ajpdb.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:

ajPdbtospReadAllRawNew Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.

ajPdbtospReadNew Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

ajPdbtospReadCNew Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.

ajPdbtospReadAllNew Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.

ajCmapReadINew Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.

ajCmapReadCNew Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.

ajCmapReadAllNew Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.

ajCmapReadNew Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.

ajVdwallReadNew Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

ajHetReadNew Read heterogen dictionary, the Het object is allocated.

ajHetReadRawNew Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.

ajPdbReadFirstModelNew Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

ajPdbReadAllModelsNew Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.

ajPdbReadNew Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

ajPdbReadoldNew Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.

ajPdbReadoldFirstModelNew Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.

ajAtomNew Atom object constructor. This is normally called by the ajChainNew function.

ajResidueNew Residue object constructor. This is normally called by the ajChainNew function.

ajChainNew Chain object constructor. This is normally called by the ajPdbNew function

ajPdbNew Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).

ajHetentNew Hetent object constructor.

ajHetNew Het object constructor.

ajVdwallNew Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.

ajVdwresNew Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.

ajCmapNew Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.

ajPdbtospNew Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

Function ajPdbtospReadAllRawNew

Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.

Prototype

AjPList ajPdbtospReadAllRawNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file

AjPList RETURN AJAX List of AJAX PDB to Swiss-Prot (AjPPdbtosp) objects

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file
`AjPList`		RETURN	AJAX List of AJAX PDB to Swiss-Prot (AjPPdbtosp) objects

From EMBOSS 2.9.0

Function ajPdbtospReadNew

Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Prototype

AjPPdbtosp ajPdbtospReadNew (
      AjPFile inf,
      const AjPStr entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const AjPStr entry Input Pdb id

AjPPdbtosp RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const AjPStr`	`entry`	Input	Pdb id
`AjPPdbtosp`		RETURN	True on success

From EMBOSS 2.9.0

Function ajPdbtospReadCNew

Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.

Prototype

AjPPdbtosp ajPdbtospReadCNew (
      AjPFile inf,
      const char* entry
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

const char* entry Input Pdb id

AjPPdbtosp RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`const char*`	`entry`	Input	Pdb id
`AjPPdbtosp`		RETURN	True on success

From EMBOSS 2.9.0

Function ajPdbtospReadAllNew

Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.

Prototype

AjPList ajPdbtospReadAllNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

AjPList RETURN List of Pdbtosp objects.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`AjPList`		RETURN	List of Pdbtosp objects.

From EMBOSS 2.9.0

Function ajCmapReadINew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.

Prototype

AjPCmap ajCmapReadINew (
      AjPFile inf,
      ajint chn,
      ajint mod
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

ajint chn Input Chain number

ajint mod Input Model number

AjPCmap RETURN Pointer to new Cmap object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`ajint`	`chn`	Input	Chain number
`ajint`	`mod`	Input	Model number
`AjPCmap`		RETURN	Pointer to new Cmap object.

From EMBOSS 2.9.0

Function ajCmapReadCNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.

Prototype

AjPCmap ajCmapReadCNew (
      AjPFile inf,
      char chn,
      ajint mod
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

char chn Input Chain number

ajint mod Input Model number

AjPCmap RETURN Pointer to new Cmap object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`char`	`chn`	Input	Chain number
`ajint`	`mod`	Input	Model number
`AjPCmap`		RETURN	Pointer to new Cmap object.

From EMBOSS 2.9.0

Function ajCmapReadAllNew

Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.

Prototype

AjPList ajCmapReadAllNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

AjPList RETURN List of Cmap objects.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`AjPList`		RETURN	List of Cmap objects.

From EMBOSS 3.0.0

Function ajCmapReadNew

Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.

Prototype

AjPCmap ajCmapReadNew (
      AjPFile inf,
      ajint mode,
      ajint chn,
      ajint mod
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream.

ajint mode Input Mode, either CMAP_MODE_I (treat chn arg as an integer) or CMAP_MODE_C (treat chn arg as a character).

ajint chn Input Chain identifier / number.

ajint mod Input Model number.

