top_includes in the function minimize() does not work

[RlyehAD]

In md.py, there's a function for energy minimization called minimize(). The three necessary args of it are struct, top and top_includes. The comments there suggest that top_includes is a list of dirs in which .itp ff files are searched. Assuming it's a list of str of path to the dirs, it does not make sense at line 215 where the list is input to another function called data_tofile () so the itp files can be copied to the temporary dir with .gro and .top files. However, according to the code in data_tofile(), the input should be a single file otherwise the error "expected either Dataset, ndarray or file path as src" is raised.

The error can be repeated by running the following code in the test dir with a terminal:

python

import os
import proto_md 

struct = "../sample/SpaceWarping/Struct/1PRT.gro"  
struct = os.path.abspath(struct) 

top = "../sample/SpaceWarping/Top/1PRT.top"
top = os.path.abspath(top)

top_includes = "../sample/SpaceWarping/Top"
top_includes = os.path.abspath(top_includes)

os.path.isdir(top_includes) #This will return True

proto_md.md.minimize(struct=struct, top=top, top_includes=[top_includes]) 

[anabiman]

Please post the error returned from running the code snippet.

[RlyehAD]

Hi, the error returned is

Traceback (most recent call last): 
 File "<stdin>", line 1, in <module>           
 File "/home/******/miniconda3/envs/mmic/lib/python3.9/site-packages/proto_md/md.py", line 215, in minimize                                                                                                          data_tofile(i, dirname=dirname)      
 File "/home/******/miniconda3/envs/mmic/lib/python3.9/site-packages/proto_md/util/util.py", line 94, in data_tofile       
 raise TypeError(       
 TypeError: expected either Dataset, ndarray or file path as src  

[anabiman]

top_includes should be a list of files to include for the topology and not the dir. In the docstrings for data_tofile, you'll notice that fid can be None only when dealing with the h5py datasets. In other words, if your itp files are h5py datasets, then your code should work.