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Re: [OpenBabel-scripting] SMARTS excluding

[Pascal M. <pas...@gm...>]

Hi,

> Hi have tried the following:
> alcohol = pybel.Smarts('[OX2H]')
> ketone = pybel.Smarts('[#6][CX3](=O)[#6]')
> carboxylic_acid =  pybel.Smarts('[CX3](=O)[OX2H1]')
> Which finds an alcohol a ketone and a carboxylic acid and it should only
> find a carboxylic acid.

Indeed, [CX3](=O)[OX2H1] is correct and find only carboxylic acid.


> If I try the following:
> which should not find a alcohol or ketone if they are part of a carboxylic
> acid
> alcohol = pybel.Smarts('[OX2H];!$[CX3](=O)[OX2H1]')

I think that the first atom after the $ sign should be the atom you
consider --> O and not C in your exemple.

So:
[OX2H1;!$(OC=O)]
[OX2H1;!$([OX2H1]C=O)]

But what about avoiding "!" for more easy to read expression:
alcool = pybel.Smarts("[OX2H][CX4,c]")
alcoolCH = pybel.Smarts("[OX2H][CX4][H]")

Regards,
Pascal

Re: [OpenBabel-scripting] SMARTS excluding

[Jurgens de B. <deb...@gm...>]

Hi have tried the following:

alcohol = pybel.Smarts('[OX2H]')
ketone = pybel.Smarts('[#6][CX3](=O)[#6]')
carboxylic_acid =  pybel.Smarts('[CX3](=O)[OX2H1]')

Which finds an alcohol a ketone and a carboxylic acid and it should only
find a carboxylic acid.

If I try the following:
which should not find a alcohol or ketone if they are part of a carboxylic
acid
alcohol = pybel.Smarts('[OX2H];!$[CX3](=O)[OX2H1]')
ketone = pybel.Smarts('[#6][CX3](=O)[#6];!$[CX3](=O)[OX2H1]')


I get "Invalid Smart" which is probably my fault.


Thanks


On 24 August 2011 10:34, Pascal Muller <pas...@gm...> wrote:

> Hi,
>
> > I am searching for a number of active groups in molecules using smarts
> and
> > it so happens that some of the groups overlap. Thus would it be possible
> to
> > write a smart stating to find a group but it should not be part of
> another
> > group.
> > smartA = "Some Smart"
> > SmartB ='SecondSmart not part of SmartA'
>
> smartA = C(F)(F)F)
>
> smartB = A[#6;!$(C(F)(F)F)]
> (Aliphatic atom single-bonded to any carbon which isn't a trifluromethyl
> carbon)
>
> http://www.daylight.com/dayhtml_tutorials/languages/smarts/#LOGIC
> "!" means "not" - but I guess you already knew that... Doesn't it
> match your needs?
>
> Regards,
> Pascal
>



-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] SMARTS excluding

[Pascal M. <pas...@gm...>]

Hi,

> I am searching for a number of active groups in molecules using smarts and
> it so happens that some of the groups overlap. Thus would it be possible to
> write a smart stating to find a group but it should not be part of another
> group.
> smartA = "Some Smart"
> SmartB ='SecondSmart not part of SmartA'

smartA = C(F)(F)F)

smartB = A[#6;!$(C(F)(F)F)]
(Aliphatic atom single-bonded to any carbon which isn't a trifluromethyl carbon)

http://www.daylight.com/dayhtml_tutorials/languages/smarts/#LOGIC
"!" means "not" - but I guess you already knew that... Doesn't it
match your needs?

Regards,
Pascal

[OpenBabel-scripting] SMARTS excluding

[Jurgens de B. <deb...@gm...>]

Hi,

I am searching for a number of active groups in molecules using smarts and
it so happens that some of the groups overlap. Thus would it be possible to
write a smart stating to find a group but it should not be part of another
group.

smartA = "Some Smart"
SmartB ='SecondSmart not part of SmartA'

Thanks

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

[OpenBabel-scripting] extracting SMARTS from SMILES molecule

[Gonzalo H. <gon...@gm...>]

Hi, I've been working on extracting a SMARTS string from a molecule centered
on a given atom and to a given number of shells. So far, I can do it but the
possition of the substituents depend on the atoms Idx's.  I would like to
canonalized the SMARTS in some way so they are the same string when the same
environment is extracted from different molecules.

