diff qed.py @ 3:52a8d34dd08f draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 943ff93be2257426d69a8406ed55c838495ecf3f"
author bgruening
date Fri, 30 Jul 2021 12:51:45 +0000
parents ab73abead7fa
children
line wrap: on
line diff
--- a/qed.py	Tue Jul 28 08:47:05 2020 -0400
+++ b/qed.py	Fri Jul 30 12:51:45 2021 +0000
@@ -1,20 +1,22 @@
 #!/usr/bin/env python
-__all__ = ['weights_max', 'weights_mean', 'weights_none', 'default']
+__all__ = ["weights_max", "weights_mean", "weights_none", "default"]
 
-# RDKit
-from rdkit.Chem import Descriptors
-from rdkit import Chem
-
+import argparse
+import os
+import re
+import sys
 # General
 from copy import deepcopy
 from math import exp, log
-import sys, os, re
-import argparse
+
+from rdkit import Chem
+# RDKit
+from rdkit.Chem import Descriptors
 
 
 class SilicosItError(Exception):
     """Base class for exceptions in Silicos-it code"""
-    pass
+
 
 class WrongArgument(SilicosItError):
     """
@@ -24,172 +26,175 @@
         function -- function in which error occurred
         msg      -- explanation of the error
     """
+
     def __init__(self, function, msg):
         self.function = function
         self.msg = msg
 
+
 def check_filetype(filepath):
     mol = False
     possible_inchi = True
     for line_counter, line in enumerate(open(filepath)):
         if line_counter > 10000:
             break
-        if line.find('$$$$') != -1:
-            return 'sdf'
-        elif line.find('@<TRIPOS>MOLECULE') != -1:
-            return 'mol2'
-        elif line.find('ligand id') != -1:
-            return 'drf'
-        elif possible_inchi and re.findall('^InChI=', line):
-            return 'inchi'
-        elif re.findall('^M\s+END', line):
+        if line.find("$$$$") != -1:
+            return "sdf"
+        elif line.find("@<TRIPOS>MOLECULE") != -1:
+            return "mol2"
+        elif line.find("ligand id") != -1:
+            return "drf"
+        elif possible_inchi and re.findall("^InChI=", line):
+            return "inchi"
+        elif re.findall("^M\s+END", line):  # noqa W605
             mol = True
         # first line is not an InChI, so it can't be an InChI file
         possible_inchi = False
 
     if mol:
-        # END can occures before $$$$, so and SDF file will 
+        # END can occures before $$$$, so and SDF file will
         # be recognised as mol, if you not using this hack'
-        return 'mol'
-    return 'smi'
+        return "mol"
+    return "smi"
 
-AliphaticRings = Chem.MolFromSmarts('[$([A;R][!a])]')
+
+AliphaticRings = Chem.MolFromSmarts("[$([A;R][!a])]")
 
 AcceptorSmarts = [
-    '[oH0;X2]',
-    '[OH1;X2;v2]',
-    '[OH0;X2;v2]',
-    '[OH0;X1;v2]',
-    '[O-;X1]',
-    '[SH0;X2;v2]',
-    '[SH0;X1;v2]',
-    '[S-;X1]',
-    '[nH0;X2]',
-    '[NH0;X1;v3]',
-    '[$([N;+0;X3;v3]);!$(N[C,S]=O)]'
-    ]
+    "[oH0;X2]",
+    "[OH1;X2;v2]",
+    "[OH0;X2;v2]",
+    "[OH0;X1;v2]",
+    "[O-;X1]",
+    "[SH0;X2;v2]",
+    "[SH0;X1;v2]",
+    "[S-;X1]",
+    "[nH0;X2]",
+    "[NH0;X1;v3]",
+    "[$([N;+0;X3;v3]);!$(N[C,S]=O)]",
+]
 Acceptors = []
 for hba in AcceptorSmarts:
     Acceptors.append(Chem.MolFromSmarts(hba))
 
