00001 /********************************************************************** 00002 residue.h - Defines for residue properties, names, etc. 00003 00004 Copyright (C) 2001, 2002 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.sourceforge.net/> 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 /********************************************************************** 00021 Global arrays Residue, ElemDesc and function GetResidueNumber were 00022 obtained in part or whole from RasMol2 by Roger Sayle. 00023 ***********************************************************************/ 00024 00025 #ifndef OB_RESIDUE_H 00026 #define OB_RESIDUE_H 00027 00028 #include <openbabel/babelconfig.h> 00029 00030 #ifndef EXTERN 00031 # define EXTERN extern 00032 #endif 00033 00034 #include <vector> 00035 #include <string> 00036 00037 #include <openbabel/base.h> 00038 00039 namespace OpenBabel { 00040 00041 class OBAtom; 00043 typedef std::vector<OBAtom*>::iterator OBAtomIterator; 00044 class OBBond; 00046 typedef std::vector<OBBond*>::iterator OBBondIterator; 00047 00048 // Class OBResidue 00049 // class introduction in residue.cpp 00050 class OBAPI OBResidue : public OBBase 00051 { 00052 public: 00053 00055 OBResidue(void); 00057 OBResidue(const OBResidue &); 00059 virtual ~OBResidue(void); 00060 00061 OBResidue &operator=(const OBResidue &); 00062 00064 void AddAtom(OBAtom *atom); 00066 void InsertAtom(OBAtom *atom); 00068 void RemoveAtom(OBAtom *atom); 00073 bool Clear(); 00074 00079 void SetName(const std::string &resname); 00081 void SetNum(const unsigned int resnum); 00083 void SetChain(const char chain); 00085 void SetChainNum(const unsigned int chainnum); 00088 void SetIdx(const unsigned int idx); 00089 00092 void SetAtomID(OBAtom *atom, const std::string &id); 00093 void SetHetAtom(OBAtom *atom, bool hetatm); 00095 void SetSerialNum(OBAtom *atom, unsigned int sernum); 00096 00098 std::string GetName(void) const; 00100 unsigned int GetNum(void) const; 00102 unsigned int GetNumAtoms() const; 00104 char GetChain(void) const; 00106 unsigned int GetChainNum(void) const; 00108 unsigned int GetIdx(void) const; 00110 unsigned int GetResKey(void) const; 00111 00113 std::vector<OBAtom*> GetAtoms(void) const; 00116 std::vector<OBBond*> GetBonds(bool exterior= true)const; 00117 00120 std::string GetAtomID(OBAtom *atom) const; 00122 unsigned GetSerialNum(OBAtom *atom) const; 00123 00126 bool GetAminoAcidProperty(int) const; 00129 bool GetAtomProperty(OBAtom *a, int) const; 00132 bool GetResidueProperty(int) const; 00133 00135 bool IsHetAtom(OBAtom *atom) const; 00138 bool IsResidueType(int) const; 00139 00141 00142 00143 OBAtomIterator BeginAtoms() { return _atoms.begin(); } 00145 OBAtomIterator EndAtoms() { return _atoms.end(); } 00148 OBAtom *BeginAtom(std::vector<OBAtom*>::iterator &i); 00151 OBAtom *NextAtom(std::vector<OBAtom*>::iterator &i); 00153 00154 protected: // members 00155 00156 unsigned int _idx; 00157 char _chain; 00158 unsigned int _aakey; 00159 unsigned int _reskey; 00160 unsigned int _resnum; 00161 std::string _resname; 00162 00163 std::vector<bool> _hetatm; 00164 std::vector<std::string> _atomid; 00165 std::vector<OBAtom*> _atoms; 00166 std::vector<unsigned int> _sernum; 00167 // Now in OBBase 00168 // std::vector<OBGenericData*> _vdata; //!