Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi Niko,
I tried this piece of code adapted from the doctest and got the same
result (table is fine, but no rendering of molecules):
from rdkit.Chem import PandasTools
import pandas as pd
import os
from rdkit import RDConfig
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
antibiotics = pd.DataFrame(columns=['Name','Smiles'])
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C','Name':'Penicilline
G'}, ignore_index=True)#Penicilline G
antibiotics =
antibiotics.append({'Smiles':'CC1(C2CC3C(C(=O)C(=C(C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O','Name':'Tetracycline'},
ignore_index=True)#Tetracycline
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)C(C3=CC=CC=C3)N)C(=O)O)C','Name':'Ampicilline'},
ignore_index=True)#Ampicilline
PandasTools.AddMoleculeColumnToFrame(antibiotics,'Smiles','Molecule',includeFingerprints=True)
display(HTML(antibiotics.to_html()))
The img tag and the png encoding themselves are fine. If I paste one in
a simple html page and open it with the same browser the molecule is
rendered.
Best,
Markus
On 05/08/2013 09:03 AM, Fechner, Nikolas wrote:
Hi Markus,
Could you try the examples that are included as doctests in the
PandasTools.py module? These should definitely work and show rendered
molecules in the tables.
Best,
Niko
From: Markus Hartenfeller markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com
Date: Tuesday, May 7, 2013 1:40 PM
To: rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want to paste the whole beast. The fields contain
the full strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had problems with *very*
long png strings, because the pandas maximal column width applies to
the string, which is what is stored in the dataframe, before the
image rendering. As an effect the truncated png string was shown in
the table (exactly the ...' ending shown in your example).
You could try manually setting the maximal width very high (e.g.
pandas.set_option(display.max_colwidth,10)). This should be
done automatically by the PandasTools, which sets it the len(PNG)+100
for the longest string found during rendering, but because this
rarely had an impact I could very well have overseen some problems
with this strategy.
Best,
Niko
On May 7, 2013 at 1:13 PM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Thanks again for your reply. That's what I have tried:
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
df = PandasTools.LoadSDF('test.sdf', includeFingerprints=False)
display(HTML(df.to_html()))
So it is a dataframe and .to_html() works fine in general. I see all
sdf fields. It's just that the molecule column contains string value
of this kind:
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
The notebook somehow does not realize that it is an html tag with an
image, but instead renders it as a normal string (just like before
with the single molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
Just for clarification, are you trying to render a dataframe or a
series/single column? The pandas series object has no to_html()
method and is therefore rendered as string only. Moreover, if you
select a single column, e.g. 'ROMol' from a dataframe by
df['ROMol'] you will get a series object that is rendered as
string. If you select a set of columns you get a dataframe, for
which the HTML rendering should work. The latter also works for a
single column if you enclose in double brackets df[ *[*'ROMol'
*]*], which will give a single-column dataframe. This took me some
time to figure out and the silent conversion that sometimes occurs
can be quite confusing.
Best,
Niko
On May 7, 2013 at 11:33 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Thanks for your help, Niko. Importing the iPythonConsole from
rdkit + removing the 'print' command did the trick for a single
molecule :)
Unfortunately, molecules in data frames are still shown as
strings, even when forcing html rendering. I will try to get this
working and report here if I make any progress. In case somebody
has already faced the same problem please let me know.
Best,
Markus
On 05/07/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem,
there are two things: You
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi Markus,
Sorry, but I am running a bit out of ideas. Could you check whether the
structures are rendered if you write the dataframe.to_html() to a file and
open that as a webpage. If this works than it probably has to do something with
the ipython environment (btw, which version are you using?).
Best,
Niko
On May 8, 2013 at 9:51 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Hi Niko,
I tried this piece of code adapted from the doctest and got the same result
(table is fine, but no rendering of molecules):
from rdkit.Chem import PandasTools
import pandas as pd
import os
from rdkit import RDConfig
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
antibiotics = pd.DataFrame(columns=['Name','Smiles'])
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C','Name':'Penicilline
G'}, ignore_index=True)#Penicilline G
antibiotics =
antibiotics.append({'Smiles':'CC1(C2CC3C(C(=O)C(=C(C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O','Name':'Tetracycline'},
ignore_index=True)#Tetracycline
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)C(C3=CC=CC=C3)N)C(=O)O)C','Name':'Ampicilline'},
ignore_index=True)#Ampicilline
PandasTools.AddMoleculeColumnToFrame(antibiotics,'Smiles','Molecule',includeFingerprints=True)
display(HTML(antibiotics.to_html()))
The img tag and the png encoding themselves are fine. If I paste one in a
simple html page and open it with the same browser the molecule is rendered.
