Bug: Ligand file in a folder causes exception

[schackartk]

If the ligand pdb file is in a folder instead of the root of the repo, an exception occurs:

$ ls ligands/
my_ligand.pdb

$ python main.py --run_num=1 --mode='full dock' --aptamerSeq='GCGCGCGCGATATATAT' --ligand='ligands/my_ligand.pdb' --ligandType='other' --ligandSeq=''
Starting Fresh Run 1
Traceback (most recent call last):
  File "main.py", line 229, in <module>
    opendna = opendna(params)  # instantiate the class
  File "/home/ken/personal/E2EDNA2/opendna.py", line 53, in __init__
    self.setup()  # if we don't need a workdir & MMB files (eg, give a 3D structure), don't make one.
  File "/home/ken/personal/E2EDNA2/opendna.py", line 179, in setup
    copyfile(self.targetPDB, self.workDir + '/' + self.targetPDB)
  File "/home/ken/personal/E2EDNA2/env/lib/python3.7/shutil.py", line 121, in copyfile
    with open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/home/ken/personal/E2EDNA2/localruns/run1/ligands/my_ligand.pdb'

I don't see any reason that the ligand file should not be in a folder, so this should not fail.

[taoliu032]

This is because the pipeline will copy the provided file specified by --ligand into the workdir. Here there is a folder named "ligands" in your code directory but there isn't a "ligands" folder in the workdir. So the copyfile commands runs into problem.

[taoliu032]

To resolve this, either extract the filename from --ligand and store it as self.targetPDB or explicitly create a folder in workdir. I think the former option is better. A quick and dirty way can be like this: splitting the string by /, and copying the pdb file from its folder to the code directory:

# args.ligand is 'ligands/my_ligand.pdb'
params['target ligand'] = args.ligand.split('/')[-1]  # params['target ligand'] is 'my_ligand.pdb'
copyfile(args.ligand, params['target ligand'])