emboss-lib 6.6.0-1 / usr / lib / emboss / include / ajdomain.h

/* @include ajdomain **********************************************************
**
** AJAX objects for handling protein domain data.
** Scop, Cath and Domain objects.
**
** @author: Copyright (C) 2004 Jon Ison (jison@hgmp.mrc.ac.uk)
** @version $Revision: 1.26 $
** @modified $Date: 2012/04/12 20:36:39 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library 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
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA  02110-1301,  USA.
**
******************************************************************************/

#ifndef AJDOMAIN_H
#define AJDOMAIN_H

/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */

#include "ajdefine.h"
#include "ajstr.h"
#include "ajlist.h"
#include "ajfile.h"
#include "ajpdb.h"
#include "ajreg.h"
#include "ajseqwrite.h"

AJ_BEGIN_DECLS




/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */




/* @enum AjEDomainType ********************************************************
**
** AJAX Domain Type enumeration
**
** @value ajEDomainTypeNULL NULL
** @value ajEDomainTypeCATH CATH
** @value ajEDomainTypeSCOP SCOP
** @@
******************************************************************************/

typedef enum AjODomainType
{
    ajEDomainTypeNULL,
    ajEDomainTypeCATH,
    ajEDomainTypeSCOP
} AjEDomainType;




/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */




/* @data AjPScop **************************************************************
**
** AJAX SCOP object
**
** Holds SCOP database data
**
** @alias AjSScop
** @alias AjOScop
**
** @attr Entry [AjPStr] Domain identifier code
** @attr Pdb [AjPStr] Corresponding pdb identifier code
** @attr Class [AjPStr] SCOP class name as an AjPStr
** @attr Fold [AjPStr] SCOP fold  name as an AjPStr
** @attr Superfamily [AjPStr]  SCOP superfamily name as an AjPStr
** @attr Family [AjPStr] SCOP family name as an AjPStr
** @attr Domain [AjPStr] SCOP domain name as an AjPStr
** @attr Source [AjPStr] SCOP source (species) as an AjPStr
** @attr Chain [char*] Chain identifiers
** @attr Start [AjPStr*] PDB residue number of first residue in domain
** @attr End [AjPStr*] PDB residue number of last residue in domain
** @attr Sse [AjPStr] Secondary structure element map
** @attr Sss [AjPStr] Secondary structure element string
** @attr Number [ajuint] Number of chains from which this domain is comprised
** @attr Sunid_Class [ajint] SCOP sunid for class
** @attr Sunid_Fold [ajint] SCOP sunid for fold
** @attr Sunid_Superfamily [ajint] SCOP sunid for superfamily
** @attr Sunid_Family [ajint] SCOP sunid for family
** @attr Sunid_Domain [ajint] SCOP sunid for domain
** @attr Sunid_Source [ajint] SCOP sunid for species
** @attr Sunid_Domdat [ajint] SCOP sunid for domain data
**
** @attr Acc [AjPStr] Accession number of sequence entry
** @attr Spr [AjPStr] Swissprot code of sequence entry
** @attr SeqPdb [AjPStr] Sequence (from PDB) as string
** @attr SeqSpr [AjPStr] Sequence (from swissprot) as string
** @attr Startd [ajint] Start of sequence relative to full
** length swissprot sequence
** @attr Endd [ajint] End of sequence relative to full length
** swissprot sequence
** @attr Score [float] Used by misc. algorithms for scoring the domain
** @attr Padding [char[4]] Padding to alignment boundary
**
** @new    ajScopNew Scop default constructor
** @new    ajScopReadNew Scop constructor from reading DCF format file
** @new    ajScopReadCNew Scop constructor from reading DCF format file
** @delete ajScopDel Default Scop destructor
** @assign ajScopCopy Replicates a Scop object
** @use    ajScopMatchSunid Sort Scop objects by Sunid_Family element
** @use    ajScopMatchScopid Sort Scop objects by Entry element
** @use    ajScopMatchPdbId Sort Scop objects by Pdb element
** @use    embScopToPdbid  Read a scop identifier code and writes the
**         equivalent PDB identifier code
** @use    embScopToSp  Read a scop identifier code and writes the
**         equivalent swissprot identifier code
** @use    embScopToAcc  Read a scop identifier code and writes the
**         equivalent accession number
** @use    ajScopArrFindScopid Binary search for Entry element over array
**         of Scop objects
** @use    ajScopArrFindSunid Binary search for Sunid_Family element over
**         array of Scop objects
** @use    ajScopArrFindPdbid Binary search for Pdb element over array of
**         Scop objects
** @new    ajScopReadAllNew Construct list of Scop objects from reading DCF
**         format file
** @new  ajScopReadAllRawNew Construct list of Scop objects from reading
**         raw SCOP parsable files
** @output ajScopWrite Write Scop object to DCF format file
** @output ajPdbWriteDomain Writes a CCF format file for a SCOP domain
** @output ajPdbWriteDomainRaw Writes a PDB-format file for a SCOP domain
** @output ajPdbWriteDomainRecordRaw Writes lines to a PDB format file for
**         a domain
** @@
******************************************************************************/

