HI all
Thank you Noel for your mail, and updating about the issue babel has with
tricycle compounds and bond order.
I appreciate your reply
Vinay
--- On Thu, 1/28/10, Noel O'Boyle <baoille...@gmail.com> wrote:
From: Noel O'Boyle <baoille...@gmail.com>
Subject: Re: [Open Babel] Unexpected result - by obprop
To: "Robert DeLisle" <rkdeli...@gmail.com>
Cc: "babel" <openbabel-discuss@lists.sourceforge.net>
Received: Thursday, January 28, 2010, 9:42 PM
I'm currently away but your assessment that " It appears that babel is having
issues with the bonding pattern (due to aromaticity detection?) of the
tricycle." is
quite possible looking at the SMILES string. If so, it's a known issue that we
are addressing but it's a major piece of work (Craig James has been working on
this).
- Noel
2010/1/28 Robert DeLisle <rkdeli...@gmail.com>
Just curious - I didn't see any response after my message (copied below).. I
was wondering what the resolution was.
-Kirk
On Tue, Jan 26, 2010 at 10:20 AM, Robert DeLisle <rkdeli...@gmail.com> wrote:
To help clarify a bit, I did some experiments with Vinay's original files as
follows:
Starting with example.sdf and generating a cannonical SMILES string, then
generating properties from both:
babel -isdf example.sdf -ocan example.can
obprop example.sdf
name ZINC20816447
formula C21H32N7O2
mol_weight 414.524
exact_mass 414.262
canonical_SMILES C/C=C/CN1CC[NH+](CC1)
CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C ZINC20816447
InChI
InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
num_atoms 62
num_bonds 65
num_residues 0
sequence -
num_rings
4
logP 0.5869
PSA 73.91
MR 128.186
obprop example.can
name ZINC20816447
formula C21H32N7O2
mol_weight 414.524
exact_mass 414.262
canonical_SMILES C/C=C/CN1CC[NH+](CC1)CC[n]
1c2nc3N(C)[C](=O)=[N](C[C]
=O)=c3n2c(C)c1C ZINC20816447
InChI
InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
num_atoms 62
num_bonds 65
num_residues 0
sequence -
num_rings 4
logP 0.4349
PSA 79.65
MR 131.945
Notice that the logP, PSA, and MR are different between the two.
Also, if you generate a new sdf from the babel generated canonical SMILES:
babel --gen3D -ican example.can -osdf example.new.sdf
you get a different bonding pattern. See attached. It appears that babel is
having issues with the bonding pattern (due to aromaticity detection?) of the
tricycle.
-Kirk
On Tue, Jan 26, 2010 at 8:33 AM, Vinay M <vi...@ymail.com> wrote:
HI All
Those two are same compound, I have used babel to convert from SDF to
Canonicals and then calculated molecular properties.
Vinay
--- On Tue, 1/26/10, Noel O'Boyle <baoille...@gmail.com> wrote:
From: Noel O'Boyle <baoille...@gmail.com>
Subject: Re: [Open Babel] Unexpected result - by obprop
To: "Vinay M" <vi...@ymail.com>
Cc: "babel" <openbabel-discuss@lists.sourceforge.net>
Received: Tuesday, January 26, 2010, 9:18 AM
Hello Vinay,
Perhaps example.sdf and example.smi represent different compounds..
- Noel
2010/1/25 Vinay M <vi...@ymail.com>
Hi all
I have been using babel for various molecular calculations and conversions.
I have noticed an unexpected error during conversion and with obprop
calculation. When i use cannonical smiles as input for obprop, I get a
different canonical output, its entirely a different compund and if i use sdf
as input, I got a different canonical string. The following is an example.
SDF was converted to cannonicals by babel- Using babel -isdf filename -ocan
filename.can
Example one where, I have used Canonical smiles as the input for obprop.
1.
[vi...@vinay_pc testing]$ ls
can_from_sdf.can example.can example.sdf
[vi...@vinay_pc testing]$ obprop example.can > obprop_can_input
==============================
*** Open Babel Warning in InChI code
ZINC20816447 :Accepted unusual valence(s):
N(4); C(5); Proton(s) added/removed
Example two, where in I have used sdf as input file for obprop
2.
[vi...@vinay_pc testing]$ obprop example.sdf > obprop_sdf_input
==============================
*** Open Babel Warning in InChI code
ZINC20816447 :Proton(s) added/removed
[vi...@vinay_pc testing]$ ls
can_from_sdf.can example.can example.sdf obprop_can_input obprop_sdf_input
Differences in canonical strings from different input files.
[vi...@vinay_pc testing]$ more obprop_can_input
name ZINC20816447
formula C21H32N7O2
mol_weight 414.524
exact_mass 414.262
canonical_SMILES C/C=C/CN1CC[NH+](CC1)CC[n]1c2nc3N(C)[C](=O)=[N](C[C]
=O)=c3n2c(C)c1C ZINC20816447
InChI
InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
num_atoms 62
num_bonds 65
num_residues 0
sequence -
num_rings 4
logP 0.4349
PSA 79.65
MR 131.945
$$$$
This is sdf as input file,
[vi...@vinay_pc testing]$ more
obprop_sdf_input
name ZINC20816447
formula C21H32N7O2
mol_weight 414.524
exact_mass 414.262
canonical_SMILES C/C=C/CN1CC[NH+](CC1)CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C
ZINC20816447
InChI
InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
num_atoms 62
num_bonds 65
num_residues 0
sequence -
num_rings
4
logP 0.5869
PSA 73.91
MR 128.186
$$$$
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