soedinglab / CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
http://www.ncbi.nlm.nih.gov/pubmed/25064567
GNU Affero General Public License v3.0
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Why not use the -b argument to generate BRAW files? #36

Open geqj opened 2 years ago

geqj commented 2 years ago

Hello, I have a question to ask you, when I used ccmpred example.mat -b example.braw command to generate braw file, there was an error. Error: unknown option b at argument index 22 So I can't generate my own BRAW file. But I see that your source code has the -b parameter. #ifdef MSGPACK printf("\t-b BRAWFLE\tStore raw prediction matrix in msgpack format in BRAWFLE\n"); May I ask what is the cause of this problem? Any thoughts would be greatly appreciated! Thanks.

mintuos commented 1 year ago

me too when I use this ./ccmpred -h, there are not -b options

Usage: ./ccmpred [options] input.aln output.mat Options: -n NUMITER Compute a maximum of NUMITER operations [default: 50] -e EPSILON Set convergence criterion for minimum decrease in the last K iterations to EPSILON [default: 0.01] -k LASTK Set K parameter for convergence criterion to LASTK [default: 5]

-i INIFILE  Read initial weights from INIFILE
-r RAWFILE  Store raw prediction matrix in RAWFILE

-w IDTHRES  Set sequence reweighting identity threshold to IDTHRES [default: 0.8]
-l LFACTOR  Set pairwise regularization coefficients to LFACTOR * (L-1) [default: 0.2]
-A          Disable average product correction (APC)
-R          Re-normalize output matrix to [0,1]
-h          Display help
ylx0925 commented 1 year ago

I have met this problem,and I installed it from the latest branch.If you solved the problem,can you teach me?