< Custom data 00169 }; // OBResidue 00170 00172 typedef std::vector<OBResidue*>::iterator OBResidueIterator; 00173 00175 // Global Definitions 00177 00178 #define MAXSETNO 40 00179 #define MAXELEM 1024 00180 #define MINELEM 29 00181 #define MAXRES 100 00182 #define MINRES 54 00183 00185 // Amino Acid Definitions 00187 00188 #define AA_ALA (1<<1) 00189 #define AA_GLY (1<<2) 00190 #define AA_LEU (1<<3) 00191 #define AA_SER (1<<4) 00192 #define AA_VAL (1<<5) 00193 #define AA_THR (1<<6) 00194 #define AA_LYS (1<<7) 00195 #define AA_ASP (1<<8) 00196 #define AA_ILE (1<<9) 00197 #define AA_ASN (1<<10) 00198 #define AA_GLU (1<<11) 00199 #define AA_PRO (1<<12) 00200 #define AA_ARG (1<<13) 00201 #define AA_PHE (1<<14) 00202 #define AA_GLN (1<<15) 00203 #define AA_TYR (1<<16) 00204 #define AA_HIS (1<<17) 00205 #define AA_CYS (1<<18) 00206 #define AA_MET (1<<19) 00207 #define AA_TRP (1<<20) 00208 00210 // Amino Acid Property Definitions 00212 #define IS_ACIDIC(x) ((x) & ((AA_ASP)|(AA_GLU))) 00213 #define IS_ACYCLIC(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \ 00214 (AA_VAL)|(AA_THR)|(AA_LYS)|(AA_ASP)| \ 00215 (AA_ILE)|(AA_ASN)|(AA_GLU)|(AA_GLN)| \ 00216 (AA_CYS)|(AA_MET))) 00217 #define IS_ALIPHATIC(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_ILE)|(AA_LEU)| \ 00218 (AA_VAL))) 00219 #define IS_AROMATIC(x) ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR))) 00220 #define IS_BASIC(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS))) 00221 #define IS_BURIED(x) ((x) & ((AA_ALA)|(AA_CYS)|(AA_ILE)|(AA_LEU)| \ 00222 (AA_MET)|(AA_PHE)|(AA_TRP)|(AA_VAL))) 00223 #define IS_CHARGED(x) ((x) & ((AA_ASP)|(AA_GLU)|(AA_ARG)|(AA_HIS)| \ 00224 (AA_LYS))) 00225 #define IS_CYCLIC(x) ((x) & ((AA_HIS)|(AA_PHE)|(AA_PRO)|(AA_TRP)| \ 00226 (AA_TYR))) 00227 #define IS_HYDROPHOBIC(x) ((x) & ((AA_ALA)|(AA_LEU)|(AA_VAL)|(AA_ILE)| \ 00228 (AA_PRO)|(AA_PHE)|(AA_MET)|(AA_TRP))) 00229 #define IS_LARGE(x) ((x) & ((AA_ARG)|(AA_PHE)|(AA_GLN)|(AA_TYR)| \ 00230 (AA_HIS)|(AA_LEU)|(AA_LYS)|(AA_ILE)| \ 00231 (AA_GLU)|(AA_MET)|(AA_TRP))) 00232 #define IS_MEDIUM(x) ((x) & ((AA_VAL)|(AA_THR)|(AA_ASP)|(AA_ASN)| \ 00233 (AA_PRO)|(AA_CYS))) 00234 #define IS_NEGATIVE(x) ((x) & ((AA_ASP)|(AA_GLU))) 00235 #define IS_NEUTRAL(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)| \ 00236 (AA_VAL)|(AA_THR)|(AA_PHE)|(AA_GLN)| \ 00237 (AA_TYR)|(AA_HIS)|(AA_CYS)|(AA_MET)| \ 00238 (AA_TRP)|(AA_ILE)|(AA_ASN)|(AA_PRO))) 00239 #define IS_POLAR(x) ((x) & ((AA_ASP)|(AA_ILE)|(AA_ASN)|(AA_GLU)| \ 