[Open Babel] Converting sybyl line notation to smiles or sdf
Dear, I have a library of ~60,000 structures defined in SLN (sybyl line notation) and I need to convert these in smiles or sdf format. I don't believe that Open Babel can help me on that (unless I missed it), so are there any other tools (preferably on Mac OS X) that can do this? Thx in advance. Hans De Winter Silicos NV -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Converting sybyl line notation to smiles or sdf
It's not quite the same but see http://blueobelisk.shapado.com/questions/convert-sln-to-smarts and links therein. - Noel On 18 March 2011 07:52, Hans De Winter wrote: > Dear, > > I have a library of ~60,000 structures defined in SLN (sybyl line > notation) and I need to convert these in smiles or sdf format. I don't > believe that Open Babel can help me on that (unless I missed it), so > are there any other tools (preferably on Mac OS X) that can do this? > > Thx in advance. > > Hans De Winter > Silicos NV > > > > -- > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Fragment indexing and generation
Hey everyone, I am kind of new to openbabel, but I was wondering if there is a way to produce fragments given one or more molecules. And if not, anything close to what openbabel supports An example is like the one on the openbabel documention page at address: http://openbabel.org/docs/2.3.0/Cheminf101/search.html#what-is-indexing Thanks, Andi -- View this message in context: http://forums.openbabel.org/Fragment-indexing-and-generation-tp3385311p3385311.html Sent from the General discussion mailing list archive at Nabble.com. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Python Openbabel Module Difficulties
Hello,
I am currently struggling with a particular interaction in openbabel.
When I run the following python code, the obConversion object correctly
reads X, but it just stalls on Y.
***
import openbabel
import sys
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "can")
mol = openbabel.OBMol()
X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
obConversion.ReadString(mol, X)
sys.stdout.write("X read\n")
mol2 = openbabel.OBMol()
Y =
"c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
obConversion.ReadString(mol2, Y)
sys.stdout.write("Y read\n")
***
Is there an explanation or a fix for this?
Thank you for your time,
- Brad Calhoun, Washington University in St Louis, Pathology
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Re: [Open Babel] Fragment indexing and generation
Fragments could mean a lot of things, but see http://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html for examples of code (by others) for Murcko and RECAP fragmentation. Also, see the "s" option of fingerprint FP2 as described at http://openbabel.org/docs/dev/FileFormats/Fingerprint_format.html. - Noel On 17 March 2011 18:40, andi wrote: > Hey everyone, I am kind of new to openbabel, but I was wondering if there is > a way to produce fragments given one or more molecules. And if not, anything > close to what openbabel supports > > An example is like the one on the openbabel documention page at address: > > http://openbabel.org/docs/2.3.0/Cheminf101/search.html#what-is-indexing > > Thanks, > > Andi > > -- > View this message in context: > http://forums.openbabel.org/Fragment-indexing-and-generation-tp3385311p3385311.html > Sent from the General discussion mailing list archive at Nabble.com. > > -- > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Python Openbabel Module Difficulties
Hi Brad,
It works for me, but it takes 10 seconds. It also uncovers a bug - the
system is not detected as aromatic.
Is this a real molecule?
- Noel
On 17 March 2011 17:53, Bradley Calhoun wrote:
> Hello,
> I am currently struggling with a particular interaction in openbabel.
> When I run the following python code, the obConversion object correctly
> reads X, but it just stalls on Y.
> ***
> import openbabel
> import sys
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "can")
> mol = openbabel.OBMol()
> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
> obConversion.ReadString(mol, X)
> sys.stdout.write("X read\n")
> mol2 = openbabel.OBMol()
> Y =
> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
> obConversion.ReadString(mol2, Y)
> sys.stdout.write("Y read\n")
> ***
> Is there an explanation or a fix for this?
> Thank you for your time,
> - Brad Calhoun, Washington University in St Louis, Pathology
> --
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> ___
> OpenBabel-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
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___
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Re: [Open Babel] Python Openbabel Module Difficulties
I have to wonder then what the difference is. I ran the code again to make
sure, and the program sat for 30 minutes without any progress.
I added a few other molecules that cause the same response. (seeming to
hang)
These are all real molecules. The Substance IDs 23587365, 34132506,
and 34132507 can be searched at the PubChem website.