Best,
Markus
On 05/08/2013 09:03 AM, Fechner, Nikolas wrote:
Hi Markus,
Could you try the examples that are included as doctests in the
PandasTools.py module? These should definitely work and show rendered
molecules in the tables.
Best,
Niko
From: Markus Hartenfeller markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com
Date: Tuesday, May 7, 2013 1:40 PM
To: rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want to paste the whole beast. The fields contain the full
strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had
problems with *very* long png strings, because the pandas
maximal column width applies to the string, which is what is
stored in the dataframe, before the image rendering. As an
effect the truncated png string was shown in the table
(exactly the ...' ending shown in your example).
You could try manually setting the maximal width very high (e.g.
pandas.set_option(display.max_colwidth,10)). This should be done
automatically by the PandasTools, which sets it the len(PNG)+100 for the
longest string found during rendering, but because this rarely had an
impact I could very well have overseen some problems with this strategy.
Best,
Niko
On May 7, 2013 at 1:13 PM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Thanks again for your reply. That's what I have tried:
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
df = PandasTools.LoadSDF('test.sdf',
includeFingerprints=False)
display(HTML(df.to_html()))
So it is a dataframe and .to_html() works fine in general. I
see all sdf fields. It's just that the molecule column contains string
value of this kind:
img
src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
The notebook somehow does not realize that it is an html tag
with an image, but instead renders it as a normal string (just like
before with the single molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
Just for clarification, are you
trying to render a dataframe or a series/single
column? The pandas series object has no
to_html() method and is therefore rendered
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi,
Strange, I'm also using pandas 0.10.1, but it seems pretty obvious to me
that the problem is related to that, although it's not exactly clear to
me now why it should not happen at your system but on only on mine then :)
For the others following the conversation: Sorry for being sloppy and
discussing with Niko directly and in German, but I wanted to check the
hypothesis with him first to spare you the additional email traffic and
just let you know the result once we found the problem:
When printing out the html code to a file as Niko suggested I realized
that '' and '' at the beginning and the end of the img tag are masked
in the html code as 'lt;' and 'gt;'. This makes the html parser of the
browser ignore them (and at the same time displaying the correct
characters in the string in the table). Unmasking them in the html code
gives the correct renderings of the molecules.
Best,
Markus
On 05/08/2013 11:25 AM, Nikolas Fechner wrote:
Hi Markus,
Nice find! That could very likely be the cause for the problem. I just
saw that in the very recent version 0.11 (22. April 2013) a new
attribute was introduced to the pandas to_html() method that should
have exactly that effect.
*escape : boolean, default True*
*Convert the characters , , and to HTML-safe sequences.*
This wasn't there in versions 0.10/0.10.1, which is what I was using
so far. Are you using pandas 0.11? I will update my pandas and check
that and if necessary find a way to deal with this in the PandasTools.
Thanks for finding that.
Best,
Niko
**
**
On May 8, 2013 at 10:59 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Hi Niko,
Ich weiss jetzt denke ich woran es liegt: Im Anhang findest du 2
files: antibiotics.html ist der direkte print-out von python. Die
Zeichen '' und '' am Anfang und am Ende des img tags sind im Code
html-maskiert, also durch 'lt;' bzw. 'gt;' ersetzt. Deshalb werden
sie im Browser auch 'normal' angezeigt. Wenn ich sie durch die ASCII
Zeichen ersetze (wie im File _antibiotics.html) zeigt der browser die
Strukturen korrekt an.
Wenn du mal Zeit dafuer hast: Kannst du das im code nachvollziehen?
Cheers,
Markus
On 05/08/2013 10:29 AM, Nikolas Fechner wrote:
Hi Markus,
Sorry, but I am running a bit out of ideas. Could you check whether
the structures are rendered if you write the dataframe.to_html()
to a file and open that as a webpage. If this works than it probably
has to do something with the ipython environment (btw, which version
are you using?).
