plmc

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Haven't coded in C for years - please check my header files etc are sensible :) Added weights file reading, weights file validation (checking there is the correct number of...

loodvn

Focus sequence non-functional if alphabet provided

1

When alphabet is specified, all sequence positions are modeled ignoring uppercase/lowercase Without alphabet ( assumes protein alphabet = a problem for RNAs ) ``` plmc -c my.model -f target_seq -t...

njrollins

This change just removes the hard coding of alphabet to be codesAA for removing lowerCase and '.' gaps.

joshuaroll

Hi, would it be possible to offer plmc as a conda package?

Zethson

Hello, I'm trying to run the program with the EVcouplings pipeline, but the related bug comes from the plmc tool The program just loaded my .a2m file before dumped the...

Nautilus567

I was a bit confused by `--gapignore Exclude first alphabet character from potential calculations` and then realized it didn't correspond to what I had seen on the command line... Anyhow,...

smsaladi

new version gives error when compling in linux

1

Hi, compiling this new version in linux (with ot without openmp) yelds an error: In file included from src/plm.c:15: src/include/plm.h:106:20: error: field ‘start’ has incomplete type 106 | struct timeval...

eagalpern

Confusion on -theta flag ?

1

This may seem obvious, but does the -t flag of say 0.2 do the evolutionary reweighting for us? I just feel like I'm always confused for all these methods ......

brycejoh16

How to get a2m MSA?

1

I am really new to MSA, would you mind telling me how to get the a2m file that this package required? Thank you very much.

jackhu3301

Gradient optimization: ROUNDING_ERROR

3

hi, with plmc usage my calculation ran to 90 steps but then terminated with the following error. Found focus OsNIP2-1 as sequence 1 255 valid sequences out of 255 298...

Yogesh1-11