AjPCmap RETURN True on success (an object read)

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream.
`ajint`	`mode`	Input	Mode, either CMAP_MODE_I (treat chn arg as an integer) or CMAP_MODE_C (treat chn arg as a character).
`ajint`	`chn`	Input	Chain identifier / number.
`ajint`	`mod`	Input	Model number.
`AjPCmap`		RETURN	True on success (an object read)

From EMBOSS 2.9.0

Function ajVdwallReadNew

Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).

Prototype

AjPVdwall ajVdwallReadNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Input file stream

AjPVdwall RETURN Pointer to Vdwall object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Input file stream
`AjPVdwall`		RETURN	Pointer to Vdwall object.

From EMBOSS 2.9.0

Function ajHetReadNew

Read heterogen dictionary, the Het object is allocated.

Prototype

AjPHet ajHetReadNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to Het file

AjPHet RETURN Het object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to Het file
`AjPHet`		RETURN	Het object.

From EMBOSS 2.9.0

Function ajHetReadRawNew

Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.

Prototype

AjPHet ajHetReadRawNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to dictionary

AjPHet RETURN True on success

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to dictionary
`AjPHet`		RETURN	True on success

From EMBOSS 2.9.0

Function ajPdbReadFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadFirstModelNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to clean coordinate file

AjPPdb RETURN Pointer to Pdb object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to clean coordinate file
`AjPPdb`		RETURN	Pointer to Pdb object.

From EMBOSS 2.9.0

Function ajPdbReadAllModelsNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.

Prototype

AjPPdb ajPdbReadAllModelsNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to clean coordinate file

AjPPdb RETURN Pointer to Pdb object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to clean coordinate file
`AjPPdb`		RETURN	Pointer to Pdb object.

From EMBOSS 3.0.0

Function ajPdbReadNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadNew (
      AjPFile inf,
      ajint mode
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to clean coordinate file

ajint mode Input Mode. 0==Read first model only. 1==Read all models.

AjPPdb RETURN Pointer to Pdb object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to clean coordinate file
`ajint`	`mode`	Input	Mode. 0==Read first model only. 1==Read all models.
`AjPPdb`		RETURN	Pointer to Pdb object.

From EMBOSS 2.9.0

Function ajPdbReadoldNew

Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.

Prototype

AjPPdb ajPdbReadoldNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to clean coordinate file

AjPPdb RETURN Pointer to Pdb object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to clean coordinate file
`AjPPdb`		RETURN	Pointer to Pdb object.

From EMBOSS 3.0.0

Function ajPdbReadoldFirstModelNew

Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.

Prototype

AjPPdb ajPdbReadoldFirstModelNew (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to clean coordinate file

AjPPdb RETURN Pointer to Pdb object.

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	Pointer to clean coordinate file
`AjPPdb`		RETURN	Pointer to Pdb object.

From EMBOSS 3.0.0

Function ajAtomNew

Atom object constructor. This is normally called by the ajChainNew function.

Prototype

AjPAtom ajAtomNew (
      void
);

Type Name Read/Write Description

AjPAtom RETURN Pointer to an atom object

Type	Name	Read/Write	Description
`AjPAtom`		RETURN	Pointer to an atom object

From EMBOSS 1.8.0

Function ajResidueNew

Residue object constructor. This is normally called by the ajChainNew function.

Prototype

AjPResidue ajResidueNew (
      void
);

Type Name Read/Write Description

AjPResidue RETURN Pointer to a Residue object

Type	Name	Read/Write	Description
`AjPResidue`		RETURN	Pointer to a Residue object

From EMBOSS 3.0.0

Function ajChainNew

Chain object constructor. This is normally called by the ajPdbNew function

Prototype

AjPChain ajChainNew (
      void
);

Type Name Read/Write Description

AjPChain RETURN Pointer to a chain object

Type	Name	Read/Write	Description
`AjPChain`		RETURN	Pointer to a chain object

From EMBOSS 1.8.0

Function ajPdbNew

Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).

