ajdomain.c

Section: Constructors

These constructors return a pointer to a new instance of an object.

Functions:

ajCathReadAllNew Reads a DCF file (domain classification file) for CATH domains. This file is in DCF format (see documentation for DOMAINATRIX "cathparse" application) and creates a list of Cath objects for the entire content.

ajCathReadAllRawNew Reads the CATH parsable files (dir.cla.scop.txt & dir.des.scop.txt) and writes a list of Cath objects.

ajCathReadCNew Read a Cath object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).

ajCathReadNew Read a Cath object from a DCF file (domain classification file) which is in DCF format (see documentation for DOMAINATRIX "cathparse" application).

ajDomainReadAllNew Reads the DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and creates a list of Domain objects for the entire content.

ajScopReadAllNew Reads the DCF file (domain classification file) of SCOP domains. The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application). The function creates a list of cop objects for the entire content.

ajScopReadAllRawNew Reads the SCOP parsable files (dir.cla.scop.txt & dir.des.scop.txt) and creates a list of Scop objects.

ajCathNew Cath object constructor. Fore-knowledge of the number of chain segments the domain is comprised of is required.

ajDomainNew Domain object constructor. Fore-knowledge of the number of chains (SCOP domains) or chain segments (CATH domains) the domain is comprised of is required. This is normally called by the ajDomainReadCNew / ajDomainReadNew functions.

ajScopNew Scop object constructor. Fore-knowledge of the number of chains is required. This is normally called by the ajScopReadCNew / ajScopReadNew functions.

ajDomainReadNew Read a Domain object from a DCF file (domain classification file - see documentation for DOMAINATRIX "scopparse" application).

ajScopReadNew Read a Scop object from a DCF file (domain classification file). The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application).

ajDomainReadCNew Read a Domain object from a DCF (domain classification file; see documentation for DOMAINATRIX "scopparse" application).

ajScopReadCNew Read a Scop object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "scopparse" application).

Function ajCathReadAllNew

Reads a DCF file (domain classification file) for CATH domains. This file is in DCF format (see documentation for DOMAINATRIX "cathparse" application) and creates a list of Cath objects for the entire content.

Prototype

AjPList ajCathReadAllNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to CATH classification file

AjPList RETURN List of Cath objects.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to CATH classification file
`AjPList`		RETURN	List of Cath objects.

From EMBOSS 2.9.0

Function ajCathReadAllRawNew

Reads the CATH parsable files (dir.cla.scop.txt & dir.des.scop.txt) and writes a list of Cath objects.

Prototype

AjPList ajCathReadAllRawNew (
      AjPFile cathf,
      AjPFile domf,
      AjPFile namesf,
      AjPFile flog
);

Type Name Read/Write Description

AjPFile cathf Modify Cath class file

AjPFile domf Modify Cath domain file

AjPFile namesf Modify Output file

AjPFile flog Modify Log file

AjPList RETURN List of Scop objects.

Type	Name	Read/Write	Description
`AjPFile`	`cathf`	Modify	Cath class file
`AjPFile`	`domf`	Modify	Cath domain file
`AjPFile`	`namesf`	Modify	Output file
`AjPFile`	`flog`	Modify	Log file
`AjPList`		RETURN	List of Scop objects.

From EMBOSS 2.9.0

Function ajCathReadCNew

Read a Cath object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).

Prototype

AjPCath ajCathReadCNew (
      AjPFile inf,
      const char* entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const char* entry Input CATH id of entry to retrieve (or "*" for next domain in file).

AjPCath RETURN Cath object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const char*`	`entry`	Input	CATH id of entry to retrieve (or "*" for next domain in file).
`AjPCath`		RETURN	Cath object.

From EMBOSS 2.9.0

Function ajCathReadNew

Read a Cath object from a DCF file (domain classification file) which is in DCF format (see documentation for DOMAINATRIX "cathparse" application).

Prototype

AjPCath ajCathReadNew (
      AjPFile inf,
      const AjPStr entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const AjPStr entry Input CATH id of entry to retrieve (or "*" for next domain in file).

AjPCath RETURN Cath object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const AjPStr`	`entry`	Input	CATH id of entry to retrieve (or "*" for next domain in file).
`AjPCath`		RETURN	Cath object.

