NCBI C Toolkit Cross Reference

C/biostruc/mkbioseq.h

  1 /* mkbioseq.h
  2  *
  3  * ===========================================================================
  4  *
  5  *                            PUBLIC DOMAIN NOTICE
  6  *            National Center for Biotechnology Information (NCBI)
  7  *
  8  *  This software/database is a "United States Government Work" under the
  9  *  terms of the United States Copyright Act.  It was written as part of
 10  *  the author's official duties as a United States Government employee and
 11  *  thus cannot be copyrighted.  This software/database is freely available
 12  *  to the public for use. The National Library of Medicine and the U.S.
 13  *  Government do not place any restriction on its use or reproduction.
 14  *  We would, however, appreciate having the NCBI and the author cited in
 15  *  any work or product based on this material
 16  *
 17  *  Although all reasonable efforts have been taken to ensure the accuracy
 18  *  and reliability of the software and data, the NLM and the U.S.
 19  *  Government do not and cannot warrant the performance or results that
 20  *  may be obtained by using this software or data. The NLM and the U.S.
 21  *  Government disclaim all warranties, express or implied, including
 22  *  warranties of performance, merchantability or fitness for any particular
 23  *  purpose.
 24  *
 25  * ===========================================================================
 26  *
 27  * File Name: mkbioseq.h
 28  *
 29  * Author: Ken Addess
 30  *
 31  * $Log: mkbioseq.h,v $
 32  * Revision 6.1  1998/07/17 18:56:01  madej
 33  * Created by Ken Addess.
 34  *
 35  */
 36 
 37 /*****************************************************************************
 38 *
 39 *   mkbioseq.h
 40 *
 41 *****************************************************************************/
 42 
 43 #ifndef _MKBIOSEQ_
 44 #define _MKBIOSEQ_
 45 
 46 #include <ncbi.h>
 47 #include <asn.h>
 48 #include <mmdbapi.h>
 49 
 50 #include "strimprt.h"
 51 #define MAXNUM 50
 52 
 53 SeqEntryPtr LIBCALL CreateSeqEntry PROTO 
 54 ((BiostrucSourcePtr bssp, BiostrucGraphPtr bsgp, BiostrucModelPtr bsmp, ValNodePtr descr, Int4 nchn));
 55 SeqIdPtr LIBCALL MakePDBId PROTO((BiostrucSourcePtr bssp, MoleculeGraphPtr mgp, DbtagPtr dtp));
 56 SeqIdPtr LIBCALL MakeLocalID PROTO((Int4 mid, MoleculeGraphPtr mgp, DbtagPtr dtp));
 57 SeqIdPtr LIBCALL MakeGId PROTO((Int4 gi));
 58 BiostrucPtr LIBCALL readBiostruc PROTO((CharPtr filename, Int2 mode, Int4 mdlLvl));
 59 ValNodePtr LIBCALL MakeBioseqDescr PROTO((MoleculeGraphPtr mgp, ValNodePtr bioseq_descr));
 60 Uint1 LIBCALL MakeBioseqMol PROTO((MoleculeGraphPtr mgp));
 61 Int4 LIBCALL CountNumOfResidues PROTO((MoleculeGraphPtr mgp));
 62 Boolean LIBCALL isBiopoly PROTO((Int4 molecule_id, MoleculeGraphPtr currentbp));
 63 Boolean LIBCALL isHet PROTO((Int4 molecule_id, MoleculeGraphPtr currenthet));
 64 Int4 LIBCALL getHetIdx PROTO((Int4 molecule_id, MoleculeGraphPtr currenthet));
 65 ByteStorePtr LIBCALL AddSeqData PROTO((MoleculeGraphPtr mgp, Uint1 mol, Int4 length, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary));
 66 CharPtr LIBCALL getStdOlcode PROTO
 67 ((Int4 standard_graphs_id, Int4 residue_graph_id, BiostrucResidueGraphSetPtr std));
 68 CharPtr LIBCALL getNstdOlcode PROTO((ResidueGraphPtr nrg));
 69 ResidueGraphPtr LIBCALL getNstdResGraph PROTO((Int4 rgid, BiostrucGraphPtr bsgp));
 70 CharPtr LIBCALL rmvSpace PROTO((CharPtr str));
 71 SeqAnnotPtr LIBCALL AddNstdSeqAnnot PROTO((MoleculeGraphPtr mgp, SeqIdPtr id, BiostrucGraphPtr bsgp));
 72 Boolean LIBCALL isNstd PROTO((ResidueGraphPtr rgp));
 73 SeqAnnotPtr LIBCALL AddSecDomToSeqAnnot PROTO((BiostrucFeaturePtr bsfp, CharPtr name, SeqAnnotPtr seq_annot, SeqIdPtr id, Int4 num));
 74 Int4 LIBCALL findChnidx PROTO((Int4 mol_id, Int4 nbp, MoleculeGraphPtr bp));
 75 ValNodePtr LIBCALL MakeHetValNode PROTO((MoleculeGraphPtr nhet, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg));
 76 CharPtr LIBCALL getResNam PROTO((ResidueGraphPntrPtr rgpp, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg));
 77 CharPtr LIBCALL getResComm PROTO((ResidueGraphPntrPtr rgpp, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg));
 78 SeqAnnotPtr LIBCALL AddHetToSeqAnnot 
 79 PROTO((SeqAnnotPtr seq_annot, SeqIdPtr id, ValNodePtr hetval, ValNodePtr pvnThePoints, Int4 rescount));
 80 SeqAnnotPtr LIBCALL AddDisulToSeqAnnot PROTO((SeqAnnotPtr seq_annot, Int4 residx1, Int4 residx2, SeqIdPtr id1, SeqIdPtr id2));
 81 Int4 LIBCALL 
 82 getAtomElementIdx PROTO ((Int4 molecule_id, Int4 residue_id, Int4 atom_id, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary));
 83 ResidueGraphPtr LIBCALL getResGraph PROTO((ResidueGraphPntrPtr rgpp, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary));
 84 
 85 
 86 #endif
 87
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