ajdomain.c

Section: Constructors

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

Functions: ajCathReadAllNew ajCathReadAllRawNew ajCathReadCNew ajCathReadNew ajDomainReadAllNew ajScopReadAllNew ajScopReadAllRawNew ajCathNew ajDomainNew ajScopNew ajDomainReadNew ajScopReadNew ajDomainReadCNew ajScopReadCNew

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.

Synopsis

Prototype
AjPList ajCathReadAllNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to CATH classification file
AjPList RETURNList of Cath objects.

Input & Output
inf:(Modify)Pointer to CATH classification file
Returns
AjPList:List of Cath objects.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathReadAllRawNew

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFilecathfModifyCath class file
AjPFiledomfModifyCath domain file
AjPFilenamesfModifyOutput file
AjPFileflogModifyLog file
AjPList RETURNList of Scop objects.

Input & Output
cathf:(Modify)Cath class file
domf:(Modify)Cath domain file
namesf:(Modify)Output file
flog:(Modify)Log file
Returns
AjPList:List of Scop objects.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathReadCNew

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const char*entryInputCATH id of entry to retrieve (or "*" for next domain in file).
AjPCath RETURNCath object.

Input
entry:(Input)CATH id of entry to retrieve (or "*" for next domain in file).
Input & Output
inf:(Modify)Input file stream
Returns
AjPCath:Cath object.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathReadNew

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

Synopsis

Prototype
AjPCath ajCathReadNew (
      AjPFile inf,
      const AjPStr entry
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const AjPStrentryInputCATH id of entry to retrieve (or "*" for next domain in file).
AjPCath RETURNCath object.

Input
entry:(Input)CATH id of entry to retrieve (or "*" for next domain in file).
Input & Output
inf:(Modify)Input file stream
Returns
AjPCath:Cath object.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

Prototype
AjPList ajDomainReadAllNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to DOMAIN classification file
AjPList RETURNList of domain objects or NULL (file read problem).

Input & Output
inf:(Modify)Pointer to DOMAIN classification file
Returns
AjPList:List of domain objects or NULL (file read problem).

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

Prototype
AjPList ajScopReadAllNew (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to SCOP classification file
AjPList RETURNList of scop objects or NULL (file read problem).

Input & Output
inf:(Modify)Pointer to SCOP classification file
Returns
AjPList:List of scop objects or NULL (file read problem).

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopReadAllRawNew

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFileclafModifyScop class file
AjPFiledesfModifyScop description file
AjBoolomitInputTrue if domains of 1 chain only are output
AjPList RETURNList of Scop objects.

Input
omit:(Input)True if domains of 1 chain only are output
Input & Output
claf:(Modify)Scop class file
desf:(Modify)Scop description file
Returns
AjPList:List of Scop objects.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathNew

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

Synopsis

Prototype
AjPCath ajCathNew (
      ajint n
);

TypeNameRead/WriteDescription
ajintnInputNo. of chain segments
AjPCath RETURNPointer to a Cath object

Input
n:(Input)No. of chain segments
Returns
AjPCath:Pointer to a Cath object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

Prototype
AjPDomain ajDomainNew (
      ajint n,
      ajint type
);

TypeNameRead/WriteDescription
ajintnInputNumber of chains (SCOP) or chain segments (CATH)
ajinttypeInputEither ajSCOP (1) or ajCATH (2)
AjPDomain RETURNPointer to a Domain object

Input
n:(Input)Number of chains (SCOP) or chain segments (CATH)
type:(Input)Either ajSCOP (1) or ajCATH (2)
Returns
AjPDomain:Pointer to a Domain object

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopNew

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

Synopsis

Prototype
AjPScop ajScopNew (
      ajint chains
);

TypeNameRead/WriteDescription
ajintchainsInputNumber of chains
AjPScop RETURNPointer to a Scop object

Input
chains:(Input)Number of chains
Returns
AjPScop:Pointer to a Scop object

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainReadNew

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

Synopsis

Prototype
AjPDomain ajDomainReadNew (
      AjPFile inf,
      const AjPStr entry
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream.
const AjPStrentryInputDomain id of domain to read (or "*" for next domain in file).
AjPDomain RETURNDomain object.

Input
entry:(Input)Domain id of domain to read (or "*" for next domain in file).
Input & Output
inf:(Modify)Input file stream.
Returns
AjPDomain:Domain object.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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).

Synopsis

Prototype
AjPScop ajScopReadNew (
      AjPFile inf,
      const AjPStr entry
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream.
const AjPStrentryInputSCOP id of domain to read (or "*" for next domain in file).
AjPScop RETURNScop object.

Input
entry:(Input)SCOP id of domain to read (or "*" for next domain in file).
Input & Output
inf:(Modify)Input file stream.
Returns
AjPScop:Scop object.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainReadCNew

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const char*entryInputDomain id of domain to parse
ajintdtypeInputType of domain (ajSCOP or ajCATH) in the DCF file, or '0' if not sure.
AjPDomain RETURNDomain object or NULL (file read problem).

