Re: [Rdkit-discuss] Phosphate containing mol2 files
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Re: [Rdkit-discuss] Phosphate containing mol2 files
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From: Stiefl, N. <nik...@no...> - 2012-06-28 21:01:17
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Dear Simone,
Thanks for your feedback. As some might know at some point I implemented the Mol2 parser. During my search for a good description of the mol2 file format I had to learn that there is not a really good one and (because of this I assume) many software will have different answers for the same molecule in mol2 (even different tools from Tripos will result in different mol2 files).
So – what we decided on at that point was that we will use the corina mol2 format since at least here we can do a proper testing (this is also found in the code docs). Jhere is some simple examples that explain the warning you see.
stiefni2@camm31 ~ ->echo 'CCOP(=O)(=O)[O-]' | corina -i t=smiles -o t=mol2
# Name: NoName
# Creating user name: stiefni2
# Creation time: 28. 06. 2012 22:55
# Modifying user name: stiefni2
# Modification time: 28. 06. 2012 22:55
# Program: corina 3.48 0006 22.01.2010
@<TRIPOS>MOLECULE
NoName
7 6 0 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 -0.0187 1.5258 0.0104 C.3
2 C2 0.0021 -0.0041 0.0020 C.3
3 O3 0.6709 -0.4649 -1.1737 O.3
4 P4 0.8773 -2.0258 -1.5102 P.3
5 O5 2.2183 -2.2222 -2.2057 O.2
6 O6 0.8528 -2.8315 -0.2177 O.2
7 O7 -0.2438 -2.5004 -2.4258 O.3
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 4 5 2
5 4 6 2
6 4 7 1
# End of record
stiefni2@camm31 ~ ->echo 'CCOS(=O)(=O)[O-]' | corina -i t=smiles -o t=mol2
# Name: NoName
# Creating user name: stiefni2
# Creation time: 28. 06. 2012 22:55
# Modifying user name: stiefni2
# Modification time: 28. 06. 2012 22:55
# Program: corina 3.48 0006 22.01.2010
@<TRIPOS>MOLECULE
NoName
7 6 0 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 -0.0187 1.5258 0.0104 C.3
2 C2 0.0021 -0.0041 0.0020 C.3
3 O3 0.6709 -0.4649 -1.1737 O.3
4 S4 0.7506 -1.9806 -1.2867 S.o2
5 O5 1.7444 -2.2735 -2.3078 O.co2
6 O6 1.1484 -2.4784 0.0210 O.co2
7 O7 -0.5752 -2.4432 -1.6667 O.co2
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 1
4 4 5 ar
5 4 6 ar
6 4 7 ar
# End of record
stiefni2@camm31 ~ ->echo 'CCC(=O)[O-]' | corina -i t=smiles -o t=mol2
# Name: NoName
# Creating user name: stiefni2
# Creation time: 28. 06. 2012 22:58
# Modifying user name: stiefni2
# Modification time: 28. 06. 2012 22:58
# Program: corina 3.48 0006 22.01.2010
@<TRIPOS>MOLECULE
NoName
5 4 0 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 -0.0187 1.5258 0.0104 C.3
2 C2 0.0021 -0.0041 0.0020 C.3
3 C3 0.7309 -0.5033 1.2229 C.2
4 O4 1.1912 0.2909 2.0254 O.co2
5 O5 0.8604 -1.7014 1.4082 O.co2
@<TRIPOS>BOND
1 1 2 1
2 2 3 1
3 3 4 ar
4 3 5 ar
# End of record
I know this is not a very helpful answer for you at this moment, however, in order to stay within the corina mol2 format the code should stay like this. Obviously if anybody wants to go on and improve the code they are more than welcome to do so.
Ciao
Nik
From: Simone Fulle <sim...@in...<mailto:sim...@in...>>
Date: Thu, 28 Jun 2012 16:02:10 +0100
To: <rdk...@li...<mailto:rdk...@li...>>
Subject: [Rdkit-discuss] Phosphate containing mol2 files
Dear RDKitters,
I have a set of ligands in mol2 format which contain phosphate groups. I am reading them in by typing:
rdkMol = Chem.MolFromMol2File(inmol2file, sanitize=True, removeHs=False)
and get the following warning message: "warning - O.co2 with non C.2 or S.o2 neighbor."
The reason for the message is that I have P.3 atoms bound to O.co2's and Mol2FileParser.cpp (in $RDKIT/Code/GraphMol/FileParsers) is (at least in my version) only postprocessing carboxylates or sulphates groups.
Changing line 292 in Mol2FileParser.cpp into ' if (tATT=="C.2" || tATT=="S.o2" || tATT=="P.3"){ '
allows me to postprocess the phosphate containing ligands. If my change is only part of the solution I would be really grateful to hear about it. In any case I guess it's s.th<http://s.th>. which should be changed in the code distribution.
Kind regards,
Simone
--
Dr. Simone Fulle
Post-doctoral Researcher
InhibOx, Ltd
Oxford Centre for Innovation, Suites F14-F16
New Road
Oxford, OX1 1BY, UK
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