drrdom/pmapper

3D pharmacophore signatures and fingerprints

pmapper's Issues

Caching documentation typo

Hi DrrDom,

Nice work with pmapper, I am looking forward working with it a bit more in the future. I just wanted to point out a typo in the readme.md and documentation. To turn on caching, the P constructor needs the variable "cached" as opposed to "cache", it's super minor but I thought I'd let you know. :)

Best Wishes,
Matt

.pma to .xyz format?

Hi,

Is it possible to convert .pma to .xyz format using pmapper or psearch?

Please suggest.

Regards,
Suneel

psearch functionality

Hello

I see a reference to a "psearch" functionality for high throughput pharmacophore screening, but can't seem to find it anywhere. Can that be shared? If not, what are the best ways to screen a large collection of molecules (1M+) against a few point pharmacophore?

Hi, would you supply the script of speed test?

Thank you for sharing your code. would you supply the script of speed test?

Visualize the models?

Hi,

Thanks for sharing the script and nice tutorial on how to generate pharmacophore models. Will it be possible to view (pymol or nglview) the generated pharmacophore models for analysis purpose. I have tried to generate .xyz file and but wasnt successful. Any help will be appreciated!.

Thanks in advance.

Regards,
Suneel

Extending pmapper functionality to protein residues

Would it be possible to extend this functionality to create pharmacophores for proteins? Specifically, I'm looking to create pharmacophores for protein pockets based on PDB structures alone, and convert those to fingerprints. It appears that the smarts patterns could be modified to those matching protein residues, but the underlying functionality seems to work on a per-atom level, and not a per-object--is that true?

problem about get_features_count()

Hi authors,

Thanks for providing the open source code for getting the pharmacophore signature.

While I found that the 'pharmacophore counts' which obtained with the use of get_features_count() contains only 6 classes: feature_names_dict = {'HBD': 'D', 'HBA': 'A', 'NI': 'N', 'PI': 'P', 'H': 'H', 'AR': 'a'}. I wonder that what's the relationship between those abbreviations and [positive, negative, acceptor, donor, aromatic, sulfur, neutral] ? How can I get all the 8 features?

Thanks for your time and help!

best,
User
March 31, 2022

ligandscout

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