 StructuralAlertSmarts = [
-    '*1[O,S,N]*1',
-    '[S,C](=[O,S])[F,Br,Cl,I]',
-    '[CX4][Cl,Br,I]',
-    '[C,c]S(=O)(=O)O[C,c]',
-    '[$([CH]),$(CC)]#CC(=O)[C,c]',
-    '[$([CH]),$(CC)]#CC(=O)O[C,c]',
-    'n[OH]',
-    '[$([CH]),$(CC)]#CS(=O)(=O)[C,c]',
-    'C=C(C=O)C=O',
-    'n1c([F,Cl,Br,I])cccc1',
-    '[CH1](=O)',
-    '[O,o][O,o]',
-    '[C;!R]=[N;!R]',
-    '[N!R]=[N!R]',
-    '[#6](=O)[#6](=O)',
-    '[S,s][S,s]',
-    '[N,n][NH2]',
-    'C(=O)N[NH2]',
-    '[C,c]=S',
-    '[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]',
-    'C1(=[O,N])C=CC(=[O,N])C=C1',
-    'C1(=[O,N])C(=[O,N])C=CC=C1',
-    'a21aa3a(aa1aaaa2)aaaa3',
-    'a31a(a2a(aa1)aaaa2)aaaa3',
-    'a1aa2a3a(a1)A=AA=A3=AA=A2',
-    'c1cc([NH2])ccc1',
-    '[Hg,Fe,As,Sb,Zn,Se,se,Te,B,Si,Na,Ca,Ge,Ag,Mg,K,Ba,Sr,Be,Ti,Mo,Mn,Ru,Pd,Ni,Cu,Au,Cd,Al,Ga,Sn,Rh,Tl,Bi,Nb,Li,Pb,Hf,Ho]',
-    'I',
-    'OS(=O)(=O)[O-]',
-    '[N+](=O)[O-]',
-    'C(=O)N[OH]',
-    'C1NC(=O)NC(=O)1',
-    '[SH]',
-    '[S-]',
-    'c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]',
-    'c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]',
-    '[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1',
-    '[CR1]1[CR1][CR1]cc[CR1][CR1]1',
-    '[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1',
-    '[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1',
-    '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
-    '[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1',
-    'C#C',
-    '[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]',
-    '[$([N+R]),$([n+R]),$([N+]=C)][O-]',
-    '[C,c]=N[OH]',
-    '[C,c]=NOC=O',
-    '[C,c](=O)[CX4,CR0X3,O][C,c](=O)',
-    'c1ccc2c(c1)ccc(=O)o2',
-    '[O+,o+,S+,s+]',
-    'N=C=O',
-    '[NX3,NX4][F,Cl,Br,I]',
-    'c1ccccc1OC(=O)[#6]',
-    '[CR0]=[CR0][CR0]=[CR0]',
-    '[C+,c+,C-,c-]',
-    'N=[N+]=[N-]',
-    'C12C(NC(N1)=O)CSC2',
-    'c1c([OH])c([OH,NH2,NH])ccc1',
-    'P',
-    '[N,O,S]C#N',
-    'C=C=O',
-    '[Si][F,Cl,Br,I]',
-    '[SX2]O',
-    '[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)',
-    'O1CCCCC1OC2CCC3CCCCC3C2',
-    'N=[CR0][N,n,O,S]',
-    '[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2',
-    'C=[C!r]C#N',
-    '[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1',
-    '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1',
-    '[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])',
-    '[OH]c1ccc([OH,NH2,NH])cc1',
-    'c1ccccc1OC(=O)O',
