ajpdbio.c

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.

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 logf
);

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
logf:(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).

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Input & output

These functions are used for formatted input and output 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.

Synopsis

Prototype

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

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 succcess

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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 succcess

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function ajPdbWriteAllRaw

Writes a pdb file for a protein.

Synopsis

Prototype

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

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 succcess

Description

Writes a pdb file for a protein.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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 succcess

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Miscellaneous

These functions may have diverse functions that do not fit into the other categories.

Function BaseAa3ToAa1

Takes a 3 character amino acid code and writes a char with the corresponding single letter code.

Synopsis

Prototype

AjBool BaseAa3ToAa1 (
      char* aa1,
      const AjPStr aa3
);

Input

aa3:(Input)AjPStr object (3 letter code)

Output

aa1:(Output)Single letter identifier of amino acid

Returns

AjBool:True on succcess

Description

Takes a 3 character amino acid code and writes a char with the corresponding single letter code.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0