ajpdbio.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: ajPdbReadRawNew

Function ajPdbReadRawNew

Reads a pdb file and returns a pointer to a filled Pdb object.

The pdb id is derived from the file name and extension of the pdb file (these are passed in by argument).

Synopsis

Prototype

AjPPdb ajPdbReadRawNew (
      AjPFile inf,
      const AjPStr pdbid,
      ajint min_chain_size,
      ajint max_mismatch,
      ajint max_trim,
      AjBool camask,
      AjBool camask1,
      AjBool atommask,
      AjPFile flog
);

Type Name Read/Write Description

AjPFile inf Modify Pointer to pdb file

const AjPStr pdbid Input PDB id code of pdb file

ajint min_chain_size Input Minimum number of amino acids in a chain

ajint max_mismatch Input Maximum number of permissible mismatches between the ATOM and SEQRES sequences

ajint max_trim Input Max. no. residues to trim when checking for missing N- or C-terminal ATOM or SEQRES sequences.

AjBool camask Input Whether to mask non-amino acid groups within protein chains which do not have a C-alpha atom.

AjBool camask1 Input Whether to mask amino acid residues within protein chains which do not have a C-alpha atom.

AjBool atommask Input Whether to mask residues or groups in protein chains with a single atom only.

AjPFile flog Modify Pointer to log file (build diagnostics)

AjPPdb RETURN pdb object pointer, or NULL on failure.

Type	Name	Read/Write	Description
AjPFile	inf	Modify	Pointer to pdb file
const AjPStr	pdbid	Input	PDB id code of pdb file
ajint	min_chain_size	Input	Minimum number of amino acids in a chain
ajint	max_mismatch	Input	Maximum number of permissible mismatches between the ATOM and SEQRES sequences
ajint	max_trim	Input	Max. no. residues to trim when checking for missing N- or C-terminal ATOM or SEQRES sequences.
AjBool	camask	Input	Whether to mask non-amino acid groups within protein chains which do not have a C-alpha atom.
AjBool	camask1	Input	Whether to mask amino acid residues within protein chains which do not have a C-alpha atom.
AjBool	atommask	Input	Whether to mask residues or groups in protein chains with a single atom only.
AjPFile	flog	Modify	Pointer to log file (build diagnostics)
AjPPdb		RETURN	pdb object pointer, or NULL on failure.

Input

pdbid:	(Input)	PDB id code of pdb file
min_chain_size:	(Input)	Minimum number of amino acids in a chain
max_mismatch:	(Input)	Maximum number of permissible mismatches between the ATOM and SEQRES sequences
max_trim:	(Input)	Max. no. residues to trim when checking for missing N- or C-terminal ATOM or SEQRES sequences.
camask:	(Input)	Whether to mask non-amino acid groups within protein chains which do not have a C-alpha atom.
camask1:	(Input)	Whether to mask amino acid residues within protein chains which do not have a C-alpha atom.
atommask:	(Input)	Whether to mask residues or groups in protein chains with a single atom only.

Input & Output

inf:	(Modify)	Pointer to pdb file
flog:	(Modify)	Pointer to log file (build diagnostics)

Returns

AjPPdb:

pdb object pointer, or NULL on failure.

Description

Reads a pdb file and returns a pointer to a filled Pdb object.

The pdb id is derived from the file name and extension of the pdb file (these are passed in by argument).

Availability

In release 6.4.0

Section: Input & output

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

Functions: ajPdbWriteDomainRecordRaw ajPdbWriteRecordRaw ajPdbWriteAllRaw ajPdbWriteDomainRaw

Function ajPdbWriteDomainRecordRaw

Writes lines to a PDB file. What is written depends upon the mode: ajHEADER_DOMAIN Header line for domain PDB file. ajSEQRES_DOMAIN SEQRES records for domain. ajATOMPDB_DOMAIN ATOM records for domain using original residue numbers. ajATOMIDX_DOMAIN ATOM records for domain using residues numbers that give correct index into SEQRES sequence.