-    '[SX2H0][N]',
-    'c12ccccc1(SC(S)=N2)',
-    'c12ccccc1(SC(=S)N2)',
-    'c1nnnn1C=O',
-    's1c(S)nnc1NC=O',
-    'S1C=CSC1=S',
-    'C(=O)Onnn',
-    'OS(=O)(=O)C(F)(F)F',
-    'N#CC[OH]',
-    'N#CC(=O)',
-    'S(=O)(=O)C#N',
-    'N[CH2]C#N',
-    'C1(=O)NCC1',
-    'S(=O)(=O)[O-,OH]',
-    'NC[F,Cl,Br,I]',
-    'C=[C!r]O',
-    '[NX2+0]=[O+0]',
-    '[OR0,NR0][OR0,NR0]',
-    'C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]',
-    '[CX2R0][NX3R0]',
-    'c1ccccc1[C;!R]=[C;!R]c2ccccc2',
-    '[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]',
-    '[s,S,c,C,n,N,o,O]~[n+,N+](~[s,S,c,C,n,N,o,O])(~[s,S,c,C,n,N,o,O])~[s,S,c,C,n,N,o,O]',
-    '[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]',
-    '[*]=[N+]=[*]',
-    '[SX3](=O)[O-,OH]',
-    'N#N',
-    'F.F.F.F',
-    '[R0;D2][R0;D2][R0;D2][R0;D2]',
-    '[cR,CR]~C(=O)NC(=O)~[cR,CR]',
-    'C=!@CC=[O,S]',
-    '[#6,#8,#16][C,c](=O)O[C,c]',
-    'c[C;R0](=[O,S])[C,c]',
-    'c[SX2][C;!R]',
-    'C=C=C',
-    'c1nc([F,Cl,Br,I,S])ncc1',
-    'c1ncnc([F,Cl,Br,I,S])c1',
-    'c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])',
-    '[C,c]S(=O)(=O)c1ccc(cc1)F',
-    '[15N]',
-    '[13C]',
-    '[18O]',
-    '[34S]'
-    ]
+    "*1[O,S,N]*1",
+    "[S,C](=[O,S])[F,Br,Cl,I]",
+    "[CX4][Cl,Br,I]",
+    "[C,c]S(=O)(=O)O[C,c]",
+    "[$([CH]),$(CC)]#CC(=O)[C,c]",
+    "[$([CH]),$(CC)]#CC(=O)O[C,c]",
+    "n[OH]",
+    "[$([CH]),$(CC)]#CS(=O)(=O)[C,c]",
+    "C=C(C=O)C=O",
+    "n1c([F,Cl,Br,I])cccc1",
+    "[CH1](=O)",
+    "[O,o][O,o]",
+    "[C;!R]=[N;!R]",
+    "[N!R]=[N!R]",
+    "[#6](=O)[#6](=O)",
+    "[S,s][S,s]",
+    "[N,n][NH2]",
+    "C(=O)N[NH2]",
+    "[C,c]=S",
+    "[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]=[$([CH2]),$([CH][CX4]),$(C([CX4])[CX4])]",
+    "C1(=[O,N])C=CC(=[O,N])C=C1",
+    "C1(=[O,N])C(=[O,N])C=CC=C1",
+    "a21aa3a(aa1aaaa2)aaaa3",
+    "a31a(a2a(aa1)aaaa2)aaaa3",
+    "a1aa2a3a(a1)A=AA=A3=AA=A2",
+    "c1cc([NH2])ccc1",
+    "[Hg,Fe,As,Sb,Zn,Se,se,Te,B,Si,Na,Ca,Ge,Ag,Mg,K,Ba,Sr,Be,Ti,Mo,Mn,Ru,Pd,Ni,Cu,Au,Cd,Al,Ga,Sn,Rh,Tl,Bi,Nb,Li,Pb,Hf,Ho]",
+    "I",
+    "OS(=O)(=O)[O-]",
+    "[N+](=O)[O-]",
+    "C(=O)N[OH]",
+    "C1NC(=O)NC(=O)1",
+    "[SH]",
+    "[S-]",
+    "c1ccc([Cl,Br,I,F])c([Cl,Br,I,F])c1[Cl,Br,I,F]",
+    "c1cc([Cl,Br,I,F])cc([Cl,Br,I,F])c1[Cl,Br,I,F]",
+    "[CR1]1[CR1][CR1][CR1][CR1][CR1][CR1]1",
+    "[CR1]1[CR1][CR1]cc[CR1][CR1]1",
+    "[CR2]1[CR2][CR2][CR2][CR2][CR2][CR2][CR2]1",
