pdbparse

 

Function

Parses pdb files and writes cleaned-up protein coordinate files

Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

Usage

Here is a sample session with pdbparse:

% pdbparse

Command line arguments

   Mandatory qualifiers:
  [-pdb]               string     Location of pdb files (pdb format input)
  [-pdbextn]           string     Extension of pdb files (pdb format input)
   -nocamask           boolean    The group will not appear in either the CO
                                  or SQ records of the clean coordinate file
   -nocamaska          boolean    The amino acid will not appear in the CO
                                  record but will still be present in the SQ
                                  record of the clean coordinate file
   -atommask           boolean    The amino acid will appear not appear in the
                                  CO record but will still be present in the
                                  SQ record of the clean coordinate file
  [-cpdb]              string     Location of coordinate files (embl format
                                  output)
  [-cpdbextn]          string     Extension of coordinate files (embl format
                                  output)
   -errf               outfile    Name of log file for the build

   Optional qualifiers:
   -chnsiz             integer    Minimum number of residues in a chain for it
                                  to be parsed

   Advanced qualifiers:
   -[no]cpdbnaming     boolean    Use pdbid code to name files
   -maxmis             integer    Maximum number of permissible mismatches
                                  between the ATOM and SEQRES sequences

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-pdb]
(Parameter 1)
Location of pdb files (pdb format input) Any string is accepted ./
[-pdbextn]
(Parameter 2)
Extension of pdb files (pdb format input) Any string is accepted .ent
-nocamask The group will not appear in either the CO or SQ records of the clean coordinate file Yes/No No
-nocamaska The amino acid will not appear in the CO record but will still be present in the SQ record of the clean coordinate file Yes/No No
-atommask The amino acid will appear not appear in the CO record but will still be present in the SQ record of the clean coordinate file Yes/No No
[-cpdb]
(Parameter 3)
Location of coordinate files (embl format output) Any string is accepted ./
[-cpdbextn]
(Parameter 4)
Extension of coordinate files (embl format output) Any string is accepted .pxyz
-errf Name of log file for the build Output file pdbparse.log
Optional qualifiers Allowed values Default
-chnsiz Minimum number of residues in a chain for it to be parsed Any integer value 5
Advanced qualifiers Allowed values Default
-[no]cpdbnaming Use pdbid code to name files Yes/No Yes
-maxmis Maximum number of permissible mismatches between the ATOM and SEQRES sequences Any integer value 3

Input file format

Output file format

Data files

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
aaindexextractExtract data from AAINDEX
cutgextractExtract data from CUTG
domainerReads protein coordinate files and writes domains coordinate files
funkyReads clean coordinate files and writes file of protein-heterogen contact data
groupsRemoves redundant hits from a scop families file
hetparseConverts raw dictionary of heterogen groups to a file in embl-like format
nrscopeConverts redundant EMBL-format SCOP file to non-redundant one
pdbtospConvert raw swissprot:pdb equivalence file to embl-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopeConvert raw scop classification file to embl-like format
scopnrRemoves redundant domains from a scop classification file
scopparseConverts raw scop classification files to a file in embl-like format
scopseqsAdds pdb and swissprot sequence records to a scop classification file
tfextractExtract data from TRANSFAC

Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (date) - author.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments