00001 /********************************************************************** 00002 atom.h - Handle OBAtom class. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison 00006 Some portions Copyright (C) 2003 by Michael Banck 00007 00008 This file is part of the Open Babel project. 00009 For more information, see <http://openbabel.sourceforge.net/> 00010 00011 This program is free software; you can redistribute it and/or modify 00012 it under the terms of the GNU General Public License as published by 00013 the Free Software Foundation version 2 of the License. 00014 00015 This program is distributed in the hope that it will be useful, 00016 but WITHOUT ANY WARRANTY; without even the implied warranty of 00017 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00018 GNU General Public License for more details. 00019 ***********************************************************************/ 00020 00021 #ifndef OB_ATOM_H 00022 #define OB_ATOM_H 00023 00024 #include <openbabel/babelconfig.h> 00025 00026 #ifndef EXTERN 00027 # define EXTERN extern 00028 #endif 00029 00030 #include <vector> 00031 #include <string> 00032 00033 #include <openbabel/base.h> 00034 #include <openbabel/residue.h> 00035 00036 namespace OpenBabel 00037 { 00038 00039 class OBBond; 00040 class OBMol; 00041 00043 typedef OBAtom OBNodeBase; 00045 typedef std::vector<OBBond*>::iterator OBBondIterator; 00047 typedef std::vector<OBAtom*>::iterator OBAtomIterator; 00048 00049 //ATOM Property Macros (flags) 00051 #define OB_4RING_ATOM (1<<1) 00053 #define OB_3RING_ATOM (1<<2) 00055 #define OB_AROMATIC_ATOM (1<<3) 00057 #define OB_RING_ATOM (1<<4) 00059 #define OB_CSTEREO_ATOM (1<<5) 00061 #define OB_ACSTEREO_ATOM (1<<6) 00063 #define OB_DONOR_ATOM (1<<7) 00065 #define OB_ACCEPTOR_ATOM (1<<8) 00067 #define OB_CHIRAL_ATOM (1<<9) 00069 #define OB_POS_CHIRAL_ATOM (1<<10) 00071 #define OB_NEG_CHIRAL_ATOM (1<<11) 00073 #define OB_ATOM_HAS_NO_H (1<<12) 00074 // 13-16 currently unused 00075 00076 // Class OBAtom 00077 // class introduction in atom.cpp 00078 class OBAPI OBAtom: public OBBase 00079 { 00080 protected: 00081 char _ele; 00082 char _impval; 00083 char _type[6]; 00084 short _fcharge; 00085 unsigned short _isotope; 00086 short _spinmultiplicity; 00087 00088 unsigned int _idx; 00089 OBMol *_parent; 00090 std::vector<OBBond*> _vbond; 00091 00092 unsigned int _cidx; 00093 unsigned short _hyb; 00094 unsigned short _flags; 00095 double _pcharge; 00096 double **_c; 00097 mutable vector3 _v; 00098 OBResidue *_residue; 00099 00101 int GetFlag() const { return(_flags); } 00103 void SetFlag(int flag) { _flags |= flag; } 00105 bool HasFlag(int flag) { return((_flags & flag) ? true : false); } 00106 00107 public: 00109 bool Visit; 00110 00112 OBAtom(); 00114 virtual ~OBAtom(); 00116 OBAtom &operator = (OBAtom &); 00119 bool Clear(); 00120 00122 00123 00124 void SetIdx(int idx) { _idx = idx; _cidx = (idx-1)*3; } 00126 void SetHyb(int hyb) { _hyb = hyb; } 00128 void SetAtomicNum(int atomicnum) { _ele = (char)atomicnum; } 00130 void SetIsotope(unsigned int iso); 00132 void SetImplicitValence(int val) { _impval = (char)val; } 00134 void IncrementImplicitValence() { _impval++; } 00136 void DecrementImplicitValence() { _impval--; } 00138 void SetFormalCharge(int fcharge) { _fcharge = fcharge; } 00140 void SetSpinMultiplicity(short spin){ _spinmultiplicity = spin; } 