Prototype

AjPPdb ajPdbNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of chains in this pdb file

AjPPdb RETURN Pointer to a pdb object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of chains in this pdb file
`AjPPdb`		RETURN	Pointer to a pdb object

From EMBOSS 1.8.0

Function ajHetentNew

Hetent object constructor.

Prototype

AjPHetent ajHetentNew (
      void
);

Type Name Read/Write Description

AjPHetent RETURN Pointer to a Hetent object

Type	Name	Read/Write	Description
`AjPHetent`		RETURN	Pointer to a Hetent object

From EMBOSS 2.9.0

Function ajHetNew

Het object constructor.

Prototype

AjPHet ajHetNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of entries in dictionary.

AjPHet RETURN Pointer to a Het object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of entries in dictionary.
`AjPHet`		RETURN	Pointer to a Het object

From EMBOSS 2.9.0

Function ajVdwallNew

Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.

Prototype

AjPVdwall ajVdwallNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of residues

AjPVdwall RETURN Pointer to a Vdwall object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of residues
`AjPVdwall`		RETURN	Pointer to a Vdwall object

From EMBOSS 2.9.0

Function ajVdwresNew

Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.

Prototype

AjPVdwres ajVdwresNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of atoms

AjPVdwres RETURN Pointer to a Vdwres object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of atoms
`AjPVdwres`		RETURN	Pointer to a Vdwres object

From EMBOSS 2.9.0

Function ajCmapNew

Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.

Prototype

AjPCmap ajCmapNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Dimension of contact map

AjPCmap RETURN Pointer to a Cmap object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Dimension of contact map
`AjPCmap`		RETURN	Pointer to a Cmap object

From EMBOSS 2.9.0

Function ajPdbtospNew

Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

Prototype

AjPPdbtosp ajPdbtospNew (
      ajuint n
);

Type Name Read/Write Description

ajuint n Input Number of entries

AjPPdbtosp RETURN Pointer to a Pdbtosp object

Type	Name	Read/Write	Description
`ajuint`	`n`	Input	Number of entries
`AjPPdbtosp`		RETURN	Pointer to a Pdbtosp object

From EMBOSS 2.9.0

Section: 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:

ajAtomDel Destructor for an AJAX Atom object.

ajResidueDel Destructor for an AJAX Residue object.

ajChainDel Destructor for an AJAX Chain object.

ajPdbDel Destructor for an AJAX PDB object.

ajHetentDel Destructor for an AJAX Hetent object.

ajHetDel Destructor for an AJAX Het object.

ajVdwallDel Destructor for an AJAX Vdwall object.

ajVdwresDel Destructor for an AJAX Vdwres object.

ajCmapDel Destructor for an AJAX Cmap object.

ajPdbtospDel Destructor for an AJAX Pdbtosp object.

Function ajAtomDel

Destructor for an AJAX Atom object.

Prototype

void ajAtomDel (
      AjPAtom* Patom
);

Type Name Read/Write Description

AjPAtom* Patom Delete AJAX Atom address

void RETURN

Type	Name	Read/Write	Description
`AjPAtom*`	`Patom`	Delete	AJAX Atom address
`void`		RETURN

From EMBOSS 1.8.0

Function ajResidueDel

Destructor for an AJAX Residue object.

Prototype

void ajResidueDel (
      AjPResidue* Presidue
);

Type Name Read/Write Description

AjPResidue* Presidue Delete AJAX Residue address

void RETURN

Type	Name	Read/Write	Description
`AjPResidue*`	`Presidue`	Delete	AJAX Residue address
`void`		RETURN

From EMBOSS 3.0.0

Function ajChainDel

Destructor for an AJAX Chain object.

Prototype

void ajChainDel (
      AjPChain* Pchain
);

Type Name Read/Write Description

AjPChain* Pchain Delete AJAX Chain address

void RETURN

Type	Name	Read/Write	Description
`AjPChain*`	`Pchain`	Delete	AJAX Chain address
`void`		RETURN

From EMBOSS 1.8.0

Function ajPdbDel

Destructor for an AJAX PDB object.

