Comments (2)
Hi @dwbaron,
Thank you for the feedback, we are glad that you liked our work!
-
Yes, all the input fragments should be in the same pdb, mol, mol2 or sdf file. Please check examples here: https://huggingface.co/spaces/igashov/DiffLinker/tree/main/examples
-
Yes, you can pass the information about atoms to be connected specifying their IDs in
--anchors
argument (comma-separated numbers, e.g.--anchors 4,12,20
). To get the right IDs, you can open your file with fragments in PyMOL and show atom ID labels (as shown in the figure below).
Please let me know if you have other questions!
from difflinker.
Hi @dwbaron,
Thank you for the feedback, we are glad that you liked our work!
- Yes, all the input fragments should be in the same pdb, mol, mol2 or sdf file. Please check examples here: https://huggingface.co/spaces/igashov/DiffLinker/tree/main/examples
- Yes, you can pass the information about atoms to be connected specifying their IDs in
--anchors
argument (comma-separated numbers, e.g.--anchors 4,12,20
). To get the right IDs, you can open your file with fragments in PyMOL and show atom ID labels (as shown in the figure below).![]()
Please let me know if you have other questions!
Thanks for u help, it solved the problems~
from difflinker.
Related Issues (12)
- How to sample with protein backbones?? HOT 2
- AttributeError: can't set attribute
- Evaluation for reproducing the paper's result HOT 5
- I can't download these models HOT 1
- cannot repeat the process of fragment generation HOT 6
- Question:given the limitation of pocket but without limitataion of --anchors HOT 2
- The format of the fragment file
- can I run cpu mode to generate linkers? HOT 1
- sascorer.py calls removed RDkit module - ModuleNotFoundError: No module named 'rdkit.six' HOT 1
- Calculating the "Clash Metric" as Described in Your Paper
- Larger segments as input HOT 1
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