os.symlink() gets passed relative paths, which creates a wrongly pointed symlink - for example you will have called os.symlink('manual_pdb/X.pdb', 'structures/pdb/X.pdb'), which will create the structures/pdb/X.pdb symlink pointing to a file that would have had to be at structures/pdb/manual_pdb/X.pdb.
This is used when the --structure_paths argument is used with gather_templates to point to your local directory containing (some) of the pdb and sift files.
Will fix by passing absolute paths to os.symlink() ?
Here: https://github.com/choderalab/ensembler/blob/master/ensembler/initproject.py#L443
os.symlink()gets passed relative paths, which creates a wrongly pointed symlink - for example you will have calledos.symlink('manual_pdb/X.pdb', 'structures/pdb/X.pdb'), which will create thestructures/pdb/X.pdbsymlink pointing to a file that would have had to be atstructures/pdb/manual_pdb/X.pdb.This is used when the
--structure_pathsargument is used withgather_templatesto point to your local directory containing (some) of the pdb and sift files.Will fix by passing absolute paths to
os.symlink()?