Do you have any idea how to do this?

Thanks you,

Gonzalo.



-- 

---
"For the determined mind, it's not a matter of 'if' it's a matter of 'when'"
T. Sanchez

Re: [OpenBabel-scripting] Determine Atoms are in same ring

[Geoffrey H. <ge...@ge...>]

On Aug 18, 2011, at 5:28 AM, Jurgens de Bruin wrote:

> What I would like to know is which atoms belong to the same Ring-Structure. Any help on how to do this would be great.

Well, I'd get mol.GetSSSR() and then loop through all the atoms in each OBRing:
http://openbabel.org/api/2.3/classOpenBabel_1_1OBRing.shtml

Hope that helps,
-Geoff

Re: [OpenBabel-scripting] Distance between atoms

[Jurgens de B. <deb...@gm...>]

Thanks

On 16 August 2011 18:11, Geoffrey Hutchison <ge...@ge...>wrote:

> > I would like to determine if 2 functional groups are within 1 atom from
> each other.
>
> My suggestion would actually be a modified SMARTS using the "*" character
> for the one atom. For example:
>
> [O*O] # matches two oxygens bonded to the same atom
> [O**O] # matches two oxygens on neighboring atoms
>
> Hope that helps,
> -Geoff




-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

[OpenBabel-scripting] Determine Atoms are in same ring

[Jurgens de B. <deb...@gm...>]

Hi all,

I have the following SMART : [NX3;H2,H1;!$(NC=O);R] to find intracyclic
amines. Given the following SMILES: C1NC(CNC1)C2CNCCN2 I get the following
results:
[(2,), (5,), (9,), (12,)]

What I would like to know is which atoms belong to the same Ring-Structure.
Any help on how to do this would be great.




-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] Distance between atoms

[Geoffrey H. <ge...@ge...>]

> I would like to determine if 2 functional groups are within 1 atom from each other. 

My suggestion would actually be a modified SMARTS using the "*" character for the one atom. For example:

[O*O] # matches two oxygens bonded to the same atom
[O**O] # matches two oxygens on neighboring atoms

Hope that helps,
-Geoff

[OpenBabel-scripting] Distance between atoms

[Jurgens de B. <deb...@gm...>]

Hi,

I would like to determine if 2 functional groups are within 1 atom from each
other.

Is their a way I can calculate the distance between two atoms in order to do
this or are their any other suggestions?

Thanks

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

[OpenBabel-scripting] SMARTS

[Jurgens de B. <deb...@gm...>]

Hi,

Would like some help on writing SMARTS:

I would like a SMART for urea currently I have the following :
[NX3][NX3][CX3]=[OX1] but this does not seem to be able to find urea in a
structure. Any help on witting SMARTS would help. Had a loop and the
Daylight website but a bit more on designing SMARTS would help.

Thanks

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

Re: [OpenBabel-scripting] openbabel python example on Wiki Question

[Noel O'B. <bao...@gm...>]

What happens when you try that?

- Noel

On 22 July 2011 20:35, phani ghanakota <gph...@ya...> wrote:

> Hi,
>
> I was following the python openbabel example given on the open babel wiki
> below.
>
> >>> import openbabel>>> conv=openbabel.OBConversion()>>> conv.OpenInAndOutFiles("1200mols.smi","index.fs")True>>> conv.SetInAndOutFormats("smi","fs")True>>> conv.Convert()This will prepare an index of 1200mols.smi and may take some time...It took 6 seconds1192>>> conv.CloseOutFile()>>> conv.OpenInAndOutFiles("index.fs","results.smi")True>>> conv.SetInAndOutFormats("fs","smi")True>>> conv.AddOption("s",conv.GENOPTIONS,"C=CC#N")>>> conv.Convert()10 candidates from fingerprint search phase1202>>> f=open("results.smi")>>> f.read()'OC(=O)C(=Cc1ccccc1)C#N\t298\nN#CC(=Cc1ccccc1)C#N\t490\nO=N(=O)c1cc(ccc1)C=C(C#N)C#N\t491\nClc1ccc(cc1)C=C(C#N)C#N\t492\nClc1ccc(c(c1)Cl)C=C(C#N)C#N\t493\nClc1ccc(cc1Cl)C=C(C#N)C#N\t494\nBrc1ccc(cc1)C=C(C#N)C#N\t532\nClc1ccccc1C=C(C#N)C#N\t542\nN#CC(=CC=Cc1occc1)C#N\t548\nCCOC(=O)C(C#N)=C(C)C\t1074\n'
>
>
> If I wanted to change the fingerprint from the default FP2 to MACCS
> what would be the command that I would have to use.
>
> I am guessing it might be
>
> conv.AddOption("f",conv.OUTOPTIONS,"MACCS")
>
> could you confirm if this is right?
>
> Thanks,
> Phani.
>
>
>
> ------------------------------------------------------------------------------
> 10 Tips for Better Web Security
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Re: [OpenBabel-scripting] Fwd: importing pybel

