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/********************************************************************** |
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chains.h - Parse for macromolecule chains and residues |
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#ifndef OB_CHAINS_H |
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#define OB_CHAINS_H |
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|
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#define MaxMonoAtom 20 |
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#define MaxMonoBond 20 |
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|
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namespace OpenBabel |
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{ |
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|
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class OBAtom; |
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class OBMol; |
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|
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//! Structure for atomic patterns (templates) in residues for OBChainsParser |
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//! Implementation and documentation in chains.cpp |
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typedef struct Template Template; |
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|
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//! \brief Perceives peptide or nucleotide chains and residues in an OBMol |
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// |
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//! Perceive peptide or nucleotide chains and residues from atom connectivity. |
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//! Based on original RasMol code by Roger Sayle and modified by Joe Corkery. |
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//! For more on Roger's original talk, see: |
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//! http://www.daylight.com/meetings/mug96/sayle/sayle.html |
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class OBAPI OBChainsParser |
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{ |
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public: |
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|
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OBChainsParser(void); |
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~OBChainsParser(void); |
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|
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//! Perceive macromolecular (peptide and nucleotide) residues and chains |
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//! \param mol - the molecule to parse and update |
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//! \param nukeSingleResidue - if only one residue is found, clear information |
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//! default = false -- single residue files should still be recognized. |
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bool PerceiveChains(OBMol &mol, bool nukeSingleResidue = false); |
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private: // internal methods |
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|
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bool DetermineHetAtoms(OBMol &); |
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bool DetermineConnectedChains(OBMol &); |
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bool DeterminePeptideBackbone(OBMol &); |
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bool DeterminePeptideSidechains(OBMol &); |
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bool DetermineNucleicBackbone(OBMol &); |
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bool DetermineNucleicSidechains(OBMol &); |
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bool DetermineHydrogens(OBMol &); |
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|
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void SetupMol(OBMol &); |
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void SetResidueInformation(OBMol &, bool nukeSingleResidue); |
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void ClearResidueInformation(OBMol &); |
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void CleanupMol(void); |
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|
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void AssignResidue(OBMol &, int, int, int); |
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int IdentifyResidue(void *, OBMol &, int, int); // ByteCode * |
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void DefineMonomer(void **, int, char *); // ByteCode ** |
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int IdentifyElement(char *); |
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|
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bool MatchConstraint(OBAtom *, int); |
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bool Match2Constraints(Template *, OBAtom *, OBAtom *); |
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bool Match3Constraints(Template *, OBAtom *, OBAtom *, OBAtom *); |
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bool Match4Constraints(Template *, OBAtom *, OBAtom *, OBAtom *, OBAtom *); |
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|
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void ConstrainBackbone(OBMol &, Template *, int); |
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|
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int RecurseChain(OBMol &, int, int); |
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void TraceNucleicChain(OBMol &, int, int); |
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void TracePeptideChain(OBMol &, int, int); |
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|
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char *ParseSmiles(char *, int); |
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private: // members |
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void *PDecisionTree; // ByteCode * |
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void *NDecisionTree; // ByteCode * |
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|
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int ResMonoAtom[MaxMonoAtom]; |
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int ResMonoBond[MaxMonoBond]; |
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|
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unsigned short *bitmasks; |
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unsigned char *resids; |
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unsigned char *flags; |
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bool *hetflags; |
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short *atomids; |
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short *resnos; |
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short *sernos; //!< array of residue serial numbers |
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char *hcounts; |
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char *chains; |
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}; |
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|
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} |
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#endif // OB_CHAINS_H |
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|
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//! \file chains.h |
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//! \brief Parse for macromolecule chains and residues. |
