Open Babel: residue.h Source File

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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.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 /**********************************************************************
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);
00082     void    SetNum(const std::string  resnum);
00084     void    SetChain(const char chain);
00086     void    SetChainNum(const unsigned int chainnum);
00089     void    SetIdx(const unsigned int idx);
00090 
00093     void    SetAtomID(OBAtom *atom, const std::string &id);
00094     void    SetHetAtom(OBAtom *atom, bool hetatm);
00096     void    SetSerialNum(OBAtom *atom, unsigned int sernum);
00097 
00099     std::string    GetName(void)                  const;
00101     unsigned int    GetNum(void);
00102     std::string     GetNumString(void);
00104     unsigned int   GetNumAtoms()                  const;
00106     char           GetChain(void)                 const;
00108     unsigned int   GetChainNum(void)              const;
00110     unsigned int   GetIdx(void)                   const;
00112     unsigned int   GetResKey(void)                const;
00113 
00115     std::vector<OBAtom*> GetAtoms(void)           const;
00118     std::vector<OBBond*> GetBonds(bool exterior= true)const;
00119 
00122     std::string    GetAtomID(OBAtom *atom)        const;
00124     unsigned       GetSerialNum(OBAtom *atom)     const;
00125 
00128     bool           GetAminoAcidProperty(int)      const;
00131     bool           GetAtomProperty(OBAtom *a, int) const;
00134     bool           GetResidueProperty(int)        const;
00135 
00137     bool           IsHetAtom(OBAtom *atom)        const;
00140     bool           IsResidueType(int)             const;
00141 
00143 
00144 
00145     OBAtomIterator BeginAtoms()   { return _atoms.begin(); }
00147     OBAtomIterator EndAtoms()     { return _atoms.end();   }
00150     OBAtom *BeginAtom(std::vector<OBAtom*>::iterator &i);
00153     OBAtom *NextAtom(std::vector<OBAtom*>::iterator &i);
00155 
00156   protected: // members
00157 
00158     unsigned int              _idx;   
00159     char                      _chain; 
00160     unsigned int              _aakey; 
00161     unsigned int              _reskey;
00162     std::string               _resnum;
00163     std::string               _resname;
00164 
00165     std::vector<bool>         _hetatm;
00166     std::vector<std::string>  _atomid;
00167     std::vector<OBAtom*>      _atoms; 
00168     std::vector<unsigned int> _sernum;
00169     // Now in OBBase
00170     //    std::vector<OBGenericData*> _vdata; //!< Custom data
00171   }; // OBResidue
00172 
00174   typedef std::vector<OBResidue*>::iterator OBResidueIterator;
00175 
00177   // Global Definitions
00179 
00180 #define MAXSETNO 40
00181 #define MAXELEM  1024
00182 #define MINELEM  29
00183 #define MAXRES   100
00184 #define MINRES   54
00185 
00187   // Amino Acid Definitions
00189 
00190 #define AA_ALA (1<<1)
00191 #define AA_GLY (1<<2)
00192 #define AA_LEU (1<<3)
00193 #define AA_SER (1<<4)
00194 #define AA_VAL (1<<5)
00195 #define AA_THR (1<<6)
00196 #define AA_LYS (1<<7)