Prototype

void ajPdbDel (
      AjPPdb* Ppdb
);

Type Name Read/Write Description

AjPPdb* Ppdb Delete AJAX PDB address

void RETURN

Type	Name	Read/Write	Description
`AjPPdb*`	`Ppdb`	Delete	AJAX PDB address
`void`		RETURN

From EMBOSS 1.8.0

Function ajHetentDel

Destructor for an AJAX Hetent object.

Prototype

void ajHetentDel (
      AjPHetent* Phetent
);

Type Name Read/Write Description

AjPHetent* Phetent Delete AJAX Hetent address

void RETURN

Type	Name	Read/Write	Description
`AjPHetent*`	`Phetent`	Delete	AJAX Hetent address
`void`		RETURN

From EMBOSS 2.9.0

Function ajHetDel

Destructor for an AJAX Het object.

Prototype

void ajHetDel (
      AjPHet* Phet
);

Type Name Read/Write Description

AjPHet* Phet Delete AJAX Het address

void RETURN

Type	Name	Read/Write	Description
`AjPHet*`	`Phet`	Delete	AJAX Het address
`void`		RETURN

From EMBOSS 2.9.0

Function ajVdwallDel

Destructor for an AJAX Vdwall object.

Prototype

void ajVdwallDel (
      AjPVdwall* Pvdwall
);

Type Name Read/Write Description

AjPVdwall* Pvdwall Delete AJAX Vdwall address

void RETURN

Type	Name	Read/Write	Description
`AjPVdwall*`	`Pvdwall`	Delete	AJAX Vdwall address
`void`		RETURN

From EMBOSS 2.9.0

Function ajVdwresDel

Destructor for an AJAX Vdwres object.

Prototype

void ajVdwresDel (
      AjPVdwres* Pvdwres
);

Type Name Read/Write Description

AjPVdwres* Pvdwres Delete AJAX Vdwres address

void RETURN

Type	Name	Read/Write	Description
`AjPVdwres*`	`Pvdwres`	Delete	AJAX Vdwres address
`void`		RETURN

From EMBOSS 2.9.0

Function ajCmapDel

Destructor for an AJAX Cmap object.

Prototype

void ajCmapDel (
      AjPCmap* Pcmap
);

Type Name Read/Write Description

AjPCmap* Pcmap Delete AJAX Cmap address

void RETURN

Type	Name	Read/Write	Description
`AjPCmap*`	`Pcmap`	Delete	AJAX Cmap address
`void`		RETURN

From EMBOSS 2.9.0

Function ajPdbtospDel

Destructor for an AJAX Pdbtosp object.

Prototype

void ajPdbtospDel (
      AjPPdbtosp* Ppdbtosp
);

Type Name Read/Write Description

AjPPdbtosp* Ppdbtosp Delete AJAX Pdbtosp address

void RETURN

Type	Name	Read/Write	Description
`AjPPdbtosp*`	`Ppdbtosp`	Delete	AJAX Pdbtosp address
`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:

ajAtomCopy Copies the data from an AJAX Atom object to an AJAX Atom object; the new object is created if needed.

ajResidueCopy Copies the data from a Residue object to an Residue object; the new object is created if needed.

ajAtomListCopy Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.

ajResidueListCopy Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.

ajPdbCopy Copies data from one AHAX PDB object to another; the new object is always created.

Function ajAtomCopy

Copies the data from an AJAX Atom object to an AJAX Atom object; the new object is created if needed.

Prototype

AjBool ajAtomCopy (
      AjPAtom* Pto,
      const AjPAtom from
);

Type Name Read/Write Description

AjPAtom* Pto Output AJAX Atom address

const AjPAtom from Input AJAX Atom

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPAtom*`	`Pto`	Output	AJAX Atom address
`const AjPAtom`	`from`	Input	AJAX Atom
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Function ajResidueCopy

Copies the data from a Residue object to an Residue object; the new object is created if needed.

Prototype

AjBool ajResidueCopy (
      AjPResidue* Pto,
      const AjPResidue from
);

Type Name Read/Write Description

AjPResidue* Pto Output AJAX Residue address

const AjPResidue from Input AJAX Residue

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPResidue*`	`Pto`	Output	AJAX Residue address
`const AjPResidue`	`from`	Input	AJAX Residue
`AjBool`		RETURN	True on success

From EMBOSS 3.0.0

Function ajAtomListCopy

Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.