+    "[CR2]1[CR2][CR2]cc[CR2][CR2][CR2]1",
+    "[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1",
+    "[CH2R2]1N[CH2R2][CH2R2][CH2R2][CH2R2][CH2R2][CH2R2]1",
+    "C#C",
+    "[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]@[CR2]@[CR2]@[OR2,NR2]",
+    "[$([N+R]),$([n+R]),$([N+]=C)][O-]",
+    "[C,c]=N[OH]",
+    "[C,c]=NOC=O",
+    "[C,c](=O)[CX4,CR0X3,O][C,c](=O)",
+    "c1ccc2c(c1)ccc(=O)o2",
+    "[O+,o+,S+,s+]",
+    "N=C=O",
+    "[NX3,NX4][F,Cl,Br,I]",
+    "c1ccccc1OC(=O)[#6]",
+    "[CR0]=[CR0][CR0]=[CR0]",
+    "[C+,c+,C-,c-]",
+    "N=[N+]=[N-]",
+    "C12C(NC(N1)=O)CSC2",
+    "c1c([OH])c([OH,NH2,NH])ccc1",
+    "P",
+    "[N,O,S]C#N",
+    "C=C=O",
+    "[Si][F,Cl,Br,I]",
+    "[SX2]O",
+    "[SiR0,CR0](c1ccccc1)(c2ccccc2)(c3ccccc3)",
+    "O1CCCCC1OC2CCC3CCCCC3C2",
+    "N=[CR0][N,n,O,S]",
+    "[cR2]1[cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2][cR2]1[cR2]2[cR2][cR2][cR2]([Nv3X3,Nv4X4])[cR2][cR2]2",
+    "C=[C!r]C#N",
+    "[cR2]1[cR2]c([N+0X3R0,nX3R0])c([N+0X3R0,nX3R0])[cR2][cR2]1",
+    "[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2]c([N+0X3R0,nX3R0])[cR2]1",
+    "[cR2]1[cR2]c([N+0X3R0,nX3R0])[cR2][cR2]c1([N+0X3R0,nX3R0])",
+    "[OH]c1ccc([OH,NH2,NH])cc1",
+    "c1ccccc1OC(=O)O",
+    "[SX2H0][N]",
+    "c12ccccc1(SC(S)=N2)",
+    "c12ccccc1(SC(=S)N2)",
+    "c1nnnn1C=O",
+    "s1c(S)nnc1NC=O",
+    "S1C=CSC1=S",
+    "C(=O)Onnn",
+    "OS(=O)(=O)C(F)(F)F",
+    "N#CC[OH]",
+    "N#CC(=O)",
+    "S(=O)(=O)C#N",
+    "N[CH2]C#N",
+    "C1(=O)NCC1",
+    "S(=O)(=O)[O-,OH]",
+    "NC[F,Cl,Br,I]",
+    "C=[C!r]O",
+    "[NX2+0]=[O+0]",
+    "[OR0,NR0][OR0,NR0]",
+    "C(=O)O[C,H1].C(=O)O[C,H1].C(=O)O[C,H1]",
+    "[CX2R0][NX3R0]",
+    "c1ccccc1[C;!R]=[C;!R]c2ccccc2",
+    "[NX3R0,NX4R0,OR0,SX2R0][CX4][NX3R0,NX4R0,OR0,SX2R0]",
+    "[s,S,c,C,n,N,o,O]~[n+,N+](~[s,S,c,C,n,N,o,O])(~[s,S,c,C,n,N,o,O])~[s,S,c,C,n,N,o,O]",
+    "[s,S,c,C,n,N,o,O]~[nX3+,NX3+](~[s,S,c,C,n,N])~[s,S,c,C,n,N]",
+    "[*]=[N+]=[*]",
+    "[SX3](=O)[O-,OH]",
+    "N#N",
+    "F.F.F.F",
+    "[R0;D2][R0;D2][R0;D2][R0;D2]",
+    "[cR,CR]~C(=O)NC(=O)~[cR,CR]",
+    "C=!@CC=[O,S]",
+    "[#6,#8,#16][C,c](=O)O[C,c]",
+    "c[C;R0](=[O,S])[C,c]",
+    "c[SX2][C;!R]",
+    "C=C=C",
+    "c1nc([F,Cl,Br,I,S])ncc1",
+    "c1ncnc([F,Cl,Br,I,S])c1",
+    "c1nc(c2c(n1)nc(n2)[F,Cl,Br,I])",
+    "[C,c]S(=O)(=O)c1ccc(cc1)F",
+    "[15N]",
+    "[13C]",
+    "[18O]",
+    "[34S]",
+]
 