From EMBOSS 2.9.0

Function ajDomainReadAllNew

Reads the DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and creates a list of Domain objects for the entire content.

Prototype

AjPList ajDomainReadAllNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to DOMAIN classification file

AjPList RETURN List of domain objects or NULL (file read problem).

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to DOMAIN classification file
`AjPList`		RETURN	List of domain objects or NULL (file read problem).

From EMBOSS 3.0.0

Function ajScopReadAllNew

Reads the DCF file (domain classification file) of SCOP domains. The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application). The function creates a list of cop objects for the entire content.

Prototype

AjPList ajScopReadAllNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to SCOP classification file

AjPList RETURN List of scop objects or NULL (file read problem).

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to SCOP classification file
`AjPList`		RETURN	List of scop objects or NULL (file read problem).

From EMBOSS 2.9.0

Function ajScopReadAllRawNew

Reads the SCOP parsable files (dir.cla.scop.txt & dir.des.scop.txt) and creates a list of Scop objects.

Prototype

AjPList ajScopReadAllRawNew (
      AjPFile claf,
      AjPFile desf,
      AjBool omit
);

Type Name Read/Write Description

AjPFile claf Modify Scop class file

AjPFile desf Modify Scop description file

AjBool omit Input True if domains of 1 chain only are output

AjPList RETURN List of Scop objects.

Type	Name	Read/Write	Description
`AjPFile`	`claf`	Modify	Scop class file
`AjPFile`	`desf`	Modify	Scop description file
`AjBool`	`omit`	Input	True if domains of 1 chain only are output
`AjPList`		RETURN	List of Scop objects.

From EMBOSS 2.9.0

Function ajCathNew

Cath object constructor. Fore-knowledge of the number of chain segments the domain is comprised of is required.

Prototype

AjPCath ajCathNew (
      ajint n
);

Type Name Read/Write Description

ajint n Input No. of chain segments

AjPCath RETURN Pointer to a Cath object

Type	Name	Read/Write	Description
`ajint`	`n`	Input	No. of chain segments
`AjPCath`		RETURN	Pointer to a Cath object

From EMBOSS 2.9.0

Function ajDomainNew

Domain object constructor. Fore-knowledge of the number of chains (SCOP domains) or chain segments (CATH domains) the domain is comprised of is required. This is normally called by the ajDomainReadCNew / ajDomainReadNew functions.

Prototype

AjPDomain ajDomainNew (
      ajint n,
      ajint type
);

Type Name Read/Write Description

ajint n Input Number of chains (SCOP) or chain segments (CATH)

ajint type Input Either ajSCOP (1) or ajCATH (2)

AjPDomain RETURN Pointer to a Domain object

Type	Name	Read/Write	Description
`ajint`	`n`	Input	Number of chains (SCOP) or chain segments (CATH)
`ajint`	`type`	Input	Either ajSCOP (1) or ajCATH (2)
`AjPDomain`		RETURN	Pointer to a Domain object

From EMBOSS 3.0.0

Function ajScopNew

Scop object constructor. Fore-knowledge of the number of chains is required. This is normally called by the ajScopReadCNew / ajScopReadNew functions.

Prototype

AjPScop ajScopNew (
      ajint chains
);

Type Name Read/Write Description

ajint chains Input Number of chains

AjPScop RETURN Pointer to a Scop object

Type	Name	Read/Write	Description
`ajint`	`chains`	Input	Number of chains
`AjPScop`		RETURN	Pointer to a Scop object

From EMBOSS 1.8.0

Function ajDomainReadNew

Read a Domain object from a DCF file (domain classification file - see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjPDomain ajDomainReadNew (
      AjPFile inf,
      const AjPStr entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream.

const AjPStr entry Input Domain id of domain to read (or "*" for next domain in file).

AjPDomain RETURN Domain object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream.
`const AjPStr`	`entry`	Input	Domain id of domain to read (or "*" for next domain in file).
`AjPDomain`		RETURN	Domain object.

