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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