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:
ajPdbReadRawNewReads 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
);

TypeNameRead/WriteDescription
AjPFileinfModifyPointer to pdb file
const AjPStrpdbidInputPDB id code of pdb file
ajintmin_chain_sizeInputMinimum number of amino acids in a chain
ajintmax_mismatchInputMaximum number of permissible mismatches between the ATOM and SEQRES sequences
ajintmax_trimInputMax. no. residues to trim when checking for missing N- or C-terminal ATOM or SEQRES sequences.
AjBoolcamaskInputWhether to mask non-amino acid groups within protein chains which do not have a C-alpha atom.
AjBoolcamask1InputWhether to mask amino acid residues within protein chains which do not have a C-alpha atom.
AjBoolatommaskInputWhether to mask residues or groups in protein chains with a single atom only.
AjPFileflogModifyPointer to log file (build diagnostics)
AjPPdb RETURNpdb 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:
ajPdbWriteDomainRecordRawWrites 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.
ajPdbWriteRecordRawWrites 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.
ajPdbWriteAllRawWrites a pdb file for a protein.
ajPdbWriteDomainRawWrites 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
);

TypeNameRead/WriteDescription
ajintmodeInputMode that controls what is printed: one of ajHEADER_DOMAIN, ajSEQRES_DOMAIN, ajATOMPDB_DOMAIN, ajATOMIDX_DOMAIN
const AjPPdbpdbInputPdb object
ajintmodInputModel number
const AjPScopscopInputScop object for domain
AjPFileoutfOutputOutput file stream
AjPFileerrfOutputOutput file stream for error messages
AjBool RETURNTrue 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
);

TypeNameRead/WriteDescription
ajintmodeInputMode that controls what is printed: one of ajSEQRES_CHAIN, ajATOMPDB_CHAIN, ajATOMIDX_CHAIN, ajHETEROGEN, ajHEADER, ajTITLE,ajCOMPND,ajSOURCE, ajEMPTYREMARK,ajRESOLUTION.
const AjPPdbpdbInputPdb object
ajintmodInputModel number.
ajintchnInputChain number.
AjPFileoutfOutputOutput file stream
AjPFileerrfOutputOutput file stream for error messages
AjBool RETURNTrue 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
);

TypeNameRead/WriteDescription
ajintmodeInputEither ajPdb or ajIDX if the original or corrected residue number is to be used.
const AjPPdbpdbInputPdb object
AjPFileoutfOutputOutput file stream
AjPFileerrfOutputOutput file stream for error messages
AjBool RETURNTrue 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
);

TypeNameRead/WriteDescription
ajintmodeInputEither ajPDB or ajIDX if the original or corrected residue number is to be used.
const AjPPdbpdbInputPdb object
const AjPScopscopInputScop object
AjPFileoutfOutputOutput file stream
AjPFileerrfOutputOutput file stream for error messages
AjBool RETURNTrue on success

From EMBOSS 2.9.0