Hi
Commands used for the example file. I have attached the file, kindly have a
look at it.
Vinay
--- On Fri, 1/22/10, Vinay M <[email protected]> wrote:
From: Vinay M <[email protected]>
Subject: Re: [Open Babel] Unexpected result - by obprop
To: "Noel O'Boyle" <[email protected]>
Received: Friday, January 22, 2010, 4:34 PM
--- On Thu, 1/21/10, Noel O'Boyle <[email protected]> wrote:
From: Noel O'Boyle <[email protected]>
Subject: Re: [Open Babel] Unexpected result - by obprop
To: "Vinay M" <[email protected]>
Cc: "babel" <[email protected]>
Received: Thursday, January 21, 2010, 6:10 PM
2010/1/21 Vinay M <[email protected]>
Hi everyone
I have bee using babel for molecular calculations and conversion.
I encountered unexpected results when I used babel for conversion and for
Molecular calculation.
babel -isdf XXX -ocan this the commend used for conversion, from sdf to
canonical
When we again convert the sdf output to cannonical, we get different cannonical
smiles.
I don't understand. Can you provide the exact command line you used for each
conversion using the filenames in your .tar.gz?
And in obprop.
if we use canonical smiles as input for obprop calculations we get all the
molecular calculations and canonical strings.
When we use the same compound, but sdf as input for obporp we get a different
canonical smiles, and i have checked those two compunds, there bond order are
changed.
I have attached the example files with which i have worked. Kindly have a look.
Kindly respond to this issue.
Vinay
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http://www.flickr.com/gift/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
$$$$
This is sdf as input file,
[vi...@vinay_pc testing]$ more obprop_sdf_input
name ZINC20816447
formula C21H32N7O2
mol_weight 414.524
exact_mass 414.262
canonical_SMILES C/C=C/CN1CC[NH+](CC1)CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C
ZINC20816447
InChI
InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
num_atoms 62
num_bonds 65
num_residues 0
sequence -
num_rings 4
logP 0.5869
PSA 73.91
MR 128.186
$$$$
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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