Prototype

AjBool ajAtomListCopy (
      AjPList* Pto,
      const AjPList from
);

Type Name Read/Write Description

AjPList* Pto Output AJAX List of AJAX Atom objects to write

const AjPList from Input List of Atom objects to read

AjBool RETURN True if list was copied ok.

Type	Name	Read/Write	Description
`AjPList*`	`Pto`	Output	AJAX List of AJAX Atom objects to write
`const AjPList`	`from`	Input	List of Atom objects to read
`AjBool`		RETURN	True if list was copied ok.

From EMBOSS 2.9.0

Function ajResidueListCopy

Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.

Prototype

AjBool ajResidueListCopy (
      AjPList* to,
      const AjPList from
);

Type Name Read/Write Description

AjPList* to Output List of Residue objects to write

const AjPList from Input List of Residue objects to read

AjBool RETURN True if list was copied ok.

Type	Name	Read/Write	Description
`AjPList*`	`to`	Output	List of Residue objects to write
`const AjPList`	`from`	Input	List of Residue objects to read
`AjBool`		RETURN	True if list was copied ok.

From EMBOSS 3.0.0

Function ajPdbCopy

Copies data from one AHAX PDB object to another; the new object is always created.

Prototype

AjBool ajPdbCopy (
      AjPPdb* Pto,
      const AjPPdb from
);

Type Name Read/Write Description

AjPPdb* Pto Output AJAX PDB address

const AjPPdb from Input AJAX PDB

AjBool RETURN True on success

Type	Name	Read/Write	Description
`AjPPdb*`	`Pto`	Output	AJAX PDB address
`const AjPPdb`	`from`	Input	AJAX PDB
`AjBool`		RETURN	True on success

From EMBOSS 2.9.0

Section: Operators

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

Functions:

ajResidueSSEnv Assigns secondary structure environment of an AJAX Residue

ajResidueEnv1 Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv2 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv3 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv4 Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv5 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv6 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv7 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv8 Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv9 Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv10 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv11 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv12 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv13 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv14 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv15 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajResidueEnv16 Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

ajPdbGetEStrideType Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Function ajResidueSSEnv

Assigns secondary structure environment of an AJAX Residue

Prototype

AjBool ajResidueSSEnv (
      const AjPResidue residue,
      char* SEnv,
      AjPFile flog
);

Type Name Read/Write Description

const AjPResidue residue Input AJAX Residue

char* SEnv Output Character for the Secondary structure environment

AjPFile flog Output Log file

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPResidue`	`residue`	Input	AJAX Residue
`char*`	`SEnv`	Output	Character for the Secondary structure environment
`AjPFile`	`flog`	Output	Log file
`AjBool`		RETURN	ajTrue on success

From EMBOSS 3.0.0

Function ajResidueEnv1

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv1 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

Type Name Read/Write Description

const AjPResidue residue Input AJAX Residue

char SEnv Input Secondary structure environment code

AjPStr* OEnv Output Character for the overall environment class

AjPFile flog Output Log file

ajint RETURN Number of environments

Type	Name	Read/Write	Description
`const AjPResidue`	`residue`	Input	AJAX Residue
`char`	`SEnv`	Input	Secondary structure environment code
`AjPStr*`	`OEnv`	Output	Character for the overall environment class
`AjPFile`	`flog`	Output	Log file
`ajint`		RETURN	Number of environments

From EMBOSS 3.0.0

Function ajResidueEnv2

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv2 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

Type	Name	Read/Write	Description
`const AjPResidue`	`residue`	Input	AJAX Residue
`char`	`SEnv`	Input	Secondary structure environment code
`AjPStr*`	`OEnv`	Output	Character for the overall environment class
`AjPFile`	`flog`	Output	Log file
`ajint`		RETURN	Number of environments

From EMBOSS 3.0.0

Function ajResidueEnv3

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv3 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

