first version

script/add_hydrogen.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+'''
+@file        :add_hydrogen.py
+@Description:       : add hydrogen in pymol
+@Date     :2022/10/24 11:17:11
+@Author      :hotwa
+@version      :1.0
+'''
+from pymol import cmd
+from openbabel import pybel
+"""
+conda install -c conda-forge pymol-open-source openbabel --yes
+"""
+
+def add_polar_hydrogen(file, out_file,read_fmt = 'mol2', pymol_obj='sele',
+    save_format='mol2',tool = 'pymol'):
+    """add_polar_hydrogen _summary_
+
+    _extended_summary_
+
+    Arguments:
+        file {pathlike} -- input file path
+        out_file {pathlike} -- output file
+
+    Keyword Arguments:
+        read_fmt {string} -- the format of read file (default: {'mol2'})
+        pymol_obj {string } -- add polar hydrogen object name, ligand ID (default: {'sele'})
+        save_format {string} -- the format of save file (default: {'mol2'})
+        tool {string} -- the tool of add polar hydrogens (default: {'pymol'})
+
+    Returns:
+        _type_ -- path or None
+    """
+    if tool == 'pymol':
+        cmd.reinitialize("everything")
+        cmd.load(filename=file, format=read_fmt)
+        cmd.h_add(pymol_obj) # add all hydrogens in this molecular
+        cmd.remove(f"{pymol_obj} & hydro & not nbr. (don.|acc.)") # remove no-polar-hydrogen
+        cmd.save(filename=out_file,selection=pymol_obj, format=save_format)
+        return out_file
+    elif tool == 'pybel':
+        omol = list(pybel.readfile(format = 'mol2', filename = file))[0]
+        omol.OBMol.AddPolarHydrogens()
+        omol.write('mol2',out_file,overwrite=True)
+        return out_file
+    else:
+        return None