chains.h

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/**********************************************************************
chains.h - Parse for macromolecule chains and residues

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
Some portions Copyright (C) 2008 by Tim Vandermeersch

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_CHAINS_H
#define OB_CHAINS_H

#define MaxMonoAtom 20
#define MaxMonoBond 20

#include <openbabel/babelconfig.h>
#include <vector>

namespace OpenBabel
{

  class OBAtom;
  class OBMol;

  // implementation in chains.cpp
  struct Template;
  typedef struct Template Template;

  class OBAPI OBChainsParser
  {
    public:

      OBChainsParser(void);
      ~OBChainsParser(void);

      bool PerceiveChains(OBMol &mol, bool nukeSingleResidue = false);

    private: // internal methods



      bool DetermineHetAtoms(OBMol &);



      bool DetermineConnectedChains(OBMol &);
      unsigned int RecurseChain(OBMol &mol, unsigned int i, int c);



      bool DeterminePeptideBackbone(OBMol &);
      void ConstrainBackbone(OBMol &mol, Template *templ, int tmax);
      bool MatchConstraint(OBAtom *atom, int mask);
      bool Match2Constraints(Template *templ, OBAtom *na, OBAtom *nb);
      bool Match3Constraints(Template *templ, OBAtom *na, OBAtom *nb, OBAtom *nc);
      bool Match4Constraints(Template *templ, OBAtom *na, OBAtom *nb, OBAtom *nc, OBAtom *nd);
      void TracePeptideChain(OBMol &mol, unsigned int i, int r);



      bool  DeterminePeptideSidechains(OBMol &);
      int IdentifyResidue(void *tree, OBMol &mol, unsigned int seed, int resno); // ByteCode *
      void  AssignResidue(OBMol &mol, int r, int c, int i);



      bool  DetermineHydrogens(OBMol &);



      void  SetResidueInformation(OBMol &, bool nukeSingleResidue);



      bool  DetermineNucleicBackbone(OBMol &);
      void  TraceNucleicChain(OBMol &, unsigned int i, int r);
      bool  DetermineNucleicSidechains(OBMol &);

      void  SetupMol(OBMol &);
      void  ClearResidueInformation(OBMol &mol);
      void CleanupMol();
      void  DefineMonomer(void **tree, int resid, const char *smiles); // ByteCode **
      int   IdentifyElement(char *ptr);
      const char *ParseSmiles(const char *smiles, int prev);
      void DumpState();

      void *PDecisionTree; 
      void *NDecisionTree; 

      int   ResMonoAtom[MaxMonoAtom];
      int   ResMonoBond[MaxMonoBond];

      std::vector<unsigned short> bitmasks;
      std::vector<bool>           visits;   
      std::vector<unsigned char>  resids;
      std::vector<unsigned char>  flags;
      std::vector<bool>           hetflags;
      std::vector<int>            atomids;
      std::vector<short>          resnos;
      std::vector<short>          sernos;   
      std::vector<char>           hcounts;
      std::vector<char>           chains;
    };

    EXTERN  OBChainsParser   chainsparser;

}
#endif // OB_CHAINS_H