[Noel O'B. <bao...@gm...>]

The Python bindings require OB to be compiled with Eigen2. See the
install instructions at
http://openbabel.org/docs/2.3.0/Installation/install.html

- Noel

On 26 July 2011 03:53, Daniel Sindhikara <sin...@gm...> wrote:
> Hi,
> I downloaded "openbabel-2.3.0.tar.gz"
> When I run that command, I get:
> otool -L
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so:
>     /Users/sindhikara/Downloads/openbabel-2.3.0/lib/libopenbabel.4.dylib
> (compatibility version 4.0.0, current version 4.0.0)
>     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
> 7.9.0)
>     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 125.2.11)
>
> Thanks!
>
>
>
> On Mon, Jul 25, 2011 at 11:49 PM, Geoffrey Hutchison
> <ge...@ge...> wrote:
>>
>> > I am running Mac OSX 10.6.8. When I e-mailed you originally I had
>> > installed "iBabel" the mac version. Since then tried installing the linux
>> > version and I suppose it installed correctly, but I still cannot import it:
>>
>> What "linux version" did you install?
>>
>> Can you run "otool -L
>> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so"
>> for me?
>>
>> Thanks,
>> -Geoff
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sin...@gm...
> Website: http://sites.google.com/site/dansindhikara/
> --
>
> ------------------------------------------------------------------------------
> Magic Quadrant for Content-Aware Data Loss Prevention
> Research study explores the data loss prevention market. Includes in-depth
> analysis on the changes within the DLP market, and the criteria used to
> evaluate the strengths and weaknesses of these DLP solutions.
> http://www.accelacomm.com/jaw/sfnl/114/51385063/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

Re: [OpenBabel-scripting] Fwd: importing pybel

[Daniel S. <sin...@gm...>]

Hi,
I downloaded "openbabel-2.3.0.tar.gz"
When I run that command, I get:
otool -L
/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so
/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so:
    /Users/sindhikara/Downloads/openbabel-2.3.0/lib/libopenbabel.4.dylib
(compatibility version 4.0.0, current version 4.0.0)
    /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
7.9.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
125.2.11)

Thanks!



On Mon, Jul 25, 2011 at 11:49 PM, Geoffrey Hutchison <
ge...@ge...> wrote:

> > I am running Mac OSX 10.6.8. When I e-mailed you originally I had
> installed "iBabel" the mac version. Since then tried installing the linux
> version and I suppose it installed correctly, but I still cannot import it:
>
> What "linux version" did you install?
>
> Can you run "otool -L
> /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so"
> for me?
>
> Thanks,
> -Geoff




-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

Re: [OpenBabel-scripting] Fwd: importing pybel

[Geoffrey H. <ge...@ge...>]

> I am running Mac OSX 10.6.8. When I e-mailed you originally I had installed "iBabel" the mac version. Since then tried installing the linux version and I suppose it installed correctly, but I still cannot import it:

What "linux version" did you install?

Can you run "otool -L /Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so" for me?