***
import openbabel
import sys
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "can")
mol = openbabel.OBMol()
X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
a =
"c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21
23587365"
b =
"c1ccc2c(c1)sc1cc3sc4c4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8c8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1c51
34132506"
c =
"c1ccc2c(c1)oc1cc3oc4c4n4c5ccc(cc5)n5c6cc7c(oc8c8n7c7ccc(cc7)n2c1cc34)cc6oc1c51
34132507"
obConversion.ReadString(mol, X)
sys.stdout.write( 'x' )
obConversion.ReadString(mol, a)
sys.stdout.write( 'a' )
obConversion.ReadString(mol, b)
sys.stdout.write( 'b' )
obConversion.ReadString(mol, c)
sys.stdout.write( 'c' )
***
- Brad
On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle wrote:
> Hi Brad,
>
> It works for me, but it takes 10 seconds. It also uncovers a bug - the
> system is not detected as aromatic.
>
> Is this a real molecule?
>
> - Noel
>
> On 17 March 2011 17:53, Bradley Calhoun
> wrote:
> > Hello,
> > I am currently struggling with a particular interaction in openbabel.
> > When I run the following python code, the obConversion object correctly
> > reads X, but it just stalls on Y.
> > ***
> > import openbabel
> > import sys
> > obConversion = openbabel.OBConversion()
> > obConversion.SetInAndOutFormats("smi", "can")
> > mol = openbabel.OBMol()
> > X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
> > obConversion.ReadString(mol, X)
> > sys.stdout.write("X read\n")
> > mol2 = openbabel.OBMol()
> > Y =
> >
> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
> > obConversion.ReadString(mol2, Y)
> > sys.stdout.write("Y read\n")
> > ***
> > Is there an explanation or a fix for this?
> > Thank you for your time,
> > - Brad Calhoun, Washington University in St Louis, Pathology
> >
> --
> > Colocation vs. Managed Hosting
> > A question and answer guide to determining the best fit
> > for your organization - today and in the future.
> > http://p.sf.net/sfu/internap-sfd2d
> > ___
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
> >
>
--
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A question and answer guide to determining the best fit
for your organization - today and in the future.
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OpenBabel-discuss mailing list
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Re: [Open Babel] Python Openbabel Module Difficulties
Maybe; you have a different version number than NoB than?
Details!Details!
On 18 March 2011 13:53, Bradley Calhoun wrote:
> I have to wonder then what the difference is. I ran the code again to make
> sure, and the program sat for 30 minutes without any progress.
>
> I added a few other molecules that cause the same response. (seeming to
> hang)
>
> These are all real molecules. The Substance IDs 23587365, 34132506,
> and 34132507 can be searched at the PubChem website.
>
> ***
> import openbabel
> import sys
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "can")
> mol = openbabel.OBMol()
> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
> a =
> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21
> 23587365"
> b =
> "c1ccc2c(c1)sc1cc3sc4c4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8c8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1c51
> 34132506"
> c =
> "c1ccc2c(c1)oc1cc3oc4c4n4c5ccc(cc5)n5c6cc7c(oc8c8n7c7ccc(cc7)n2c1cc34)cc6oc1c51
> 34132507"
>
> obConversion.ReadString(mol, X)
> sys.stdout.write( 'x' )
> obConversion.ReadString(mol, a)
> sys.stdout.write( 'a' )
> obConversion.ReadString(mol, b)
> sys.stdout.write( 'b' )
> obConversion.ReadString(mol, c)
> sys.stdout.write( 'c' )
> ***
>
> - Brad
>
>
> On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle wrote:
>
>> Hi Brad,
>>
>> It works for me, but it takes 10 seconds. It also uncovers a bug - the
>> system is not detected as aromatic.
>>
>> Is this a real molecule?
>>
>> - Noel
>>
>> On 17 March 2011 17:53, Bradley Calhoun
>> wrote:
>> > Hello,
>> > I am currently struggling with a particular interaction in openbabel.
>> > When I run the following python code, the obConversion object correctly
>> > reads X, but it just stalls on Y.