Type	Name	Read/Write	Description
`const AjPResidue`	`residue`	Input	AJAX Residue
`char`	`SEnv`	Input	Secondary structure environment code
`AjPStr*`	`OEnv`	Output	Character for the overall environment class
`AjPFile`	`flog`	Output	Log file
`ajint`		RETURN	Number of environments

From EMBOSS 3.0.0

Function ajResidueEnv4

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv4 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

Type	Name	Read/Write	Description
`const AjPResidue`	`residue`	Input	AJAX Residue
`char`	`SEnv`	Input	Secondary structure environment code
`AjPStr*`	`OEnv`	Output	Character for the overall environment class
`AjPFile`	`flog`	Output	Log file
`ajint`		RETURN	Number of environments

From EMBOSS 3.0.0

Function ajResidueEnv5

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv5 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv6

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv6 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv7

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv7 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv8

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv8 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv9

Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv9 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv10

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv10 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv11

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv11 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv12

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv12 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv13

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv13 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv14

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv14 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv15

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv15 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajResidueEnv16

Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.

Prototype

ajint ajResidueEnv16 (
      const AjPResidue residue,
      char SEnv,
      AjPStr* OEnv,
      AjPFile flog
);

From EMBOSS 3.0.0

Function ajPdbGetEStrideType

Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Prototype

ajint ajPdbGetEStrideType (
      const AjPPdb pdb,
      ajuint chn,
      AjPStr* EStrideType
);

Type Name Read/Write Description

const AjPPdb pdb Input AJAX PDB object

ajuint chn Input Chain number

AjPStr* EStrideType Output String to hold secondary structure

ajint RETURN Length (residues) of array that was written or -1 (for an error)

From EMBOSS 2.9.0

Section: Reporters

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

Functions:

ajPdbChnidToNum Finds the chain number for a given chain identifier in a pdb structure

ajPdbtospArrFindPdbid Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Function ajPdbChnidToNum

Finds the chain number for a given chain identifier in a pdb structure

Prototype

AjBool ajPdbChnidToNum (
      char identifier,
      const AjPPdb pdb,
      ajuint* chn
);

Type Name Read/Write Description

char identifier Input Chain identifier

const AjPPdb pdb Input Pdb object

ajuint* chn Output Chain number

AjBool RETURN True on success

From EMBOSS 2.9.0

Function ajPdbtospArrFindPdbid

Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Prototype

ajint ajPdbtospArrFindPdbid (
      AjPPdbtosp const* array,
      ajint size,
      const AjPStr identifier
);

Type Name Read/Write Description

AjPPdbtosp const* array Input Array of AjOPdbtosp objects

ajint size Input Size of array

const AjPStr identifier Input Search term

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

From EMBOSS 2.9.0

Section: Input & output

These functions are used for formatted input and output to file.

Functions:

ajPdbWriteAll Writes a clean coordinate file for a protein.

ajPdbWriteSegment Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.

ajHetWrite Writes the contents of a Het object to file.

ajPdbtospWrite Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

ajCmapWrite Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).

ajPdbExit Cleanup of Pdb function internals.

Function ajPdbWriteAll

Writes a clean coordinate file for a protein.

Prototype

AjBool ajPdbWriteAll (
      AjPFile outf,
      const AjPPdb pdb
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const AjPPdb pdb Input AJAX PDB object

AjBool RETURN True on success

From EMBOSS 1.9.0

Function ajPdbWriteSegment

Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.

Prototype

AjBool ajPdbWriteSegment (
      AjPFile outf,
      const AjPPdb pdb,
      const AjPStr segment,
      char chnid,
      const AjPStr domain,
      AjPFile errf
);

Type Name Read/Write Description

AjPFile outf Output Output file stream

const AjPPdb pdb Input Pdb object

const AjPStr segment Input Sequence of segment to print out.

char chnid Input Chain id of segment

const AjPStr domain Input Domain code for segment

AjPFile errf Output Output file stream for error messages

AjBool RETURN True on success

From EMBOSS 3.0.0

Function ajHetWrite

Writes the contents of a Het object to file.