 StructuralAlerts = []
 for smarts in StructuralAlertSmarts:
@@ -200,26 +205,167 @@
 #     rows[8]:     MW, ALOGP, HBA, HBD, PSA, ROTB, AROM, ALERTS
 #     columns[7]: A, B, C, D, E, F, DMAX
 # ALOGP parameters from Gregory Gerebtzoff (2012, Roche)
-pads1 = [    [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
-            [0.486849448, 186.2293718, 2.066177165, 3.902720615, 1.027025453, 0.913012565, 145.4314800],
-            [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],    
-            [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
-            [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
-            [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
-            [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
-            [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140]        ]
+pads1 = [
+    [
+        2.817065973,
+        392.5754953,
+        290.7489764,
+        2.419764353,
+        49.22325677,
+        65.37051707,
+        104.9805561,
+    ],
+    [
+        0.486849448,
+        186.2293718,
+        2.066177165,
+        3.902720615,
+        1.027025453,
+        0.913012565,
+        145.4314800,
+    ],
+    [
+        2.948620388,
+        160.4605972,
+        3.615294657,
+        4.435986202,
+        0.290141953,
+        1.300669958,
+        148.7763046,
+    ],
+    [
+        1.618662227,
+        1010.051101,
+        0.985094388,
+        0.000000001,
+        0.713820843,
+        0.920922555,
+        258.1632616,
+    ],
+    [
+        1.876861559,
+        125.2232657,
+        62.90773554,
+        87.83366614,
+        12.01999824,
+        28.51324732,
+        104.5686167,
+    ],
+    [
+        0.010000000,
+        272.4121427,
+        2.558379970,
+        1.565547684,
+        1.271567166,
+        2.758063707,
+        105.4420403,
+    ],
+    [
+        3.217788970,
+        957.7374108,
+        2.274627939,
+        0.000000001,
+        1.317690384,
+        0.375760881,
+        312.3372610,
+    ],
+    [
+        0.010000000,
+        1199.094025,
+        -0.09002883,
+        0.000000001,
+        0.185904477,
+        0.875193782,
+        417.7253140,
+    ],
+]
 # ALOGP parameters from the original publication
-pads2 = [    [2.817065973, 392.5754953, 290.7489764, 2.419764353, 49.22325677, 65.37051707, 104.9805561],
-            [3.172690585, 137.8624751, 2.534937431, 4.581497897, 0.822739154, 0.576295591, 131.3186604],
-            [2.948620388, 160.4605972, 3.615294657, 4.435986202, 0.290141953, 1.300669958, 148.7763046],    
-            [1.618662227, 1010.051101, 0.985094388, 0.000000001, 0.713820843, 0.920922555, 258.1632616],
-            [1.876861559, 125.2232657, 62.90773554, 87.83366614, 12.01999824, 28.51324732, 104.5686167],
-            [0.010000000, 272.4121427, 2.558379970, 1.565547684, 1.271567166, 2.758063707, 105.4420403],
-            [3.217788970, 957.7374108, 2.274627939, 0.000000001, 1.317690384, 0.375760881, 312.3372610],
-            [0.010000000, 1199.094025, -0.09002883, 0.000000001, 0.185904477, 0.875193782, 417.7253140]        ]
+pads2 = [
+    [
+        2.817065973,
+        392.5754953,
+        290.7489764,
+        2.419764353,
+        49.22325677,
+        65.37051707,
+        104.9805561,
+    ],
+    [
+        3.172690585,
+        137.8624751,
+        2.534937431,
+        4.581497897,
+        0.822739154,
+        0.576295591,
+        131.3186604,
+    ],
+    [
+        2.948620388,
+        160.4605972,
+        3.615294657,
+        4.435986202,
+        0.290141953,
+        1.300669958,
+        148.7763046,
+    ],
+    [
+        1.618662227,
+        1010.051101,
+        0.985094388,
+        0.000000001,
+        0.713820843,
+        0.920922555,
+        258.1632616,
+    ],
+    [
+        1.876861559,
+        125.2232657,
+        62.90773554,
+        87.83366614,
+        12.01999824,
+        28.51324732,
+        104.5686167,
+    ],
+    [
+        0.010000000,
+        272.4121427,
+        2.558379970,
+        1.565547684,
+        1.271567166,
+        2.758063707,
+        105.4420403,
+    ],
+    [
+        3.217788970,
+        957.7374108,
+        2.274627939,
+        0.000000001,
+        1.317690384,
+        0.375760881,
+        312.3372610,
+    ],
+    [
+        0.010000000,
+        1199.094025,
+        -0.09002883,
+        0.000000001,
+        0.185904477,
+        0.875193782,
+        417.7253140,
+    ],
+]
+
 
