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pdbparse |
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)
% pdbparse
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 |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
cutgextract | Extract data from CUTG |
domainer | Reads protein coordinate files and writes domains coordinate files |
funky | Reads clean coordinate files and writes file of protein-heterogen contact data |
groups | Removes redundant hits from a scop families file |
hetparse | Converts raw dictionary of heterogen groups to a file in embl-like format |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
tfextract | Extract data from TRANSFAC |