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Re: [OpenBabel-scripting] Ruby bindings for OBDepict

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

On 11 May 2011 11:50, Christoph Helma <he...@in...> wrote:
> PS: I also had to change Init_OpenBabel to Init_openbabel at line 49795
> of openbabel-ruby.cpp. This problem has been fixed in OpenBabel 2.2.3,
> but it reappeared in 2.3.0

Fixed in r4468.

Re: [OpenBabel-scripting] Ruby bindings for OBDepict

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

After googling, I see that RMagick may be a better way to convert from
SVG to PNG from Ruby.

- Noel

On 14 May 2011 18:32, Noel O'Boyle <bao...@gm...> wrote:
> Rather than use OBPainter or OBDepict, why not convert to SVG as
> normal, and then use a cairo interface to draw as a PNG. This is what
> I am doing for the python interface, eg.
>
> import cairo
> import rsvg
>
> h = rsvg.Handle("test.svg")
> s = cairo.ImageSurface(cairo.FORMAT_ARGB32, 100, 100)
> ctx = cairo.Context(s)
> h.render_cairo(ctx)
> s.write_to_png("test.png")
>
> These are GTK libraries. Maybe you can find similar libraries in Ruby?
>
> - Noel
>
> On 11 May 2011 11:50, Christoph Helma <he...@in...> wrote:
>> I wanted to substitute CDK/JChemPaint with OBDepict in our ruby based
>> webservices, but it seems that OBDepict (and also OBPaint) do not have
>> ruby bindings (other classes like OBMol or OBConversion work fine):
>>
>> depict = OpenBabel::OBDepict.new
>> NameError: uninitialized constant OpenBabel::OBDepict
>>        from (irb):1
>>
>> It seems that OBDepict is missing from scripts/ruby/openbabel-ruby.cpp
>> which changes would I need to make to create ruby bindings for OBDepict
>> (my SWIG knowledge is rather weak)?
>>
>> Best regards,
>> Christoph
>>
>> PS: I also had to change Init_OpenBabel to Init_openbabel at line 49795
>> of openbabel-ruby.cpp. This problem has been fixed in OpenBabel 2.2.3,
>> but it reappeared in 2.3.0
>>
>> ------------------------------------------------------------------------------
>> Achieve unprecedented app performance and reliability
>> What every C/C++ and Fortran developer should know.
>> Learn how Intel has extended the reach of its next-generation tools
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>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>

Re: [OpenBabel-scripting] Ruby bindings for OBDepict

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

Rather than use OBPainter or OBDepict, why not convert to SVG as
normal, and then use a cairo interface to draw as a PNG. This is what
I am doing for the python interface, eg.

import cairo
import rsvg

h = rsvg.Handle("test.svg")
s = cairo.ImageSurface(cairo.FORMAT_ARGB32, 100, 100)
ctx = cairo.Context(s)
h.render_cairo(ctx)
s.write_to_png("test.png")

These are GTK libraries. Maybe you can find similar libraries in Ruby?

- Noel

On 11 May 2011 11:50, Christoph Helma <he...@in...> wrote:
> I wanted to substitute CDK/JChemPaint with OBDepict in our ruby based
> webservices, but it seems that OBDepict (and also OBPaint) do not have
> ruby bindings (other classes like OBMol or OBConversion work fine):
>
> depict = OpenBabel::OBDepict.new
> NameError: uninitialized constant OpenBabel::OBDepict
>        from (irb):1
>
> It seems that OBDepict is missing from scripts/ruby/openbabel-ruby.cpp
> which changes would I need to make to create ruby bindings for OBDepict
> (my SWIG knowledge is rather weak)?
>
> Best regards,
> Christoph
>
> PS: I also had to change Init_OpenBabel to Init_openbabel at line 49795
> of openbabel-ruby.cpp. This problem has been fixed in OpenBabel 2.2.3,
> but it reappeared in 2.3.0
>
> ------------------------------------------------------------------------------
> Achieve unprecedented app performance and reliability
> What every C/C++ and Fortran developer should know.
> Learn how Intel has extended the reach of its next-generation tools
> to help boost performance applications - inlcuding clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Unable to open gzipped files on windows from python

[Adrià C. M. <sso...@gm...>]

I also noticed today that this bug also happens in linux (Debian and ubuntu
at least) with OB < 2.3. It doesn't happen to me with OB 2.3 on debian, but
it does with OB 2.3 on windows...

