|
|
scorecmapdir |
Standard (Mandatory) qualifiers:
[-cmapdir] dirlist Directory of cleaned-chain contact map files
[-scoredcmapdir] outdir Directory where scored contact map files
will be written
[-outfileextension] string Appended to end of all output file names
Additional (Optional) qualifiers:
-contactscoringfile matrixf Matrix of scores for frequency of contacts
between specific amino acid residue types
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers: (none)
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-cmapdir] (Parameter 1) |
Directory of cleaned-chain contact map files | Directory with files | ./contacttest/cmap |
| [-scoredcmapdir] (Parameter 2) |
Directory where scored contact map files will be written | Output directory | ./contacttest/scored_cmap |
| [-outfileextension] (Parameter 3) |
Appended to end of all output file names | Any string is accepted | .cmap2 |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -contactscoringfile | Matrix of scores for frequency of contacts between specific amino acid residue types | Comparison matrix file in EMBOSS data path | ./contacttest/testLOscores26Apr05.dat |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Under development, no example input file(s) yet
Under development, no example output file(s) yet
| Program name | Description |
|---|---|
| contactcount | Count specific versus non-specific contacts |
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainreso | Remove low resolution domains from a DCF file |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| psiphi | Phi and psi torsion angles from protein coordinates |
| rocon | Generates a hits file from comparing two DHF files |
| rocplot | Performs ROC analysis on hits files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Removes fragment sequences from DHF files |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generates DHF files from keyword search of UniProt |
| siggen | Generates a sparse protein signature from an alignment |
| siggenlig | Generate ligand-binding signatures from a CON file |
| sigscan | Generate hits (DHF file) from a signature search |
| sigscanlig | Search ligand-signature library & write hits (LHF file) |