From EMBOSS 3.0.0

Function ajScopReadNew

Read a Scop object from a DCF file (domain classification file). The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjPScop ajScopReadNew (
      AjPFile inf,
      const AjPStr entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream.

const AjPStr entry Input SCOP id of domain to read (or "*" for next domain in file).

AjPScop RETURN Scop object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream.
`const AjPStr`	`entry`	Input	SCOP id of domain to read (or "*" for next domain in file).
`AjPScop`		RETURN	Scop object.

From EMBOSS 2.9.0

Function ajDomainReadCNew

Read a Domain object from a DCF (domain classification file; see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjPDomain ajDomainReadCNew (
      AjPFile inf,
      const char* entry,
      ajint dtype
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const char* entry Input Domain id of domain to parse

ajint dtype Input Type of domain (ajSCOP or ajCATH) in the DCF file, or '0' if not sure.

AjPDomain RETURN Domain object or NULL (file read problem).

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const char*`	`entry`	Input	Domain id of domain to parse
`ajint`	`dtype`	Input	Type of domain (ajSCOP or ajCATH) in the DCF file, or '0' if not sure.
`AjPDomain`		RETURN	Domain object or NULL (file read problem).

From EMBOSS 3.0.0

Function ajScopReadCNew

Read a Scop object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjPScop ajScopReadCNew (
      AjPFile inf,
      const char* entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const char* entry Input SCOP id of domain to parse

AjPScop RETURN Scop object or NULL (file read problem).

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const char*`	`entry`	Input	SCOP id of domain to parse
`AjPScop`		RETURN	Scop object or NULL (file read problem).

From EMBOSS 2.9.0

Section: Structure Destructors

These destructors functions receive the address of the instance to be deleted. The original pointer is set to NULL so is ready for re-use.

Functions:

ajDomainDel Destructor for domain object.

ajScopDel Destructor for scop object.

ajCathDel Destructor for Cath object. Fore-knowledge of the number of chain segments domain is comprised of is required.

Function ajDomainDel

Destructor for domain object.

Prototype

void ajDomainDel (
      AjPDomain* ptr
);

Type Name Read/Write Description

AjPDomain* ptr Delete Domain object pointer

void RETURN

Type	Name	Read/Write	Description
`AjPDomain*`	`ptr`	Delete	Domain object pointer
`void`		RETURN

From EMBOSS 3.0.0

Function ajScopDel

Destructor for scop object.

Prototype

void ajScopDel (
      AjPScop* ptr
);

Type Name Read/Write Description

AjPScop* ptr Delete Scop object pointer

void RETURN

Type	Name	Read/Write	Description
`AjPScop*`	`ptr`	Delete	Scop object pointer
`void`		RETURN

From EMBOSS 1.8.0

Function ajCathDel

Destructor for Cath object. Fore-knowledge of the number of chain segments domain is comprised of is required.

Prototype

void ajCathDel (
      AjPCath* ptr
);

Type Name Read/Write Description

AjPCath* ptr Delete Cath object pointer

void RETURN

Type	Name	Read/Write	Description
`AjPCath*`	`ptr`	Delete	Cath object pointer
`void`		RETURN

From EMBOSS 2.9.0

Section: Assignments

These functions overwrite the instance provided as the first argument A NULL value is always acceptable so these functions are often used to create a new instance by assignment.

Functions:

ajDomainCopy Copies the contents from one Domain object to another.

ajCathCopy Copies the contents from one Cath object to another.

ajScopCopy Copies the contents from one Scop object to another.

Function ajDomainCopy

Copies the contents from one Domain object to another.

Prototype

AjBool ajDomainCopy (
      AjPDomain* to,
      const AjPDomain from
);

Type Name Read/Write Description

AjPDomain* to Output Domain object pointer

const AjPDomain from Input Domain object

AjBool RETURN True if copy was successful.

Type	Name	Read/Write	Description
`AjPDomain*`	`to`	Output	Domain object pointer
`const AjPDomain`	`from`	Input	Domain object
`AjBool`		RETURN	True if copy was successful.

From EMBOSS 3.0.0

Function ajCathCopy

Copies the contents from one Cath object to another.