On debian I forgot to upgrade the python-openbabel package (the python
bindings) alongside the rest of OB, but it surprisingly worked (if the
commandline works, I would have thought of this as a bug on the bindings...
but it disappeared when upgrading just libopenbabel).

2011/5/7 Chris Morley <c.m...@ga...>

> On 05/05/2011 21:12, Geoffrey Hutchison wrote:
> >> I was writing an application in python which reads and writes some data
> stored in gzipped sdf and mol2 files. These files are gzipped, and I can use
> them directly with pybel.readfile in linux without problems with OB 2.3.
> However, when I try the same on MS Windows with OB 2.3 and python 2.7.1,
> when I try to read a sdf file I just get a warning like this:
> >
> > There is no support for gzip on Windows -- the C++ code used for libz has
> a known bug. (Our intent is that we'll switch to the Boost::Iostreams, which
> offers a much more robust gzip and bzip2 implementation).
>
> That's not quite right. On the Windows commandline and GUI, gzipped
> files are read ok.  It is writing of compressed files that is not
> supported because of this bug.
>
> However I find the same problem as Adrià Cereto-Massagué
>  when using Python on Windows with most gzipped files. The files are
> all read ok in the OpenBabel GUI. But strangely this file
> http://dalkescientific.com/writings/benzodiazepine.sdf.gz works ok for
> me. I'll open a bug report.
>
> Chris
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
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> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
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> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>



-- 
*Adrià Cereto Massagué*
Biotechnology student
Universitat Rovira i Virgili

Languages: Català, Español, English, Français, Deutsch, Português, Esperanto

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[OpenBabel-scripting] Ruby bindings for OBDepict

[Christoph H. <he...@in...>]

I wanted to substitute CDK/JChemPaint with OBDepict in our ruby based
webservices, but it seems that OBDepict (and also OBPaint) do not have
ruby bindings (other classes like OBMol or OBConversion work fine):

depict = OpenBabel::OBDepict.new
NameError: uninitialized constant OpenBabel::OBDepict
        from (irb):1

It seems that OBDepict is missing from scripts/ruby/openbabel-ruby.cpp
which changes would I need to make to create ruby bindings for OBDepict
(my SWIG knowledge is rather weak)?

Best regards,
Christoph

PS: I also had to change Init_OpenBabel to Init_openbabel at line 49795
of openbabel-ruby.cpp. This problem has been fixed in OpenBabel 2.2.3,
but it reappeared in 2.3.0

Re: [OpenBabel-scripting] doing energy minimization

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

See the code that pybel uses for Molecule.localopt().

- Noel

On 7 May 2011 12:09, saad khan <sk...@gm...> wrote:
> I have a large database of organic compounds which i need to minimize using
> 10000 steps of steepest descent with another 10000 steps of conjugate
> gradient. I wanted to automate this process using open-babel and its python
> bindings but i don't see any examples of energy minimization in pybel please
> suggest me what to do.
>
> thank you
> --
> saad
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

Re: [OpenBabel-scripting] Unable to open gzipped files on windows from python

[Chris M. <c.m...@ga...>]

On 05/05/2011 21:12, Geoffrey Hutchison wrote:
>> I was writing an application in python which reads and writes some data stored in gzipped sdf and mol2 files. These files are gzipped, and I can use them directly with pybel.readfile in linux without problems with OB 2.3. However, when I try the same on MS Windows with OB 2.3 and python 2.7.1, when I try to read a sdf file I just get a warning like this:
>
> There is no support for gzip on Windows -- the C++ code used for libz has a known bug. (Our intent is that we'll switch to the Boost::Iostreams, which offers a much more robust gzip and bzip2 implementation).

