ajpdbio.c

Section: Constructors

Functions:

ajPdbReadRawNew

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

Function ajPdbReadRawNew

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.

From EMBOSS 2.9.0

Section: Input & output

Functions:

ajPdbWriteDomainRecordRaw	Writes lines to a PDB file. What is written depends upon the mode: ajEPdbioModeHeaderDomain Header line for domain PDB file. ajEPdbioModeSeqresDomain SEQRES records for domain. ajEPdbioModeAtomPdbDomain ATOM records for domain using original residue numbers. ajEPdbioModeAtomIdxDomain ATOM records for domain using residues numbers that give correct index into SEQRES sequence.
ajPdbWriteRecordRaw	Writes lines in pdb format to a PDB file. What is written depends upon the mode: ajEPdbioModeSeqResChain SEQRES records for a chain. ajEPdbioModeAtomPdbChain ATOM records for chain using original residue numbers. ajEPdbioModeAtomIdxChain ATOM records for domain using residues numbers that give correct index into SEQRES sequence. ajEPdbioModeHeterogen ATOM line for a heterogen (small ligand). ajEPdbioModeHeader Header line. ajEPdbioModeTitle Title line. ajEPdbioModeCompnd COMPND records (info. on compound) ajEPdbioModeSource SOURCE records (info. on protein source) ajEPdbioModeEmptyRemark An empty REMARK record. ajEPdbioModeResolution Record with resolution of the structure.
ajPdbWriteAllRaw	Writes a pdb file for a protein.
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.

Function ajPdbWriteDomainRecordRaw

Prototype

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

Type	Name	Read/Write	Description
AjEPdbioMode	mode	Modify	Mode that controls what is printed: one of ajEPdbioModeHeaderDomain, ajEPdbioModeSeqresDomain, ajEPdbioModeAtomPdbDomain, ajEPdbioModeAtomIdxDomain
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

From EMBOSS 2.9.0

Function ajPdbWriteRecordRaw

Prototype

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

Type	Name	Read/Write	Description
AjEPdbioMode	mode	Modify	Mode that controls what is printed: one of ajEPdbioModeSeqResChain, ajEPdbioModeAtomPdbChain, ajEPdbioModeAtomIdxChain, ajEPdbioModeHeterogen, ajEPdbioModeHeader, ajEPdbioModeTitle, ajEPdbioModeCompnd, ajEPdbioModeSource, ajEPdbioModeEmptyRemark, ajEPdbioModeResolution.
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

From EMBOSS 2.9.0

Function ajPdbWriteAllRaw

Prototype

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

Type	Name	Read/Write	Description
AjEPdbMode	mode	Modify	AJAX PDB Mode enumeration, either ajEPdbModePdb or ajEPdbModeIdx 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

From EMBOSS 2.9.0

Function ajPdbWriteDomainRaw

Prototype

AjBool ajPdbWriteDomainRaw (
      AjEPdbMode mode,
      const AjPPdb pdb,
      const AjPScop scop,
      AjPFile outf,
      AjPFile errf
);

Type	Name	Read/Write	Description
AjEPdbMode	mode	Modify	AJAX PDB Mode enumeration, either ajEPdbModePdb or ajEPdbModeIdx 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

From EMBOSS 2.9.0