ajdmx

Data type AjPScophit

Holds data associated with a protein / domain sequence. Includes SCOP classification records.

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

Alias name(s)

Name
AjSScophit
AjOScophit

Attributes

Name	Type	Description
Class	AjPStr	Class name
Architecture	AjPStr	CATH classification.
Topology	AjPStr	CATH classification.
Fold	AjPStr	Fold name
Superfamily	AjPStr	Superfamily name
Family	AjPStr	Family name
Type	ajuint	Type, either ajSCOP (1) or ajCATH (2).
Sunid_Family	ajuint	Domain identifier of node (e.g. family or superfamily) represented.
Seq	AjPStr	Sequence as string
Start	ajuint	Start of sequence or signature alignment relative to full length swissprot sequence
End	ajuint	End of sequence or signature alignment relative to full length swissprot sequence
Acc	AjPStr	Accession number of sequence entry
Spr	AjPStr	Swissprot code of sequence entry
Dom	AjPStr	SCOP or CATH database identifier code of entry.
Typeobj	AjPStr	Bibliographic information ... objective
Typesbj	AjPStr	Bibliographic information ... subjective
Model	AjPStr	String for model type (HMM, Gribskov etc)
Group	AjPStr	'REDUNDANT' or 'NON_REDUNDANT'
Rank	ajuint	Rank order of hit
Score	float	Score of hit
Eval	float	E-value of hit
Pval	float	p-value of hit
Alg	AjPStr	Alignment, e.g. of a signature to the sequence
Target	AjBool	True if the Scophit is targeted for removal from a list of Scophit objects
Target2	AjBool	Also used for garbage collection
Priority	AjBool	True if the Scop hit is high priority
Padding	char[4]	Padding to alignment boundary

Constructor(s)

Name	Description
ajDmxScophitNew	Default Scophit object constructor.

Destructor(s)

Name	Description
ajDmxScophitDel	Default Scophit object destructor.
ajDmxScophitDelWrap	Wrapper to destructor for Scophit object for use with generic functions.

Assignment(s)

Name	Description
ajDmxScophitListCopy	Reads a list of Scophit structures and returns a pointer to a duplicate of the list.

Operator(s)

Name	Description
ajDmxScophitCheckTarget	Checks to see if the Target element of a Scophit object == ajTrue.

Modifier(s)

Name	Description
ajDmxScophitTarget	Sets the Target element of a Scophit object to True.
ajDmxScophitTarget2	Sets the Target2 element of a Scophit object to True.
ajDmxScophitTargetLowPriority	Sets the Target element of a Scophit object to True if its Priority is low.

Operator(s)

Name	Description
ajDmxScophitCompSpr	Function to sort Scophit object by Spr element.
ajDmxScophitCompStart	Function to sort Scophit object by Spr element.
ajDmxScophitCompEnd	Function to sort Scophit object by End element.
ajDmxScophitCompClass	Function to sort Scophit object by Class element.
ajDmxScophitCompFold	Function to sort Scophit object by Fold element.
ajDmxScophitCompSfam	Function to sort Scophit object by Superfamily element.
ajDmxScophitCompFam	Function to sort Scophit object by Family element.
ajDmxScophitCompAcc	Function to sort Scophit objects by Acc element.
ajDmxScophitCompSunid	Function to sort Scophit objects by Sunid element.
ajDmxScophitCompScore	Function to sort Scophit objects by Score element.
ajDmxScophitCompPval	Function to sort Scophit objects by Pval element.
ajDmxScopSeqFromSunid	Writes a sequence corresponding to a Scop domain given a Sunid for the domain. The sequence is taken from one of a list of Scop objects that is provided.

Output

Name	Description
ajDmxScophitsWrite	Write contents of a list of Scophits to an output file.
ajDmxScophitsWriteFasta	Write contents of a list of Scophits to an output file in extended FASTA format.

Input

Name	Description
ajDmxScophitReadFasta	Read a Scophit object from a file in extended FASTA format.

Assignment(s)

Name	Description
ajDmxScophitCopy	Copies the contents from one Scophit object to another.

Data type AjPScopalg

Holds data associated with a structure alignment. Now adapted to hold CATH domain data also by addition of Type, Architecture and Topology elements.

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

Alias name(s)

Name
AjSScopalg
AjOScopalg

Attributes

Name	Type	Description
Class	AjPStr	Class name
Architecture	AjPStr	CATH classification.
Topology	AjPStr	CATH classification.
Fold	AjPStr	Fold name
Superfamily	AjPStr	Superfamily name
Family	AjPStr	Family name (SCOP only)
Sunid_Family	ajuint	SCOP sunid for family
width	ajuint	Width (residues) of widest part of alignment
Type	ajuint	Type of domains, either ajSCOP (1) or ajCATH (2).
N	ajuint	No. of sequences in alignment
Codes	AjPStr*	Array of domain id codes of sequences
Seqs	AjPStr*	Array of sequences
Post_similar	AjPStr	Post_similar line from alignment
Positions	AjPStr	Array of integers from 'Position' line in alignment, used for manual specification of signature positions

Constructor(s)

Name	Description
ajDmxScopalgRead	Read a Scopalg object from a file.

Output

Name	Description
ajDmxScopalgWrite	Write a Scopalg object to file in clustal format annotated with SCOP classification info.
ajDmxScopalgWriteClustal	Writes a Scopalg object to file in clustal format (just the alignment without the SCOP classification information).
ajDmxScopalgWriteClustal2	Writes a Scopalg object to file in clustal format (just the alignment without the SCOP classification information).
ajDmxScopalgWriteFasta	Writes a Scopalg object to file in clustal format (just the alignment without the SCOP classification information).

Constructor(s)

Name	Description
ajDmxScopalgNew	Scopalg object constructor.

Destructor(s)

Name	Description
ajDmxScopalgDel	Scopalg object destructor.

Input

Name	Description
ajDmxScopalgGetseqs	Read a Scopalg object and writes an array of AjPStr containing the sequences without gaps.