That's not quite right. On the Windows commandline and GUI, gzipped 
files are read ok.  It is writing of compressed files that is not 
supported because of this bug.

However I find the same problem as Adrià Cereto-Massagué
  when using Python on Windows with most gzipped files. The files are 
all read ok in the OpenBabel GUI. But strangely this file 
http://dalkescientific.com/writings/benzodiazepine.sdf.gz works ok for 
me. I'll open a bug report.

Chris

[OpenBabel-scripting] doing energy minimization

[saad k. <sk...@gm...>]

I have a large database of organic compounds which i need to minimize using
10000 steps of steepest descent with another 10000 steps of conjugate
gradient. I wanted to automate this process using open-babel and its python
bindings but i don't see any examples of energy minimization in pybel please
suggest me what to do.

thank you
-- 
saad

Re: [OpenBabel-scripting] level of MNA descriptors

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

Plugins are best called directly on a molecule with something like:

gen2d = OBOp.FindType("gen2d") # Looks up the plugin and returns it
gen2d.Do(mymol) # Calls the plugin on your molecule

- Noel

On 6 May 2011 23:22, dave.nunn <dav...@gm...> wrote:
> Did anyone get a Perl version that works? I've been attempting something
> analogous using:
>
> $OBConversion->SetOutFormat('sdf');
> $OBConversion->AddOption('gen2d',
> $Chemistry::OpenBabel::OBConversion::GENOPTIONS);
> but $OBConversion->WriteString($OBMol) warns about missing coords and gives
> me all 0.0000
>
> --
> View this message in context: http://forums.openbabel.org/level-of-MNA-descriptors-tp3472849p3504475.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] level of MNA descriptors

[dave.nunn <dav...@gm...>]

Did anyone get a Perl version that works? I've been attempting something
analogous using:

$OBConversion->SetOutFormat('sdf');
$OBConversion->AddOption('gen2d',
$Chemistry::OpenBabel::OBConversion::GENOPTIONS);
but $OBConversion->WriteString($OBMol) warns about missing coords and gives
me all 0.0000

--
View this message in context: http://forums.openbabel.org/level-of-MNA-descriptors-tp3472849p3504475.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] Unable to open gzipped files on windows from python

[Adrià C. M. <sso...@gm...>]

El 5 de maig de 2011 22:12, Geoffrey Hutchison <ge...@ge...> ha
escrit:

> > I was writing an application in python which reads and writes some data
> stored in gzipped sdf and mol2 files. These files are gzipped, and I can use
> them directly with pybel.readfile in linux without problems with OB 2.3.
> However, when I try the same on MS Windows with OB 2.3 and python 2.7.1,
> when I try to read a sdf file I just get a warning like this:
>
> There is no support for gzip on Windows -- the C++ code used for libz has a
> known bug. (Our intent is that we'll switch to the Boost::Iostreams, which
> offers a much more robust gzip and bzip2 implementation).
>
> Since you're accessing from Python, I'd suggest using Python to un-gzip and
> then read from that string using OBConversion::ReadString().
>
> Hope that helps,
> -Geoff


Thank you for your reply.
I think i'm going to simply tell the user that gzipped files are not
supported on windows,as they can be quite large files (like 15 MB), which
would use quite a lot of RAM. Or maybe I can work out  a different
workaround, like writing the unzipped files to a temporary place...

Anyways, thank you for your answer, it helped :)

Adrià Cereto-Massagué

-- 
*Adrià Cereto Massagué*
Biotechnology student
Universitat Rovira i Virgili

Languages: Català, Español, English, Français, Deutsch, Português, Esperanto

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Re: [OpenBabel-scripting] Unable to open gzipped files on windows from python

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

> I was writing an application in python which reads and writes some data stored in gzipped sdf and mol2 files. These files are gzipped, and I can use them directly with pybel.readfile in linux without problems with OB 2.3. However, when I try the same on MS Windows with OB 2.3 and python 2.7.1, when I try to read a sdf file I just get a warning like this:

There is no support for gzip on Windows -- the C++ code used for libz has a known bug. (Our intent is that we'll switch to the Boost::Iostreams, which offers a much more robust gzip and bzip2 implementation).