Input
entry:(Input)Domain id of domain to parse
dtype:(Input)Type of domain (ajSCOP or ajCATH) in the DCF file, or '0' if not sure.
Input & Output
inf:(Modify)Input file stream
Returns
AjPDomain:Domain object or NULL (file read problem).

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopReadCNew

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

Synopsis

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

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
const char*entryInputSCOP id of domain to parse
AjPScop RETURNScop object or NULL (file read problem).

Input
entry:(Input)SCOP id of domain to parse
Input & Output
inf:(Modify)Input file stream
Returns
AjPScop:Scop object or NULL (file read problem).

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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 ajScopDel ajCathDel

Function ajDomainDel

Destructor for domain object.

Synopsis

Prototype
void ajDomainDel (
      AjPDomain* ptr
);

TypeNameRead/WriteDescription
AjPDomain*ptrDeleteDomain object pointer
void RETURN

Output
ptr:(Delete)Domain object pointer
Returns
void:No return value

Description

Destructor for domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopDel

Destructor for scop object.

Synopsis

Prototype
void ajScopDel (
      AjPScop* ptr
);

TypeNameRead/WriteDescription
AjPScop*ptrDeleteScop object pointer
void RETURN

Output
ptr:(Delete)Scop object pointer
Returns
void:No return value

Description

Destructor for scop object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathDel

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

Synopsis

Prototype
void ajCathDel (
      AjPCath* ptr
);

TypeNameRead/WriteDescription
AjPCath*ptrDeleteCath object pointer
void RETURN

Output
ptr:(Delete)Cath object pointer
Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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 ajCathCopy ajScopCopy

Function ajDomainCopy

Copies the contents from one Domain object to another.

Synopsis

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

TypeNameRead/WriteDescription
AjPDomain*toOutputDomain object pointer
const AjPDomainfromInputDomain object
AjBool RETURNTrue if copy was successful.

Input
from:(Input)Domain object
Output
to:(Output)Domain object pointer
Returns
AjBool:True if copy was successful.

Description

Copies the contents from one Domain object to another.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathCopy

Copies the contents from one Cath object to another.

Synopsis

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

TypeNameRead/WriteDescription
AjPCath*toOutputCath object pointer
const AjPCathfromInputCath object
AjBool RETURNTrue if copy was successful.

Input
from:(Input)Cath object
Output
to:(Output)Cath object pointer
Returns
AjBool:True if copy was successful.

Description

Copies the contents from one Cath object to another.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopCopy

Copies the contents from one Scop object to another.

Synopsis

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

TypeNameRead/WriteDescription
AjPScop*toOutputScop object pointer
const AjPScopfromInputScop object
AjBool RETURNTrue if copy was successful.

Input
from:(Input)Scop object
Output
to:(Output)Scop object pointer
Returns
AjBool:True if copy was successful.

Description

Copies the contents from one Scop object to another.

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Operators

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

Functions: ajScopMatchSunid ajScopMatchScopid ajScopMatchPdbId ajCathMatchPdbId

Function ajScopMatchSunid

Function to sort Scop objects by Sunid_Family.

Synopsis

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

TypeNameRead/WriteDescription
const void*entry1InputPointer to Scop object 1
const void*entry2InputPointer 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.

Input
entry1:(Input)Pointer to Scop object 1
entry2:(Input)Pointer to Scop object 2
Returns
ajint:-1 if Start1 should sort before Start2, +1 if the Start2 should sort first. 0 if they are identical.

Description

Function to sort Scop objects by Sunid_Family.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopMatchScopid

Function to sort Scop objects by Entry element.

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Scop object 1
const void*hit2InputPointer 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.

Input
hit1:(Input)Pointer to Scop object 1
hit2:(Input)Pointer to Scop object 2
Returns
ajint:-1 if Entry1 should sort before Entry2, +1 if the Entry2 should sort first. 0 if they are identical in length and content.

Description

Function to sort Scop objects by Entry element.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajScopMatchPdbId

Function to sort Scop objects by Pdb element.

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Scop object 1
const void*hit2InputPointer 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.

Input
hit1:(Input)Pointer to Scop object 1
hit2:(Input)Pointer to Scop object 2
Returns
ajint:-1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

Description

Function to sort Scop objects by Pdb element.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajCathMatchPdbId

Function to sort Cath objects by Pdb element.

Synopsis

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

TypeNameRead/WriteDescription
const void*hit1InputPointer to Cath object 1
const void*hit2InputPointer 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.

Input
hit1:(Input)Pointer to Cath object 1
hit2:(Input)Pointer to Cath object 2
Returns
ajint:-1 if Pdb1 should sort before Pdb2, +1 if the Pdb2 should sort first. 0 if they are identical in length and content.

Description

Function to sort Cath objects by Pdb element.

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Reporters

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

Functions: ajDomainGetId ajDomainGetSeqPdb ajDomainGetSeqSpr ajDomainGetPdb ajDomainGetAcc ajDomainGetSpr ajDomainGetN ajScopArrFindScopid ajScopArrFindSunid ajScopArrFindPdbid ajCathArrFindPdbid

Function ajDomainGetId

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

Synopsis

Prototype
AjPStr ajDomainGetId (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetSeqPdb

Returns the pdb sequence from a Domain object.

