ajdomain

Data type AjPScop

Holds scop database data

AjPScop is implemented as a pointer to a C data structure.

Alias name(s)

Name	Description
AjSScop
AjOScop

Attributes

Name	Type	Description
Entry	Domain identifer code.
Pdb	Corresponding pdb identifier code.
Class	SCOP class name as an AjPStr.
Fold	SCOP fold name as an AjPStr.
Superfamily	SCOP superfamily name as an AjPStr.
Family	SCOP family name as an AjPStr.
Domain	SCOP domain name as an AjPStr.
Source	SCOP source (species) as an AjPStr.
Chain	Chain identifiers.
Start	PDB residue number of first residue in domain.
End	PDB residue number of last residue in domain.
Sse	Secondary structure element map
Sss	Secondary structure element string
N	No. chains from which this domain is comprised.
Sunid_Class	SCOP sunid for class.
Sunid_Fold	SCOP sunid for fold.
Sunid_Superfamily	SCOP sunid for superfamily.
Sunid_Family	SCOP sunid for family.
Sunid_Domain	SCOP sunid for domain.
Sunid_Source	SCOP sunid for species.
Sunid_Domdat	SCOP sunid for domain data.
Acc	Accession number of sequence entry.
Spr	Swissprot code of sequence entry.
SeqPdb	Sequence (from PDB) as string.
SeqSpr	Sequence (from swissprot) as string.
Startd	Start of sequence relative to full length swissprot sequence.
Endd	End of sequence relative to full length swissprot sequence.
Score	Used by misc. algorithms for scoring the domain.
Padding	Padding to alignment boundary

Constructor(s)

Name	Description
ajScopNew	Scop default constructor.
ajScopReadNew	Scop constructor from reading DCF format file.
ajScopReadCNew	Scop constructor from reading DCF format file.

Destructor(s)

Name	Description
ajScopDel	Default Scop destructor.

Assignment(s)

Name	Description
ajScopCopy	Replicates a Scop object.

Operator(s)

Name	Description
ajScopMatchSunid	Sort Scop objects by Sunid_Family element.
ajScopMatchScopid	Sort Scop objects by Entry element.
ajScopMatchPdbId	Sort Scop objects by Pdb element.
embScopToPdbid	Read a scop identifier code and writes the equivalent PDB identifier code.
embScopToSp	Read a scop identifier code and writes the equivalent swissprot identifier code.
embScopToAcc	Read a scop identifier code and writes the equivalent accession number.
ajScopArrFindScopid	Binary search for Entry element over array of Scop objects.
ajScopArrFindSunid	Binary search for Sunid_Family element over array of Scop objects.
ajScopArrFindPdbid	Binary search for Pdb element over array of Scop objects.

Constructor(s)

Name	Description
ajScopReadAllNew	Construct list of Scop objects from reading DCF format file.
ajScopReadAllRawNew	Construct list of Scop objects from reading raw SCOP parsable files.

Output

Name	Description
ajScopWrite	Write Scop object to DCF format file.
ajPdbWriteDomain	Writes a CCF format file for a SCOP domain.
ajPdbWriteDomainRaw	Writes a PDB-format file for a SCOP domain.
ajPdbWriteDomainRecordRaw	Writes lines to a PDB format file for a domain.

Data type AjPCath

Holds cath database data

AjPScop is implemented as a pointer to a C data structure.

Alias name(s)

Name	Description
AjSCath
AjOCath

Attributes

Name	Type	Description
DomainID	Domain identifer code
Pdb	Corresponding PDB identifer code
Class	CATH class name as an AjPStr
Architecture	CATH architecture name as an AjPStr
Topology	CATH topology name as an AjPStr
Superfamily	CATH homologous superfamily name as an AjPStr
Length	No. of residues in domain
NSegment	No. of chain segments domain is comprised of
Start	PDB residue number of 1st residue in segment
End	PDB residue number of last residue in segment
Class_Id	CATH class no. as an ajint
Arch_Id	CATH architecture no.as an ajint
Topology_Id	CATH topology no. as an ajint
Superfamily_Id	CATH superfamily no. as an ajint
Family_Id	CATH family no. as an ajint
NIFamily_Id	CATH near identical family no. as an ajint
Acc	Accession number of sequence entry.
Spr	Swissprot code of sequence entry.
SeqPdb	Sequence (from PDB) as string.
SeqSpr	Sequence (from swissprot) as string.
IFamily_Id	CATH identical family no. as an ajint
Startd	Start of sequence relative to full length swissprot sequence.
Endd	End of sequence relative to full length swissprot sequence.
Chain	Chain identifier
Padding	Padding to alignment boundary

Constructor(s)

Name	Description
ajCathNew	Default Cath constructor
ajCathReadCNew	Cath constructor from reading DCF format file.
ajCathReadNew	Cath constructor from reading DCF format file.

Destructor(s)

Name	Description
ajCathDel	Default Cath destructor

Assignment(s)

Name	Description
ajCathCopy	Replicates a Scop object.

Operator(s)

Name	Description
ajCathArrFindPdbid	Binary search for Pdb element over array of Cath objects.
ajCathMatchPdbId	Sort Cath objects by Pdb element.

Constructor(s)

Name	Description
ajCathReadAllNew	Construct list of Cath objects from reading DCF format file.
ajCathReadAllRawNew	Construct list of Cath objects from reading raw CATH parsable files.

Other related data structure(s)

Name	Description
ajCathWrite	Write Cath object to DCF format file.

Data type AjPDomain

Holds an entry from a DCF file (domain classification file)

AjPDomain is implemented as a pointer to a C data structure.

Alias name(s)

Name	Description
AjSDomain
AjODomain

Attributes

Name	Type	Description
Scop	Scop object pointer.
Cath	Cath object pointer.
Type	Type, either ajSCOP (1) or ajCATH (2).
Padding	Padding to alignment boundary

Constructor(s)

Name	Description
ajDomainNew	Default Domain constructor.
ajDomainReadNew	Domain constructor from reading DCF format file.
ajDomainReadCNew	Domain constructor from reading DCF format file.
ajDomainReadAllNew	Construct list of Domain objects from reading DCF format file.

Destructor(s)

Name	Description
ajDomainDel	Default Domain destructor.

Output

Name	Description
ajDomainWrite	Write Domain object to DCF format file.

Other related data structure(s)

Name	Description
ajDomainDCFType	Assertains type of domains (ajSCOP or ajCATH) in a DCF file.

Assignment(s)

Name	Description
ajDomainCopy	Replicates a Domain object.

Cast(s)

Name	Description
ajDomainGetId	Returns domain id, either DomainID element (Cath object) or Entry (Scop object).
ajDomainGetSeqPdb	Returns the PDB sequence from a Domain object.
ajDomainGetSeqSpr	Returns the swissprot sequence from a Domain object.
ajDomainGetPdb	Returns the PDB identifier code corresponding to the domain
ajDomainGetAcc	Returns the accession number corresponding to the domain.
ajDomainGetSpr	Returns the swissprot code corresponding to the domain.
ajDomainGetN	Returns no. chains or chain segments in a domain, either NSegment element (Cath domains) or N element (Scop domains).