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 <[email protected]>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 <[email protected]> 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 <[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: Tuesday, January 26, 2010, 9:18 AM
>>
>>
>> Hello Vinay,
>>
>> Perhaps example.sdf and example.smi represent different compounds..
>>
>> - Noel
>>
>> 2010/1/25 Vinay M <[email protected] <http://mc/[email protected]>
>> >
>>
>>> 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
>>> $$$$
>>>
>>>
>>> This is sdf as input file,
>>>
>>> [vi...@vinay_pc testing]$ more obprop_sdf_input
>>> name ZINC20816447
>>> formula C21H32N7O2
>>> mol_weight 414.524
>>> exact_mass 414.262
>>> canonical_SMILES
>>> C/C=C/CN1CC[NH+](CC1)CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C ZINC20816447
>>>
>>> InChI
>>> InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
>>>
>>> num_atoms 62
>>> num_bonds 65
>>> num_residues 0
>>> sequence -
>>> num_rings 4
>>> logP 0.5869
>>> PSA 73.91
>>> MR 128.186
>>> $$$$
>>>
>>> ------------------------------
>>>
>>> *Yahoo! Canada Toolbar :* Search from anywhere on the web and bookmark
>>> your favourite sites. Download it now! <http://ca.toolbar.yahoo.com/>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The Planet: dedicated and managed hosting, cloud storage, colocation
>>> Stay online with enterprise data centers and the best network in the
>>> business
>>> Choose flexible plans and management services without long-term contracts
>>> Personal 24x7 support from experience hosting pros just a phone call
>>> away.
>>> http://p.sf.net/sfu/theplanet-com
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> [email protected]<http://mc/[email protected]>
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>
>> ------------------------------
>>
>> *Yahoo! Canada Toolbar :* Search from anywhere on the web and bookmark
>> your favourite sites. Download it now! <http://ca.toolbar..yahoo.com/>
>>
>>
>> ------------------------------------------------------------------------------
>> The Planet: dedicated and managed hosting, cloud storage, colocation
>> Stay online with enterprise data centers and the best network in the
>> business
>> Choose flexible plans and management services without long-term contracts
>> Personal 24x7 support from experience hosting pros just a phone call away.
>> http://p.sf.net/sfu/theplanet-com
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
------------------------------------------------------------------------------
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com
_______________________________________________
OpenBabel-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
