1 /********************************************************************************************************** 2 Copyright (c) 2002-2013 Abdul-Rahman Allouche. All rights reserved 3 4 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated 5 documentation files (the Gabedit), to deal in the Software without restriction, including without limitation 6 the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, 7 and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 8 9 The above copyright notice and this permission notice shall be included in all copies or substantial portions 10 of the Software. 11 12 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED 13 TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL 14 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 15 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 16 DEALINGS IN THE SOFTWARE. 17 ************************************************************************************************************/ 18 19 #ifndef __GABEDIT_MOLECULARMECHANICS_H__ 20 #define __GABEDIT_MOLECULARMECHANICS_H__ 21 22 typedef struct _AmberParameters AmberParameters; 23 typedef struct _AmberAtomTypes AmberAtomTypes; 24 typedef struct _AmberBondStretchTerms AmberBondStretchTerms; 25 typedef struct _AmberAngleBendTerms AmberAngleBendTerms; 26 typedef struct _AmberDihedralAngleTerms AmberDihedralAngleTerms; 27 typedef struct _AmberImproperTorsionTerms AmberImproperTorsionTerms; 28 typedef struct _AmberNonBondedTerms AmberNonBondedTerms; 29 typedef struct _AmberHydrogenBondedTerms AmberHydrogenBondedTerms; 30 typedef struct _AmberPairWiseTerms AmberPairWiseTerms; 31 32 /************************************/ 33 struct _AmberAtomTypes 34 { 35 gchar* name; 36 gchar* symbol; 37 gint number; 38 gdouble masse; 39 gdouble polarisability; 40 gchar* description; 41 }; 42 /************************************/ 43 struct _AmberBondStretchTerms 44 { 45 gint numbers[2]; 46 gdouble equilibriumDistance; 47 gdouble forceConstant; 48 }; 49 /************************************/ 50 struct _AmberAngleBendTerms 51 { 52 gint numbers[3]; 53 gdouble equilibriumAngle; 54 gdouble forceConstant; 55 }; 56 /************************************/ 57 struct _AmberDihedralAngleTerms 58 { 59 gint numbers[4]; 60 gint nSomme; 61 gdouble* divisor; 62 gdouble* barrier; 63 gdouble* phase; 64 gdouble* n; 65 }; 66 /************************************/ 67 struct _AmberImproperTorsionTerms 68 { 69 gint numbers[4]; 70 gdouble barrier; 71 gdouble phase; 72 gdouble n; 73 }; 74 /************************************/ 75 struct _AmberNonBondedTerms 76 { 77 gint number; 78 gdouble r; 79 gdouble epsilon; 80 }; 81 /************************************/ 82 struct _AmberHydrogenBondedTerms 83 { 84 gint numbers[2]; 85 gdouble c; 86 gdouble d; 87 }; 88 /************************************/ 89 struct _AmberPairWiseTerms 90 { 91 gint numbers[2]; 92 gdouble a; 93 gdouble beta; 94 gdouble c6; 95 gdouble c8; 96 gdouble c10; 97 gdouble b; 98 }; 99 /************************************/ 100 struct _AmberParameters 101 { 102 gint numberOfTypes; 103 AmberAtomTypes* atomTypes; 104 105 gint numberOfStretchTerms; 106 AmberBondStretchTerms* bondStretchTerms; 107 108 gint numberOfBendTerms; 109 AmberAngleBendTerms* angleBendTerms; 110 111 gint numberOfDihedralTerms; 112 AmberDihedralAngleTerms* dihedralAngleTerms; 113 114 gint numberOfImproperTorsionTerms; 115 AmberImproperTorsionTerms* improperTorsionTerms; 116 117 gint numberOfNonBonded; 118 AmberNonBondedTerms* nonBondedTerms; 119 120 gint numberOfHydrogenBonded; 121 AmberHydrogenBondedTerms* hydrogenBondedTerms; 122 123 gint numberOfPairWise; 124 AmberPairWiseTerms* pairWiseTerms; 125 }; 126 /************************************/ 127 ForceField createAmberModel(GeomDef* geom,gint Natoms,ForceFieldOptions forceFieldOptions); 128 ForceField createPairWiseModel(GeomDef* geom,gint Natoms,ForceFieldOptions forceFieldOptions); 129 void loadAmberParameters(); 130 void saveAmberParameters(); 131 AmberParameters* getPointerAmberParameters(); 132 void setPointerAmberParameters(AmberParameters* ptr); 133 AmberParameters newAmberParameters(); 134 gchar** getListMMTypes(gint* nlist); 135 136 #endif /* __GABEDIT_MOLECULARMECHANICS_H__ */ 137 138