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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Aug 17 16:54:12 2019
@author: [email protected]
@calculate ErG fps, more info: https://pubs.acs.org/doi/full/10.1021/ci050457y#
"""
_type = 'Pharmacophore-based'
import numpy as np
from rdkit.Chem import AllChem
## get info from : https://github.com/rdkit/rdkit/blob/d41752d558bf7200ab67b98cdd9e37f1bdd378de/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp
Donor = ["[N;!H0;v3,v4&+1]", "[O,S;H1;+0]", "[n&H1&+0]"]
Acceptor = ["[O,S;H1;v2;!$(*-*=[O,N,P,S])]", "[O;H0;v2]", "[O,S;v1;-]",
"[N;v3;!$(N-*=[O,N,P,S])]", "[n&H0&+0]", "[o;+0;!$([o]:n);!$([o]:c:n)]"]
Positive = ["[#7;+]", "[N;H2&+0][$([C,a]);!$([C,a](=O))]",
"[N;H1&+0]([$([C,a]);!$([C,a](=O))])[$([C,a]);!$([C,a](=O))]",
"[N;H0&+0]([C;!$(C(=O))])([C;!$(C(=O))])[C;!$(C(=O))]"]
Negative = ["[C,S](=[O,S,P])-[O;H1,-1]"]
Hydrophobic = ["[C;D3,D4](-[CH3])-[CH3]", "[S;D2](-C)-C"]
Aromatic = ["a"]
PROPERTY_KEY = ["Donor", "Acceptor", "Positive", "Negative", "Hydrophobic", "Aromatic"]
def GetPharmacoErGFPs(mol, fuzzIncrement=0.3, maxPath=21, binary=True, return_bitInfo=False):
'''
https://pubs.acs.org/doi/full/10.1021/ci050457y#
return maxPath*21 bits
size(v) = (n(n + 1)/2) * (maxDist - minDist + 1)
'''
minPath = 1
arr = AllChem.GetErGFingerprint(mol, fuzzIncrement=fuzzIncrement, maxPath=maxPath, minPath=minPath)
arr = arr.astype(np.float32)
if binary:
arr = arr.astype(np.bool_)
if return_bitInfo:
bitInfo = []
for i in range(len(PROPERTY_KEY)):
for j in range(i, len(PROPERTY_KEY)):
for path in range(minPath, maxPath + 1):
triplet = (PROPERTY_KEY[i], PROPERTY_KEY[j], path)
bitInfo.append(triplet)
return arr, bitInfo
return arr
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