Added functionality to spatiotemporal #1096
Conversation
| if os.path.exists(exp_comp_map[prot]): | ||
| exp = pd.read_csv(exp_comp_map[prot]) | ||
| else: | ||
| raise Exception( |
There was a problem hiding this comment.
Personally I wouldn't bother with this check (since Python will raise an exception anyway if the file does not exist, or is unreadable) but if you want to, I would recommend catching the original exception rather than using os.path.exists (as this avoids race conditions). Certainly use a more specific exception like IOError or FileNotFoundError instead of Exception.
| if not isinstance(match_final_state, bool): | ||
| raise TypeError("match_final_state should be of type bool") | ||
| # make output_dir if necessary | ||
| if len(output_dir) > 0: |
There was a problem hiding this comment.
Can be simplified to simply if output_dir:
There was a problem hiding this comment.
No, because if len(output_dir) == 0, uses cwd
| os.chdir(output_dir) | ||
| else: | ||
| os.mkdir(output_dir) | ||
| os.chdir(output_dir) |
There was a problem hiding this comment.
A little inelegant since you chdir in both branches. Would be cleaner if the chdir were outside the if.
| if prot in template_dict.keys(): | ||
| keep_prots.extend(template_dict[prot]) | ||
| else: | ||
| raise Exception("Protein " + prot + ' does not exist in template_dict\nClosing...') |
There was a problem hiding this comment.
KeyError would be more appropriate here.
Added prepare_protein_library, which prepares protein topologies and configurations for all snapshots from topology and configuration information about the final snapshot.