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

Function ajPdbReadRawNew

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

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.

From EMBOSS 2.9.0

Section: Input & output

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

Functions:

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.

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.

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

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.

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

From EMBOSS 2.9.0

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.

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

From EMBOSS 2.9.0

Function ajPdbWriteAllRaw

Writes a pdb file for a protein.

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

From EMBOSS 2.9.0

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.

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

From EMBOSS 2.9.0

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.
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.
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.