Prototype

AjBool ajHetWrite (
      AjPFile outf,
      const AjPHet het,
      AjBool dogrep
);

Type Name Read/Write Description

AjPFile outf Output Output file

const AjPHet het Input AJAX Het

AjBool dogrep Input Flag (True if we are to write 'cnt' element of the Het object to file).

AjBool RETURN True on success

From EMBOSS 2.9.0

Function ajPdbtospWrite

Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).

Prototype

AjBool ajPdbtospWrite (
      AjPFile outf,
      const AjPList list
);

Type Name Read/Write Description

AjPFile outf Output Output file

const AjPList list Input List of Pdbtosp objects

AjBool RETURN True of file was written ok.

From EMBOSS 2.9.0

Function ajCmapWrite

Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).

Prototype

AjBool ajCmapWrite (
      AjPFile outf,
      const AjPCmap cmap
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream.

const AjPCmap cmap Input Cmap object pointer.

AjBool RETURN True on success (object was written successfully)

From EMBOSS 3.0.0

Function ajPdbExit

Cleanup of Pdb function internals.

Prototype

void ajPdbExit (
      void
);

Type Name Read/Write Description

void RETURN

From EMBOSS 6.1.0

ajPdbtospReadAllRawNew	Reads the swissprot:pdb equivalence table available at URL (1) (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt and returns the data as a list of Pdbtosp objects.
ajPdbtospReadNew	Read a Pdbtosp object from a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).
ajPdbtospReadCNew	Read a Pdbtosp object from a file in embl-like format. Memory for the object is allocated.
ajPdbtospReadAllNew	Read all the Pdbtosp objects in a file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application) and writes a list of these objects. It then sorts the list by PDB id.
ajCmapReadINew	Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as an integer. If the arguments mod and chn are both 0, the function will read the next Cmap in the file.
ajCmapReadCNew	Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). Takes the chain identifier as a character.
ajCmapReadAllNew	Read every Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application) and returns a list of these objects.
ajCmapReadNew	Read a Cmap object from a file in CON format (see documentation for DOMAINATRIX "contacts" application). This is not usually called by the user, who uses ajCmapReadINew or ajCmapReadCNew instead. If mode==CMAP_MODE_I, chn==0 and mod==0, the function will read the next Cmap in the file.
ajVdwallReadNew	Read a Vdwall object from a file in embl-like format (see documentation for the EMBASSY DOMAINATRIX package).
ajHetReadNew	Read heterogen dictionary, the Het object is allocated.
ajHetReadRawNew	Reads a dictionary of heterogen groups available at http://pdb.rutgers.edu/het_dictionary.txt and writes a Het object.
ajPdbReadFirstModelNew	Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.
ajPdbReadAllModelsNew	Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for all models is read.
ajPdbReadNew	Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) and writes a filled Pdb object. Data for the first model only is read in.
ajPdbReadoldNew	Reads a clean coordinate file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object.
ajPdbReadoldFirstModelNew	Reads a clean coordinate file file (see documentation for DOMAINATRIX "pdbparse" application) lacking residue-level description in RE records and writes a filled Pdb object. Data for the first model only is read in.
ajAtomNew	Atom object constructor. This is normally called by the ajChainNew function.
ajResidueNew	Residue object constructor. This is normally called by the ajChainNew function.
ajChainNew	Chain object constructor. This is normally called by the ajPdbNew function
ajPdbNew	Pdb object constructor. Fore-knowledge of the number of chains is required. This is normally called by the functions that read PDB files or clean coordinate files (see embpdb.c & embpdbraw.c).
ajHetentNew	Hetent object constructor.
ajHetNew	Het object constructor.
ajVdwallNew	Vdwall object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of residues is required.
ajVdwresNew	Vdwres object constructor. This is normally called by the ajVdwallReadNew function. Fore-knowledge of the number of atoms is required.
ajCmapNew	Cmap object constructor. This is normally called by the ajCmapReadNew function. Fore-knowledge of the dimension (number of residues) for the contact map is required.
ajPdbtospNew	Pdbtosp object constructor. Fore-knowledge of the number of entries is required. This is normally called by the ajPdbtospReadCNew / ajPdbtospReadNew functions.

