antibody.py: output_cter_constraint(base,prefix,decoy) inconsistently omits decoy information

[smoe]

Hello,

I found this while I was commenting all the functions in antibody.py, see pull request #31 .

The function output_cter_constraint(base,prefix,decoy) is meant to add information in a text file for a separate tool to interpret and further improve a cognate .pdb file. The routine is passed a decoy number, but that information is not used in line
https://github.com/RosettaCommons/tools/blob/master/antibody/antibody.py#L1286
where the file is created. Consequently, since the invocation is clearly dependent on that decoy number on line

tools/antibody/antibody.py

Line 1246 in 9db2953

output_cter_constraint(cter, prefix, decoy)

there is some information overwritten. The decoy also needs to be added here

tools/antibody/antibody.py

Line 1306 in 9db2953

commandline = '%s/kink_constraints.py %s/model.pdb' % (script_dir, prefix)

Cheers,

Steffen