embsig

Data type EmbPSigpos

Holds data for compiled signature position

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

Alias name(s)

Name
EmbSSigpos
EmbOSigpos

Attributes

Name	Type	Description
gsiz	ajuint*	Gap sizes
gpen	float*	Gap penalties
subs	float*	Residue match values
ngaps	ajuint	No. of gaps
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
embSigposNew	Default Sigdat object constructor

Destructor(s)

Name	Description
embSigposDel	Default Sigdat object destructor

Data type EmbPSigdat

Holds empirical data for an (uncompiled) signature position. Important: Functions which manipulate this structure rely on the data in the gap arrays (gsiz and grfq) being filled in order of increasing gap size.

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

Alias name(s)

Name
EmbSSigdat
EmbOSigdat

Attributes

Name	Type	Description
rids	AjPChar	Residue id's
rfrq	AjPUint	Residue frequencies
nres	ajuint	No. diff. types of residue
nenv	ajuint	No. diff. types of environment
eids	AjPStr*	Environment id's
efrq	AjPUint	Environment frequencies
gsiz	AjPUint	Gap sizes
gfrq	AjPUint	Frequencies of gaps of each size
ngap	ajuint	No. diff. sizes of empirical gap
wsiz	ajuint	Window size for this gap

Constructor(s)

Name	Description
embSigdatNew	Default Sigdat object constructor

Destructor(s)

Name	Description
embSigdatDel	Default Sigdat object destructor

Data type EmbPSignature

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

Alias name(s)

Name
EmbSSignature
EmbOSignature

Attributes

Name	Type	Description
Type	ajuint	Type, either ajSCOP (1) or ajCATH (2) for domain signatures, or ajLIGAND (3) for ligand signatures.
Typesig	ajuint	Type, either aj1D (1) or aj3D (2) for sequence or structure-based signatures respectively.
Class	AjPStr	SCOP classification.
Architecture	AjPStr	CATH classification.
Topology	AjPStr	CATH classification.
Fold	AjPStr	SCOP classification.
Superfamily	AjPStr	SCOP classification.
Family	AjPStr	SCOP classification.
Sunid_Family	ajuint	SCOP sunid for family.
npos	ajuint	No. of signature positions.
pos	EmbPSigpos*	Array of derived data for puropses of alignment.
dat	EmbPSigdat*	Array of empirical data.
Id	AjPStr	Protein id code.
Domid	AjPStr	Domain id code.
Ligid	AjPStr	Ligand id code.
Desc	AjPStr	Description of ligand (ajLIGAND only)
ns	ajuint	No. of sites (ajLIGAND only)
sn	ajuint	Site number (ajLIGAND only)
np	ajuint	No. of patches (ajLIGAND only)
pn	ajuint	Patch number (ajLIGAND only)
minpatch	ajuint	Max. patch size (residues) (ajLIGAND only)
maxgap	ajuint	Min. gap distance (residues) (ajLIGAND only)

Constructor(s)

Name	Description
embSignatureNew	Default Signature constructor

Destructor(s)

Name	Description
embSignatureDel	Default Signature destructor

Output

Name	Description
embSignatureWrite	Write signature to file.

Input

Name	Description
embSignatureReadNew	Construct a Signature object from reading a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Output

Name	Description
embSignatureWrite	Write a Signature object to a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Input

Name	Description
embSignatureHitsRead	Construct a Hitlist object from reading a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Output

Name	Description
embSignatureHitsWrite	Writes a list of Hit objects to a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Modifier(s)

Name	Description
embSignatureCompile	Compiles a Signature object. The signature must first have been allocated by using the embSignatureNew function.

Operator(s)

Name	Description
embSignatureAlignSeq	Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling embSignatureCompile. Write a Hit object with the result.
embSignatureAlignSeqall	Performs an alignment of a signature to protein sequences. The signature must have first been compiled by calling embSignatureCompile. Write a list of Hit objects with the result.

