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scopreso |
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)
% scopreso
Mandatory qualifiers: [-cpdbpath] string Location of domain coordinate files for input (embl-like format) [-cpdbextn] string Extension of coordinate files (embl-like format) [-scopinf] infile Name of SCOP data file for input (embl-like format) -threshold float Threshold for inclusion (Angstroms) [-scopoutf] outfile Name of SCOP data file for output Optional qualifiers: (none) Advanced qualifiers: (none) 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 | |
---|---|---|---|
[-cpdbpath] (Parameter 1) |
Location of domain coordinate files for input (embl-like format) | Any string is accepted | ./ |
[-cpdbextn] (Parameter 2) |
Extension of coordinate files (embl-like format) | Any string is accepted | .pxyz |
[-scopinf] (Parameter 3) |
Name of SCOP data file for input (embl-like format) | Input file | Escop.dat |
-threshold | Threshold for inclusion (Angstroms) | Any numeric value | 2.8 |
[-scopoutf] (Parameter 4) |
Name of SCOP data file for output | Output file | Escop_2.8.dat |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
Program name | Description |
---|---|
contacts | Reads coordinate files and writes files of intra-chain residue-residue contact data |
dichet | Parse dictionary of heterogen groups |
hmmgen | Generates a hidden Markov model for each alignment in a directory |
interface | Reads coordinate files and writes files of inter-chain residue-residue contact data |
profgen | Generates various profiles for each alignment in a directory |
psiblasts | Runs PSI-BLAST given scopalign alignments |
scopalign | Generate alignments for families in a scop classification file by using STAMP |
scoprep | Reorder scop classificaiton file so that the representative structure of each family is given first |
seqalign | Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments |
seqsearch | Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments |
seqsort | Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file |
seqwords | Generate file of hits for scop families by searching swissprot with keywords |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigscan | Scans a signature against swissprot and writes a signature hits files |