00142 void SetType(const char *type); 00144 void SetType(std::string &type); 00146 void SetPartialCharge(double pcharge){ _pcharge = pcharge; } 00148 void SetVector(const vector3 &v); 00150 void SetVector(const double x,const double y,const double z); 00152 void SetCoordPtr(double **c) { _c = c; _cidx = (GetIdx()-1)*3; } 00154 void SetVector(); 00156 void SetResidue(OBResidue *res) { _residue=res; } 00158 void SetParent(OBMol *ptr) { _parent=ptr; } 00160 void SetAromatic() { SetFlag(OB_AROMATIC_ATOM); } 00162 void UnsetAromatic() { _flags &= (~(OB_AROMATIC_ATOM)); } 00164 void SetClockwiseStereo() { SetFlag(OB_CSTEREO_ATOM|OB_CHIRAL_ATOM); } 00166 void SetAntiClockwiseStereo() { SetFlag(OB_ACSTEREO_ATOM|OB_CHIRAL_ATOM); } 00168 void SetPositiveStereo() { SetFlag(OB_POS_CHIRAL_ATOM|OB_CHIRAL_ATOM); } 00170 void SetNegativeStereo() { SetFlag(OB_NEG_CHIRAL_ATOM|OB_CHIRAL_ATOM); } 00172 void UnsetStereo() 00173 { 00174 _flags &= ~(OB_ACSTEREO_ATOM); 00175 _flags &= ~(OB_CSTEREO_ATOM); 00176 _flags &= ~(OB_POS_CHIRAL_ATOM); 00177 _flags &= ~(OB_NEG_CHIRAL_ATOM); 00178 _flags &= ~(OB_CHIRAL_ATOM); 00179 } 00181 void SetInRing() { SetFlag(OB_RING_ATOM); } 00183 void SetChiral() { SetFlag(OB_CHIRAL_ATOM); } 00185 void ClearCoordPtr() { _c = NULL; _cidx=0; } 00187 00189 00190 00191 int GetFormalCharge() const { return(_fcharge); } 00193 unsigned int GetAtomicNum() const { return((unsigned int)_ele); } 00195 unsigned short int GetIsotope() const { return(_isotope); } 00198 int GetSpinMultiplicity() const { return(_spinmultiplicity); } 00201 double GetAtomicMass() const; 00204 double GetExactMass() const; 00206 unsigned int GetIdx() const { return((int)_idx); } 00209 unsigned int GetCoordinateIdx() const { return((int)_cidx); } 00211 unsigned int GetCIdx() const { return((int)_cidx); } 00213 unsigned int GetValence() const 00214 { 00215 return((_vbond.empty()) ? 0 : _vbond.size()); 00216 } 00218 unsigned int GetHyb() const; 00220 unsigned int GetImplicitValence() const; 00222 unsigned int GetHvyValence() const; 00224 unsigned int GetHeteroValence() const; 00226 char *GetType(); 00227 00229 double GetX() { return(x()); } 00231 double GetY() { return(y()); } 00233 double GetZ() { return(z()); } 00234 00235 // These methods check to see if there is a coordinate pointer 00236 // or an internal vector (e.g., SetCoordPtr()) 00238 double x() { 00239 if (_c) return((*_c)[_cidx]); 00240 else return _v.x(); 00241 } 00243 double y() { 00244 if (_c) return((*_c)[_cidx+1]); 00245 else return _v.y(); 00246 } 00248 double z() { 00249 if (_c) return((*_c)[_cidx+2]); 00250 else return _v.z(); 00251 } 00256 double *GetCoordinate(){ 00257 if (_c) return(&(*_c)[_cidx]); 00258 else return NULL; 00259 } 00261 vector3 &GetVector(); 00262 const vector3 &GetVector() const; 00264 double GetPartialCharge(); 00266 OBResidue *GetResidue(); 00268 OBMol *GetParent() {return((OBMol*)_parent);} 00271 bool GetNewBondVector(vector3 &v,double length); 00274 OBBond *GetBond(OBAtom *); 00279 OBAtom *GetNextAtom(); 00281 00283 00284 00285 OBBondIterator BeginBonds() 00286 { return(_vbond.begin()); } 00288 OBBondIterator EndBonds() 00289 { return(_vbond.end()); } 00292 OBBond *BeginBond(OBBondIterator &i); 00295 OBBond *NextBond(OBBondIterator &i); 00298 OBAtom *BeginNbrAtom(OBBondIterator &i); 00301 OBAtom *NextNbrAtom(OBBondIterator &i); 00303 00305 double GetDistance(int index); 00307 double GetDistance(OBAtom*); 00309 double GetAngle(int b, int c); 00311 double GetAngle(OBAtom *b, OBAtom *c); 00312 00314 00315 00317 void NewResidue() 00318 { 00319 if (!