Thanks,
-Geoff

[OpenBabel-scripting] Fwd: importing pybel

[Daniel S. <sin...@gm...>]

---------- Forwarded message ----------
From: Daniel Sindhikara <sin...@gm...>
Date: Mon, Jul 25, 2011 at 4:29 PM
Subject: Re: [OpenBabel-scripting] importing pybel
To: Noel O'Boyle <bao...@gm...>


I am running Mac OSX 10.6.8. When I e-mailed you originally I had installed
"iBabel" the mac version. Since then tried installing the linux version and
I suppose it installed correctly, but I still cannot import it:

16:25:32 [danpc: ~]$ python2.7
Python 2.7.2 (default, Jun 21 2011, 13:19:45)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py",
line 16, in <module>
    import openbabel as ob
  File
"/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/openbabel.py",
line 70, in <module>
    _openbabel = swig_import_helper()
  File
"/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/openbabel.py",
line 66, in swig_import_helper
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError:
dlopen(/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so,
2): Symbol not found: __ZTVN9OpenBabel20OBRMSDConformerScoreE
  Referenced from:
/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so
  Expected in: flat namespace
 in
/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/_openbabel.so




On Wed, Jul 13, 2011 at 10:19 PM, Noel O'Boyle <bao...@gm...> wrote:

> Hi Dan,
>
> What operating system? How did you install Open Babel?
>
> - Noel
>
> On 11 July 2011 12:28, Daniel Sindhikara <sin...@gm...> wrote:
> > Hello,
> >   I'm somewhat new to python but would like to use pybel. I have
> openbabel
> > installed, but I'm not sure exactly how to get pybel working. Do I need
> to
> > install pybel separately? Is it included in some package? I can't find a
> > download link for it. Of course if I try "import pybel" I get: Traceback
> > (most recent call last):
> >   File "<pyshell#0>", line 1, in <module>
> >     import pybel
> > ImportError: No module named pybel
> >
> > Thanks for any help!
> > --Dan
> >
> >
> >
> ------------------------------------------------------------------------------
> > AppSumo Presents a FREE Video for the SourceForge Community by Eric
> > Ries, the creator of the Lean Startup Methodology on "Lean Startup
> > Secrets Revealed." This video shows you how to validate your ideas,
> > optimize your ideas and identify your business strategy.
> > http://p.sf.net/sfu/appsumosfdev2dev
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
>



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
 --



-- 
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sin...@gm...
Website: http://sites.google.com/site/dansindhikara/
--

[OpenBabel-scripting] openbabel python example on Wiki Question

[phani g. <gph...@ya...>]

Hi, 

I was following the python openbabel example given on the open babel wiki below. 
>>> import openbabel
>>> conv=openbabel.OBConversion()
>>> conv.OpenInAndOutFiles("1200mols.smi","index.fs")
True
>>> conv.SetInAndOutFormats("smi","fs")
True
>>> conv.Convert()
This will prepare an index of 1200mols.smi and may take some time...
It took 6 seconds
1192
>>> conv.CloseOutFile()
>>> conv.OpenInAndOutFiles("index.fs","results.smi")
True
>>> conv.SetInAndOutFormats("fs","smi")
True
>>> conv.AddOption("s",conv.GENOPTIONS,"C=CC#N")
>>> conv.Convert()
10 candidates from fingerprint search phase
1202
>>> f=open("results.smi")
>>> f.read()
'OC(=O)C(=Cc1ccccc1)C#N\t298\nN#CC(=Cc1ccccc1)C#N\t490\nO=N(=O)c1cc(ccc1)C=C(C#N
)C#N\t491\nClc1ccc(cc1)C=C(C#N)C#N\t492\nClc1ccc(c(c1)Cl)C=C(C#N)C#N\t493\nClc1c
cc(cc1Cl)C=C(C#N)C#N\t494\nBrc1ccc(cc1)C=C(C#N)C#N\t532\nClc1ccccc1C=C(C#N)C#N\t
542\nN#CC(=CC=Cc1occc1)C#N\t548\nCCOC(=O)C(C#N)=C(C)C\t1074\n'


If I wanted to change the fingerprint from the default FP2 to MACCS
what would be the command that I would have to use. 

I am guessing it might be 

conv.AddOption("f",conv.OUTOPTIONS,"MACCS")

could you confirm if this is right? 

Thanks,
Phani. 

Re: [OpenBabel-scripting] importing pybel

[Noel O'B. <bao...@gm...>]

Hi Dan,

What operating system? How did you install Open Babel?

