Random structure generation fails if no ligand is specified

[fredauski]

Dear all,

I'm running into a problem trying to recreate the generation of random structures as shown in Fig. 19 in the User's Manual (v1.0).

Here's the input file fig19.in (copied from Fig. 19):

-coord 6
-ligalign 1
-rundir runs_fig19/
-spin 1
-ligctg build
-rgen 10
-distort 0
-lignum 4
-core Fe
-liggrp all
-geometry oct
-rkHs yes
-oxstate 0

and here the Traceback after running molsimplify -i fig19.in:

TensorFlow connection successful
Input file detected, reading arguments from input file
molSimplify is starting!

************************************************************
******** Welcome to molSimplify! Let's get started. ********
************************************************************


The directory for  this calculation is: runs_fig19/
Checking input...
WARNING: No ligand numbers specified. Defaulting to 6 of the first ligand and 0 of all others.
Traceback (most recent call last):
  File "/Users/user/.pyenv/versions/molSimplify/bin/molsimplify", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/user/.pyenv/versions/3.12.4/envs/molSimplify/lib/python3.12/site-packages/molSimplify/__main__.py", line 184, in main
    startgen(sys.argv, False, gui)
  File "/Users/user/.pyenv/versions/3.12.4/envs/molSimplify/lib/python3.12/site-packages/molSimplify/Scripts/generator.py", line 170, in startgen
    emsg = checkinput(args)
           ^^^^^^^^^^^^^^^^
  File "/Users/user/.pyenv/versions/3.12.4/envs/molSimplify/lib/python3.12/site-packages/molSimplify/Scripts/inparse.py", line 164, in checkinput
    for lig in args.lig[1:]:
               ~~~~~~~~^^^^
TypeError: 'NoneType' object is not subscriptable

The input from Fig. 17 works like a charm.

Is there still a way of generating structures with all random ligands?

[dbkchu]

Hi @fredauski,

Please refer to the tutorials on our website rather than the manual (which is very outdated). Random structure generation is not tested and may not work well (see issue #179)... We will try to restore this functionality, but I am not sure when we will get to it.

If you would like to use random ligands right now, you would likely need to use molSimplify in a Python script and randomly select ligands outside the calls to molSimplify.

[gianmarco-terrones]

Piggybacking off of this, you can add custom ligands for use by adding XYZ or MOL files to the molSimplify/Ligands folder, and adding lines to the ligands.dict file.

Also, an alternative to using the command line for molSimplify structure generation is startgen_pythonic, in case that is useful. For example:

from molSimplify.Scripts.generator import startgen_pythonic

input_dict = {
'-core': 'ir',
'-lig': f'{some_bidentate_ligand} {another_bidentate_ligand}',
'-ligocc': '2 1',
'-oxstate': '3',
'-geometry': 'oct',
'-coord': '6',
'-spin': '1',
}

startgen_pythonic(input_dict=input_dict, write=True)

[fredauski]

Thank you all for the tips, I will implement what I need in Python with the startgen_pythonic function.

Feel free to close this issue if it is of no further relevance to you guys!