typedef struct AjSScop
{
    AjPStr Entry;
    AjPStr Pdb;
    AjPStr Class;
    AjPStr Fold;
    AjPStr Superfamily;
    AjPStr Family;
    AjPStr Domain;
    AjPStr Source;

    char   *Chain;
    AjPStr *Start;
    AjPStr *End;

    AjPStr Sse;
    AjPStr Sss;

    ajuint Number;

    ajint Sunid_Class;
    ajint Sunid_Fold;
    ajint Sunid_Superfamily;
    ajint Sunid_Family;
    ajint Sunid_Domain;
    ajint Sunid_Source;
    ajint Sunid_Domdat;

    AjPStr Acc;
    AjPStr Spr;
    AjPStr SeqPdb;
    AjPStr SeqSpr;
    ajint Startd;
    ajint Endd;

    float Score;
    char Padding[4];
} AjOScop;

#define AjPScop AjOScop*




/* @data AjPCath **************************************************************
**
** Ajax cath object
**
** Holds cath database data
**
** AjPScop is implemented as a pointer to a C data structure.
**
**
**
** @alias AjSCath
** @alias AjOCath
**
**
**
** @attr DomainID       [AjPStr]  Domain identifier code
** @attr Pdb            [AjPStr]  Corresponding PDB identifier code
** @attr Class          [AjPStr]  CATH class name as an AjPStr
** @attr Architecture   [AjPStr]  CATH architecture name as an AjPStr
** @attr Topology       [AjPStr]  CATH topology name as an AjPStr
** @attr Superfamily    [AjPStr]  CATH homologous superfamily name as an AjPStr
** @attr Length         [ajint]   No. of residues in domain
** @attr NSegment       [ajuint]  Number of chain segments domain is comprised of
** @attr Start          [AjPStr*] PDB residue number of 1st residue in segment
** @attr End            [AjPStr*] PDB residue number of last residue in segment
** @attr Class_Id       [ajint]   CATH class no. as an ajint
** @attr Arch_Id        [ajint]   CATH architecture no.as an ajint
** @attr Topology_Id    [ajint]   CATH topology no. as an ajint
** @attr Superfamily_Id [ajint]   CATH superfamily no. as an ajint
** @attr Family_Id      [ajint]   CATH family no. as an ajint
** @attr NIFamily_Id    [ajint]   CATH near identical family no. as an ajint
**
** @attr Acc                [AjPStr]  Accession number of sequence entry.
** @attr Spr                [AjPStr]  Swissprot code of sequence entry.
** @attr SeqPdb             [AjPStr]  Sequence (from PDB) as string.
** @attr SeqSpr             [AjPStr]  Sequence (from swissprot) as string.
** @attr IFamily_Id     [ajint]   CATH identical family no. as an ajint
**
** @attr Startd             [ajint]   Start of sequence relative to full
**                                    length swissprot sequence.
** @attr Endd               [ajint]   End of sequence relative to full length
**                                    swissprot sequence.
** @attr Chain              [char]    Chain identifier
** @attr Padding            [char[3]] Padding to alignment boundary
**
**
** @new    ajCathNew Default Cath constructor
** @new    ajCathReadCNew Cath constructor from reading DCF format file.
** @new    ajCathReadNew Cath constructor from reading DCF format file.
** @delete ajCathDel Default Cath destructor
** @assign ajCathCopy Replicates a Scop object.
** @use    ajCathArrFindPdbid Binary search for Pdb element over array of
**         Cath objects.
** @use    ajCathMatchPdbId Sort Cath objects by Pdb element.
** @new    ajCathReadAllNew Construct list of Cath objects from reading DCF
**         format file.
** @new    ajCathReadAllRawNew Construct list of Cath objects from reading
**         raw CATH parsable files.
** @other  ajCathWrite Write Cath object to DCF format file.
**
** @@
******************************************************************************/

