-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.
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
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.