#!/usr/bin/python
# encoding: utf-8

#	Jan 2011	(markus kossner)	Cleaned up the code, added some documentation
#	somwhere around Aug 2008	(markus kossner)	created
#    
#    This script extracts the molecular framework for a database of molecules.
#    You can use two modes (hard coded): 
#    - Scaff:	The molecular frame is extracted
#    - RedScaff:	All linking chains between rings are deleted. The rings are directly connected.
#    
#    You can comment in/out the code snippets indicated by the comments 
#    to force each atom of the frame to be a Carbon.
#    
#    Usage: Frames.py <database.sdf>
#    Output: 
#    - sd files containing all molecules belonging to one frame (1.sdf, 2.sdf etc)
#    - frames.smi containing the (caninical) smiles and count of occurrence
#
from __future__ import print_function

import os,sys
from Chem import AllChem as Chem

def flatten(x):
    """flatten(sequence) -> list
    Returns a single, flat list which contains all elements retrieved
    from the sequence and all nested sub-sequences (iterables).
    Examples:
    >>> [1, 2, [3,4], (5,6)]
    [1, 2, [3, 4], (5, 6)]
    >>> flatten([[[1,2,3], (42,None)], [4,5], [6], 7, MyVector(8,9,10)])
    [1, 2, 3, 42, None, 4, 5, 6, 7, 8, 9, 10]"""
    result = []
    for el in x:
        if hasattr(el, "__iter__") and not isinstance(el, basestring):
            result.extend(flatten(el))
        else:
            result.append(el)
    return result


def GetFrame(mol, mode='Scaff'):
	'''return a ganeric molecule defining the reduced scaffold of the input mol.
	mode can be 'Scaff' or 'RedScaff':
	
	Scaff	->	chop off the side chains and return the scaffold
	
	RedScaff	->	remove all linking chains and connect the rings 
	directly at the atoms where the linker was
	'''
	
	ring = mol.GetRingInfo()
	RingAtoms = flatten(ring.AtomRings())
	NonRingAtoms = [ atom.GetIdx() for atom in mol.GetAtoms() if atom.GetIdx() not in RingAtoms ]
	RingNeighbors = []
	Paths = []
	for NonRingAtom in NonRingAtoms:
		for neighbor in mol.GetAtomWithIdx(NonRingAtom).GetNeighbors():
			if neighbor.GetIdx() in RingAtoms:
				RingNeighbors.append(NonRingAtom)
				Paths.append([neighbor.GetIdx(),NonRingAtom]) #The ring Atoms having a non ring Nieghbor will be the start of a walk
				break
	PosConnectors = [x for x in NonRingAtoms if x not in RingNeighbors] #Only these Atoms are potential starting points of a Linker chain
	#print 'PosConnectors:'
	#print PosConnectors	
	Framework = [ x for x in RingAtoms ]
	#Start a list of pathways which we will have to walk 
	#print 'Path atoms:'
	#print Paths
	Linkers = []
	while len(Paths)>0:
		NewPaths = []
		for P in Paths:
			if P == None:
				print('ooh')
			else:
				for neighbor in mol.GetAtomWithIdx(P[-1]).GetNeighbors():
					if neighbor.GetIdx() not in P:
						if neighbor.GetIdx() in NonRingAtoms:
							n = P[:]
							n.append(neighbor.GetIdx())
							NewPaths.append(n[:])
						elif neighbor.GetIdx() in RingAtoms:
							#print 'adding the following path to Framework:'
							#print P
							n = P[:]
							n.append(neighbor.GetIdx())
							Linkers.append(n)
							Framework=Framework+P[:]

		Paths = NewPaths[:]
	#print 'Linkers:',Linkers
	#print 'RingAtoms:',RingAtoms
	#em.AddBond(3,4,Chem.BondType.SINGLE)
	if mode == 'RedScaff':
		Framework = list(set(Framework))
		todel = []
		NonRingAtoms.sort(reverse=True)
		em = Chem.EditableMol(mol)
		BondsToAdd = [ sorted([i[0],i[-1]]) for i in Linkers ]
		mem = []
		for i in BondsToAdd:
			if i not in mem:
				em.AddBond(i[0],i[1],Chem.BondType.SINGLE)
				mem.append(i)
		for i in NonRingAtoms:
			todel.append(i)
		for i in todel:
			em.RemoveAtom(i)
		m = em.GetMol()
		#===================================#
		#  Now do the flattening of atoms and bonds!
		#  Any heavy atom will become a carbon and any bond will become a single bond!	#
		#===================================#
#		for atom in m.GetAtoms():                                                 #
#			atom.SetAtomicNum(6)                                                    #
#			atom.SetFormalCharge(0)                                                #
#		for bond in m.GetBonds():                                                   #
#			bond.SetBondType(Chem.BondType.SINGLE)                 #
#		Chem.SanitizeMol(m)                                                          #
		#===================================#
		return m

	if mode == 'Scaff':
		Framework = list(set(Framework))
		todel = []
		NonRingAtoms.sort(reverse=True)
		for i in NonRingAtoms:
			if i != None:
				if i not in Framework:
					todel.append(i)
		em = Chem.EditableMol(mol)
		for i in todel:
			em.RemoveAtom(i)
		m = em.GetMol()
		#===================================#
		#  Now do the flattening of atoms and bonds!
		#  Any heavy atom will become a carbon and any bond will become a single bond!!		#
		#===================================#
#		for atom in m.GetAtoms():                                                 #
#			atom.SetAtomicNum(6)                                                    #
#			atom.SetFormalCharge(0)                                                #
#		for bond in m.GetBonds():                                                   #
#			bond.SetBondType(Chem.BondType.SINGLE)                 #
#		Chem.SanitizeMol(m)                                                          #
		#===================================#
		return m

if __name__=='__main__':
	if len(sys.argv) < 2:
		print("No input file provided: Frames.py filetosprocess.ext")
		sys.exit(1)


	suppl = Chem.SDMolSupplier(sys.argv[1])
	FrameDict = {}

	for mol in suppl:
		m = GetFrame(mol)
		cansmiles = Chem.MolToSmiles(m, isomericSmiles=True)
		if FrameDict.has_key(cansmiles):
			FrameDict[cansmiles].append(mol)
		else:
			FrameDict[cansmiles]=[mol,]

	counter=0
	w=open('frames.smi','w')
	for key,item in FrameDict.items():
		counter+=1
		d=Chem.SDWriter(str(counter)+'.sdf')
		for i in item:
			i.SetProp('Scaffold',key)
			i.SetProp('Cluster',str(counter))
			d.write(i)
		print(key,len(item))
		w.write(key+'\t'+str(len(item))+'\n')
	w.close
	print('number of Clusters: %d' %(counter))