Prototype

AjBool ajCathCopy (
      AjPCath* to,
      const AjPCath from
);

Type Name Read/Write Description

AjPCath* to Output Cath object pointer

const AjPCath from Input Cath object

AjBool RETURN True if copy was successful.

Type	Name	Read/Write	Description
`AjPCath*`	`to`	Output	Cath object pointer
`const AjPCath`	`from`	Input	Cath object
`AjBool`		RETURN	True if copy was successful.

From EMBOSS 3.0.0

Function ajScopCopy

Copies the contents from one Scop object to another.

Prototype

AjBool ajScopCopy (
      AjPScop* to,
      const AjPScop from
);

Type Name Read/Write Description

AjPScop* to Output Scop object pointer

const AjPScop from Input Scop object

AjBool RETURN True if copy was successful.

Type	Name	Read/Write	Description
`AjPScop*`	`to`	Output	Scop object pointer
`const AjPScop`	`from`	Input	Scop object
`AjBool`		RETURN	True if copy was successful.

From EMBOSS 2.9.0

Section: Operators

These functions use the contents of an instance but do not make any changes.

Functions:

ajScopMatchSunid Function to sort Scop objects by Sunid_Family.

ajScopMatchScopid Function to sort Scop objects by Entry element.

ajScopMatchPdbId Function to sort Scop objects by Pdb element.

ajCathMatchPdbId Function to sort Cath objects by Pdb element.

Function ajScopMatchSunid

Function to sort Scop objects by Sunid_Family.

Prototype

ajint ajScopMatchSunid (
      const void* entry1,
      const void* entry2
);

Type Name Read/Write Description

const void* entry1 Input Pointer to Scop object 1

const void* entry2 Input Pointer to Scop object 2

ajint RETURN -1 if Start1 should sort before Start2, +1 if the Start2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`entry1`	Input	Pointer to Scop object 1
`const void*`	`entry2`	Input	Pointer to Scop object 2
`ajint`		RETURN	-1 if Start1 should sort before Start2, +1 if the Start2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajScopMatchScopid

Function to sort Scop objects by Entry element.

Prototype

ajint ajScopMatchScopid (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Scop object 1

const void* hit2 Input Pointer to Scop object 2

ajint RETURN -1 if Entry1 should sort before Entry2, +1 if the Entry2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scop object 1
`const void*`	`hit2`	Input	Pointer to Scop object 2
`ajint`		RETURN	-1 if Entry1 should sort before Entry2, +1 if the Entry2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajScopMatchPdbId

Function to sort Scop objects by Pdb element.

Prototype

ajint ajScopMatchPdbId (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Scop object 1

const void* hit2 Input Pointer to Scop object 2

ajint RETURN -1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scop object 1
`const void*`	`hit2`	Input	Pointer to Scop object 2
`ajint`		RETURN	-1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajCathMatchPdbId

Function to sort Cath objects by Pdb element.

Prototype

ajint ajCathMatchPdbId (
      const void* hit1,
      const void* hit2
);

Type Name Read/Write Description

const void* hit1 Input Pointer to Cath object 1

const void* hit2 Input Pointer to Cath object 2

ajint RETURN -1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Cath object 1
`const void*`	`hit2`	Input	Pointer to Cath object 2
`ajint`		RETURN	-1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Section: Reporters

These functions return the contents of an instance but do not make any changes.

Functions:

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 element from a Domain object.

ajDomainGetAcc Returns the Acc element from a Domain object.

ajDomainGetSpr Returns the Spr element from a Domain object.

ajDomainGetN Returns no. chains or chain segments in a domain, either NSegment element (Cath domains) or N element (Scop domains).

ajScopArrFindScopid Performs a binary search for a SCOP domain id over an array of Scop structures (which of course must first have been sorted). This is a case-insensitive search.

ajScopArrFindSunid Performs a binary search for a SCOP sunid over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.

ajScopArrFindPdbid Performs a binary search for a SCOP domain id over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.

ajCathArrFindPdbid Performs a binary search for a CATH domain id over an array of Cath structures (which of course must first have been sorted). This is a case-insensitive search.

Function ajDomainGetId

Returns domain id, either DomainID element (Cath object) or Entry (Scop object).