Synopsis

Prototype

AjBool ajPdbWriteDomainRecordRaw (
      ajint mode,
      const AjPPdb pdb,
      ajint mod,
      const AjPScop scop,
      AjPFile outf,
      AjPFile errf
);

Type Name Read/Write Description

ajint mode Input Mode that controls what is printed: one of ajHEADER_DOMAIN, ajSEQRES_DOMAIN, ajATOMPDB_DOMAIN, ajATOMIDX_DOMAIN

const AjPPdb pdb Input Pdb object

ajint mod Input Model number

const AjPScop scop Input Scop object for domain

AjPFile outf Output Output file stream

AjPFile errf Output Output file stream for error messages

AjBool RETURN True on success

Type	Name	Read/Write	Description
ajint	mode	Input	Mode that controls what is printed: one of ajHEADER_DOMAIN, ajSEQRES_DOMAIN, ajATOMPDB_DOMAIN, ajATOMIDX_DOMAIN
const AjPPdb	pdb	Input	Pdb object
ajint	mod	Input	Model number
const AjPScop	scop	Input	Scop object for domain
AjPFile	outf	Output	Output file stream
AjPFile	errf	Output	Output file stream for error messages
AjBool		RETURN	True on success

Input

mode:	(Input)	Mode that controls what is printed: one of ajHEADER_DOMAIN, ajSEQRES_DOMAIN, ajATOMPDB_DOMAIN, ajATOMIDX_DOMAIN
pdb:	(Input)	Pdb object
mod:	(Input)	Model number
scop:	(Input)	Scop object for domain

Output

outf:	(Output)	Output file stream
errf:	(Output)	Output file stream for error messages

Returns

AjBool:

True on success

Description

Availability

In release 6.4.0

Function ajPdbWriteRecordRaw

Writes lines in pdb format to a PDB file. What is written depends upon the mode: ajSEQRES_CHAIN SEQRES records for a chain. ajATOMPDB_CHAIN ATOM records for chain using original residue numbers. ajATOMIDX_CHAIN ATOM records for domain using residues numbers that give correct index into SEQRES sequence. ajHETEROGEN ATOM line for a heterogen (small ligand). ajHEADER Header line. ajTITLE Title line. ajCOMPND COMPND records (info. on compound) ajSOURCE SOURCE records (info. on protein source) ajEMPTYREMARK An empty REMARK record. ajRESOLUTION Record with resolution of the structure.

Synopsis

Prototype

AjBool ajPdbWriteRecordRaw (
      ajint mode,
      const AjPPdb pdb,
      ajint mod,
      ajint chn,
      AjPFile outf,
      AjPFile errf
);

Type Name Read/Write Description

ajint mode Input Mode that controls what is printed: one of ajSEQRES_CHAIN, ajATOMPDB_CHAIN, ajATOMIDX_CHAIN, ajHETEROGEN, ajHEADER, ajTITLE,ajCOMPND,ajSOURCE, ajEMPTYREMARK,ajRESOLUTION.

const AjPPdb pdb Input Pdb object

ajint mod Input Model number.

ajint chn Input Chain number.

AjPFile outf Output Output file stream

AjPFile errf Output Output file stream for error messages

AjBool RETURN True on success

Type	Name	Read/Write	Description
ajint	mode	Input	Mode that controls what is printed: one of ajSEQRES_CHAIN, ajATOMPDB_CHAIN, ajATOMIDX_CHAIN, ajHETEROGEN, ajHEADER, ajTITLE,ajCOMPND,ajSOURCE, ajEMPTYREMARK,ajRESOLUTION.
const AjPPdb	pdb	Input	Pdb object
ajint	mod	Input	Model number.
ajint	chn	Input	Chain number.
AjPFile	outf	Output	Output file stream
AjPFile	errf	Output	Output file stream for error messages
AjBool		RETURN	True on success

Input

mode:	(Input)	Mode that controls what is printed: one of ajSEQRES_CHAIN, ajATOMPDB_CHAIN, ajATOMIDX_CHAIN, ajHETEROGEN, ajHEADER, ajTITLE,ajCOMPND,ajSOURCE, ajEMPTYREMARK,ajRESOLUTION.
pdb:	(Input)	Pdb object
mod:	(Input)	Model number.
chn:	(Input)	Chain number.

