ajdmx.c

Section: Constructors

All constructors return a pointer to a new instance. It is the responsibility of the user to first destroy any previous instance. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions:

ajDmxScophitNew Scophit object constructor.

ajDmxScopalgNew Scopalg object constructor. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.

ajDmxScopalgRead Read a Scopalg object from a file.

Function ajDmxScophitNew

Scophit object constructor.

Prototype

AjPScophit ajDmxScophitNew (
      void
);

Type Name Read/Write Description

AjPScophit RETURN Pointer to a Scophit object

Type	Name	Read/Write	Description
`AjPScophit`		RETURN	Pointer to a Scophit object

From EMBOSS 2.9.0

Function ajDmxScopalgNew

Scopalg object constructor. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.

Prototype

AjPScopalg ajDmxScopalgNew (
      ajint n
);

Type Name Read/Write Description

ajint n Input Number of sequences

AjPScopalg RETURN Pointer to a Scopalg object

Type	Name	Read/Write	Description
`ajint`	`n`	Input	Number of sequences
`AjPScopalg`		RETURN	Pointer to a Scopalg object

From EMBOSS 2.9.0

Function ajDmxScopalgRead

Read a Scopalg object from a file.

Prototype

AjBool ajDmxScopalgRead (
      AjPFile inf,
      AjPScopalg* thys
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

AjPScopalg* thys Output Scopalg object

AjBool RETURN True if the file contained any data, even an empty alignment. False if the file did not contain a 'TY' record, which is taken to indicate a domain alignment file.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`AjPScopalg*`	`thys`	Output	Scopalg object
`AjBool`		RETURN	True if the file contained any data, even an empty alignment. False if the file did not contain a 'TY' record, which is taken to indicate a domain alignment file.

From EMBOSS 2.9.0

Section: Structure Destructors

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

Functions:

ajDmxScophitDel Destructor for Scophit object.

ajDmxScophitDelWrap Wrapper to destructor for Scophit object for use with generic functions.

ajDmxScopalgDel Destructor for Scopalg object.

Function ajDmxScophitDel

Destructor for Scophit object.

Prototype

void ajDmxScophitDel (
      AjPScophit* pthis
);

Type Name Read/Write Description

AjPScophit* pthis Output Scophit object pointer

void RETURN

Type	Name	Read/Write	Description
`AjPScophit*`	`pthis`	Output	Scophit object pointer
`void`		RETURN

From EMBOSS 2.9.0

Function ajDmxScophitDelWrap

Wrapper to destructor for Scophit object for use with generic functions.

Prototype

void ajDmxScophitDelWrap (
      void** ptr
);

Type Name Read/Write Description

void** ptr Delete Object pointer

void RETURN

Type	Name	Read/Write	Description
`void**`	`ptr`	Delete	Object pointer
`void`		RETURN

From EMBOSS 2.9.0

Function ajDmxScopalgDel

Destructor for Scopalg object.

Prototype

void ajDmxScopalgDel (
      AjPScopalg* pthis
);

Type Name Read/Write Description

AjPScopalg* pthis Delete Scopalg object pointer

void RETURN

Type	Name	Read/Write	Description
`AjPScopalg*`	`pthis`	Delete	Scopalg 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:

ajDmxScophitListCopy Read a list of Scophit structures and returns a pointer to a duplicate of the list.

ajDmxScophitCopy Copies the contents from one Scophit object to another.

Function ajDmxScophitListCopy

Read a list of Scophit structures and returns a pointer to a duplicate of the list.

Prototype

AjPList ajDmxScophitListCopy (
      const AjPList ptr
);

Type Name Read/Write Description

const AjPList ptr Input List of Scophit objects

AjPList RETURN True on success (list was duplicated ok)

Type	Name	Read/Write	Description
`const AjPList`	`ptr`	Input	List of Scophit objects
`AjPList`		RETURN	True on success (list was duplicated ok)

From EMBOSS 2.9.0

Function ajDmxScophitCopy

Copies the contents from one Scophit object to another.

Prototype

AjBool ajDmxScophitCopy (
      AjPScophit* to,
      const AjPScophit from
);

Type Name Read/Write Description

AjPScophit* to Output Scophit object pointer

const AjPScophit from Input Scophit object

AjBool RETURN True if copy was successful.

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

From EMBOSS 2.9.0

Section: Modifiers

These functions use the contents of an instance and update them.

Functions:

ajDmxScophitTargetLowPriority Sets the Target element of a Scophit object to True if its Priority is low.

ajDmxScophitTarget2 Sets the Target2 element of a Scophit object to True.

ajDmxScophitTarget Sets the Target element of a Scophit object to True.