Prototype

AjPStr ajDomainGetId (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetSeqPdb

Returns the pdb sequence from a Domain object.

Prototype

AjPStr ajDomainGetSeqPdb (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetSeqSpr

Returns the swissprot sequence from a Domain object.

Prototype

AjPStr ajDomainGetSeqSpr (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetPdb

Returns the Pdb element from a Domain object.

Prototype

AjPStr ajDomainGetPdb (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetAcc

Returns the Acc element from a Domain object.

Prototype

AjPStr ajDomainGetAcc (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetSpr

Returns the Spr element from a Domain object.

Prototype

AjPStr ajDomainGetSpr (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

AjPStr RETURN Or NULL on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`AjPStr`		RETURN	Or NULL on error.

From EMBOSS 3.0.0

Function ajDomainGetN

Returns no. chains or chain segments in a domain, either NSegment element (Cath domains) or N element (Scop domains).

Prototype

ajint ajDomainGetN (
      const AjPDomain obj
);

Type Name Read/Write Description

const AjPDomain obj Input Domain object

ajint RETURN Or -1 on error.

Type	Name	Read/Write	Description
`const AjPDomain`	`obj`	Input	Domain object
`ajint`		RETURN	Or -1 on error.

From EMBOSS 3.0.0

Function ajScopArrFindScopid

Performs a binary search for a SCOP domain id over an array of Scop structures (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajScopArrFindScopid (
      AjPScop const* arr,
      ajint siz,
      const AjPStr id
);

Type Name Read/Write Description

AjPScop const* arr Input Array of AjPScop objects

ajint siz Input Size of array

const AjPStr id Input Search term

ajint RETURN Index of first Scop object found with a SCOP domain id matching id, or -1 if id is not found.

Type	Name	Read/Write	Description
`AjPScop const*`	`arr`	Input	Array of AjPScop objects
`ajint`	`siz`	Input	Size of array
`const AjPStr`	`id`	Input	Search term
`ajint`		RETURN	Index of first Scop object found with a SCOP domain id matching id, or -1 if id is not found.

From EMBOSS 2.9.0

Function ajScopArrFindSunid

Performs a binary search for a SCOP sunid over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajScopArrFindSunid (
      AjPScop const* arr,
      ajint siz,
      ajint id
);

Type Name Read/Write Description

AjPScop const* arr Input Array of Scop objects

ajint siz Input Size of array

ajint id Input Search term

ajint RETURN Index of first Scop object found with an PDB code matching id, or -1 if id is not found.

Type	Name	Read/Write	Description
`AjPScop const*`	`arr`	Input	Array of Scop objects
`ajint`	`siz`	Input	Size of array
`ajint`	`id`	Input	Search term
`ajint`		RETURN	Index of first Scop object found with an PDB code matching id, or -1 if id is not found.

From EMBOSS 2.9.0

Function ajScopArrFindPdbid

Performs a binary search for a SCOP domain id over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajScopArrFindPdbid (
      AjPScop const* arr,
      ajint siz,
      const AjPStr id
);

Type	Name	Read/Write	Description
`AjPScop const*`	`arr`	Input	Array of AjPScop objects
`ajint`	`siz`	Input	Size of array
`const AjPStr`	`id`	Input	Search term
`ajint`		RETURN	Index of first Scop object found with a PDB code matching id, or -1 if id is not found.

From EMBOSS 2.9.0

Function ajCathArrFindPdbid

Performs a binary search for a CATH domain id over an array of Cath structures (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajCathArrFindPdbid (
      AjPCath const* arr,
      ajint siz,
      const AjPStr id
);

Type Name Read/Write Description

AjPCath const* arr Input Array of AjPCath objects

ajint siz Input Size of array

const AjPStr id Input Search term

ajint RETURN Index of first Cath object found with a PDB code matching id, or -1 if id is not found.

Type	Name	Read/Write	Description
`AjPCath const*`	`arr`	Input	Array of AjPCath objects
`ajint`	`siz`	Input	Size of array
`const AjPStr`	`id`	Input	Search term
`ajint`		RETURN	Index of first Cath object found with a PDB code matching id, or -1 if id is not found.