Since you're accessing from Python, I'd suggest using Python to un-gzip and then read from that string using OBConversion::ReadString().

Hope that helps,
-Geoff

[OpenBabel-scripting] Unable to open gzipped files on windows from python

[Adrià C. M. <sso...@gm...>]

Hi,
I was writing an application in python which reads and writes some data
stored in gzipped sdf and mol2 files. These files are gzipped, and I can use
them directly with pybel.readfile in linux without problems with OB 2.3.
However, when I try the same on MS Windows with OB 2.3 and python 2.7.1,
when I try to read a sdf file I just get a warning like this:

-------------
>>> mols = pybel.readfile('sdf','test_file.sdf.gz')
>>> mols.next().title()
==============================
*** Open Babel Warning  in OpenBabel::MDLFormat::ReadMolecule
  WARNING: Problems reading a MDL file
Missing data following atom specification in atom block

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
StopIteration
>>>
--------------------

With other formats (such as mol2) I don't even get a warning; it just
silently fails and returns an empty iterator:

--------------------
>>> mols = pybel.readfile('mol2','test_file.mol2.gz')
>>> mols.next().title()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
StopIteration
>>>
----------------------

Is this behaviour a known bug or limitation or am I doing something wrong?
I've tested it in windows XP, Windows 7 and even on wine, always with latest
packages of OB, python and OB python bindings, and is always reproducible.

Thanks in advance,

Adrià Cereto-Massagué

-- 
*Adrià Cereto Massagué*
Biotechnology student
Universitat Rovira i Virgili

Languages: Català, Español, English, Français, Deutsch, Português, Esperanto

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Re: [OpenBabel-scripting] level of MNA descriptors

[Igor F. <igo...@gm...>]

Noel,

Good call, this works!

Thank you,
Igor


On Tue, 2011-04-26 at 15:55 +0100, Noel O'Boyle wrote:
> In Python, I have either:
> 
>    conv.SetOptions("L\"0\"", conv.OUTOPTIONS)
> or
>    conv.SetOptions('L"1"', conv.OUTOPTIONS)
> 
> In other words, if you use double quotation marks, you need to escape
> the inner double quotation marks.
> 
> - Noel
> 
> On 26 April 2011 15:43, Igor Filippov <igo...@gm...> wrote:
> > Noel,
> >
> > Hmmm, I'm not sure how to parse this into Perl.
> > Is it different from what I've tried (I put the line from my script in
> > the previous email)?
> >
> > Igor
> >
> > On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
> >> The API docs say:
> >>     SetOptions: Set several single character options of specified type
> >> from string like ab"btext"c"ctext".
> >>
> >> Have you tried this?
> >>
> >> - Noel
> >>
> >> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> >> > Can anybody advise how to set up the level of MNA descriptors in Perl?
> >> >
> >> > I tried
> >> > $obconversion->SetOptions('L3',
> >> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
> >> >
> >> > It doesn't seem to do the trick.
> >> >
> >> > Regards,
> >> > Igor
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > Fulfilling the Lean Software Promise
> >> > Lean software platforms are now widely adopted and the benefits have been
> >> > demonstrated beyond question. Learn why your peers are replacing JEE
> >> > containers with lightweight application servers - and what you can gain
> >> > from the move. http://p.sf.net/sfu/vmware-sfemails
> >> > _______________________________________________
> >> > OpenBabel-scripting mailing list
> >> > Ope...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >> >
> >
> >
> >

Re: [OpenBabel-scripting] level of MNA descriptors

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

In Python, I have either:

   conv.SetOptions("L\"0\"", conv.OUTOPTIONS)
or
   conv.SetOptions('L"1"', conv.OUTOPTIONS)

In other words, if you use double quotation marks, you need to escape
the inner double quotation marks.