Best,
Niko
On May 8, 2013 at 9:51 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Hi Niko,
I tried this piece of code adapted from the doctest and got the
same result (table is fine, but no rendering of molecules):
from rdkit.Chem import PandasTools
import pandas as pd
import os
from rdkit import RDConfig
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
antibiotics = pd.DataFrame(columns=['Name','Smiles'])
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C','Name':'Penicilline
G'}, ignore_index=True)#Penicilline G
antibiotics =
antibiotics.append({'Smiles':'CC1(C2CC3C(C(=O)C(=C(C3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O','Name':'Tetracycline'},
ignore_index=True)#Tetracycline
antibiotics =
antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)C(C3=CC=CC=C3)N)C(=O)O)C','Name':'Ampicilline'},
ignore_index=True)#Ampicilline
PandasTools.AddMoleculeColumnToFrame(antibiotics,'Smiles','Molecule',includeFingerprints=True)
display(HTML(antibiotics.to_html()))
The img tag and the png encoding themselves are fine. If I paste
one in a simple html page and open it with the same browser the
molecule is rendered.
Best,
Markus
On 05/08/2013 09:03 AM, Fechner, Nikolas wrote:
Hi Markus,
Could you try the examples that are included as doctests in the
PandasTools.py module? These should definitely work and show
rendered molecules in the tables.
Best,
Niko
From: Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com
Date: Tuesday, May 7, 2013 1:40 PM
To: rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
mailto:rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] New module for RDKit - PANDAS
integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want to paste the whole beast. The fields
contain the full strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had problems with
*very* long png strings, because the pandas maximal column width
applies to the string, which is what is stored in the dataframe,
before the image rendering. As an effect the truncated png string
was shown
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think this
is going to be useful for many rdkit users. I'm looking forward to using
it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython
notebook though (both in tables and by just printing out a single molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
...
a very long string with the base64 encoding of the image, but not the
image itself. Plotting from matplotlib works fine. Did I forget to
import something, or could it be a browser issue? I am using centOS 6
and Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows
for using RDKit molecule objects directly in pandas dataframes. Pandas
(http://pandas.pydata.org/) is a python library that offers table-like
datacontainers, which are incredibly useful for anything related to
data mining. Moreover, it integrates nicely with the ipython notebook
producing rendered HTML tables for the dataframes. The RDKit
integration allows to have molecule-type columns and functionality to
perform substructure-based row filtering directly on the pandas table.
Additionally, if a dataframe is exported as HTML or shown within an
ipython notebook, the molecules in the table are rendered as 2D
structures.
The new module is available in the current SF trunk and contains a
doctest header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug reports,
comments, ideas... are very much appreciated.
Best,
Nikolas
--
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi Markus,
glad you think it could be useful :). Regarding the problem, there are two
things: You have to import the RDKit IPythonConsole to enable the molecule
rendering (from rdkit.Chem.Draw import IPythonConsole) and if you trigger the
output using 'print' the notebook will always use string rendering (AFAIK). Just
try 'm' alone (instead of 'print m'). Alternatively, you can always force the
notebook to do a HTML rendering (useful for large dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think this is
going to be useful for many rdkit users. I'm looking forward to using it in
the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython notebook
though (both in tables and by just printing out a single molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
a very long string with the base64 encoding of the image, but not the image
itself. Plotting from matplotlib works fine. Did I forget to import something,
or could it be a browser issue? I am using centOS 6 and Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows for
using RDKit molecule objects directly in pandas dataframes. Pandas (
http://pandas.pydata.org/ http://pandas.pydata.org/ ) is a python library
that offers table-like datacontainers, which are incredibly useful for
anything related to data mining. Moreover, it integrates nicely with the
ipython notebook producing rendered HTML tables for the dataframes. The
RDKit integration allows to have molecule-type columns and functionality to
perform substructure-based row filtering directly on the pandas table.
Additionally, if a dataframe is exported as HTML or shown within an ipython
notebook, the molecules in the table are rendered as 2D structures.
The new module is available in the current SF trunk and contains a
doctest header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug reports,
comments, ideas... are very much appreciated.
Best,
Nikolas
--
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for
building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
http://www2.precog.com/precogplatform/slashdotnewsletter
___
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Rdkit-discuss@lists.sourceforge.net
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Graph Databases is the definitive new guide to graph databases and
their applications. This 200-page book is written by three acclaimed
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Download your free book today!
