rotamer.h
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00001 /********************************************************************** 00002 rotamer.h - Handle rotamer list data. 00003 00004 Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison 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 This program is distributed in the hope that it will be useful, 00015 but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 GNU General Public License for more details. 00018 ***********************************************************************/ 00019 00020 #ifndef OB_ROTAMER_H 00021 #define OB_ROTAMER_H 00022 00023 #include <vector> 00024 #include <map> 00025 00026 #include <openbabel/mol.h> 00027 #include <openbabel/rotor.h> 00028 #include <openbabel/generic.h> 00029 00030 namespace OpenBabel 00031 { 00032 00034 // Further class introduction in rotamer.cpp 00035 class OBAPI OBRotamerList : public OBGenericData 00036 { 00038 unsigned int _NBaseCoords; 00040 std::vector<double*> _c; 00042 std::vector<std::pair<OBAtom**,std::vector<int> > > _vrotor; 00045 std::vector<std::vector<double> > _vres; 00047 std::vector<unsigned char*> _vrotamer; 00048 00049 /*Because contains OBAtom*, these aren't meaningful without knowing the parent molecule 00050 OBRotamerList(const OBRotamerList &cpy) : OBGenericData(cpy) 00051 {} 00052 OBRotamerList& operator =(const OBRotamerList &) 00053 { 00054 return *this; 00055 } 00056 */ 00057 00058 public: 00059 OBRotamerList() 00060 { 00061 _NBaseCoords=0; 00062 _type= OBGenericDataType::RotamerList; 00063 _attr="RotamerList"; 00064 } 00065 virtual OBGenericData* Clone(OBBase* parent) const; 00066 00067 ~OBRotamerList(); 00069 void Setup(OBMol&,OBRotorList&); 00074 void Setup(OBMol &mol,unsigned char*ref,int nrotors); 00076 unsigned int NumRotors() const 00077 { 00078 return (unsigned int)_vrotor.size(); 00079 } 00081 unsigned int NumRotamers() const 00082 { 00083 return (unsigned int)_vrotamer.size(); 00084 } 00086 void AddRotamer(double*); 00088 void AddRotamer(int *key); 00090 void AddRotamer(std::vector<int> key); 00092 void AddRotamer(unsigned char *key); 00094 void AddRotamers(unsigned char *arr,int nconf); 00096 void GetReferenceArray(unsigned char*) const; 00097 00099 00100 std::vector<unsigned char*>::iterator BeginRotamer() 00101 { 00102 return _vrotamer.begin(); 00103 } 00104 std::vector<unsigned char*>::iterator EndRotamer() 00105 { 00106 return _vrotamer.end(); 00107 } 00109 00112 std::vector<double*> CreateConformerList(OBMol& mol); 00113 00116 void ExpandConformerList(OBMol&mol,std::vector<double*>& confs); 00117 00118 void SetCurrentCoordinates(OBMol &mol, std::vector<int> arr); 00119 00122 void SetBaseCoordinateSets(OBMol& mol) 00123 { 00124 SetBaseCoordinateSets(mol.GetConformers(), mol.NumAtoms()); 00125 } 00126 00128 00131 void SetBaseCoordinateSets(std::vector<double*> bc, unsigned int N); 00132 00134 unsigned int NumBaseCoordinateSets() const 00135 { 00136 return static_cast<unsigned int> (_c.size()); 00137 } 00138 00140 double *GetBaseCoordinateSet(unsigned int i) const 00141 { 00142 return (i<_c.size()) ? _c[i] : NULL; 00143 } 00144 00146 unsigned int NumAtoms() const 00147 { 00148 return _NBaseCoords; 00149 } 00150 }; 00151 00153 int Swab(int); 00154 00155 } 00156 00157 #endif // OB_ROTAMER_H 00158