- Noel

On 26 April 2011 15:43, Igor Filippov <igo...@gm...> wrote:
> Noel,
>
> Hmmm, I'm not sure how to parse this into Perl.
> Is it different from what I've tried (I put the line from my script in
> the previous email)?
>
> Igor
>
> On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
>> The API docs say:
>>     SetOptions: Set several single character options of specified type
>> from string like ab"btext"c"ctext".
>>
>> Have you tried this?
>>
>> - Noel
>>
>> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
>> > Can anybody advise how to set up the level of MNA descriptors in Perl?
>> >
>> > I tried
>> > $obconversion->SetOptions('L3',
>> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>> >
>> > It doesn't seem to do the trick.
>> >
>> > Regards,
>> > Igor
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Fulfilling the Lean Software Promise
>> > Lean software platforms are now widely adopted and the benefits have been
>> > demonstrated beyond question. Learn why your peers are replacing JEE
>> > containers with lightweight application servers - and what you can gain
>> > from the move. http://p.sf.net/sfu/vmware-sfemails
>> > _______________________________________________
>> > OpenBabel-scripting mailing list
>> > Ope...@li...
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >
>
>
>

Re: [OpenBabel-scripting] level of MNA descriptors

[Igor F. <igo...@gm...>]

Noel,

Hmmm, I'm not sure how to parse this into Perl.
Is it different from what I've tried (I put the line from my script in
the previous email)?

Igor

On Mon, 2011-04-25 at 10:44 +0100, Noel O'Boyle wrote:
> The API docs say:
>     SetOptions: Set several single character options of specified type
> from string like ab"btext"c"ctext".
> 
> Have you tried this?
> 
> - Noel
> 
> On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> > Can anybody advise how to set up the level of MNA descriptors in Perl?
> >
> > I tried
> > $obconversion->SetOptions('L3',
> > $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
> >
> > It doesn't seem to do the trick.
> >
> > Regards,
> > Igor
> >
> >
> > ------------------------------------------------------------------------------
> > Fulfilling the Lean Software Promise
> > Lean software platforms are now widely adopted and the benefits have been
> > demonstrated beyond question. Learn why your peers are replacing JEE
> > containers with lightweight application servers - and what you can gain
> > from the move. http://p.sf.net/sfu/vmware-sfemails
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >

Re: [OpenBabel-scripting] level of MNA descriptors

[Chris M. <c.m...@ga...>]

The function you need is AddOption

Chris

On 23/04/2011 04:40, Igor Filippov wrote:
> Can anybody advise how to set up the level of MNA descriptors in Perl?
>
> I tried
> $obconversion->SetOptions('L3',
> $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>
> It doesn't seem to do the trick.
>
> Regards,
> Igor
>
>
> ------------------------------------------------------------------------------
> Fulfilling the Lean Software Promise
> Lean software platforms are now widely adopted and the benefits have been
> demonstrated beyond question. Learn why your peers are replacing JEE
> containers with lightweight application servers - and what you can gain
> from the move. http://p.sf.net/sfu/vmware-sfemails
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] level of MNA descriptors

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

The API docs say:
    SetOptions: Set several single character options of specified type
from string like ab"btext"c"ctext".

Have you tried this?

- Noel

On 23 April 2011 04:40, Igor Filippov <igo...@gm...> wrote:
> Can anybody advise how to set up the level of MNA descriptors in Perl?
>
> I tried
> $obconversion->SetOptions('L3',
> $Chemistry::OpenBabel::OBConversion::OUTOPTIONS);
>
> It doesn't seem to do the trick.
>
> Regards,
> Igor
>
>
> ------------------------------------------------------------------------------
> Fulfilling the Lean Software Promise
> Lean software platforms are now widely adopted and the benefits have been
> demonstrated beyond question. Learn why your peers are replacing JEE
> containers with lightweight application servers - and what you can gain
> from the move. http://p.sf.net/sfu/vmware-sfemails
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] level of MNA descriptors

[Igor F. <igo...@gm...>]

Can anybody advise how to set up the level of MNA descriptors in Perl?

I tried
$obconversion->SetOptions('L3',
$Chemistry::OpenBabel::OBConversion::OUTOPTIONS);

It doesn't seem to do the trick.

