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