Python_scripts/canonicalization.py at master · NP-Plug-and-Play-Scripts/Python_scripts · GitHub

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#!/usr/bin/env python3
import rdkit.Chem as Chem
import rdkit.Chem.AllChem as AllChem

class SmilesFixer():
	'''
	This class stores RDKit reactions which help turn molecules with
	weird representations into ones with common ones (so they will match
	a template)
	'''
	def __init__(self):
		self.rxns = [
			# Double bonds on aromatic rings (dist 1)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][nH:3]>>[NH:1][a:2][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][nH:3]>>[NH2:1][a:2][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][nH:3]>>[OH:1][a:2][nH0:3]'),
			# Double bonds on aromatic rings (dist 2)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][a:4][nH:3]>>[NH:1][a:2][a:4][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][a:4][nH:3]>>[NH2:1][a:2][a:4][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][a:4][nH:3]>>[OH:1][a:2][a:4][nH0:3]'),
			# Double bonds on aromatic rings (dist 2)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][a:4][a:5][nH:3]>>[NH:1][a:2][a:4][a:5][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][a:4][a:5][nH:3]>>[NH2:1][a:2][a:4][a:5][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][a:4][a:5][nH:3]>>[OH:1][a:2][a:4][a:5][nH0:3]'),
			# Iminol / amide
			AllChem.ReactionFromSmarts('[NH0:1]=[C:2]-[OH:3]>>[NH1:1]-[C:2]=[OH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[C:2]-[OH:3]>>[NH2:1]-[C:2]=[OH0:3]'),
			# Thiourea
			AllChem.ReactionFromSmarts('[NH0:1]=[C:2]-[SH:3]>>[NH1:1]-[C:2]=[SH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[C:2]-[SH:3]>>[NH2:1]-[C:2]=[SH0:3]'),
			# Azide
			AllChem.ReactionFromSmarts('[NH0:1][NH0:2]=[NH0;-:3]>>[NH0;-:1]=[NH0;+:2]=[NH0;-:3]'),
			# Cyanide salts
			AllChem.ReactionFromSmarts('([K,Na;H1:1].[C;X1;H0:2]#[N:3])>>[*;H0:1][*:2]#[N:3]'),
			AllChem.ReactionFromSmarts('([Cu:1].[C;X1;H0:2]#[N:3])>>[*:1][*:2]#[N:3]'),
			# Grinards
			AllChem.ReactionFromSmarts('([MgH+:1].[C;v3:2][*:3])>>[Mg+:1][*:2][*:3]'),
			# Coordinated tin
			AllChem.ReactionFromSmarts('([SnH4:1].[C;v3:2].[C;v3:3].[C;v3:4].[C;v3:5])>>[Sn:1]([*:2])([*:3])([*:4])[*:5]'),
			AllChem.ReactionFromSmarts('([SnH3:1].[C;v3:2].[C;v3:3].[C;v3:4])>>[Sn:1]([*:2])([*:3])[*:4]'),
			AllChem.ReactionFromSmarts('([SnH2:1].[C;v3:2].[C;v3:3])>>[Sn:1]([*:2])[*:3]'),
			AllChem.ReactionFromSmarts('([SnH1:1].[C;v3:2])>>[Sn:1][*:2]'),
		]
	"""accepts 1 smile string and a boolean indicating if should remove the molecules atoms or not."""
	def fix_smiles(self, old_smiles, removeMap = True):
		'''
		For a given SMILES string, this function "fixes" common mistakes
		found in the Lowe parsed database:
		- N=c[nH] structures are turned into the normal [NH]-c[n] forms
		- iminols are turned into amides/carbamates
		It applies the reactions in self.rxns until the SMILES string doesn't change
		'''
		# Should we use stereochemistry? used to be in a seperat
		USE_STEREOCHEMISTRY = False
		mol = Chem.MolFromSmiles(old_smiles)
		if removeMap: [x.ClearProp('molAtomMapNumber') for x in mol.GetAtoms()]
		if not mol:
			return old_smiles

		new_smiles = Chem.MolToSmiles(mol, isomericSmiles = USE_STEREOCHEMISTRY)
		old_smiles = ''
		while new_smiles != old_smiles:
			old_smiles = new_smiles
			for rxn in self.rxns:
				outcomes = rxn.RunReactants((mol,))
				if not outcomes:
					continue
				else:
					mol = outcomes[0][0]
					Chem.SanitizeMol(mol)
					new_smiles = Chem.MolToSmiles(mol, isomericSmiles = USE_STEREOCHEMISTRY)
		return new_smiles