00197 #define AA_ASP (1<<8)
00198 #define AA_ILE (1<<9)
00199 #define AA_ASN (1<<10)
00200 #define AA_GLU (1<<11)
00201 #define AA_PRO (1<<12)
00202 #define AA_ARG (1<<13)
00203 #define AA_PHE (1<<14)
00204 #define AA_GLN (1<<15)
00205 #define AA_TYR (1<<16)
00206 #define AA_HIS (1<<17)
00207 #define AA_CYS (1<<18)
00208 #define AA_MET (1<<19)
00209 #define AA_TRP (1<<20)
00210 
00212   // Amino Acid Property Definitions
00214 #define IS_ACIDIC(x)      ((x) & ((AA_ASP)|(AA_GLU)))
00215 #define IS_ACYCLIC(x)     ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)|  \
00216                                   (AA_VAL)|(AA_THR)|(AA_LYS)|(AA_ASP)|  \
00217                                   (AA_ILE)|(AA_ASN)|(AA_GLU)|(AA_GLN)|  \
00218                                   (AA_CYS)|(AA_MET)))
00219 #define IS_ALIPHATIC(x)   ((x) & ((AA_ALA)|(AA_GLY)|(AA_ILE)|(AA_LEU)|  \
00220                                   (AA_VAL)))
00221 #define IS_AROMATIC(x)    ((x) & ((AA_HIS)|(AA_PHE)|(AA_TRP)|(AA_TYR)))
00222 #define IS_BASIC(x)       ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
00223 #define IS_BURIED(x)      ((x) & ((AA_ALA)|(AA_CYS)|(AA_ILE)|(AA_LEU)|  \
00224                                   (AA_MET)|(AA_PHE)|(AA_TRP)|(AA_VAL)))
00225 #define IS_CHARGED(x)     ((x) & ((AA_ASP)|(AA_GLU)|(AA_ARG)|(AA_HIS)|  \
00226                                   (AA_LYS)))
00227 #define IS_CYCLIC(x)      ((x) & ((AA_HIS)|(AA_PHE)|(AA_PRO)|(AA_TRP)|  \
00228                                   (AA_TYR)))
00229 #define IS_HYDROPHOBIC(x) ((x) & ((AA_ALA)|(AA_LEU)|(AA_VAL)|(AA_ILE)|  \
00230                                   (AA_PRO)|(AA_PHE)|(AA_MET)|(AA_TRP)))
00231 #define IS_LARGE(x)       ((x) & ((AA_ARG)|(AA_PHE)|(AA_GLN)|(AA_TYR)|  \
00232                                   (AA_HIS)|(AA_LEU)|(AA_LYS)|(AA_ILE)|  \
00233                                   (AA_GLU)|(AA_MET)|(AA_TRP)))
00234 #define IS_MEDIUM(x)      ((x) & ((AA_VAL)|(AA_THR)|(AA_ASP)|(AA_ASN)|  \
00235                                   (AA_PRO)|(AA_CYS)))
00236 #define IS_NEGATIVE(x)    ((x) & ((AA_ASP)|(AA_GLU)))
00237 #define IS_NEUTRAL(x)     ((x) & ((AA_ALA)|(AA_GLY)|(AA_LEU)|(AA_SER)|  \
00238                                   (AA_VAL)|(AA_THR)|(AA_PHE)|(AA_GLN)|  \
00239                                   (AA_TYR)|(AA_HIS)|(AA_CYS)|(AA_MET)|  \
00240                                   (AA_TRP)|(AA_ILE)|(AA_ASN)|(AA_PRO)))
00241 #define IS_POLAR(x)       ((x) & ((AA_ASP)|(AA_ILE)|(AA_ASN)|(AA_GLU)|  \
00242                                   (AA_SER)|(AA_THR)|(AA_ARG)|(AA_GLN)|  \
00243                                   (AA_CYS)|(AA_HIS)))
00244 #define IS_POSITIVE(x)    ((x) & ((AA_ARG)|(AA_HIS)|(AA_LYS)))
00245 #define IS_SMALL(x)       ((x) & ((AA_ALA)|(AA_GLY)|(AA_SER)))
00246 #define IS_SURFACE(x)     ((x) & ((AA_THR)|(AA_LYS)|(AA_ASP)|(AA_ILE)|  \
00247                                   (AA_ASN)|(AA_GLU)|(AA_PRO)|(AA_ARG)|  \
00248                                   (AA_GLY)|(AA_SER)|(AA_GLN)|(AA_TYR)|  \
00249                                   (AA_HIS)))
00250 
00252   namespace OBAminoAcidProperty
00253   {
00254         enum
00255     {
00256       ACIDIC      =  0,
00257       ACYCLIC     =  1,