Function ajDmxScophitTargetLowPriority

Sets the Target element of a Scophit object to True if its Priority is low.

Prototype

AjBool ajDmxScophitTargetLowPriority (
      AjPScophit* h
);

Type Name Read/Write Description

AjPScophit* h Modify Pointer to Scophit object

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`h`	Modify	Pointer to Scophit object
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Function ajDmxScophitTarget2

Sets the Target2 element of a Scophit object to True.

Prototype

AjBool ajDmxScophitTarget2 (
      AjPScophit* h
);

Type Name Read/Write Description

AjPScophit* h Modify Pointer to Scophit object

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`h`	Modify	Pointer to Scophit object
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Function ajDmxScophitTarget

Sets the Target element of a Scophit object to True.

Prototype

AjBool ajDmxScophitTarget (
      AjPScophit* h
);

Type Name Read/Write Description

AjPScophit* h Modify Pointer to Scophit object

AjBool RETURN True on success. False otherwise.

Type	Name	Read/Write	Description
`AjPScophit*`	`h`	Modify	Pointer to Scophit object
`AjBool`		RETURN	True on success. False otherwise.

From EMBOSS 2.9.0

Section: Operators

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

Functions:

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

Function ajDmxScophitCheckTarget

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

Prototype

AjBool ajDmxScophitCheckTarget (
      const AjPScophit ptr
);

Type Name Read/Write Description

const AjPScophit ptr Input Scophit object pointer

AjBool RETURN Returns ajTrue if the Target element of the Scophit object == ajTrue, returns ajFalse otherwise.

Type	Name	Read/Write	Description
`const AjPScophit`	`ptr`	Input	Scophit object pointer
`AjBool`		RETURN	Returns ajTrue if the Target element of the Scophit object == ajTrue, returns ajFalse otherwise.

From EMBOSS 2.9.0

Section: Reporters

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

Functions:

ajDmxScophitCompScore Function to sort Scophit objects by Score element. Usually called by ajListSort.

ajDmxScophitCompPval Function to sort AjOScophit objects by Pval record. Usually called by ajListSort.

ajDmxScophitCompAcc Function to sort Scophit objects by Acc element.

ajDmxScophitCompSunid Function to sort Scophit object by Sunid_Family.

ajDmxScophitCompSpr Function to sort Scophit object by Spr element.

ajDmxScophitCompEnd Function to sort Scophit object by End element.

ajDmxScophitCompStart Function to sort Scophit object by Start element.

ajDmxScophitCompFam Function to sort Scophit object by Family element.

ajDmxScophitCompSfam Function to sort Scophit object by Superfamily element.

ajDmxScophitCompClass Function to sort Scophit object by Class element.

ajDmxScophitCompFold Function to sort Scophit object by Fold element.

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

ajDmxScophitsWrite Write contents of a list of Scophits to an output file in embl-like format Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

ajDmxScophitsWriteFasta Write contents of a list of Scophits to an output file in DHF format Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.

ajDmxScophitReadFasta Read a Scophit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

ajDmxScopalgWrite Write a Scopalg object to file in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):

ajDmxScopalgWriteClustal Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).

ajDmxScopalgWriteClustal2 Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).

ajDmxScopalgWriteFasta Writes a Scopalg object to a specified file in FASTA format (just the alignment without the domain classification information).

Function ajDmxScophitCompScore

Function to sort Scophit objects by Score element. Usually called by ajListSort.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Hit object 1

const void* hit2 Input Pointer to Hit object 2

ajint RETURN 1 if score1<score2, 0 if score1==score2, else -1.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	1 if score1<score2, 0 if score1==score2, else -1.

From EMBOSS 2.9.0

Function ajDmxScophitCompPval

Function to sort AjOScophit objects by Pval record. Usually called by ajListSort.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Hit object 1

const void* hit2 Input Pointer to Hit object 2

ajint RETURN 1 if Pval1>Pval2, 0 if Pval1==Pval2, else -1.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Hit object 1
`const void*`	`hit2`	Input	Pointer to Hit object 2
`ajint`		RETURN	1 if Pval1>Pval2, 0 if Pval1==Pval2, else -1.

From EMBOSS 2.9.0

Function ajDmxScophitCompAcc

Function to sort Scophit objects by Acc element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Acc1 should sort before Acc2, +1 if the Acc2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Acc1 should sort before Acc2, +1 if the Acc2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajDmxScophitCompSunid

Function to sort Scophit object by Sunid_Family.

