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the original purpose and actual effect of reduce_receptors.py script file #72

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tangmaomao16 opened this issue Jul 20, 2024 · 0 comments

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@tangmaomao16
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tangmaomao16 commented Jul 20, 2024

I read the source code of the script file https://github.com/HannesStark/EquiBind/blob/main/data_preparation/reduce_receptors.py

I think the core coding is
f"reduce -Trim {rec_path} > {os.path.join(data_path, name, f'{name}_protein_obabel_reduce_tmp.pdb')}"
f"reduce -HIS {os.path.join(data_path, name, f'{name}_protein_obabel_reduce_tmp.pdb')} > {os.path.join(data_path, name, f'{name}_protein_obabel_reduce.pdb')}"

Then I search for the "reduce" command line tool document, and I find https://github.com/rlabduke/reduce/blob/master/README.usingReduce.txt

-Trim remove (rather than add) hydrogens
-HIS create NH hydrogens on HIS rings

I want to ask the authors of EquiBind. Do you want to remove most hydrogen atoms in the protein PDB file to decrease the computation of the program? But why still create NH hydrogens on HIS rings?

Please tell me the original purpose and actual effect of reduce_receptors.py script file. Thank you.

@tangmaomao16 tangmaomao16 changed the title the orginal purpose and actual effect of reduce_receptors.py script file the original purpose and actual effect of reduce_receptors.py script file Jul 20, 2024
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