Thanks, Noel. I've seen similar results in other (long forgotten)
instances. At least it is on the map - not an easy map to navigate, but a
map none the less.
-Kirk
On Thu, Jan 28, 2010 at 2:42 PM, Noel O'Boyle <[email protected]> wrote:
> 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 <[email protected]>
>
>> 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
>>>>> $$$$
>>>>>
>>>>>
>>>>> This is sdf as input file,
>>>>>
>>>>> [vi...@vinay_pc testing]$ more obprop_sdf_input
>>>>> name ZINC20816447
>>>>> formula C21H32N7O2
>>>>> mol_weight 414.524
>>>>> exact_mass 414.262
>>>>> canonical_SMILES
>>>>> C/C=C/CN1CC[NH+](CC1)CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C
>>>>> ZINC20816447
>>>>>
>>>>> InChI
>>>>> InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
>>>>>
>>>>> num_atoms 62
>>>>> num_bonds 65
>>>>> num_residues 0
>>>>> sequence -
>>>>> num_rings 4
>>>>> logP 0.5869
>>>>> PSA 73.91
>>>>> MR 128.186
>>>>> $$$$
>>>>>
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