00258       ALIPHATIC   =  2,
00259       AROMATIC    =  3,
00260       BASIC       =  4,
00261       BURIED      =  5,
00262       CHARGED     =  6,
00263       CYCLIC      =  7,
00264       HYDROPHOBIC =  8,
00265       LARGE       =  9,
00266       MEDIUM      = 10,
00267       NEGATIVE    = 11,
00268       NEUTRAL     = 12,
00269       POLAR       = 13,
00270       POSITIVE    = 14,
00271       SMALL       = 15,
00272       SURFACE     = 16
00273     };
00274   }
00275 
00277   namespace OBResidueAtomProperty
00278   {
00279     enum
00280     {
00281       ALPHA_CARBON     = 0,
00282       AMINO_BACKBONE   = 1,
00283       BACKBONE         = 2,
00284       CYSTEINE_SULPHUR = 3,
00285       LIGAND           = 4,
00286       NUCLEIC_BACKBONE = 5,
00287       SHAPELY_BACKBONE = 6,
00288       SHAPELY_SPECIAL  = 7,
00289       SIDECHAIN        = 8,
00290       SUGAR_PHOSPHATE  = 9
00291     };
00292   }
00293 
00295   // some of these are invalid or troublesome in scripting interfaces
00296   // so they are removed by the #ifndef SWIG parts
00297   // (otherwise ignore them for C++ use)
00298   namespace OBResidueIndex
00299   {
00300     enum
00301     {
00302       ALA   =  0,
00303       GLY   =  1,
00304       LEU   =  2,
00305       SER   =  3,
00306       VAL   =  4,
00307 #ifndef SWIGPERL
00308       THR   =  5,
00309 #endif
00310       LYS   =  6,
00311       ASP   =  7,
00312       ILE   =  8,
00313       ASN   =  9,
00314       GLU   = 10,
00315       PRO   = 11,
00316       ARG   = 12,
00317       PHE   = 13,
00318       GLN   = 14,
00319       TYR   = 15,
00320       HIS   = 16,
00321       CYS   = 17,
00322       MET   = 18,
00323       TRP   = 19,
00324       ASX   = 20,
00325       GLX   = 21,
00326       PCA   = 22,
00327       HYP   = 23,
00328       A     = 24,
00329       C     = 25,
00330       G     = 26,
00331       T     = 27,
00332       U     = 28,
00333       UPLUS = 29,
00334       I     = 30,
00335       _1MA  = 32,
00336       _5MC  = 32,
00337       OMC   = 33,
00338       _1MG  = 34,
00339       _2MG  = 35,
00340       M2G   = 36,
00341       _7MG  = 37,
00342       OMG   = 38,
00343       YG    = 39,
00344       H2U   = 40,
00345       _5MU  = 41,
00346       PSU   = 42,
00347       UNK   = 43,
00348       ACE   = 44,
00349       FOR   = 45,
00350       HOH   = 46,
00351       DOD   = 47,
00352       SO4   = 48,
00353       PO4   = 49,
00354       NAD   = 50,
00355       COA   = 51,
00356       NAP   = 52,
00357       NDP   = 53
00358     };
00359   }
00360 
00362   namespace OBResidueProperty
00363   {
00364     enum
00365      {
00366       AMINO        = 0,
00367       AMINO_NUCLEO = 1,
00368       COENZYME     = 2,
00369       ION          = 3,
00370       NUCLEO       = 4,
00371       PROTEIN      = 5,
00372       PURINE       = 6,
00373       PYRIMIDINE   = 7,
00374       SOLVENT      = 8,
00375       WATER        = 9
00376     };
00377   }
00378 
00380   // Global Variables
00382 
00383   EXTERN char Residue[MAXRES][4];
00384   EXTERN char ElemDesc[MAXELEM][4];
00385   EXTERN unsigned int ResNo;
00386   EXTERN unsigned int ElemNo;
00387 } // end namespace OpenBabel
00388 
00389 #endif
00390