gokit1 / gokit Goto Github PK

I am trying to following the tutorial of 1ris, by running:
python gokit.py -attype 1 -aa_pdb 1ris.pdb -skip_glycine

and got the log
in write_CB_to_native 1ris.pdb False
sopc False skipglycine, True
in get_side_chain_COM: 1ris.pdb False

Excluding glycine, res = 10
Excluding glycine, res = 35
Excluding glycine, res = 47
Excluding glycine, res = 53
Excluding glycine, res = 75
Excluding glycine, res = 76
in get_back_bone_COM 1ris.pdb
in write_CB_to_native: 1ris.pdb False
See file: native_cb.pdb with 146 atoms
CB= 70 CA= 76

I could see it generated the files native_ca.pdb and native_cb.pdb, but the two folders called MD and PATH were not generated as expected. And I also didn't get any error messages.

By the way, I had an issue to run the script with python3 which failed with
Traceback (most recent call last):
File "/lindorffgrp-isilon/wyong/temp/GoKit/gokit/gokit.py", line 1616, in
main()
File "/lindorffgrp-isilon/wyong/temp/GoKit/gokit/gokit.py", line 1583, in main
X.write_CB_to_native(pdbfile,False)
File "/lindorffgrp-isilon/wyong/temp/GoKit/gokit/gokit.py", line 251, in write_CB_to_native
CB=self.get_side_chain_COM(pdbfile,skip_glycine)
File "/lindorffgrp-isilon/wyong/temp/GoKit/gokit/gokit.py", line 230, in get_side_chain_COM
COM1=np.array(COM1).reshape(len(COM1)/2,2)
TypeError: 'float' object cannot be interpreted as an integer
But this could be fixed by replacing "/" with "//" in line 178 and 230. Hope these changes are not the reason that I couldn't get the MD and PATH folders.

Any clues?
Thanks a lot!
Yong

pip install MDTraj gives trouble on my machine (MacOS, Catalina 10.15.3)

In this case the following command works:
pip install git+https://github.com/mdtraj/mdtraj@master --user