- Noel

On 11 July 2011 12:28, Daniel Sindhikara <sin...@gm...> wrote:
> Hello,
>   I'm somewhat new to python but would like to use pybel. I have openbabel
> installed, but I'm not sure exactly how to get pybel working. Do I need to
> install pybel separately? Is it included in some package? I can't find a
> download link for it. Of course if I try "import pybel" I get: Traceback
> (most recent call last):
>   File "<pyshell#0>", line 1, in <module>
>     import pybel
> ImportError: No module named pybel
>
> Thanks for any help!
> --Dan
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] importing pybel

[Daniel S. <sin...@gm...>]

Hello,
  I'm somewhat new to python but would like to use pybel. I have openbabel
installed, but I'm not sure exactly how to get pybel working. Do I need to
install pybel separately? Is it included in some package? I can't find a
download link for it. Of course if I try "import pybel" I get: Traceback
(most recent call last):
  File "<pyshell#0>", line 1, in <module>
    import pybel
ImportError: No module named pybel

Thanks for any help!
--Dan

Re: [OpenBabel-scripting] text representation of SMARTS objects?

[Andrew F. <fa...@mo...>]

and, as an aside, it doesn't help that to access the base openbabel methods from a pybel mol object you use Pybel.Mol.OBMol, but to access the openbabel smarts methods, you need to use Pybel.Smarts.obsmarts.  :-)

On Jul 7, 2011, at 2:39 PM, Geoffrey Hutchison wrote:

>> Is there an easy way to generate a printable representation of a SMARTS query object from the object?  I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner.
> 
> Use the GetSMARTS() method?
> 
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c
> 
> Hope that helps,
> -Geoff

Re: [OpenBabel-scripting] text representation of SMARTS objects?

[Andrew F. <fa...@mo...>]

Thanks, Geoff.  (if you can't tell by the questions I ask, my C++ is basically non-existant and I get very lost, very quickly when I try to dig into the API documentation)

On Jul 7, 2011, at 2:39 PM, Geoffrey Hutchison wrote:

>> Is there an easy way to generate a printable representation of a SMARTS query object from the object?  I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner.
> 
> Use the GetSMARTS() method?
> 
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c
> 
> Hope that helps,
> -Geoff

Re: [OpenBabel-scripting] text representation of SMARTS objects?

[Geoffrey H. <ge...@ge...>]

> Is there an easy way to generate a printable representation of a SMARTS query object from the object?  I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner.

Use the GetSMARTS() method?

http://openbabel.org/api/2.3/classOpenBabel_1_1OBSmartsPattern.shtml#a52d9a732c39944ff60d06aeacb96617c

Hope that helps,
-Geoff

[OpenBabel-scripting] text representation of SMARTS objects?

[Andrew F. <fa...@mo...>]

Is there an easy way to generate a printable representation of a SMARTS query object from the object?  I guess I could carry the string representation that the query was generated from around with the query in a tuple, but I'm hoping to find something a little cleaner.

Thanks,
	Andy

[OpenBabel-scripting] Bindings compatible with Enthought Python on Windows?

[Noel O'B. <bao...@gm...>]

(ccing to the list)

I use the standard Python from Python.org. I haven't tested that the
bindings are compatible with enthought, but AFAIK everything that
works with one will work with the other.

The installer just copies three files to site-packages, pybel.py,
openbabel.py and _openbabel.pyd. These can be uninstalled from "add or
remove programs" or else manually.

- Noel

On 4 July 2011 23:46, Andrew Fant <fa...@mo...> wrote:
> Thanks, Noel.
>
> Looking through the openbabel documentation, I see that whoever wrote the windows documentation was using enthought python.  Are the binary distributions for openbabel on sourceforge compatible with enthought?  I'd try it myself, but cleaning up after bad installs on windows is such a pain that I thought I would ask an expert first.
>
> Thanks again,
>        Andy

Re: [OpenBabel-scripting] identify multi-fragment molecules in pybel?

[Noel O'B. <bao...@gm...>]

Convert to smiles and search for "." or else call
Molecule.OBMol.Separate and look at the number of components.

- Noel

On 4 July 2011 02:04, Andrew Fant <fa...@mo...> wrote:
> Is there a simple way to determine if there are multiple unlinked fragments in a molecule from pybel?  I'm trying to clean out a bunch of old compound lists that I inherited, and since I have to do it once, I might as well try to avoid doing it a second time.
>
> Thanks,
>        Andy
>
>
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