typedef struct AjSCath
{
    AjPStr  DomainID;
    AjPStr  Pdb;
    AjPStr  Class;
    AjPStr  Architecture;
    AjPStr  Topology;
    AjPStr  Superfamily;

    ajint   Length;

    ajuint  NSegment;
    AjPStr *Start;
    AjPStr *End;

    ajint   Class_Id;
    ajint   Arch_Id;
    ajint   Topology_Id;
    ajint   Superfamily_Id;
    ajint   Family_Id;
    ajint   NIFamily_Id;

    AjPStr Acc;
    AjPStr Spr;
    AjPStr SeqPdb;
    AjPStr SeqSpr;
    ajint  IFamily_Id;
    ajint  Startd;
    ajint  Endd;
    char   Chain;
    char   Padding[3];
} AjOCath;

#define AjPCath AjOCath*




/* @data AjPDomain ************************************************************
**
** Ajax Domain object.
**
** Holds an entry from a DCF file (domain classification file)
**
** AjPDomain is implemented as a pointer to a C data structure.
**
** @alias AjSDomain
** @alias AjODomain
**
** @attr Scop    [AjPScop] Scop object pointer.
** @attr Cath    [AjPCath] Cath object pointer.
** @attr Type    [AjEDomainType] AJAX Domain Type enumeration
** @attr Padding [char[4]] Padding to alignment boundary
**
** @new    ajDomainNew Default Domain constructor.
** @new    ajDomainReadNew Domain constructor from reading DCF format file.
** @new    ajDomainReadCNew Domain constructor from reading DCF format file.
** @new    ajDomainReadAllNew Construct list of Domain objects from reading DCF
**         format file.
** @delete ajDomainDel Default Domain destructor.
** @output ajDomainWrite Write Domain object to DCF format file.
** @other  ajDomainDCFType Ascertains type of domains (ajEDomainTypeSCOP
**         or ajEDomainTypeCATH) in a DCF file.
** @assign ajDomainCopy Replicates a Domain object.
** @cast   ajDomainGetId Returns domain id, either DomainID element
**                      (Cath object) or Entry (Scop object).
** @cast   ajDomainGetSeqPdb Returns the PDB sequence from a Domain object.
** @cast   ajDomainGetSeqSpr Returns the swissprot sequence from a
**                           Domain object.
** @cast   ajDomainGetPdb Returns the PDB identifier code corresponding to the
**                        domain
** @cast   ajDomainGetAcc Returns the accession number corresponding to the
**                        domain.
** @cast   ajDomainGetSpr Returns the swissprot code corresponding to the
**                        domain.
** @cast   ajDomainGetN  Returns no. chains or chain segments in a domain,
** either NSegment element (Cath domains) or N element (Scop domains).
** @@
******************************************************************************/

typedef struct AjSDomain
{
    AjPScop Scop;
    AjPCath Cath;
    AjEDomainType Type;
    char Padding[4];
} AjODomain;

#define AjPDomain AjODomain*




/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */




/*
** Prototype definitions
*/

/* ======================================================================= */
/* =========================== Scop object =============================== */
/* ======================================================================= */

void     ajDomainDummyFunction(void);
AjPScop  ajScopNew(ajuint n);
void     ajScopDel(AjPScop *Pscop);
AjBool   ajScopCopy(AjPScop *Pto, const AjPScop from);

ajint    ajScopArrFindScopid(AjPScop const *array, ajint size,
                             const AjPStr identifier);
ajint    ajScopArrFindSunid(AjPScop const *array, ajint size,
                            ajint identifier);
ajint    ajScopArrFindPdbid(AjPScop const *array, ajint size,
                            const AjPStr identifier);

ajint    ajScopMatchScopid(const void *item1, const void *item2);
ajint    ajScopMatchPdbId(const void *item1, const void *item2);
ajint    ajScopMatchSunid(const void *item1, const void *item2);