ajAtomDel	Destructor for an AJAX Atom object.
ajResidueDel	Destructor for an AJAX Residue object.
ajChainDel	Destructor for an AJAX Chain object.
ajPdbDel	Destructor for an AJAX PDB object.
ajHetentDel	Destructor for an AJAX Hetent object.
ajHetDel	Destructor for an AJAX Het object.
ajVdwallDel	Destructor for an AJAX Vdwall object.
ajVdwresDel	Destructor for an AJAX Vdwres object.
ajCmapDel	Destructor for an AJAX Cmap object.
ajPdbtospDel	Destructor for an AJAX Pdbtosp object.

ajAtomCopy	Copies the data from an AJAX Atom object to an AJAX Atom object; the new object is created if needed.
ajResidueCopy	Copies the data from a Residue object to an Residue object; the new object is created if needed.
ajAtomListCopy	Read a list of Atom structures and writes a copy of the list. The data are copied and the list is created if necessary.
ajResidueListCopy	Read a list of Residue structures and writes a copy of the list. The data are copied and the list is created if necessary.
ajPdbCopy	Copies data from one AHAX PDB object to another; the new object is always created.

ajResidueSSEnv	Assigns secondary structure environment of an AJAX Residue
ajResidueEnv1	Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv2	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv3	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv4	Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv5	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv6	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv7	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv8	Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv9	Assigns environment based only of side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv10	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv11	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv12	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv13	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv14	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv15	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajResidueEnv16	Assigns environment based on side chain accessibility and secondary structure. Assigns environment of "*" as default.
ajPdbGetEStrideType	Reads a Pdb object and writes a string with the secondary structure. The string that is written is the same length as the full-length chain (regardless of whether coordinates for a residue were available or not) therefore it can be indexed into using residue numbers. The string is allocated if necessary. If secondary structure assignment was not available for a residue a '.' is given in the string.

Type	Name	Read/Write	Description
`const AjPPdb`	`pdb`	Input	AJAX PDB object
`ajuint`	`chn`	Input	Chain number
`AjPStr*`	`EStrideType`	Output	String to hold secondary structure
`ajint`		RETURN	Length (residues) of array that was written or -1 (for an error)

ajPdbChnidToNum	Finds the chain number for a given chain identifier in a pdb structure
ajPdbtospArrFindPdbid	Performs a binary search for a PDB code over an array of Pdbtosp structures (which of course must first have been sorted). This is a case-insensitive search.

Type	Name	Read/Write	Description
`char`	`identifier`	Input	Chain identifier
`const AjPPdb`	`pdb`	Input	Pdb object
`ajuint*`	`chn`	Output	Chain number
`AjBool`		RETURN	True on success

Type	Name	Read/Write	Description
`AjPPdbtosp const*`	`array`	Input	Array of AjOPdbtosp objects
`ajint`	`size`	Input	Size of array
`const AjPStr`	`identifier`	Input	Search term
`ajint`		RETURN	Index of first Pdbtosp object found with an PDB code matching id, or -1 if id is not found.

ajPdbWriteAll	Writes a clean coordinate file for a protein.
ajPdbWriteSegment	Writes a clean coordinate file for a segment, e.g. a domain. The segment corresponds to a sequence that is passed to the function. In the clean coordinate file, the coordinates are presented as belonging to a single chain. Coordinates for heterogens are NOT written to file.
ajHetWrite	Writes the contents of a Het object to file.
ajPdbtospWrite	Reads a list of Pdbtosp objects, e.g. taken from the swissprot:pdb equivalence table available at URL: (1) http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt) and writes the list out to file in embl-like format (see documentation for DOMAINATRIX "pdbtosp" application).
ajCmapWrite	Write a Cmap object to file in CON format (see documentation for DOMAINATRIX "contacts" application).
ajPdbExit	Cleanup of Pdb function internals.

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Output	Output file stream
`const AjPPdb`	`pdb`	Input	AJAX PDB object
`AjBool`		RETURN	True on success