Prototype

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

Type Name Read/Write Description

const void* entry1 Input Pointer to AjOScophit object 1

const void* entry2 Input Pointer to AjOScophit object 2

ajint RETURN -1 if Sunid_Family1 < Sunid_Family2, +1 if the Sunid_Family2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`entry1`	Input	Pointer to AjOScophit object 1
`const void*`	`entry2`	Input	Pointer to AjOScophit object 2
`ajint`		RETURN	-1 if Sunid_Family1 < Sunid_Family2, +1 if the Sunid_Family2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompSpr

Function to sort Scophit object by Spr element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Spr1 should sort before Spr2, +1 if the Spr2 should sort first. 0 if they are identical in length and content.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Spr1 should sort before Spr2, +1 if the Spr2 should sort first. 0 if they are identical in length and content.

From EMBOSS 2.9.0

Function ajDmxScophitCompEnd

Function to sort Scophit object by End element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if End1 should sort before End2, +1 if the End2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if End1 should sort before End2, +1 if the End2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompStart

Function to sort Scophit object by Start element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit 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*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit 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 ajDmxScophitCompFam

Function to sort Scophit object by Family element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Family1 should sort before Family2, +1 if the Family2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Family1 should sort before Family2, +1 if the Family2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompSfam

Function to sort Scophit object by Superfamily element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Superfamily1 should sort before Superfamily2, +1 if the Superfamily2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Superfamily1 should sort before Superfamily2, +1 if the Superfamily2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScophitCompClass

Function to sort Scophit object by Class element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Class1 should sort before Class2, +1 if the Class2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Class1 should sort before Class2, +1 if the Class2 should sort first. 0 if they are identical.

From EMBOSS 3.0.0

Function ajDmxScophitCompFold

Function to sort Scophit object by Fold element.

Prototype

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

Type Name Read/Write Description

const void* hit1 Input Pointer to Scophit object 1

const void* hit2 Input Pointer to Scophit object 2

ajint RETURN -1 if Fold1 should sort before Fold2, +1 if the Fold2 should sort first. 0 if they are identical.

Type	Name	Read/Write	Description
`const void*`	`hit1`	Input	Pointer to Scophit object 1
`const void*`	`hit2`	Input	Pointer to Scophit object 2
`ajint`		RETURN	-1 if Fold1 should sort before Fold2, +1 if the Fold2 should sort first. 0 if they are identical.

From EMBOSS 2.9.0

Function ajDmxScopalgGetseqs

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

Prototype

ajint ajDmxScopalgGetseqs (
      const AjPScopalg thys,
      AjPStr** arr
);

Type Name Read/Write Description

const AjPScopalg thys Input Scopalg object

AjPStr** arr Output Array of AjPStr

ajint RETURN Number of sequences read

Type	Name	Read/Write	Description
`const AjPScopalg`	`thys`	Input	Scopalg object
`AjPStr**`	`arr`	Output	Array of AjPStr
`ajint`		RETURN	Number of sequences read

From EMBOSS 2.9.0

Function ajDmxScophitsWrite

Write contents of a list of Scophits to an output file in embl-like format Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool ajDmxScophitsWrite (
      AjPFile outf,
      const AjPList list
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const AjPList list Input List object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	Output file stream
`const AjPList`	`list`	Input	List object
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Function ajDmxScophitsWriteFasta

Write contents of a list of Scophits to an output file in DHF format Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.

Prototype

AjBool ajDmxScophitsWriteFasta (
      AjPFile outf,
      const AjPList list
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const AjPList list Input List object

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	Output file stream
`const AjPList`	`list`	Input	List object
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function ajDmxScophitReadFasta

Read a Scophit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Prototype

AjPScophit ajDmxScophitReadFasta (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

AjPScophit RETURN Scophit object, or NULL if the file was not in extended FASTA (DHF) format (indicated by a token count of the the lines beginning with '>').

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`AjPScophit`		RETURN	Scophit object, or NULL if the file was not in extended FASTA (DHF) format (indicated by a token count of the the lines beginning with '>').

From EMBOSS 3.0.0

Function ajDmxScopalgWrite

Write a Scopalg object to file in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):

Prototype

AjBool ajDmxScopalgWrite (
      const AjPScopalg scop,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg scop Input Scopalg object

AjPFile outf Modify Output file stream

AjBool RETURN True on success (an alignment was written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`scop`	Input	Scopalg object
`AjPFile`	`outf`	Modify	Output file stream
`AjBool`		RETURN	True on success (an alignment was written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteClustal

Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteClustal (
      const AjPScopalg align,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg align Input Scopalg object

AjPFile outf Modify Outfile file pointer

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`align`	Input	Scopalg object
`AjPFile`	`outf`	Modify	Outfile file pointer
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteClustal2

Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteClustal2 (
      const AjPScopalg align,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg align Input Scopalg object.

AjPFile outf Modify Outfile file pointer.