00240 (AA_SER)|(AA_THR)|(AA_ARG)|(AA_GLN)| \ 00241 (AA_CYS)|(AA_HIS))) 00242 #define IS_POSITIVE(x) ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS))) 00243 #define IS_SMALL(x) ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER))) 00244 #define IS_SURFACE(x) ((x) & ((AA_THR)|(AA_LYS)|(AA_ASP)|(AA_ILE)| \ 00245 (AA_ASN)|(AA_GLU)|(AA_PRO)|(AA_ARG)| \ 00246 (AA_GLY)|(AA_SER)|(AA_GLN)|(AA_TYR)| \ 00247 (AA_HIS))) 00248 00250 namespace OBAminoAcidProperty 00251 { 00252 enum 00253 { 00254 ACIDIC = 0, 00255 ACYCLIC = 1, 00256 ALIPHATIC = 2, 00257 AROMATIC = 3, 00258 BASIC = 4, 00259 BURIED = 5, 00260 CHARGED = 6, 00261 CYCLIC = 7, 00262 HYDROPHOBIC = 8, 00263 LARGE = 9, 00264 MEDIUM = 10, 00265 NEGATIVE = 11, 00266 NEUTRAL = 12, 00267 POLAR = 13, 00268 POSITIVE = 14, 00269 SMALL = 15, 00270 SURFACE = 16, 00271 }; 00272 } 00273 00275 namespace OBResidueAtomProperty 00276 { 00277 enum 00278 { 00279 ALPHA_CARBON = 0, 00280 AMINO_BACKBONE = 1, 00281 BACKBONE = 2, 00282 CYSTEINE_SULPHUR = 3, 00283 LIGAND = 4, 00284 NUCLEIC_BACKBONE = 5, 00285 SHAPELY_BACKBONE = 6, 00286 SHAPELY_SPECIAL = 7, 00287 SIDECHAIN = 8, 00288 SUGAR_PHOSPHATE = 9, 00289 }; 00290 } 00291 00293 // some of these are invalid or troublesome in scripting interfaces 00294 // so they are removed by the #ifndef SWIG parts 00295 // (otherwise ignore them for C++ use) 00296 namespace OBResidueIndex 00297 { 00298 enum 00299 { 00300 ALA = 0, 00301 GLY = 1, 00302 LEU = 2, 00303 SER = 3, 00304 VAL = 4, 00305 #ifndef SWIGPERL 00306 THR = 5, 00307 #endif 00308 LYS = 6, 00309 ASP = 7, 00310 ILE = 8, 00311 ASN = 9, 00312 GLU = 10, 00313 PRO = 11, 00314 ARG = 12, 00315 PHE = 13, 00316 GLN = 14, 00317 TYR = 15, 00318 HIS = 16, 00319 CYS = 17, 00320 MET = 18, 00321 TRP = 19, 00322 ASX = 20, 00323 GLX = 21, 00324 PCA = 22, 00325 HYP = 23, 00326 A = 24, 00327 C = 25, 00328 G = 26, 00329 T = 27, 00330 U = 28, 00331 UPLUS = 29, 00332 I = 30, 00333 _1MA = 32, 00334 _5MC = 32, 00335 OMC = 33, 00336 _1MG = 34, 00337 _2MG = 35, 00338 M2G = 36, 00339 _7MG = 37, 00340 OMG = 38, 00341 YG = 39, 00342 H2U = 40, 00343 _5MU = 41, 00344 PSU = 42, 00345 UNK = 43, 00346 ACE = 44, 00347 FOR = 45, 00348 HOH = 46, 00349 DOD = 47, 00350 SO4 = 48, 00351 PO4 = 49, 00352 NAD = 50, 00353 COA = 51, 00354 NAP = 52, 00355 NDP = 53, 00356 }; 00357 } 00358 00360 namespace OBResidueProperty 00361 { 00362 enum 00363 { 00364 AMINO = 0, 00365 AMINO_NUCLEO = 1, 00366 COENZYME = 2, 00367 ION = 3, 00368 NUCLEO = 4, 00369 PROTEIN = 5, 00370 PURINE = 6, 00371 PYRIMIDINE = 7, 00372 SOLVENT = 8, 00373 WATER = 9, 00374 }; 00375 } 00376 00378 // Global Variables 00380 00381 EXTERN char Residue[MAXRES][4]; 00382 EXTERN char ElemDesc[MAXELEM][4]; 00383 EXTERN unsigned int ResNo; 00384 EXTERN unsigned int ElemNo; 00385 } // end namespace OpenBabel 00386 00387 #endif 00388
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.