual double E_Torsion(bool gradients = true) { return 0.0f; } 00382 virtual double E_OOP(bool gradients = true) { return 0.0f; } 00388 virtual double E_VDW(bool gradients = true) { return 0.0f; } 00394 virtual double E_Electrostatic(bool gradients = true) { return 0.0f; } 00396 00398 // Logging // 00400 00402 00403 00407 bool SetLogFile(std::ostream *pos); 00436 bool SetLogLevel(int level); 00438 int GetLogLevel() { return loglvl; } 00440 00442 // Structure Generation // 00444 00446 00447 00464 void SystematicRotorSearch(); 00465 00467 // Energy Minimization // 00469 00471 00472 00484 vector3 LineSearch(OBAtom *atom, vector3 &direction); 00499 void SteepestDescent(int steps, double econv = 1e-6f, int method = OBFF_ANALYTICAL_GRADIENT); 00527 void SteepestDescentInitialize(int steps = 1000, double econv = 1e-6f, int method = OBFF_ANALYTICAL_GRADIENT); 00543 bool SteepestDescentTakeNSteps(int n); 00559 void ConjugateGradients(int steps, double econv = 1e-6f, int method = OBFF_ANALYTICAL_GRADIENT); 00586 void ConjugateGradientsInitialize(int steps = 1000, double econv = 1e-6f, int method = OBFF_ANALYTICAL_GRADIENT); 00601 bool ConjugateGradientsTakeNSteps(int n); 00603 00605 // Validation // 00607 00609 00610 00611 virtual bool Validate() { return false; } 00616 virtual bool ValidateGradients() { return false; } 00621 vector3 ValidateGradientError(vector3 &numgrad, vector3 &anagrad); 00623 00625 // Vector Analysis // 00627 00629 00630 00636 static double VectorLengthDerivative(vector3 &a, vector3 &b); 00643 static double VectorAngleDerivative(vector3 &a, vector3 &b, vector3 &c); 00651 static double VectorTorsionDerivative(vector3 &a, vector3 &b, vector3 &c, vector3 &d); 00653 00658 void kludge() 00659 { 00660 PluginIter<OBForceField> it; 00661 (++it)->SetLogLevel(1); 00662 if(it)it.ID(); 00663 } 00664 00665 }; // class OBForceField 00666 00667 }// namespace OpenBabel 00668 00669 #endif // OB_FORCEFIELD_H 00670
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.