stereo.h
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00001 /********************************************************************** 00002 stereo.h - OBStereo & OBStereoBase 00003 00004 Copyright (C) 2009-2010 by Tim Vandermeersch 00005 00006 This file is part of the Open Babel project. 00007 For more information, see <http://openbabel.org/> 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; either version 2 of the License, or 00012 (at your option) any later version. 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 You should have received a copy of the GNU General Public License 00020 along with this program; if not, write to the Free Software 00021 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 00022 02110-1301, USA. 00023 **********************************************************************/ 00024 #ifndef OB_STEREO_H 00025 #define OB_STEREO_H 00026 00027 #include <openbabel/base.h> // OBGenericData 00028 #include <openbabel/isomorphism.h> // Automorphisms 00029 #include <vector> 00030 #include <map> 00031 #include <set> 00032 #include <climits> // UINT_MAX 00033 00034 namespace OpenBabel { 00035 00038 00075 struct OBAPI OBStereo 00076 { 00080 enum Type { 00081 CisTrans = (1<<0), 00082 ExtendedCisTrans = (1<<1), 00083 SquarePlanar = (1<<2), 00084 Tetrahedral = (1<<3), 00085 ExtendedTetrahedral = (1<<4), 00086 TrigonalBipyramidal = (1<<5), 00087 Octahedral = (1<<6) 00088 }; 00089 00094 enum BondDirection { // Values taken from MDL format 00095 NotStereo = 0, 00096 UpBond = 1, 00097 DownBond = 6, 00098 UnknownDir = 4 00099 }; 00100 00108 enum Shape { 00109 ShapeU = 1, 00110 ShapeZ = 2, 00111 Shape4 = 3 00112 }; 00113 00119 enum View 00120 { 00121 ViewFrom = 1, 00122 ViewTowards = 2 00123 }; 00124 00130 enum Winding { 00131 Clockwise = 1, 00132 AntiClockwise = 2, 00133 UnknownWinding = 3 00134 }; 00135 00137 00138 00145 typedef unsigned long Ref; 00149 enum { 00150 NoRef = UINT_MAX, 00151 ImplicitRef = UINT_MAX - 1 00152 }; 00156 typedef std::vector<Ref> Refs; 00160 typedef Refs::iterator RefIter; 00164 typedef Refs::const_iterator ConstRefIter; 00166 00168 00169 00175 static Refs MakeRefs(Ref ref1, Ref ref2, Ref ref3, Ref ref4 = NoRef) 00176 { 00177 Refs refs(3); 00178 refs[0] = ref1; 00179 refs[1] = ref2; 00180 refs[2] = ref3; 00181 if (ref4 != NoRef) 00182 refs.push_back(ref4); 00183 return refs; 00184 } 00197 static bool ContainsSameRefs(const Refs &refs1, const Refs &refs2); 00201 static bool ContainsRef(const Refs &refs, unsigned long ref); 00203 00205 00206 00226 static int NumInversions(const Refs &refs); 00236 static void Permutate(Refs &refs, int i, int j); 00248 static Refs Permutated(const Refs &refs, int i, int j); 00250 00251 }; 00252 00258 struct OBStereoUnit 00259 { 00264 OBStereoUnit() : type(static_cast<OBStereo::Type>(0)), id(OBStereo::NoRef), para(false) 00265 { 00266 } 00267 00271 OBStereoUnit(OBStereo::Type _type, unsigned long _id, bool _para = false) : 00272 type(_type), id(_id), para(_para) 00273 { 00274 } 00275 00276 OBStereo::Type type; 00277 unsigned long id; 00278 bool para; 00279 }; 00287 typedef std::vector<OBStereoUnit> OBStereoUnitSet; 00294 typedef std::vector<OBStereoUnitSet> OBStereoUnitSetOfSets; 00295 00296 00297 // fwd decl 00298 class OBMol; 00321 class OBAPI OBStereoBase : public OBGenericData 00322 { 00323 public: 00330 OBStereoBase(OBMol *mol) : 00331 OBGenericData("StereoData", OBGenericDataType::StereoData, perceived), 00332 m_mol(mol), m_specified(true) 00333 { 00334 } 00338 virtual ~OBStereoBase() { m_mol = 0; } 00339 00341 00342 00346 OBMol* GetMolecule() const { return m_mol; } 