From EMBOSS 2.9.0

Section: Input and Output

These functions use the contents of an instance but do not make any changes.

Functions:

ajPdbWriteDomain Writes a clean coordinate file for a SCOP domain. Where coordinates for multiple models (e.g. NMR structures) are given, data for model 1 are written. In the clean file, the coordinates are presented as belonging to a single chain regardless of how many chains the domain comprised. Coordinates for heterogens are NOT written to file.

ajCathWrite Write contents of a Cath object to an output DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).

ajDomainWrite Write contents of a Domain object to an output file in DCF format (see documentation for DOMAINATRIX "scopparse" application).

ajScopWrite Write contents of a Scop object to a DCF file (domain classification file). The DCF file uses DCF format (see documentation for DOMAINATRIX "scopparse" application).

Function ajPdbWriteDomain

Writes a clean coordinate file for a SCOP domain. Where coordinates for multiple models (e.g. NMR structures) are given, data for model 1 are written. In the clean file, the coordinates are presented as belonging to a single chain regardless of how many chains the domain comprised. Coordinates for heterogens are NOT written to file.

Prototype

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

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const AjPPdb pdb Input Pdb object

const AjPScop scop Input Scop object

AjPFile errf Modify Output file stream for error messages

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const AjPPdb`	`pdb`	Input	Pdb object
`const AjPScop`	`scop`	Input	Scop object
`AjPFile`	`errf`	Modify	Output file stream for error messages
`AjBool`		RETURN	True on success

From EMBOSS 1.9.0

Function ajCathWrite

Write contents of a Cath object to an output DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).

Prototype

AjBool ajCathWrite (
      AjPFile outf,
      const AjPCath obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const AjPCath obj Input Cath object

AjBool RETURN True if file was written ok.

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const AjPCath`	`obj`	Input	Cath object
`AjBool`		RETURN	True if file was written ok.

From EMBOSS 2.9.0

Function ajDomainWrite

Write contents of a Domain object to an output file in DCF format (see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjBool ajDomainWrite (
      AjPFile outf,
      const AjPDomain obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const AjPDomain obj Input Domain object

AjBool RETURN True if file was written ok.

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const AjPDomain`	`obj`	Input	Domain object
`AjBool`		RETURN	True if file was written ok.

From EMBOSS 3.0.0

Function ajScopWrite

Write contents of a Scop object to a DCF file (domain classification file). The DCF file uses DCF format (see documentation for DOMAINATRIX "scopparse" application).

Prototype

AjBool ajScopWrite (
      AjPFile outf,
      const AjPScop obj
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

const AjPScop obj Input Scop object

AjBool RETURN True if file was written ok.

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`const AjPScop`	`obj`	Input	Scop object
`AjBool`		RETURN	True if file was written ok.

From EMBOSS 1.8.0

Section: Miscellaneous

These functions may have diverse functions that do not fit into the other categories.

Functions:

ajDomainDCFType Reads a DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and ascertains the type of domains (ajSCOP or ajCATH) within.

ajDomainExit Cleanup of Domain function internals.

ajDomainDummyFunction Dummy function to catch all unused functions defined in the ajdomain source file.

Function ajDomainDCFType

Reads a DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and ascertains the type of domains (ajSCOP or ajCATH) within.

Prototype

ajint ajDomainDCFType (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

ajint RETURN ajSCOP, ajCATH or -1 (error) as appropriate.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`ajint`		RETURN	ajSCOP, ajCATH or -1 (error) as appropriate.

From EMBOSS 3.0.0

Function ajDomainExit

Cleanup of Domain function internals.

Prototype

void ajDomainExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.1.0

Function ajDomainDummyFunction

Dummy function to catch all unused functions defined in the ajdomain source file.