>> > ***
>> > import openbabel
>> > import sys
>> > obConversion = openbabel.OBConversion()
>> > obConversion.SetInAndOutFormats("smi", "can")
>> > mol = openbabel.OBMol()
>> > X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
>> > obConversion.ReadString(mol, X)
>> > sys.stdout.write("X read\n")
>> > mol2 = openbabel.OBMol()
>> > Y =
>> >
>> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
>> > obConversion.ReadString(mol2, Y)
>> > sys.stdout.write("Y read\n")
>> > ***
>> > Is there an explanation or a fix for this?
>> > Thank you for your time,
>> > - Brad Calhoun, Washington University in St Louis, Pathology
>> >
>> --
>> > Colocation vs. Managed Hosting
>> > A question and answer guide to determining the best fit
>> > for your organization - today and in the future.
>> > http://p.sf.net/sfu/internap-sfd2d
>> > ___
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>>
>
>
>
> --
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
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Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
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36-37 Pembroke Street
Oxford
OX1 1BP
UK
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This email and any files transmitted with it are confidential and intended
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please notify the sender and delete all copies from your system.
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Re: [Open Babel] Python Openbabel Module Difficulties
I am using Open Babel 2.3.0 and the most recent apt-get version of
python-openbabel, which I believe is where the openbabel python module is.
I think this is version 2.2.3. My python is 2.6.6 (we have to keep this on
the same page as python's scipy package).
- Brad
On Fri, Mar 18, 2011 at 8:57 AM, JP wrote:
> Maybe; you have a different version number than NoB than?
>
> Details!Details!
>
>
> On 18 March 2011 13:53, Bradley Calhoun wrote:
>
>> I have to wonder then what the difference is. I ran the code again to
>> make sure, and the program sat for 30 minutes without any progress.
>>
>> I added a few other molecules that cause the same response. (seeming to
>> hang)
>>
>> These are all real molecules. The Substance IDs 23587365, 34132506,
>> and 34132507 can be searched at the PubChem website.
>>
>> ***
>> import openbabel
>> import sys
>> obConversion = openbabel.OBConversion()
>> obConversion.SetInAndOutFormats("smi", "can")
>> mol = openbabel.OBMol()
>> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
>> a =
>> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21
>> 23587365"
>> b =
>> "c1ccc2c(c1)sc1cc3sc4c4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8c8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1c51
>> 34132506"
>> c =
>> "c1ccc2c(c1)oc1cc3oc4c4n4c5ccc(cc5)n5c6cc7c(oc8c8n7c7ccc(cc7)n2c1cc34)cc6oc1c51
>> 34132507"
>>
>> obConversion.ReadString(mol, X)
>> sys.stdout.write( 'x' )
>> obConversion.ReadString(mol, a)
>> sys.stdout.write( 'a' )
>> obConversion.ReadString(mol, b)
>> sys.stdout.write( 'b' )
>> obConversion.ReadString(mol, c)
>> sys.stdout.write( 'c' )
>> ***
>>
>> - Brad
>>
>>
>> On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle wrote:
>>
>>> Hi Brad,
>>>
>>> It works for me, but it takes 10 seconds. It also uncovers a bug - the
>>> system is not detected as aromatic.
>>>
>>> Is this a real molecule?
>>>
>>> - Noel
>>>
>>> On 17 March 2011 17:53, Bradley Calhoun
>>> wrote:
>>> > Hello,
>>> > I am currently struggling with a particular interaction in openbabel.
>>> > When I run the following python code, the obConversion object correctly
>>> > reads X, but it just stalls on Y.
>>> > ***
>>> > import openbabel
>>> > import sys
>>> > obConversion = openbabel.OBConversion()
>>> > obConversion.SetInAndOutFormats("smi", "can")
>>> > mol = openbabel.OBMol()
>>> > X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
>>> > obConversion.ReadString(mol, X)
>>> > sys.stdout.write("X read\n")
>>> > mol2 = openbabel.OBMol()
>>> > Y =
>>> >
>>> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
>>> > obConversion.ReadString(mol2, Y)
>>> > sys.stdout.write("Y read\n")
>>> > ***
>>> > Is there an explanation or a fix for this?
>>> > Thank you for your time,
>>> > - Brad Calhoun, Washington University in St Louis, Pathology
>>> >
>>> --
>>> > Colocation vs. Managed Hosting
>>> > A question and answer guide to determining the best fit
>>> > for your organization - today and in the future.
