scorecmapdir

 

Function

Contact scores for cleaned protein chain contact files

Description

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Algorithm

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Usage

Under development, no final example yet

Command line arguments

   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)

Input file format

scorecmapdir reads any normal sequence USAs.

Under development, no example input file(s) yet

Output file format

scorecmapdir outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Under development, no example output file(s) yet

Data files

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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
contactcountCount specific versus non-specific contacts
contactsGenerate intra-chain CON files from CCF files
domainalignGenerate alignments (DAF file) for nodes in a DCF file
domainrepReorder DCF file to identify representative structures
domainresoRemove low resolution domains from a DCF file
interfaceGenerate inter-chain CON files from CCF files
libgenGenerate discriminating elements from alignments
matgen3dGenerate a 3D-1D scoring matrix from CCF files
psiphiPhi and psi torsion angles from protein coordinates
roconGenerates a hits file from comparing two DHF files
rocplotPerforms ROC analysis on hits files
seqalignExtend alignments (DAF file) with sequences (DHF file)
seqfraggleRemoves fragment sequences from DHF files
seqsearchGenerate PSI-BLAST hits (DHF file) from a DAF file
seqsortRemove ambiguous classified sequences from DHF files
seqwordsGenerates DHF files from keyword search of UniProt
siggenGenerates a sparse protein signature from an alignment
siggenligGenerate ligand-binding signatures from a CON file
sigscanGenerate hits (DHF file) from a signature search
sigscanligSearch ligand-signature library & write hits (LHF file)

Author(s)

Damian Counsell (d.counsell © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

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

Comments

None