_residue) 00320 _residue = new OBResidue; 00321 } 00323 void AddResidue(OBResidue *res) { SetResidue(res); } 00325 void DeleteResidue(){ 00326 if (_residue) { 00327 delete _residue; 00328 _residue = NULL; // Make sure to clear that a residue existed 00329 } 00330 } 00332 void AddBond(OBBond *bond) { _vbond.push_back(bond); } 00335 void InsertBond(OBBondIterator &i, OBBond *bond) 00336 { 00337 _vbond.insert(i, bond); 00338 } 00340 bool DeleteBond(OBBond* bond); 00342 void ClearBond() {_vbond.clear();} 00344 00346 00347 00350 bool HtoMethyl(); 00353 bool SetHybAndGeom(int); 00355 void ForceNoH() {SetFlag(OB_ATOM_HAS_NO_H);} 00357 bool HasNoHForced() {return HasFlag(OB_ATOM_HAS_NO_H);} 00359 00361 00362 00363 unsigned int CountFreeOxygens() const; 00365 unsigned int ImplicitHydrogenCount() const; 00367 unsigned int ExplicitHydrogenCount(bool ExcludeIsotopes=false) const; 00369 unsigned int MemberOfRingCount() const; 00371 unsigned int MemberOfRingSize() const; 00373 unsigned int CountRingBonds() const; 00375 double SmallestBondAngle(); 00377 double AverageBondAngle(); 00379 unsigned int BOSum() const; 00382 unsigned int KBOSum() const; 00384 bool HasResidue() { return(_residue != NULL); } 00386 bool IsHydrogen() { return(GetAtomicNum() == 1); } 00388 bool IsCarbon() { return(GetAtomicNum() == 6); } 00390 bool IsNitrogen() { return(GetAtomicNum() == 7); } 00392 bool IsOxygen() { return(GetAtomicNum() == 8); } 00394 bool IsSulfur() { return(GetAtomicNum() == 16);} 00396 bool IsPhosphorus() { return(GetAtomicNum() == 15);} 00398 bool IsAromatic() const; 00400 bool IsInRing() const; 00402 bool IsInRingSize(int) const; 00405 bool IsHeteroatom(); 00407 bool IsNotCorH(); 00409 bool IsConnected(OBAtom*); 00412 bool IsOneThree(OBAtom*); 00415 bool IsOneFour(OBAtom*); 00417 bool IsCarboxylOxygen(); 00419 bool IsPhosphateOxygen(); 00421 bool IsSulfateOxygen(); 00423 bool IsNitroOxygen(); 00425 bool IsAmideNitrogen(); 00428 bool IsPolarHydrogen(); 00431 bool IsNonPolarHydrogen(); 00434 bool IsAromaticNOxide(); 00436 bool IsChiral(); 00438 bool IsAxial(); 00440 bool IsClockwise() { return(HasFlag(OB_CSTEREO_ATOM)); } 00442 bool IsAntiClockwise() { return(HasFlag(OB_ACSTEREO_ATOM)); } 00444 bool IsPositiveStereo() { return(HasFlag(OB_POS_CHIRAL_ATOM)); } 00446 bool IsNegativeStereo() { return(HasFlag(OB_NEG_CHIRAL_ATOM)); } 00448 bool HasChiralitySpecified() 00449 { return(HasFlag(OB_CSTEREO_ATOM|OB_ACSTEREO_ATOM)); } 00451 bool HasChiralVolume() 00452 { return(HasFlag(OB_POS_CHIRAL_ATOM|OB_NEG_CHIRAL_ATOM)); } 00454 bool IsHbondAcceptor(); 00456 bool IsHbondDonor(); 00458 bool IsHbondDonorH(); 00463 bool HasAlphaBetaUnsat(bool includePandS=true); 00465 bool HasBondOfOrder(unsigned int bo); 00467 int CountBondsOfOrder(unsigned int bo); 00469 bool HasNonSingleBond(); 00471 bool HasSingleBond() { return(HasBondOfOrder(1)); } 00473 bool HasDoubleBond() { return(HasBondOfOrder(2)); } 00475 bool HasAromaticBond() { return(HasBondOfOrder(5)); } 00477 bool MatchesSMARTS(const char *); 00479 00480 }; // class OBAtom 00481 00482 }// namespace OpenBabel 00483 00484 #endif // OB_ATOM_H 00485
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.