Synopsis

Prototype
AjPStr ajDomainGetSeqPdb (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

Returns the pdb sequence from a Domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetSeqSpr

Returns the swissprot sequence from a Domain object.

Synopsis

Prototype
AjPStr ajDomainGetSeqSpr (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

Returns the swissprot sequence from a Domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetPdb

Returns the Pdb element from a Domain object.

Synopsis

Prototype
AjPStr ajDomainGetPdb (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

Returns the Pdb element from a Domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetAcc

Returns the Acc element from a Domain object.

Synopsis

Prototype
AjPStr ajDomainGetAcc (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

Returns the Acc element from a Domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetSpr

Returns the Spr element from a Domain object.

Synopsis

Prototype
AjPStr ajDomainGetSpr (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
AjPStr RETURNOr NULL on error.

Input
obj:(Input)Domain object
Returns
AjPStr:Or NULL on error.

Description

Returns the Spr element from a Domain object.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainGetN

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

Synopsis

Prototype
ajint ajDomainGetN (
      const AjPDomain obj
);

TypeNameRead/WriteDescription
const AjPDomainobjInputDomain object
ajint RETURNOr -1 on error.

Input
obj:(Input)Domain object
Returns
ajint:Or -1 on error.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPScop const*arrInputArray of AjPScop objects
ajintsizInputSize of array
const AjPStridInputSearch term
ajint RETURNIndex of first Scop object found with a SCOP domain id matching id, or -1 if id is not found.

Input
arr:(Input)Array of AjPScop objects
siz:(Input)Size of array
id:(Input)Search term
Returns
ajint:Index of first Scop object found with a SCOP domain id matching id, or -1 if id is not found.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPScop const*arrInputArray of Scop objects
ajintsizInputSize of array
ajintidInputSearch term
ajint RETURNIndex of first Scop object found with an PDB code matching id, or -1 if id is not found.

Input
arr:(Input)Array of Scop objects
siz:(Input)Size of array
id:(Input)Search term
Returns
ajint:Index of first Scop object found with an PDB code matching id, or -1 if id is not found.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPScop const*arrInputArray of AjPScop objects
ajintsizInputSize of array
const AjPStridInputSearch term
ajint RETURNIndex of first Scop object found with a PDB code matching id, or -1 if id is not found.

Input
arr:(Input)Array of AjPScop objects
siz:(Input)Size of array
id:(Input)Search term
Returns
ajint:Index of first Scop object found with a PDB code matching id, or -1 if id is not found.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPCath const*arrInputArray of AjPCath objects
ajintsizInputSize of array
const AjPStridInputSearch term
ajint RETURNIndex of first Cath object found with a PDB code matching id, or -1 if id is not found.

Input
arr:(Input)Array of AjPCath objects
siz:(Input)Size of array
id:(Input)Search term
Returns
ajint:Index of first Cath object found with a PDB code matching id, or -1 if id is not found.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Input and Output

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

Functions: ajPdbWriteDomain ajCathWrite ajDomainWrite ajScopWrite

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.

Synopsis

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

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const AjPPdbpdbInputPdb object
const AjPScopscopInputScop object
AjPFileerrfModifyOutput file stream for error messages
AjBool RETURNTrue on success

Input
pdb:(Input)Pdb object
scop:(Input)Scop object
Input & Output
outf:(Modify)Output file stream
errf:(Modify)Output file stream for error messages
Returns
AjBool:True on success

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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).

Synopsis

Prototype
AjBool ajCathWrite (
      AjPFile outf,
      const AjPCath obj
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const AjPCathobjInputCath object
AjBool RETURNTrue if file was written ok.

Input
obj:(Input)Cath object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True if file was written ok.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainWrite

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

Synopsis

Prototype
AjBool ajDomainWrite (
      AjPFile outf,
      const AjPDomain obj
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const AjPDomainobjInputDomain object
AjBool RETURNTrue if file was written ok.

Input
obj:(Input)Domain object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True if file was written ok.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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).

Synopsis

Prototype
AjBool ajScopWrite (
      AjPFile outf,
      const AjPScop obj
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file stream
const AjPScopobjInputScop object
AjBool RETURNTrue if file was written ok.

Input
obj:(Input)Scop object
Input & Output
outf:(Modify)Output file stream
Returns
AjBool:True if file was written ok.

Description

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).

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Miscellaneous

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

Functions: ajDomainDCFType ajDomainExit ajDomainDummyFunction

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.

Synopsis

Prototype
ajint ajDomainDCFType (
      AjPFile inf
);

TypeNameRead/WriteDescription
AjPFileinfModifyInput file stream
ajint RETURNajSCOP, ajCATH or -1 (error) as appropriate.

Input & Output
inf:(Modify)Input file stream
Returns
ajint:ajSCOP, ajCATH or -1 (error) as appropriate.

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainExit

Cleanup of Domain function internals.

Synopsis

Prototype
void ajDomainExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleanup of Domain function internals.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajDomainDummyFunction

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

Synopsis

Prototype
void ajDomainDummyFunction (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0