Regards,
Igor

[OpenBabel-scripting] Last chance to apply to attend Open Babel users' workshop

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

Apply before April 22nd to attend the 2nd Open Babble
(http://openbabel.org/wiki/2nd_Open_Babble), a hands-on Open Babel
workshop presented by Open Babel developers Chris Morley, Tim
Vandermeersch and Noel O'Boyle. This will take place on July 5-6 2011
at the Unilever Centre in the Dept of Chemistry, University of
Cambridge, UK.

This is the first ever users' workshop for Open Babel, one of the most
widely used cheminformatics toolkits. Open Babble presents a unique
opportunity to learn how to make the most of Open Babel, whether you
are interested in using for converting file formats, writing scripts
to analyse molecular structures, or developing your own chemistry
software.

The workshop will start on the afternoon of the 5th July, and finish
on the evening of the 6th. The exact topics covered will depend on the
attendees’ interests but will include some or all of the following:

    * Exploiting the Open Babel command line for fast searching and
filtering of molecular databases
    * How to get the most from the Open Babel GUI
    * Getting started with Python scripting for chemistry
    * Compiling C++ programs that use Open Babel
    * Writing a new plugin for Open Babel
    * How to create a user-defined molecular fingerprint
    * Combining Open Babel with other Open Source cheminformatics toolkits

To apply, visit the workshop website at:
    http://openbabel.org/wiki/2nd_Open_Babble

Regards,
   Noel O'Boyle (on behalf of Open Babble organisers)

Re: [OpenBabel-scripting] Duplicate Molecules

[Marc C. <mar...@gm...>]

Jurgens

You should be aware that Tc=1 does not guarantee that two compounds are identical, only that they could be identical. Due to the finite fingerprint length used in the comparison it is possible that the same bits will be set for non-identical structures, especially if you fold the fingerprints.

To say this another way - identical compounds must have the same fingerprints, but compounds with the same fingerprints are not necessarily identical.

Marc


On 29/03/2011, at 10:43 PM, Jurgens de Bruin <deb...@gm...> wrote:

> Hi All,
> 
> I do hope some light can be shed on the following...
> 
> I have a .sdf file that contains 2483 molecules when I run the following command ">babel in.sdf out.sdf --unique" it finds 255 duplicated, which is possible. 
> 
> When I try and do the same using python code by calculating the Tanimoto coefficient between two compounds (Tc = 1 would indicate a duplicate) I don't find any duplicated. How is this possible? 
> Python code below:
> 
> mport openbabel
> import pybel
> import csv
> from pybel import *
> 
> 
> def createFPS():
>     
>     before = 0
>     Phytochemicals = []
>     
>     for phyto in readfile("sdf","./phyto3000.sdf"):
>         Phytochemical = {}
>         before += 1
>         fps = phyto.calcfp()
>         Phytochemical["Name"] = phyto.title
>         Phytochemical["FPS"] = fps
>         Phytochemicals.append(Phytochemical)
>     
>     print "Phytochemicals in original sdf:",before
>     
>     return Phytochemicals
>         
>         
> def fDuplicated(Phytochemicals):
>     
>     stop = len(Phytochemicals)
>     count = 0
>     for x in range(0, stop):
>         for z in range(0, stop):
>             if x != z:
>                 Tc = Phytochemicals[x]['FPS'] | Phytochemicals[z]['FPS']
>         if Tc == 1:
>             print "Tc equalto 1"
>             count += 1
>             
>     print "Total Tc equal to 1",count
>     
> 
> Phytochemicals = createFPS()
> fDuplicated(Phytochemicals)
> 
> -- 
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
> 
> Jurgens de Bruin
> ------------------------------------------------------------------------------
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Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

[Igor F. [Contr] <fil...@ma...>]

Geoff,

It's not a huge deal, but it could be very useful.
If it is added to 2.3.1 can you give a simple example how to use it from
Perl?

