Ifg contribution (#1813)

* ifg contribution

* ifg python file

* Delete settings.json

* Update README

Contrib/IFG/README

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+IFG Algorithm.
+
+Implementation of
+
+    An algorithm to identify functional groups in organic molecules
+    Peter Ertl
+
+    https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0225-z
+
+
+Authors:
+    Richard Hall,
+    Guillaume Godin modified function output to be more readable
+
+
+    Usage:
+    ```python
+        # return the list of IFG (atomIds, atoms & type) for a molecule object:
+        m = Chem.MolFromSmiles(smiles)
+        fgs = identify_functional_groups(m)
+        print fgs
+    ```
+    Output example:
+        [IFG(atomIds=(2,), atoms='n', type='cnc'),
+         IFG(atomIds=(4, 5, 6, 7), atoms='NS(=O)=O', type='cNS(c)(=O)=O'),
+         IFG(atomIds=(12,), atoms='N', type='cN'),
+         IFG(atomIds=(15,), atoms='n', type='cnc')]
+
+Notes:
+
+This implementation of Ertl paper was made by Richard Hall in summer 2017.
+Cause RDKit and Peter tool can have distinct aromaticity dectection behaviours, list
+of functionnal groups in aromatic rings may differ in presence of conjugated aromatics rings.

Contrib/IFG/ifg.py

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+# Richard hall 2017
+# IFG main code
+# Guillaume Godin 2017
+# refine output function
+# astex_ifg: identify functional groups a la Ertl, J. Cheminform (2017) 9:36
+from rdkit import Chem
+from collections import namedtuple
+
+def merge(mol, marked, aset):
+    bset = set()
+    for idx in aset:
+        atom = mol.GetAtomWithIdx(idx)
+        for nbr in atom.GetNeighbors():
+            jdx = nbr.GetIdx()
+            if jdx in marked:
+                marked.remove(jdx)
+                bset.add(jdx)
+    if not bset:
+        return
+    merge(mol, marked, bset)
+    aset.update(bset)
+
+# atoms connected by non-aromatic double or triple bond to any heteroatom
+# c=O should not match (see fig1, box 15).  I think using A instead of * should sort that out?
+PATT_DOUBLE_TRIPLE = Chem.MolFromSmarts('A=,#[!#6]')
+# atoms in non aromatic carbon-carbon double or triple bonds
+PATT_CC_DOUBLE_TRIPLE = Chem.MolFromSmarts('C=,#C')
+# acetal carbons, i.e. sp3 carbons connected to tow or more oxygens, nitrogens or sulfurs; these O, N or S atoms must have only single bonds
+PATT_ACETAL = Chem.MolFromSmarts('[CX4](-[O,N,S])-[O,N,S]')
+# all atoms in oxirane, aziridine and thiirane rings
+PATT_OXIRANE_ETC = Chem.MolFromSmarts('[O,N,S]1CC1')
+
+PATT_TUPLE = (PATT_DOUBLE_TRIPLE, PATT_CC_DOUBLE_TRIPLE, PATT_ACETAL, PATT_OXIRANE_ETC)
+
+def identify_functional_groups(mol):
+    marked = set()
+#mark all heteroatoms in a molecule, including halogens
+    for atom in mol.GetAtoms():
+        if atom.GetAtomicNum() not in (6,1): # would we ever have hydrogen?
+            marked.add(atom.GetIdx())
+
+#mark the four specific types of carbon atom
+    for patt in PATT_TUPLE:
+        for path in mol.GetSubstructMatches(patt):
+            for atomindex in path:
+                marked.add(atomindex)
+
+#merge all connected marked atoms to a single FG
+    groups = []
+    while marked:
+        grp = set([marked.pop()])
+        merge(mol, marked, grp)
+        groups.append(grp)
+
+#extract also connected unmarked carbon atoms
+    ifg = namedtuple('IFG', ['atomIds', 'atoms', 'type'])
+    ifgs = []
+    for g in groups:
+        uca = set()
+        for atomidx in g:
+            for n in mol.GetAtomWithIdx(atomidx).GetNeighbors():
+                if n.GetAtomicNum() == 6:
+                    uca.add(n.GetIdx())
+        ifgs.append(ifg(atomIds=tuple(list(g)), atoms=Chem.MolFragmentToSmiles(mol, g, canonical=True), type=Chem.MolFragmentToSmiles(mol, g.union(uca),canonical=True)))
+    return ifgs
+
+def main():
+    for ix, smiles in enumerate([
+        'Cc1nc(NS(=O)(=O)c2ccc(N)cc2)nc(C)c1', # fig1, 1
+        'NC(=N)c1ccc(C=Cc2ccc(cc2O)C(=N)N)cc1', # 2
+        'CC(=O)Nc1nnc(s1)S(=O)(=O)N', # 3
+        'NS(=O)(=O)c1cc2c(NCNS2(=O)=O)cc1Cl', # 4
+        'CNC1=Nc2ccc(Cl)cc2C(=N(=O)C1)c3ccccc3', # 5
+        'Cc1onc(c1C(=O)NC2C3SC(C)(C)C(N3C2=O)C(=O)O)c4ccccc4', # 6
+        'Clc1ccccc1C2=NCC(=O)Nc3ccc(cc23)N(=O)=O', # 7
+        'COc1cc(cc(C(=O)NCC2CCCN2CC=C)c1OC)S(=O)(=O)N', # 8
+        'Cc1ccc(Cl)c(Nc2ccccc2C(=O)O)c1Cl', # 9
+        'Clc1ccc2Oc3ccccc3N=C(N4CCNCC4)c2c1', # 10 - there is a discrepancy with the paper here!  I wonder if Peter has the ring as aromatic?
+        'FC(F)(F)CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13', # 11
+        'OCC1OC(CC1O)n2cnc3C(O)CNC=Nc32', # 12
+        'CCNC1CC(C)S(=O)(=O)c2sc(cc12)S(=O)(=O)N', # 13
+        'CC(O)C1C2C(C)C(=C(N2C1=O)C(=O)O)SC3CNC(C3)C(=O)N(C)C', # 14
+        'CC1CN(CC(C)N1)c2c(F)c(N)c3c(=O)c(cn(C4CC4)c3c2F)C(=O)O', # 15
+        'CC(=CCC1C(=O)N(N(C1=O)c2ccccc2)c3ccccc3)C', # 16
+        'Clc1ccc2N=C3NC(=O)CN3Cc2c1Cl', # 17
+        'CC(=O)NC1C(NC(=N)N)C=C(OC1C(O)C(O)CO)C(=O)O', # 18
+        'CC(O)C(O)C1CNc2nc(N)nc(O)c2N1', # 19
+        'NC1CCCCN(C1)c2c(Cl)cc3c(=O)c(cn(C4CC4)c3c2Cl)C(=O)O', # 20
+    ]):
+        m = Chem.MolFromSmiles(smiles)
+        fgs = identify_functional_groups(m)
+        print '%2d: %d fgs'%(ix+1, len(fgs)), fgs
+
+
+if __name__ == "__main__":
+    main()