 def ads(x, a, b, c, d, e, f, dmax):
-    return ((a+(b/(1+exp(-1*(x-c+d/2)/e))*(1-1/(1+exp(-1*(x-c-d/2)/f))))) / dmax)
+    return (
+        a
+        + (
+            b
+            / (1 + exp(-1 * (x - c + d / 2) / e))
+            * (1 - 1 / (1 + exp(-1 * (x - c - d / 2) / f)))
+        )
+    ) / dmax
+
 
 def properties(mol):
     """
@@ -227,25 +373,26 @@
     """
     matches = []
     if mol is None:
-        raise WrongArgument("properties(mol)", "mol argument is \'None\'")
+        raise WrongArgument("properties(mol)", "mol argument is 'None'")
     x = [0] * 9
-    x[0] = Descriptors.MolWt(mol)                                                # MW 
-    x[1] = Descriptors.MolLogP(mol)                                                # ALOGP
-    for hba in Acceptors:                                                        # HBA
+    x[0] = Descriptors.MolWt(mol)  # MW
+    x[1] = Descriptors.MolLogP(mol)  # ALOGP
+    for hba in Acceptors:  # HBA
         if mol.HasSubstructMatch(hba):
             matches = mol.GetSubstructMatches(hba)
             x[2] += len(matches)
-    x[3] = Descriptors.NumHDonors(mol)                                            # HBD
-    x[4] = Descriptors.TPSA(mol)                                                # PSA
-    x[5] = Descriptors.NumRotatableBonds(mol)                                    # ROTB
-    x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings))    # AROM
-    for alert in StructuralAlerts:                                                # ALERTS
-        if (mol.HasSubstructMatch(alert)): x[7] += 1
+    x[3] = Descriptors.NumHDonors(mol)  # HBD
+    x[4] = Descriptors.TPSA(mol)  # PSA
+    x[5] = Descriptors.NumRotatableBonds(mol)  # ROTB
+    x[6] = Chem.GetSSSR(Chem.DeleteSubstructs(deepcopy(mol), AliphaticRings))  # AROM
+    for alert in StructuralAlerts:  # ALERTS
+        if mol.HasSubstructMatch(alert):
+            x[7] += 1
     ro5_failed = 0
     if x[3] > 5:
-        ro5_failed += 1 #HBD
+        ro5_failed += 1  # HBD
     if x[2] > 10:
-        ro5_failed += 1 #HBA
+        ro5_failed += 1  # HBA
     if x[0] >= 500:
         ro5_failed += 1
     if x[1] > 5:
@@ -258,17 +405,35 @@
     d = [0.00] * 8
     if gerebtzoff:
         for i in range(0, 8):
-            d[i] = ads(p[i], pads1[i][0], pads1[i][1], pads1[i][2], pads1[i][3], pads1[i][4], pads1[i][5], pads1[i][6])
+            d[i] = ads(
+                p[i],
+                pads1[i][0],
+                pads1[i][1],
+                pads1[i][2],
+                pads1[i][3],
+                pads1[i][4],
+                pads1[i][5],
+                pads1[i][6],
+            )
     else:
         for i in range(0, 8):
-            d[i] = ads(p[i], pads2[i][0], pads2[i][1], pads2[i][2], pads2[i][3], pads2[i][4], pads2[i][5], pads2[i][6])
+            d[i] = ads(
+                p[i],
+                pads2[i][0],
+                pads2[i][1],
+                pads2[i][2],
+                pads2[i][3],
+                pads2[i][4],
+                pads2[i][5],
+                pads2[i][6],
+            )
     t = 0.0
     for i in range(0, 8):
         t += w[i] * log(d[i])
-    return (exp(t / sum(w)))
+    return exp(t / sum(w))
 
