ligandscout

[caominhtr]

How to load and read file .pml from ligandscout from your code?
I have a pharmacophore created in LigandScout and I want to open and perform virtual screening by your code

[DrrDom]

This should work

from pmapper.pharmacophore import Pharmacophore as P
p  = P()
# load LS model
p.load_ls_model('filename.pml')
# save LS model
p.save_ls_model('filename.pml', name='optional_name_visible_in_LS')

[caominhtr]

1. I encountered this error (picture attached below)
2. Is there any way to perform pharmacophore modelling by pmapper but not psearch?

File c:\Users\cowmink\Desktop\pmapper-master\pmapper\pharmacophore.py:836, in __PharmacophoreFiles.load_ls_model(self, pml_fname)
834 d = minidom.parse(pml_fname)
835 for p in d.getElementsByTagName('point'):
--> 836 feature_name = feature_names_dict[p.getAttribute('name')]
837 optional = p.getAttribute('optional')
838 disabled = p.getAttribute('disabled')

KeyError: ''

[DrrDom]

1. I do not see the full text of the error, insert full text of the error message. If the problem is in line 836, then maybe some feature names were changed in recent versions of LigandScout. This is a very experimental option to support LS files. You may attach pml-file to look on it.
2. The question is unclear. What kind of modeling do you mean?

[caominhtr]

For my 2nd question:
Is there any way to create a pharmacophore model based on multiple ligands by pmapper?

[DrrDom]

No, there is no a built-in procedure. This will require to implement a full modeling procedure.