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igashov avatar igashov commented on July 17, 2024

Hi @dwbaron,

Thank you for the feedback, we are glad that you liked our work!

  1. 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

  2. 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).

Screenshot 2022-11-10 at 16 38 44

Please let me know if you have other questions!

from difflinker.

dwbaron avatar dwbaron commented on July 17, 2024

Hi @dwbaron,

Thank you for the feedback, we are glad that you liked our work!

  1. 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
  2. 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).
Screenshot 2022-11-10 at 16 38 44

Please let me know if you have other questions!

Thanks for u help, it solved the problems~

from difflinker.

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