 
-def weights_max(mol, gerebtzoff = True, props = False):
+def weights_max(mol, gerebtzoff=True, props=False):
     """
     Calculates the QED descriptor using maximal descriptor weights.
     If props is specified we skip the calculation step and use the props-list of properties.
@@ -278,7 +443,7 @@
     return qed([0.50, 0.25, 0.00, 0.50, 0.00, 0.50, 0.25, 1.00], props, gerebtzoff)
 
 
-def weights_mean(mol, gerebtzoff = True, props = False):
+def weights_mean(mol, gerebtzoff=True, props=False):
     """
     Calculates the QED descriptor using average descriptor weights.
     If props is specified we skip the calculation step and use the props-list of properties.
@@ -288,7 +453,7 @@
     return qed([0.66, 0.46, 0.05, 0.61, 0.06, 0.65, 0.48, 0.95], props, gerebtzoff)
 
 
-def weights_none(mol, gerebtzoff = True, props = False):
+def weights_none(mol, gerebtzoff=True, props=False):
     """
     Calculates the QED descriptor using unit weights.
     If props is specified we skip the calculation step and use the props-list of properties.
@@ -298,7 +463,7 @@
     return qed([1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00], props, gerebtzoff)
 
 
-def default(mol, gerebtzoff = True):
+def default(mol, gerebtzoff=True):
     """
     Calculates the QED descriptor using average descriptor weights and Gregory Gerebtzoff parameters.
     """
@@ -307,23 +472,34 @@
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('-i', '--input', 
-                required=True, 
-                help='path to the input file name')
-    parser.add_argument("-m", "--method", 
-                dest="method",
-                choices=['max', 'mean', 'unweighted'],
-                default="mean",
-                help="Specify the method you want to use.")
-    parser.add_argument("--iformat",
-                help="Input format. It must be supported by openbabel.")
-    parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), 
-                default=sys.stdout, 
-                help="path to the result file, default it sdtout")
-    parser.add_argument("--header", dest="header", action="store_true",
-                default=False,
-                help="Write header line.")
-
+    parser.add_argument(
+        "-i", "--input", required=True, help="path to the input file name"
+    )
+    parser.add_argument(
+        "-m",
+        "--method",
+        dest="method",
+        choices=["max", "mean", "unweighted"],
+        default="mean",
+        help="Specify the method you want to use.",
+    )
+    parser.add_argument(
+        "--iformat", help="Input format. It must be supported by openbabel."
+    )
+    parser.add_argument(
+        "-o",
+        "--outfile",
+        type=argparse.FileType("w+"),
+        default=sys.stdout,
+        help="path to the result file, default it sdtout",
+    )
+    parser.add_argument(
+        "--header",
+        dest="header",
+        action="store_true",
+        default=False,
+        help="Write header line.",
+    )
 
     args = parser.parse_args()
 
