Dear Ling; Thank you for pointing out the issue with the lactam ring. I manually changed the bond types in the mol2 file and now the error is gone. The MolFromMol2File function can sanitize the molecule. However, I still have a problem with the output. Again, my code is:
mol=Chem.MolFromMol2File("%s.lig.%d.mol2"%(name, i), sanitize = True,
removeHs = False)
aromatic_6="[c,n]1[c,n][c,n][c,n][c,n][c,n]1"
aromatic_5="[c,n]1[c,n][c,n][c,n][c,n]1"
pattern6=Chem.MolFromSmarts(aromatic_6)
pattern5=Chem.MolFromSmarts(aromatic_5)
print "Pattern 6 "
lar = mol.GetSubstructMatch(pattern6)
print lar
print "Pattern 5 "
lar = mol.GetSubstructMatch(pattern5)
print lar
The output is:
Pattern 6
(0, 1, 3, 5, 7, 9)
Pattern 5
(30, 31, 32, 41, 42)
So for some reason, the pattern match for an aromatic six-membered ring returns
the conjugated lactam ring, but fails to recognize the other two (all-carbon)
aromatic rings in the system. Interesting, it correctly recognizes the
five-membered ring system. Do you have any idea's on how to address the issue?
I am attaching the hand-edited mol2 file.
Thanks!
-Sergio
From: S.L. Chan [[email protected]]
Sent: Monday, December 08, 2014 8:26 PM
To: Wong, Sergio E.; [email protected]
Subject: Re: [Rdkit-discuss] Can't kelulize
Dear Sergio,
The lactam ring (atoms 1 2 4 6 8 10) is not really aromatic. The bonds 4-6,
6-8, 8-10 should all be single rather than aromatic in the mol2 file. The
remaining three bonds in the ring should be double or single rather than
aromatic.
Ling
________________________________
From: "Wong, Sergio E." <[email protected]>
To: "[email protected]" <[email protected]>
Sent: Monday, December 8, 2014 3:27 PM
Subject: Re: [Rdkit-discuss] Can't kelulize
Dear RDKit users:
I tried reading a mol2 file using the function MolFromMol2 (). The goal of my
script is to read the molecule and find 5 or 6 membered aromatic rings. First
I got the following error:
Can't Kekulize mol
The code I used is as follows:
mol=Chem.MolFromMol2File("%s.lig.%d.mol2"%(name, i), sanitize = True, removeHs
= False)
As a work-around I tried removing the sanitize flag and did the following
mol=Chem.MolFromMol2File("%s.lig.%d.mol2"%(name, i), sanitize = False,
removeHs = False)
aromatic_6="[c,n]1[c,n][c,n][c,n][c,n][c,n]1"
aromatic_5="[c,n]1[c,n][c,n][c,n][c,n]1"
pattern6=Chem.MolFromSmarts(aromatic_6)
pattern5=Chem.MolFromSmarts(aromatic_5)
print "Pattern 6 "
lar = mol.GetSubstructMatch(pattern6)
print lar
print "Pattern 5 "
lar = mol.GetSubstructMatch(pattern5)
print lar
The output should 3 aromatic six-membered rings and 1 aromatic five-membered
ring. Instead I get only the first six-membered ring and no listing of the
five-membered ring.:
Pattern 6
(0, 1, 3, 5, 7, 9)
Pattern 5
()
So basically, I can not get around the kekulize function. I looked the mol2
file (attached) and it correctly lists the bond types as aromatic for all of
the rings. Is there a way to use the bond information from the mol2 file to
assign aromaticity?
Thanks!!
-Sergio
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MIZOLASTINE.lig.999.mol2
Description: MIZOLASTINE.lig.999.mol2
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