How to use plmDCA.m

[KotaroTsuboyama]

I guess this plmDCA.m can produce .mat file from .aln file. But, after I executed

octave plmDCA.m .aln

I got only the following message and did not get any .mat file

octave: X11 DISPLAY environment variable not set
octave: disabling GUI features

I prepared the environment the following instruction with a few modifications

git clone https://github.com/magnusekeberg/plmDCA.git
mv plmDCA/plmDCA_asymmetric_v2 plmDCA/plmDCA
mkdir plmDCA/plmDCA_asymmetric_v2
cp plmDCA.m plmDCA/plmDCA_asymmetric_v2/
cp plmDCA/plmDCA/functions/ plmDCA/plmDCA_asymmetric_v2/
cp plmDCA/plmDCA/3rd_party_code/ plmDCA/plmDCA_asymmetric_v2/
cd plmDCA/plmDCA_asymmetric_v2/functions/; for i in *.c; do octave --eval "mex $i";done
cd ../3rd_party_code/minFunc/; for i in *.c; do octave --eval "mex $i"; done`
By using those code, I made two .mex files in function folder, and three .mex files in minFunc folder.

I also noticed that the message written above did not change even after I renamed the function and 3rd_party_code folders. So, I think my plmDCA.m does not recognize those mex or c files.

How can I fix this problem? Thanks in advance!

[lumramirezch]

I made this modifications for plmDCA to work:

git clone https://github.com/magnusekeberg/plmDCA.git 

replace the original version of plmDCA.m (plmDCA_asymmetric.m) by the one provided in the alphafold_pytorch repo

rm ~/plmDCA/plmDCA_asymmetric_v2/plmDCA_asymmetric.m
cp ~/alphafold_pytorch/plmDCA.m ~/plmDCA/plmDCA_asymmetric_v2/ 

Finally run octave-cli (command line)

cd ~/plmDCA/plmDCA_asymmetric_v2/functions/ ; for i in *.c ; do octave-cli --eval "mex $i" ; done
cd ~/plmDCA/plmDCA_asymmetric_v2/3rd_party_code/minFunc/ ; for i in *.c ; do octave-cli --eval "mex $i" ; done