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Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Thanks for your help, Niko. Importing the iPythonConsole from rdkit +
removing the 'print' command did the trick for a single molecule :)
Unfortunately, molecules in data frames are still shown as strings, even
when forcing html rendering. I will try to get this working and report
here if I make any progress. In case somebody has already faced the same
problem please let me know.
Best,
Markus
On 05/07/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem, there are
two things: You have to import the RDKit IPythonConsole to enable the
molecule rendering (from rdkit.Chem.Draw import IPythonConsole) and if
you trigger the output using 'print' the notebook will always use
string rendering (AFAIK). Just try 'm' alone (instead of 'print m').
Alternatively, you can always force the notebook to do a HTML
rendering (useful for large dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think
this is going to be useful for many rdkit users. I'm looking forward
to using it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython
notebook though (both in tables and by just printing out a single
molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
a very long string with the base64 encoding of the image, but not the
image itself. Plotting from matplotlib works fine. Did I forget to
import something, or could it be a browser issue? I am using centOS 6
and Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows
for using RDKit molecule objects directly in pandas dataframes.
Pandas ( http://pandas.pydata.org/) is a python library that offers
table-like datacontainers, which are incredibly useful for anything
related to data mining. Moreover, it integrates nicely with the
ipython notebook producing rendered HTML tables for the dataframes.
The RDKit integration allows to have molecule-type columns and
functionality to perform substructure-based row filtering directly
on the pandas table. Additionally, if a dataframe is exported as
HTML or shown within an ipython notebook, the molecules in the table
are rendered as 2D structures.
The new module is available in the current SF trunk and contains a
doctest header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug reports,
comments, ideas... are very much appreciated.
Best,
Nikolas
--
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
___
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Graph Databases is the definitive new guide to graph databases and
their applications. This 200-page book is written by three acclaimed
leaders in the field. The early access version is available now.
Download your free book today!
http://p.sf.net/sfu/neotech_d2d_may___
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their applications. This 200-page book is written by three acclaimed
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Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Just for clarification, are you trying to render a dataframe or a series/single
column? The pandas series object has no to_html() method and is therefore
rendered as string only. Moreover, if you select a single column, e.g. 'ROMol'
from a dataframe by df['ROMol'] you will get a series object that is rendered as
string. If you select a set of columns you get a dataframe, for which the HTML
rendering should work. The latter also works for a single column if you enclose
in double brackets df[ ['ROMol' ]], which will give a single-column dataframe.
This took me some time to figure out and the silent conversion that sometimes
occurs can be quite confusing.
Best,
Niko
On May 7, 2013 at 11:33 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Thanks for your help, Niko. Importing the iPythonConsole from rdkit + removing
the 'print' command did the trick for a single molecule :)
Unfortunately, molecules in data frames are still shown as strings, even when
forcing html rendering. I will try to get this working and report here if I
make any progress. In case somebody has already faced the same problem please
let me know.
Best,
Markus
On 05/07/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem, there are
two things: You have to import the RDKit IPythonConsole to enable the
molecule rendering (from rdkit.Chem.Draw import IPythonConsole) and if you
trigger the output using 'print' the notebook will always use string
rendering (AFAIK). Just try 'm' alone (instead of 'print m'). Alternatively,
you can always force the notebook to do a HTML rendering (useful for large
dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think
this is going to be useful for many rdkit users. I'm looking forward to
using it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython
notebook though (both in tables and by just printing out a single
molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img
src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
a very long string with the base64 encoding of the image, but not
the image itself. Plotting from matplotlib works fine. Did I forget to
import something, or could it be a browser issue? I am using centOS 6 and
Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that
allows for using RDKit molecule objects directly in pandas dataframes.
Pandas ( http://pandas.pydata.org/ http://pandas.pydata.org/ ) is a
python library that offers table-like datacontainers, which are
incredibly useful for anything related to data mining. Moreover, it
integrates nicely with the ipython notebook producing rendered HTML
tables for the dataframes. The RDKit integration allows to have
molecule-type columns and functionality to perform substructure-based
row filtering directly on the pandas table. Additionally, if a dataframe
is exported as HTML or shown within an ipython notebook, the molecules
in the table are rendered as 2D structures.
The new module is available in the current SF trunk and
contains a doctest header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug
reports, comments, ideas... are very much appreciated.