Prototype

void ajDomainDummyFunction (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 2.9.0

ajCathReadAllNew	Reads a DCF file (domain classification file) for CATH domains. This file is in DCF format (see documentation for DOMAINATRIX "cathparse" application) and creates a list of Cath objects for the entire content.
ajCathReadAllRawNew	Reads the CATH parsable files (dir.cla.scop.txt & dir.des.scop.txt) and writes a list of Cath objects.
ajCathReadCNew	Read a Cath object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).
ajCathReadNew	Read a Cath object from a DCF file (domain classification file) which is in DCF format (see documentation for DOMAINATRIX "cathparse" application).
ajDomainReadAllNew	Reads the DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and creates a list of Domain objects for the entire content.
ajScopReadAllNew	Reads the DCF file (domain classification file) of SCOP domains. The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application). The function creates a list of cop objects for the entire content.
ajScopReadAllRawNew	Reads the SCOP parsable files (dir.cla.scop.txt & dir.des.scop.txt) and creates a list of Scop objects.
ajCathNew	Cath object constructor. Fore-knowledge of the number of chain segments the domain is comprised of is required.
ajDomainNew	Domain object constructor. Fore-knowledge of the number of chains (SCOP domains) or chain segments (CATH domains) the domain is comprised of is required. This is normally called by the ajDomainReadCNew / ajDomainReadNew functions.
ajScopNew	Scop object constructor. Fore-knowledge of the number of chains is required. This is normally called by the ajScopReadCNew / ajScopReadNew functions.
ajDomainReadNew	Read a Domain object from a DCF file (domain classification file - see documentation for DOMAINATRIX "scopparse" application).
ajScopReadNew	Read a Scop object from a DCF file (domain classification file). The DCF file is in DCF format (see documentation for DOMAINATRIX "scopparse" application).
ajDomainReadCNew	Read a Domain object from a DCF (domain classification file; see documentation for DOMAINATRIX "scopparse" application).
ajScopReadCNew	Read a Scop object from a DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "scopparse" application).

ajDomainDel	Destructor for domain object.
ajScopDel	Destructor for scop object.
ajCathDel	Destructor for Cath object. Fore-knowledge of the number of chain segments domain is comprised of is required.

ajDomainCopy	Copies the contents from one Domain object to another.
ajCathCopy	Copies the contents from one Cath object to another.
ajScopCopy	Copies the contents from one Scop object to another.

ajScopMatchSunid	Function to sort Scop objects by Sunid_Family.
ajScopMatchScopid	Function to sort Scop objects by Entry element.
ajScopMatchPdbId	Function to sort Scop objects by Pdb element.
ajCathMatchPdbId	Function to sort Cath objects by Pdb element.

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 element from a Domain object.
ajDomainGetAcc	Returns the Acc element from a Domain object.
ajDomainGetSpr	Returns the Spr element from a Domain object.
ajDomainGetN	Returns no. chains or chain segments in a domain, either NSegment element (Cath domains) or N element (Scop domains).
ajScopArrFindScopid	Performs a binary search for a SCOP domain id over an array of Scop structures (which of course must first have been sorted). This is a case-insensitive search.
ajScopArrFindSunid	Performs a binary search for a SCOP sunid over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.
ajScopArrFindPdbid	Performs a binary search for a SCOP domain id over an array of Scop objects (which of course must first have been sorted). This is a case-insensitive search.
ajCathArrFindPdbid	Performs a binary search for a CATH domain id over an array of Cath structures (which of course must first have been sorted). This is a case-insensitive search.

ajPdbWriteDomain	Writes a clean coordinate file for a SCOP domain. Where coordinates for multiple models (e.g. NMR structures) are given, data for model 1 are written. In the clean file, the coordinates are presented as belonging to a single chain regardless of how many chains the domain comprised. Coordinates for heterogens are NOT written to file.
ajCathWrite	Write contents of a Cath object to an output DCF file (domain classification file) in DCF format (see documentation for DOMAINATRIX "cathparse" application).
ajDomainWrite	Write contents of a Domain object to an output file in DCF format (see documentation for DOMAINATRIX "scopparse" application).
ajScopWrite	Write contents of a Scop object to a DCF file (domain classification file). The DCF file uses DCF format (see documentation for DOMAINATRIX "scopparse" application).

ajDomainDCFType	Reads a DCF file (domain classification file; see documentation for DOMAINATRIX "scopparse" application) and ascertains the type of domains (ajSCOP or ajCATH) within.
ajDomainExit	Cleanup of Domain function internals.
ajDomainDummyFunction	Dummy function to catch all unused functions defined in the ajdomain source file.