Make wobj.py Python3 Compatible

[Inniag]

The PyMol script for loading OBJ files is currently not compatible with the Python3 standard. This might cause errors such as this:

PyMOL>run visualise_pathway.py,main
Traceback (most recent call last):
  File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 487, in run
    run_(path, ns_main, ns_main)
  File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 532, in run_file
    execfile(file,global_ns,local_ns)
  File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 527, in execfile
    exec(co, global_ns, local_ns)
  File "visualise_pathway.py", line 89, in <module>
    obj = wobj.import_wobj(args.surface)
  File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 396, in import_wobj
    return obj_importer.read(filename)
  File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 182, in read
    cgo[key] = self.__create_cgo_object(key)
  File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 348, in __create_cgo_object
    vertex_a = self.__vertices[face["vert_idx"][0] - 1]
TypeError: 'map' object is not subscriptable

A fix has already been suggested in issue #11.

[Jeffatcunyc]

Hi Inniag,

I could not find the answer to the loading OBJ file issue with PyMol running on Python3. Could you please give me more details about how to fix it up? Thanks.

Jeff

[Jeffatcunyc]

Hi Inniag,

I just worked it out. My solution was using an old version of PyMol running on Python2. What I used is PyMol 1.8.4.0.

Best, Jeff

[calvadia]

I have the same error message. Any fix available yet?

Thank you, Carolina

[DSeiferth]

In Python 3, " map" returns an iterable object of type map, and not a subscriptible list. If you replace every map() with list(map()) in wobj.py, the script is python3 compatible. For example replace self.__materials[self.__crnt_material]["Ka"] = map(float, split_line[1:4]) with self.__materials[self.__crnt_material]["Ka"] = list(map(float, split_line[1:4]))

[DSeiferth]

I did not see the pull request made by irudayaf on 28 Aug 2019 in which he basically did the same...

[channotation]

Closed pull request #13 from @irudayaf as well now.