@@ -343,86 +519,99 @@
         # try to guess the filetype
         filetype = check_filetype(ifile)
     else:
-        filetype = args.iformat # sdf or smi
-
+        filetype = args.iformat  # sdf or smi
 
     """
         We want to store the original SMILES in the output. So in case of a SMILES file iterate over the file and convert each line separate.
     """
-    if filetype == 'sdf':
+    if filetype == "sdf":
         supplier = Chem.SDMolSupplier(ifile)
         # Process file
         if args.header:
-            args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n")
+            args.outfile.write(
+                "MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\n"
+            )
         count = 0
         for mol in supplier:
             count += 1
             if mol is None:
-                print("Warning: skipping molecule ", count, " and continuing with next.")
+                print(
+                    "Warning: skipping molecule ", count, " and continuing with next."
+                )
                 continue
             props = properties(mol)
 
-            if args.method == 'max':
+            if args.method == "max":
                 calc_qed = weights_max(mol, True, props)
-            elif args.method == 'unweighted':
+            elif args.method == "unweighted":
                 calc_qed = weights_none(mol, True, props)
             else:
                 calc_qed = weights_mean(mol, True, props)
 
-            args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n" % (
-                props[0], 
-                props[1], 
-                props[2], 
-                props[3], 
-                props[4], 
-                props[5], 
-                props[6], 
-                props[7],
-                props[8],
-                calc_qed,
-                mol.GetProp("_Name"),
-                ))
-    elif filetype == 'smi':
-        supplier = Chem.SmilesMolSupplier( ifile, " \t", 0, 1, False, True )
+            args.outfile.write(
+                "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\n"
+                % (
+                    props[0],
+                    props[1],
+                    props[2],
+                    props[3],
+                    props[4],
+                    props[5],
+                    props[6],
+                    props[7],
+                    props[8],
+                    calc_qed,
+                    mol.GetProp("_Name"),
+                )
+            )
+    elif filetype == "smi":
+        supplier = Chem.SmilesMolSupplier(ifile, " \t", 0, 1, False, True)
 
         # Process file
         if args.header:
-            args.outfile.write("MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n")
+            args.outfile.write(
+                "MW\tALOGP\tHBA\tHBD\tPSA\tROTB\tAROM\tALERTS\tLRo5\tQED\tNAME\tSMILES\n"
+            )
         count = 0
         for line in open(ifile):
-            tokens = line.strip().split('\t')
+            tokens = line.strip().split("\t")
             if len(tokens) > 1:
                 smiles, title = tokens
             else:
                 smiles = tokens[0]
-                title = ''
+                title = ""
             mol = Chem.MolFromSmiles(smiles)
             count += 1
             if mol is None:
-                print("Warning: skipping molecule ", count, " and continuing with next.")
+                print(
+                    "Warning: skipping molecule ", count, " and continuing with next."
+                )
                 continue
             props = properties(mol)
 
-            if args.method == 'max':
+            if args.method == "max":
                 calc_qed = weights_max(mol, True, props)
-            elif args.method == 'unweighted':
+            elif args.method == "unweighted":
                 calc_qed = weights_none(mol, True, props)
             else:
                 calc_qed = weights_mean(mol, True, props)
 
-            args.outfile.write( "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n" % (
-                props[0], 
-                props[1], 
-                props[2], 
-                props[3], 
-                props[4], 
-                props[5], 
-                props[6], 
-                props[7],
-                props[8],
-                calc_qed,
-                title,
-                smiles
-                ))
+            args.outfile.write(
+                "%.2f\t%.3f\t%d\t%d\t%.2f\t%d\t%d\t%d\t%s\t%.3f\t%-s\t%s\n"
+                % (
+                    props[0],
+                    props[1],
+                    props[2],
+                    props[3],
+                    props[4],
+                    props[5],
+                    props[6],
+                    props[7],
+                    props[8],
+                    calc_qed,
+                    title,
+                    smiles,
+                )
+            )
     else:
         sys.exit("Error: unknown file-type: %s" % filetype)