AjPScop  ajScopReadCNew(AjPFile inf, const char *entry);
AjPScop  ajScopReadNew(AjPFile inf, const AjPStr entry);
AjPList  ajScopReadAllNew(AjPFile inf);
AjPList  ajScopReadAllRawNew(AjPFile claf, AjPFile desf, AjBool omit);
AjBool   ajScopWrite(AjPFile outf, const AjPScop scop);

AjBool   ajPdbWriteDomain(AjPFile outf, const AjPPdb pdb,
                          const AjPScop scop, AjPFile errf);




/* ======================================================================= */
/* =========================== Cath object =============================== */
/* ======================================================================= */

AjPCath   ajCathNew(ajuint n);
void      ajCathDel(AjPCath *Pcath);
AjBool    ajCathCopy(AjPCath *Pto, const AjPCath from);

ajint     ajCathArrFindPdbid(AjPCath const *array, ajint size,
                             const AjPStr identifier);
ajint     ajCathMatchPdbId(const void *item1, const void *item2);

AjPCath   ajCathReadCNew(AjPFile inf, const char *entry);
AjPCath   ajCathReadNew(AjPFile inf, const AjPStr entry);
AjPList   ajCathReadAllNew(AjPFile inf);
AjPList   ajCathReadAllRawNew(AjPFile cathf, AjPFile domf,
                              AjPFile namesf, AjPFile flog);
AjBool    ajCathWrite(AjPFile outf, const AjPCath cath);




/* ======================================================================= */
/* =========================== Domain object ============================= */
/* ======================================================================= */

AjPDomain       ajDomainNew(ajuint n, AjEDomainType type);
AjPDomain       ajDomainReadNew(AjPFile inf, const AjPStr entry);
AjPDomain       ajDomainReadCNew(AjPFile inf, const char *entry,
                                 AjEDomainType type);
AjPList         ajDomainReadAllNew(AjPFile inf);
void            ajDomainDel(AjPDomain *Pdomain);
AjBool          ajDomainWrite(AjPFile outf, const AjPDomain domain);
AjEDomainType   ajDomainDCFType(AjPFile inf);
AjBool          ajDomainCopy(AjPDomain *Pto, const AjPDomain from);

AjPStr          ajDomainGetId(const AjPDomain domain);
AjPStr          ajDomainGetSeqPdb(const AjPDomain domain);
AjPStr          ajDomainGetSeqSpr(const AjPDomain domain);
AjPStr          ajDomainGetPdb(const AjPDomain domain);
AjPStr          ajDomainGetAcc(const AjPDomain domain);
AjPStr          ajDomainGetSpr(const AjPDomain domain);
ajint           ajDomainGetN(const AjPDomain domain);

void ajDomainExit(void);

/*
** End of prototype definitions
*/




/******************************************************************************
 **
 ** Macros for returning elements from an instance of a
 **
 ** Domain object
 **
 ******************************************************************************/

#define DOMAIN_S_Entry(ptr) ptr->Scop->Entry
#define DOMAIN_S_Pdb(ptr) ptr->Scop->Pdb
#define DOMAIN_S_Class(ptr) ptr->Scop->Class
#define DOMAIN_S_Fold(ptr) ptr->Scop->Fold
#define DOMAIN_S_Superfamily(ptr) ptr->Scop->Superfamily
#define DOMAIN_S_Family(ptr) ptr->Scop->Family
#define DOMAIN_S_Sunid_Class(ptr) ptr->Scop->Sunid_Class
#define DOMAIN_S_Sunid_Fold(ptr) ptr->Scop->Sunid_Fold
#define DOMAIN_S_Sunid_Superfamily(ptr) ptr->Scop->Sunid_Superfamily
#define DOMAIN_S_Sunid_Family(ptr) ptr->Scop->Sunid_Family
#define DOMAIN_S_Acc(ptr) ptr->Scop->Acc
#define DOMAIN_S_Spr(ptr) ptr->Scop->Spr
#define DOMAIN_S_SeqPdb(ptr) ptr->Scop->SeqPdb
#define DOMAIN_S_SeqSpr(ptr) ptr->Scop->SeqSpr
/* #define DOMAIN_S_(ptr) ptr->Scop-> */




AJ_END_DECLS

#endif /* !AJDOMAIN_H */