Best,
Nikolas
--
Precog is a next-generation analytics platform capable of
advanced
analytics on semi-structured data. The platform includes APIs
for building
apps and a phenomenal toolset for data science. Developers can
use
our toolset for easy data analysis visualization. Get a free
account!
http://www2.precog.com/precogplatform/slashdotnewsletter
http://www2.precog.com/precogplatform/slashdotnewsletter
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
When developing the module I occasionally had problems with *very* long png
strings, because the pandas maximal column width applies to the string, which is
what is stored in the dataframe, before the image rendering. As an effect the
truncated png string was shown in the table (exactly the ...' ending shown in
your example).
You could try manually setting the maximal width very high (e.g.
pandas.set_option(display.max_colwidth,10)). This should be done
automatically by the PandasTools, which sets it the len(PNG)+100 for the longest
string found during rendering, but because this rarely had an impact I could
very well have overseen some problems with this strategy.
Best,
Niko
On May 7, 2013 at 1:13 PM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Thanks again for your reply. That's what I have tried:
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
df = PandasTools.LoadSDF('test.sdf', includeFingerprints=False)
display(HTML(df.to_html()))
So it is a dataframe and .to_html() works fine in general. I see all sdf
fields. It's just that the molecule column contains string value of this kind:
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
The notebook somehow does not realize that it is an html tag with an image,
but instead renders it as a normal string (just like before with the single
molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
Just for clarification, are you trying to render a dataframe or
a series/single column? The pandas series object has no to_html()
method and is therefore rendered as string only. Moreover, if you
select a single column, e.g. 'ROMol' from a dataframe by df['ROMol']
you will get a series object that is rendered as string. If you
select a set of columns you get a dataframe, for which the HTML
rendering should work. The latter also works for a single column if
you enclose in double brackets df[ ['ROMol' ]], which will give a
single-column dataframe. This took me some time to figure out and the
silent conversion that sometimes occurs can be quite confusing.
Best,
Niko
On May 7, 2013 at 11:33 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Thanks for your help, Niko. Importing the iPythonConsole from
rdkit + removing the 'print' command did the trick for a single
molecule :)
Unfortunately, molecules in data frames are still shown as strings,
even when forcing html rendering. I will try to get this working and
report here if I make any progress. In case somebody has already faced the
same problem please let me know.
Best,
Markus
On 05/07/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem,
there are two things: You have to import the RDKit IPythonConsole to
enable the molecule rendering (from rdkit.Chem.Draw import
IPythonConsole) and if you trigger the output using 'print' the notebook
will always use string rendering (AFAIK). Just try 'm' alone (instead of
'print m'). Alternatively, you can always force the notebook to do a
HTML rendering (useful for large dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I
think this is going to be useful for many rdkit users. I'm looking
forward to using it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the
ipython notebook though (both in tables and by just printing out a
single molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img
src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
a very long string with the base64
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Sorry for the confusion, I truncated the string myself in the mail
because I did not want to paste the whole beast. The fields contain the
full strings and the tag is closed.
Best,
Markus
On 05/07/2013 01:25 PM, Nikolas Fechner wrote:
When developing the module I occasionally had problems with *very*
long png strings, because the pandas maximal column width applies to
the string, which is what is stored in the dataframe, before the image
rendering. As an effect the truncated png string was shown in the
table (exactly the ...' ending shown in your example).
You could try manually setting the maximal width very high (e.g.
pandas.set_option(display.max_colwidth,10)). This should be done
automatically by the PandasTools, which sets it the len(PNG)+100 for
the longest string found during rendering, but because this rarely had
an impact I could very well have overseen some problems with this
strategy.
Best,
Niko
On May 7, 2013 at 1:13 PM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com wrote:
Thanks again for your reply. That's what I have tried:
from rdkit import Chem
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem import PandasTools
from rdkit.Chem.Draw import IPythonConsole
from IPython.core.display import HTML
df = PandasTools.LoadSDF('test.sdf', includeFingerprints=False)
display(HTML(df.to_html()))
So it is a dataframe and .to_html() works fine in general. I see all
sdf fields. It's just that the molecule column contains string value
of this kind:
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
The notebook somehow does not realize that it is an html tag with an
image, but instead renders it as a normal string (just like before
with the single molecule).