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`align`	Input	Scopalg object.
`AjPFile`	`outf`	Modify	Outfile file pointer.
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Function ajDmxScopalgWriteFasta

Writes a Scopalg object to a specified file in FASTA format (just the alignment without the domain classification information).

Prototype

AjBool ajDmxScopalgWriteFasta (
      const AjPScopalg align,
      AjPFile outf
);

Type Name Read/Write Description

const AjPScopalg align Input A list of hit list structures.

AjPFile outf Modify Outfile file pointer

AjBool RETURN True on success (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`align`	Input	A list of hit list structures.
`AjPFile`	`outf`	Modify	Outfile file pointer
`AjBool`		RETURN	True on success (a file has been written)

From EMBOSS 2.9.0

Section: Miscellaneous

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

Functions:

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. The swissprot sequence is taken in priority over the pdb sequence.

ajDmxExit Cleanup of Dmx function internals.

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

Function 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. The swissprot sequence is taken in priority over the pdb sequence.

Prototype

AjBool ajDmxScopSeqFromSunid (
      ajint id,
      AjPStr* seq,
      const AjPList list
);

Type Name Read/Write Description

ajint id Input Search term

AjPStr* seq Output Result sequence

const AjPList list Input Sorted list of Scop objects

AjBool RETURN True if a swissprot identifier code was found for the Pdb code.

Type	Name	Read/Write	Description
`ajint`	`id`	Input	Search term
`AjPStr*`	`seq`	Output	Result sequence
`const AjPList`	`list`	Input	Sorted list of Scop objects
`AjBool`		RETURN	True if a swissprot identifier code was found for the Pdb code.

From EMBOSS 2.9.0

Function ajDmxExit

Cleanup of Dmx function internals.

Prototype

void ajDmxExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 6.1.0

Function ajDmxDummyFunction

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

Prototype

void ajDmxDummyFunction (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 2.9.0

ajDmxScophitNew	Scophit object constructor.
ajDmxScopalgNew	Scopalg object constructor. This is normally called by the ajDmxScopalgRead function. Fore-knowledge of the number of sequences is required.
ajDmxScopalgRead	Read a Scopalg object from a file.

ajDmxScophitDel	Destructor for Scophit object.
ajDmxScophitDelWrap	Wrapper to destructor for Scophit object for use with generic functions.
ajDmxScopalgDel	Destructor for Scopalg object.

ajDmxScophitListCopy	Read a list of Scophit structures and returns a pointer to a duplicate of the list.
ajDmxScophitCopy	Copies the contents from one Scophit object to another.

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

ajDmxScophitCompScore	Function to sort Scophit objects by Score element. Usually called by ajListSort.
ajDmxScophitCompPval	Function to sort AjOScophit objects by Pval record. Usually called by ajListSort.
ajDmxScophitCompAcc	Function to sort Scophit objects by Acc element.
ajDmxScophitCompSunid	Function to sort Scophit object by Sunid_Family.
ajDmxScophitCompSpr	Function to sort Scophit object by Spr element.
ajDmxScophitCompEnd	Function to sort Scophit object by End element.
ajDmxScophitCompStart	Function to sort Scophit object by Start element.
ajDmxScophitCompFam	Function to sort Scophit object by Family element.
ajDmxScophitCompSfam	Function to sort Scophit object by Superfamily element.
ajDmxScophitCompClass	Function to sort Scophit object by Class element.
ajDmxScophitCompFold	Function to sort Scophit object by Fold element.
ajDmxScopalgGetseqs	Read a Scopalg object and writes an array of AjPStr containing the sequences without gaps.
ajDmxScophitsWrite	Write contents of a list of Scophits to an output file in embl-like format Text for Class, Architecture, Topology, Fold, Superfamily and Family is only written if the text is available.
ajDmxScophitsWriteFasta	Write contents of a list of Scophits to an output file in DHF format Text for Class, Archhitecture, Topology, Fold, Superfamily and Family is only written if the text is available.
ajDmxScophitReadFasta	Read a Scophit object from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
ajDmxScopalgWrite	Write a Scopalg object to file in EMBOSS simple multiple sequence format (same as that used by clustal) annotated with domain classification as below (records are for SCOP domains in this example):
ajDmxScopalgWriteClustal	Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).
ajDmxScopalgWriteClustal2	Writes a Scopalg object to a specified file in CLUSTAL format (just the alignment without the domain classification information).
ajDmxScopalgWriteFasta	Writes a Scopalg object to a specified file in FASTA format (just the alignment without the domain classification information).

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. The swissprot sequence is taken in priority over the pdb sequence.
ajDmxExit	Cleanup of Dmx function internals.
ajDmxDummyFunction	Dummy function to catch all unused functions defined in the ajdmx source file.