Data type EmbPHit

Holds data associated with a protein / domain sequence that is generated and or manipulated by the EMBOSS applications seqsearch, seqsort, and sigscan.

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

Alias name(s)

Name
EmbSHit
EmbOHit

Attributes

Name	Type	Description
Seq	AjPStr	Sequence as string.
Start	ajuint	Start of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.
End	ajuint	End of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.
Acc	AjPStr	Accession number of sequence entry.
Spr	AjPStr	Swissprot code of sequence entry.
Dom	AjPStr	SCOP or CATH database identifier code of entry.
Rank	ajuint	Rank order of hit
Score	float	Score of hit
Eval	float	E-value of hit
Pval	float	p-value of hit
Typeobj	AjPStr	Primary (objective) classification of hit.
Typesbj	AjPStr	Secondary (subjective) classification of hit
Model	AjPStr	String for model type if used, one of PSIBLAST, HMMER, SAM, SPARSE, HENIKOFF or GRIBSKOV
Alg	AjPStr	Alignment, e.g. of a signature to the sequence
Group	AjPStr	Grouping of hit, e.g. 'REDUNDANT' or 'NON_REDUNDANT'
Target	AjBool	Used for garbage collection.
Target2	AjBool	Also used for garbage collection.
Sig	EmbPSignature	Pointer to signature object for which hit
Priority	AjBool	Also used for garbage collection.
Padding	char[4]	Padding to alignment boundary was generated. Used as a pointer only - memory is never freed or allocated to it.

Constructor(s)

Name	Description
embHitNew	Default Hit constructor
embHitReadFasta	Construct Hit object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Destructor(s)

Name	Description
embHitDel	Default Hit destructor

Assignment(s)

Name	Description
embHitMerge	Create new Hit from merging two Hit objects

Operator(s)

Name	Description
embMatchScore	Sort Hit objects by Score element.
embMatchinvScore	Sort (inverted order) Hit objects by Score element.
embMatchLigid	Sort Hit objects by Ligid element in Sig element.
embMatch	Sort Hit objects by Ligid element in Sig element.
embHitsOverlap	Checks for overlap between two Hit objects.

Data type EmbPHitlist

Holds an array of hit structures and associated SCOP classification records.

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

Alias name(s)

Name
EmbSHitlist
EmbOHitlist

Attributes

Name	Type	Description
Class	AjPStr	SCOP classification.
Architecture	AjPStr	CATH classification.
Topology	AjPStr	CATH classification.
Fold	AjPStr	SCOP classification.
Superfamily	AjPStr	SCOP classification.
Family	AjPStr	SCOP classification.
Model	AjPStr	SCOP classification.
Sunid_Family	ajuint	SCOP sunid for family.
Priority	AjBool	True if the Hitlist is high priority.
hits	EmbPHit*	Array of hits.
Type	ajuint	Domain type, either ajSCOP (1) or ajCATH (2).
N	ajuint	No. of hits.

Constructor(s)

Name	Description
embHitlistNew	Default Hitlist constructor

Destructor(s)

Name	Description
embHitlistDel	Default Hitlist destructor

Operator(s)

Name	Description
embHitlistMatchFold	Sort Hitlist objects by Fold element

Input

Name	Description
embHitlistRead	Construct Hitlist object from reading the next entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Constructor(s)

Name	Description
embHitlistReadFasta	Construct Hitlist object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Input

Name	Description
embHitlistReadNode	Construct Hitlist object from reading a specific entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Constructor(s)

Name	Description
embHitlistReadNodeFasta	Construct Hitlist object from reading a specific entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Output

Name	Description
embHitlistWrite	Write Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteSubset	Write a subset of a Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteFasta	Write Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteSubsetFasta	Write a subset of a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteHitFasta	Write a single Hit from a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Operator(s)

Name	Description
embHitlistClassify	Classifies a list of signature-sequence hits (held in a Hitlist object) according to list of target sequences (a list of Hitlist objects).