Best wishes,
Markus
On 05/07/2013 12:57 PM, Nikolas Fechner wrote:
Just for clarification, are you trying to render a dataframe or a
series/single column? The pandas series object has no to_html()
method and is therefore rendered as string only. Moreover, if you
select a single column, e.g. 'ROMol' from a dataframe by df['ROMol']
you will get a series object that is rendered as string. If you
select a set of columns you get a dataframe, for which the HTML
rendering should work. The latter also works for a single column if
you enclose in double brackets df[ *[*'ROMol' *]*], which will give
a single-column dataframe. This took me some time to figure out and
the silent conversion that sometimes occurs can be quite confusing.
Best,
Niko
On May 7, 2013 at 11:33 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Thanks for your help, Niko. Importing the iPythonConsole from rdkit
+ removing the 'print' command did the trick for a single molecule :)
Unfortunately, molecules in data frames are still shown as strings,
even when forcing html rendering. I will try to get this working
and report here if I make any progress. In case somebody has
already faced the same problem please let me know.
Best,
Markus
On 05/07/2013 10:27 AM, Nikolas Fechner wrote:
Hi Markus,
glad you think it could be useful :). Regarding the problem, there
are two things: You have to import the RDKit IPythonConsole to
enable the molecule rendering (from rdkit.Chem.Draw import
IPythonConsole) and if you trigger the output using 'print' the
notebook will always use string rendering (AFAIK). Just try 'm'
alone (instead of 'print m'). Alternatively, you can always force
the notebook to do a HTML rendering (useful for large dataframe):
from IPython.core.display import HTML
display(HTML('''any HTML string e.g. dataframe.to_html()'''))
I hope that helps.
Best,
Niko
On May 7, 2013 at 10:02 AM Markus Hartenfeller
markus.hartenfel...@molecularhealth.com
mailto:markus.hartenfel...@molecularhealth.com wrote:
Hi Nikolas,
I had a first look at the PandasTools package: very cool! I think
this is going to be useful for many rdkit users. I'm looking
forward to using it in the future. Thanks for sharing this module.
I'm having troubles to see the molecule depictions in the ipython
notebook though (both in tables and by just printing out a single
molecule).
This code in a ipython notebook
from rdkit import Chem
from rdkit.Chem import PandasTools
m=Chem.MolFromSmiles('N1CCNCC1')
print m
gives me
img src=data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAYAAAB ...
a very long string with the base64 encoding of the image, but not
the image itself. Plotting from matplotlib works fine. Did I
forget to import something, or could it be a browser issue? I am
using centOS 6 and Firefox.
Thanks in advance.
Best,
Markus
On 04/19/2013 11:56 AM, Nikolas Fechner wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that
allows for using RDKit molecule objects directly in pandas
dataframes. Pandas ( http://pandas.pydata.org/) is a python
library that offers table-like datacontainers, which
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
I just started playing around with the Pandas module, this is very cool stuff. Thanks so much Nikolas for the contribution. I definitely owe you a beer at the UGM. It might be worth noting that the you need to install PIL in order to use the Pandas module. Everything will install without a problem, but you'll get an exception like this when you try to print a dataframe without PIL. File /Users/walters/python/RDKIT_2013_04_21/rdkit/sping/PIL/pidPIL.py, line 33, in module import Image, ImageFont, ImageDraw Best, Pat On Sun, Apr 21, 2013 at 5:00 PM, Taka Seri serit...@gmail.com wrote: Dear Greg. Thank you your quick reply ! The modified version was worked without AvalonTools . That's nice tool . I appreciate your kindness. Takayuki 2013/4/22 Greg Landrum greg.land...@gmail.com Dear Takayuki, On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote: I'm interested in this work I want to use PandasTools. But I got error message, ImportError: cannot import name pyAvalonTools. I just checked in a modified version that will work when the avalon tools are not installed. If you want to install the avalon tools anyway, there's information below that shows how: So, I tried to rebuild RDKit like this. $ cmake -D RDK_BUID_AVALON_SUPPORT=ON But build was failed. -- Configuring done CMake Error at Code/cmake/Modules/RDKitUtils.cmake:35 (add_library): Cannot find source file: /common/layout.c Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:43 (rdkit_library) If anyone who has suggestion, please help me. You need to tell it where to find the source for the avalon tools. - Download the source from here: http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download - Create an avalon tools directory somewhere, for example in /usr/local/src/avalontools. - Extract the tar file in that directory. - Run cmake as follows: cmake -DAVALONTOOLS_DIR=/usr/local/src/avalontools/SourceDistribution -DRDK_BUILD_AVALON_SUPPORT=ON Best, -greg -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Hi Pat, I am glad you find it useful. Many thanks for pointing out the PIL dependency. I had installed It already for different reasons and did not think about mentioning it. Best, Niko On 22 Apr 2013, at 17:52, Patrick Walters wpwalt...