00350 virtual OBStereo::Type GetType() const = 0; 00356 void SetSpecified(bool specified) { m_specified = specified; } 00360 bool IsSpecified() const { return m_specified; } 00362 private: 00363 OBMol *m_mol; 00364 bool m_specified; 00365 }; 00366 00367 // fwd decl 00368 class OBTetrahedralStereo; 00369 class OBCisTransStereo; 00370 class OBSquarePlanarStereo; 00384 class OBAPI OBStereoFacade 00385 { 00386 public: 00394 OBStereoFacade(OBMol *mol, bool perceive = true) : 00395 m_mol(mol), m_init(false), m_perceive(perceive) 00396 { 00397 } 00398 00401 00404 unsigned int NumTetrahedralStereo(); 00409 bool HasTetrahedralStereo(unsigned long atomId); 00415 OBTetrahedralStereo* GetTetrahedralStereo(unsigned long atomId); 00417 00420 00423 unsigned int NumCisTransStereo(); 00428 bool HasCisTransStereo(unsigned long bondId); 00434 OBCisTransStereo* GetCisTransStereo(unsigned long bondId); 00436 00439 00442 unsigned int NumSquarePlanarStereo(); 00447 bool HasSquarePlanarStereo(unsigned long atomId); 00453 OBSquarePlanarStereo* GetSquarePlanarStereo(unsigned long atomId); 00455 00456 template<int StereoType> 00457 bool HasStereo(unsigned long id); 00458 template<typename T> 00459 T* GetStereo(unsigned long id); 00460 00461 00462 private: 00466 inline void EnsureInit() { if (!m_init) InitMaps(); } 00472 void InitMaps(); 00473 00474 OBMol *m_mol; 00475 bool m_init; 00476 bool m_perceive; 00477 std::map<unsigned long, OBTetrahedralStereo*> m_tetrahedralMap; 00478 std::map<unsigned long, OBCisTransStereo*> m_cistransMap; 00479 std::map<unsigned long, OBSquarePlanarStereo*> m_squarePlanarMap; 00480 }; 00481 00482 // fwd decl 00483 class OBBond; 00486 00494 OBAPI void PerceiveStereo(OBMol *mol, bool force = false); 00526 OBAPI void StereoFrom2D(OBMol *mol, 00527 std::map<OBBond*, enum OBStereo::BondDirection> *updown = NULL, bool force = false); 00544 OBAPI void StereoFrom3D(OBMol *mol, bool force = false); 00560 OBAPI void StereoFrom0D(OBMol *mol); 00562 00565 00603 OBAPI std::vector<OBTetrahedralStereo*> TetrahedralFrom3D(OBMol *mol, 00604 const OBStereoUnitSet &stereoUnits, bool addToMol = true); 00649 OBAPI std::vector<OBTetrahedralStereo*> TetrahedralFrom2D(OBMol *mol, 00650 const OBStereoUnitSet &stereoUnits, bool addToMol = true); 00670 OBAPI std::vector<OBTetrahedralStereo*> TetrahedralFrom0D(OBMol *mol, 00671 const OBStereoUnitSet &stereoUnits, bool addToMol = true); 00672 00709 OBAPI std::vector<OBCisTransStereo*> CisTransFrom3D(OBMol *mol, 00710 const OBStereoUnitSet &stereoUnits, bool addToMol = true); 00741 OBAPI std::vector<OBCisTransStereo*> CisTransFrom2D(OBMol *mol, 00742 const OBStereoUnitSet &stereoUnits, 00743 const std::map<OBBond*, enum OBStereo::BondDirection> *updown = NULL, bool addToMol = true); 00770 OBAPI bool TetStereoToWedgeHash(OBMol &mol, 00771 std::map<OBBond*, enum OBStereo::BondDirection> &updown, 00772 std::map<OBBond*, OBStereo::Ref> &from); 00784 OBAPI std::set<OBBond*> GetUnspecifiedCisTrans(OBMol& mol); 00796 OBAPI void StereoRefToImplicit(OBMol& mol, OBStereo::Ref atomId); 00810 OBAPI void ImplicitRefToStereo(OBMol& mol, OBStereo::Ref centerId, OBStereo::Ref newId); 00830 OBAPI std::vector<OBCisTransStereo*> CisTransFrom0D(OBMol *mol, 00831 const OBStereoUnitSet &stereoUnits, 00832 bool addToMol = true); 00834 00835 00838 00918 OBAPI OBStereoUnitSet FindStereogenicUnits(OBMol *mol, 00919 const std::vector<unsigned int> &symClasses); 00996 OBAPI OBStereoUnitSet FindStereogenicUnits(OBMol *mol, 00997 const std::vector<unsigned int> &symClasses, 00998 const Automorphisms &automorphisms); 01000 01150 01151 } 01152 01153 #endif 01154