Output

outf:	(Output)	Output file stream
errf:	(Output)	Output file stream for error messages

Returns

AjBool:

True on success

Description

Availability

In release 6.4.0

Function ajPdbWriteAllRaw

Writes a pdb file for a protein.

Synopsis

Prototype

AjBool ajPdbWriteAllRaw (
      ajint mode,
      const AjPPdb pdb,
      AjPFile outf,
      AjPFile errf
);

Type Name Read/Write Description

ajint mode Input Either ajPdb or ajIDX if the original or corrected residue number is to be used.

const AjPPdb pdb Input Pdb object

AjPFile outf Output Output file stream

AjPFile errf Output Output file stream for error messages

AjBool RETURN True on success

Type	Name	Read/Write	Description
ajint	mode	Input	Either ajPdb or ajIDX if the original or corrected residue number is to be used.
const AjPPdb	pdb	Input	Pdb object
AjPFile	outf	Output	Output file stream
AjPFile	errf	Output	Output file stream for error messages
AjBool		RETURN	True on success

Input

mode:	(Input)	Either ajPdb or ajIDX if the original or corrected residue number is to be used.
pdb:	(Input)	Pdb object

Output

outf:	(Output)	Output file stream
errf:	(Output)	Output file stream for error messages

Returns

AjBool:

True on success

Description

Writes a pdb file for a protein.

Availability

In release 6.4.0

Function ajPdbWriteDomainRaw

Writes a pdb file for a SCOP domain. Where coordinates for multiple models (e.g. NMR structures) are given, data for model 1 are written. Coordinates are taken from a Pdb structure, domain definition is taken from a Scop structure. In the pdb 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 ajPdbWriteDomainRaw (
      ajint mode,
      const AjPPdb pdb,
      const AjPScop scop,
      AjPFile outf,
      AjPFile errf
);

Type Name Read/Write Description

ajint mode Input Either ajPDB or ajIDX if the original or corrected residue number is to be used.

const AjPPdb pdb Input Pdb object

const AjPScop scop Input Scop object

AjPFile outf Output Output file stream

AjPFile errf Output Output file stream for error messages

AjBool RETURN True on success

Type	Name	Read/Write	Description
ajint	mode	Input	Either ajPDB or ajIDX if the original or corrected residue number is to be used.
const AjPPdb	pdb	Input	Pdb object
const AjPScop	scop	Input	Scop object
AjPFile	outf	Output	Output file stream
AjPFile	errf	Output	Output file stream for error messages
AjBool		RETURN	True on success

Input

mode:	(Input)	Either ajPDB or ajIDX if the original or corrected residue number is to be used.
pdb:	(Input)	Pdb object
scop:	(Input)	Scop object

Output

outf:	(Output)	Output file stream
errf:	(Output)	Output file stream for error messages

Returns

AjBool:

True on success

Description

Availability

In release 6.4.0

ajpdbio.c

Section: Constructors

Function ajPdbReadRawNew

Synopsis

Prototype

Input

Input & Output

Returns

Description

See Also

Availability

Section: Input & output

Function ajPdbWriteDomainRecordRaw

Synopsis

Prototype

Input

Output

Returns

Description

See Also

Availability

Function ajPdbWriteRecordRaw

Synopsis

Prototype

Input

Output

Returns

Description

See Also

Availability

Function ajPdbWriteAllRaw

Synopsis

Prototype

Input

Output

Returns

Description

See Also

Availability

Function ajPdbWriteDomainRaw

Synopsis

Prototype

Input

Output

Returns

Description

See Also

Availability