>>> > http://p.sf.net/sfu/internap-sfd2d
>>> > ___
>>> > OpenBabel-discuss mailing list
>>> > OpenBabel-discuss@lists.sourceforge.net
>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>> >
>>> >
>>>
>>
>>
>>
>> --
>> Colocation vs. Managed Hosting
>> A question and answer guide to determining the best fit
>> for your organization - today and in the future.
>> http://p.sf.net/sfu/internap-sfd2d
>> ___
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>
>
> --
>
> Jean-Paul Ebejer
> Early Stage Researcher
>
> InhibOx Ltd
> Pembroke House
> 36-37 Pembroke Street
> Oxford
> OX1 1BP
> UK
>
> (+44 / 0) 1865 262 034
>
>
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> Any unauthorised dissemination or copying of this email or its attachments,
> and any use or disclosure of any information contained in them, is strictly
> prohibited and may be illegal. If you have received this email in error
> please notify the sender and delete all copies from your system.
>
> We and our group companies accept no liability or responsibility for
> personal emails or emails unconnected with our business.
>
> Internet communications including emails and access and use of web sites
> cannot be guaranteed to be secure or error free as information can be
> intercepted, corrupted, lost or arrive late. Furthermore, while we have
> taken steps to control the spread of viruses on our systems, we cannot
> guarantee that this email and any files transmitted with it are virus free.
> No liability is
Re: [Open Babel] Python Openbabel Module Difficulties
Can you confirm that you are running OB 2.3.0?
On 18 March 2011 13:53, Bradley Calhoun wrote:
> I have to wonder then what the difference is. I ran the code again to make
> sure, and the program sat for 30 minutes without any progress.
> I added a few other molecules that cause the same response. (seeming to
> hang)
> These are all real molecules. The Substance IDs 23587365, 34132506,
> and 34132507 can be searched at the PubChem website.
> ***
> import openbabel
> import sys
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "can")
> mol = openbabel.OBMol()
> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
> a =
> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21
> 23587365"
> b =
> "c1ccc2c(c1)sc1cc3sc4c4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8c8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1c51
> 34132506"
> c =
> "c1ccc2c(c1)oc1cc3oc4c4n4c5ccc(cc5)n5c6cc7c(oc8c8n7c7ccc(cc7)n2c1cc34)cc6oc1c51
> 34132507"
> obConversion.ReadString(mol, X)
> sys.stdout.write( 'x' )
> obConversion.ReadString(mol, a)
> sys.stdout.write( 'a' )
> obConversion.ReadString(mol, b)
> sys.stdout.write( 'b' )
> obConversion.ReadString(mol, c)
> sys.stdout.write( 'c' )
> ***
> - Brad
>
> On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle wrote:
>>
>> Hi Brad,
>>
>> It works for me, but it takes 10 seconds. It also uncovers a bug - the
>> system is not detected as aromatic.
>>
>> Is this a real molecule?
>>
>> - Noel
>>
>> On 17 March 2011 17:53, Bradley Calhoun
>> wrote:
>> > Hello,
>> > I am currently struggling with a particular interaction in openbabel.
>> > When I run the following python code, the obConversion object correctly
>> > reads X, but it just stalls on Y.
>> > ***
>> > import openbabel
>> > import sys
>> > obConversion = openbabel.OBConversion()
>> > obConversion.SetInAndOutFormats("smi", "can")
>> > mol = openbabel.OBMol()
>> > X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
>> > obConversion.ReadString(mol, X)
>> > sys.stdout.write("X read\n")
>> > mol2 = openbabel.OBMol()
>> > Y =
>> >
>> > "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
>> > obConversion.ReadString(mol2, Y)
>> > sys.stdout.write("Y read\n")
>> > ***
>> > Is there an explanation or a fix for this?
>> > Thank you for your time,
>> > - Brad Calhoun, Washington University in St Louis, Pathology
>> >
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Re: [Open Babel] Python Openbabel Module Difficulties
Sorry - our emails crossed. You don't say what OS you're using, but
it's a simple matter to check to go to its website to check what
version of Open Babel the bindings are linked against. It sounds like
it's 2.2.3 but you can verify with "print
pybel.ob.OBReleaseVersion()".
