From 4393607cc2006812f40097b566980ccc28e93d35 Mon Sep 17 00:00:00 2001
From: zhangplpl <zhangpengli@dp.tech>
Date: Sun, 7 Apr 2024 18:45:20 +0800
Subject: [PATCH] del protein_prep/pdb2pdbqt.py

---
 .../modules/protein_prep/pdb2pdbqt.py         | 109 ------------------
 1 file changed, 109 deletions(-)
 delete mode 100644 unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py

diff --git a/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py b/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py
deleted file mode 100644
index e05959e..0000000
--- a/unidock_tools/src/unidock_tools/modules/protein_prep/pdb2pdbqt.py
+++ /dev/null
@@ -1,109 +0,0 @@
-from typing import Union, List
-import os
-from math import isnan, isinf
-from rdkit import Chem
-from rdkit.Chem import AllChem
-
-
-def get_pdbqt_atom_lines(mol: Chem.Mol, donors: List[int], acceptors: List[int]):
-    atom_lines = [line.replace('HETATM', 'ATOM  ')
-                  for line in Chem.MolToPDBBlock(mol).split('\n')
-                  if line.startswith('HETATM') or line.startswith('ATOM')]
-
-    pdbqt_lines = []
-    for idx, atom in enumerate(mol.GetAtoms()):
-        pdbqt_line = atom_lines[idx][:56]
-
-        pdbqt_line += '0.00  0.00    '  # append empty vdW and ele
-        # Get charge
-        charge = 0.
-        fields = ['_MMFF94Charge', '_GasteigerCharge', '_TriposPartialCharge']
-        for f in fields:
-            if atom.HasProp(f):
-                charge = atom.GetDoubleProp(f)
-                break
-        # FIXME: this should not happen, blame RDKit
-        if isnan(charge) or isinf(charge):
-            charge = 0.
-        pdbqt_line += ('%.3f' % charge).rjust(6)
-
-        # Get atom type
-        pdbqt_line += ' '
-        atomicnum = atom.GetAtomicNum()
-        atomhybridization = atom.GetHybridization()
-        atombondsnum = atom.GetDegree()
-        if atomicnum == 6 and atom.GetIsAromatic():
-            pdbqt_line += 'A '
-        elif atomicnum == 7 and idx in acceptors:
-            pdbqt_line += 'NA'
-        elif atomicnum == 8 and idx in acceptors:
-            pdbqt_line += 'OA'
-        elif atomicnum == 1 and atom.GetNeighbors()[0].GetIdx() in donors:
-            pdbqt_line += 'HD'
-        elif atomicnum == 1 and atom.GetNeighbors()[0].GetIdx() not in donors:
-            pdbqt_line += 'H '
-        elif atomicnum == 16 and (
-                (atomhybridization == Chem.HybridizationType.SP3 and atombondsnum != 4) or
-                atomhybridization == Chem.HybridizationType.SP2):
-            pdbqt_line += 'SA'
-        else:
-            if len(atom.GetSymbol()) > 1:
-                pdbqt_line += atom.GetSymbol()
-            else:
-                pdbqt_line += (atom.GetSymbol() + ' ')
-        pdbqt_lines.append(pdbqt_line)
-    return pdbqt_lines
-
-
-def receptor_mol_to_pdbqt_str(mol: Chem.Mol):
-    # make a copy of molecule
-    mol = Chem.Mol(mol)
-
-    # Identify donors and acceptors for atom typing
-    # Acceptors
-    patt = Chem.MolFromSmarts('[$([O;H1;v2]),'
-                              '$([O;H0;v2;!$(O=N-*),'
-                              '$([O;-;!$(*-N=O)]),'
-                              '$([o;+0])]),'
-                              '$([n;+0;!X3;!$([n;H1](cc)cc),'
-                              '$([$([N;H0]#[C&v4])]),'
-                              '$([N&v3;H0;$(Nc)])]),'
-                              '$([F;$(F-[#6]);!$(FC[F,Cl,Br,I])])]')
-    acceptors = list(map(lambda x: x[0], mol.GetSubstructMatches(patt, maxMatches=mol.GetNumAtoms())))
-    # Donors
-    patt = Chem.MolFromSmarts('[$([N&!H0&v3,N&!H0&+1&v4,n&H1&+0,$([$([Nv3](-C)(-C)-C)]),'
-                              '$([$(n[n;H1]),'
-                              '$(nc[n;H1])])]),'
-                              # Guanidine can be tautormeic - e.g. Arginine
-                              '$([NX3,NX2]([!O,!S])!@C(!@[NX3,NX2]([!O,!S]))!@[NX3,NX2]([!O,!S])),'
-                              '$([O,S;H1;+0])]')
-    donors = list(map(lambda x: x[0], mol.GetSubstructMatches(patt, maxMatches=mol.GetNumAtoms())))
-    AllChem.ComputeGasteigerCharges(mol)
-
-    atom_lines = get_pdbqt_atom_lines(mol, donors, acceptors)
-    assert len(atom_lines) == mol.GetNumAtoms()
-
-    pdbqt_lines = ['REMARK  Name = ' + (mol.GetProp('_Name') if mol.HasProp('_Name') else '')]
-    pdbqt_lines.extend(atom_lines)
-
-    return "\n".join(pdbqt_lines)
-
-
-def pdb2pdbqt(pdbfile: Union[str, os.PathLike], out_file: Union[str, os.PathLike]):
-    receptor_mol = Chem.MolFromPDBFile(str(pdbfile), removeHs=False)
-    pdbqt_str = receptor_mol_to_pdbqt_str(receptor_mol)
-    with open(out_file, 'w') as f:
-        f.write(pdbqt_str)
-
-
-if __name__ == "__main__":
-    import argparse
-
-    parser = argparse.ArgumentParser(description="Script to convert receptor from PDB to PDBQT format")
-    parser.add_argument("-r", "--receptor_file", type=str, required=True,
-                        help="receptor file in PDB format")
-    parser.add_argument("-o", "--out_file", type=str, required=True,
-                        help="output file in PDBQT format")
-    args = parser.parse_args()
-
-    pdb2pdbqt(args.receptor_file, args.out_file)