Many thanks,
Igor

On Tue, 2011-03-29 at 13:29 -0400, Geoffrey Hutchison wrote:
> On Mar 29, 2011, at 1:14 PM, Igor Filippov [Contr] wrote:
> 
> > The object returned by $atom->GetData() is of the type:
> > Chemistry::OpenBabel::VectorpOBGenericData
> 
> Yeah, that's not a SetData. Perl is telling us, it's vector<OBGenericData*> in the C++ datatype. But I can guarantee that entry will be empty.
> 
> You're getting things mixed up, now that I look at your script. When you read an MDL file, each atom gets an OBAliasData entry, with "AliasDataType" index.
> 
> Right now, the Perl bindings don't have a cast to AliasData*, but I can go add that. Shouldn't be much of a problem.
> 
> -Geoff

Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

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

On Mar 29, 2011, at 1:14 PM, Igor Filippov [Contr] wrote:

> The object returned by $atom->GetData() is of the type:
> Chemistry::OpenBabel::VectorpOBGenericData

Yeah, that's not a SetData. Perl is telling us, it's vector<OBGenericData*> in the C++ datatype. But I can guarantee that entry will be empty.

You're getting things mixed up, now that I look at your script. When you read an MDL file, each atom gets an OBAliasData entry, with "AliasDataType" index.

Right now, the Perl bindings don't have a cast to AliasData*, but I can go add that. Shouldn't be much of a problem.

-Geoff

Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

[Igor F. [Contr] <fil...@ma...>]

Well, obviously Xx cannot be expanded. Still I'd like to get that atom
12 (for example) has alias "Xx". I can do it in C++.
Judging by the warning message the fact that the alias was Xx got
recorded somewhere, but how to get this information out?

Best regards,
Igor

On Tue, 2011-03-29 at 13:15 -0400, Noel O'Boyle wrote:
> On 29 March 2011 18:07, Geoffrey Hutchison <ge...@ge...> wrote:
> >> TypeError in method 'toSetData', argument 1 of type
> >> 'OpenBabel::OBGenericData *'
> >>
> >> Does it mean that the argument should not be an object returned by
> >> GetData()? What should it be then?
> >
> > It's been a while since I've used the Perl bindings. What does ref($ad) return?
> >
> > Do you need to use the SetData hierarchy? I'm wondering if the extra redirection is the issue.
> 
> With the example file in the bug, I have:
> 
> C:\Users\Noel\Downloads>babel example.sdf -osmi
> ==============================
> *** Open Babel Warning  in OpenBabel::AliasData::Expand
>   Alias Xx Could not be interpreted.
>  Output may not be correct.
> C1=NCC(C(/C=C\C/*=C(/C(c2c(C=C)ccc(c2)NC(=N)c2cc(C)c(c(C)c2)*)C)\C)C)C=C1
> 
> 1 molecule converted
> 1 warnings 50 audit log messages
> 
> ...so I don't think it's related to the Perl bindings.
> 
> - Noel

Re: [OpenBabel-scripting] [Open Babel] how to access getAlias() in perl

[Igor F. [Contr] <fil...@ma...>]

Geoff,

I'd like to get the atom alias for any atom in a molecule which have
atom alias specified. I don't really care whether it's using "SetData"
but I don't know any other way.
The object returned by $atom->GetData() is of the type:
Chemistry::OpenBabel::VectorpOBGenericData

>From there on, nothing really works, I cannot get to $ad (=
Chemistry::OpenBabel::toSetData($n)) because I get the error:
TypeError in method 'toSetData', argument 1 of type
'OpenBabel::OBGenericData *'

Igor

On Tue, 2011-03-29 at 13:07 -0400, Geoffrey Hutchison wrote:
> > TypeError in method 'toSetData', argument 1 of type
> > 'OpenBabel::OBGenericData *'
> > 
> > Does it mean that the argument should not be an object returned by
> > GetData()? What should it be then? 
> 
> It's been a while since I've used the Perl bindings. What does ref($ad) return?
> 
> Do you need to use the SetData hierarchy? I'm wondering if the extra redirection is the issue.
> 
> -Geoff