I think you'll have to compile the bindings yourself.
- Noel
On 18 March 2011 14:03, Bradley Calhoun wrote:
> I am using Open Babel 2.3.0 and the most recent apt-get version of
> python-openbabel, which I believe is where the openbabel python module is.
> I think this is version 2.2.3. My python is 2.6.6 (we have to keep this on
> the same page as python's scipy package).
> - Brad
>
>
> On Fri, Mar 18, 2011 at 8:57 AM, JP wrote:
>>
>> Maybe; you have a different version number than NoB than?
>>
>> Details!Details!
>>
>> On 18 March 2011 13:53, Bradley Calhoun
>> wrote:
>>>
>>> I have to wonder then what the difference is. I ran the code again to
>>> make sure, and the program sat for 30 minutes without any progress.
>>> I added a few other molecules that cause the same response. (seeming to
>>> hang)
>>> These are all real molecules. The Substance IDs 23587365, 34132506,
>>> and 34132507 can be searched at the PubChem website.
>>> ***
>>> import openbabel
>>> import sys
>>> obConversion = openbabel.OBConversion()
>>> obConversion.SetInAndOutFormats("smi", "can")
>>> mol = openbabel.OBMol()
>>> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
>>> a =
>>> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21
>>> 23587365"
>>> b =
>>> "c1ccc2c(c1)sc1cc3sc4c4n4c5ccc(cc5)c5ccc(cc5)n5c6cc7c(sc8c8n7c7ccc(cc7)c7ccc(cc7)n2c1cc34)cc6sc1c51
>>> 34132506"
>>> c =
>>> "c1ccc2c(c1)oc1cc3oc4c4n4c5ccc(cc5)n5c6cc7c(oc8c8n7c7ccc(cc7)n2c1cc34)cc6oc1c51
>>> 34132507"
>>> obConversion.ReadString(mol, X)
>>> sys.stdout.write( 'x' )
>>> obConversion.ReadString(mol, a)
>>> sys.stdout.write( 'a' )
>>> obConversion.ReadString(mol, b)
>>> sys.stdout.write( 'b' )
>>> obConversion.ReadString(mol, c)
>>> sys.stdout.write( 'c' )
>>> ***
>>> - Brad
>>>
>>> On Fri, Mar 18, 2011 at 5:24 AM, Noel O'Boyle
>>> wrote:
Hi Brad,
It works for me, but it takes 10 seconds. It also uncovers a bug - the
system is not detected as aromatic.
Is this a real molecule?
- Noel
On 17 March 2011 17:53, Bradley Calhoun
wrote:
> Hello,
> I am currently struggling with a particular interaction in openbabel.
> When I run the following python code, the obConversion object
> correctly
> reads X, but it just stalls on Y.
> ***
> import openbabel
> import sys
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "can")
> mol = openbabel.OBMol()
> X = "Clc1c(C=NNc2ccc(Cl)c(c2)C(=O)O)1Cl"
> obConversion.ReadString(mol, X)
> sys.stdout.write("X read\n")
> mol2 = openbabel.OBMol()
> Y =
>
> "c1ccc2c(c1)ccc1cc3c4c(4c4c5c6cc7ccc8c8c7c7(c67)c5c5c(c34)c34c6c(ccc7c67)cc5c34)c21"
> obConversion.ReadString(mol2, Y)
> sys.stdout.write("Y read\n")
> ***
> Is there an explanation or a fix for this?
> Thank you for your time,
> - Brad Calhoun, Washington University in St Louis, Pathology
>
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> for your organization - today and in the future.
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>
>>>
>>>
>>>
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>>>
>>
>>
>>
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Re: [Open Babel] Fragment indexing and generation
On 3/17/11 11:40 AM, andi wrote: > Hey everyone, I am kind of new to openbabel, but I was wondering if there is > a way to produce fragments given one or more molecules. And if not, anything > close to what openbabel supports > > An example is like the one on the openbabel documention page at address: > > http://openbabel.org/docs/2.3.0/Cheminf101/search.html#what-is-indexing The choice of how to do fragments is highly dependent on why you need the fragments. For example, fragments designed for indexing a chemical database might be quite different than fragments used to predict pharmacological similarity. There is no single method that works for everyone. Craig -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