@gmail.com wrote: I just started playing around with the Pandas module, this is very cool stuff. Thanks so much Nikolas for the contribution. I definitely owe you a beer at the UGM. It might be worth noting that the you need to install PIL in order to use the Pandas module. Everything will install without a problem, but you'll get an exception like this when you try to print a dataframe without PIL. File /Users/walters/python/RDKIT_2013_04_21/rdkit/sping/PIL/pidPIL.py, line 33, in module import Image, ImageFont, ImageDraw Best, Pat On Sun, Apr 21, 2013 at 5:00 PM, Taka Seri serit...@gmail.com wrote: Dear Greg. Thank you your quick reply ! The modified version was worked without AvalonTools . That's nice tool . I appreciate your kindness. Takayuki 2013/4/22 Greg Landrum greg.land...@gmail.com Dear Takayuki, On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote: I'm interested in this work I want to use PandasTools. But I got error message, ImportError: cannot import name pyAvalonTools. I just checked in a modified version that will work when the avalon tools are not installed. If you want to install the avalon tools anyway, there's information below that shows how: So, I tried to rebuild RDKit like this. $ cmake -D RDK_BUID_AVALON_SUPPORT=ON But build was failed. -- Configuring done CMake Error at Code/cmake/Modules/RDKitUtils.cmake:35 (add_library): Cannot find source file: /common/layout.c Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:43 (rdkit_library) If anyone who has suggestion, please help me. You need to tell it where to find the source for the avalon tools. - Download the source from here: http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download - Create an avalon tools directory somewhere, for example in /usr/local/src/avalontools. - Extract the tar file in that directory. - Run cmake as follows: cmake -DAVALONTOOLS_DIR=/usr/local/src/avalontools/SourceDistribution -DRDK_BUILD_AVALON_SUPPORT=ON Best, -greg -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Dear Takayuki, On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote: I'm interested in this work I want to use PandasTools. But I got error message, ImportError: cannot import name pyAvalonTools. I just checked in a modified version that will work when the avalon tools are not installed. If you want to install the avalon tools anyway, there's information below that shows how: So, I tried to rebuild RDKit like this. $ cmake -D RDK_BUID_AVALON_SUPPORT=ON But build was failed. -- Configuring done CMake Error at Code/cmake/Modules/RDKitUtils.cmake:35 (add_library): Cannot find source file: /common/layout.c Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:43 (rdkit_library) If anyone who has suggestion, please help me. You need to tell it where to find the source for the avalon tools. - Download the source from here: http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download - Create an avalon tools directory somewhere, for example in /usr/local/src/avalontools. - Extract the tar file in that directory. - Run cmake as follows: cmake -DAVALONTOOLS_DIR=/usr/local/src/avalontools/SourceDistribution -DRDK_BUILD_AVALON_SUPPORT=ON Best, -greg -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
Dear Greg. Thank you your quick reply ! The modified version was worked without AvalonTools . That's nice tool . I appreciate your kindness. Takayuki 2013/4/22 Greg Landrum greg.land...@gmail.com Dear Takayuki, On Sun, Apr 21, 2013 at 1:30 PM, Taka Seri serit...@gmail.com wrote: I'm interested in this work I want to use PandasTools. But I got error message, ImportError: cannot import name pyAvalonTools. I just checked in a modified version that will work when the avalon tools are not installed. If you want to install the avalon tools anyway, there's information below that shows how: So, I tried to rebuild RDKit like this. $ cmake -D RDK_BUID_AVALON_SUPPORT=ON But build was failed. -- Configuring done CMake Error at Code/cmake/Modules/RDKitUtils.cmake:35 (add_library): Cannot find source file: /common/layout.c Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx Call Stack (most recent call first): External/AvalonTools/CMakeLists.txt:43 (rdkit_library) If anyone who has suggestion, please help me. You need to tell it where to find the source for the avalon tools. - Download the source from here: http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download - Create an avalon tools directory somewhere, for example in /usr/local/src/avalontools. - Extract the tar file in that directory. - Run cmake as follows: cmake -DAVALONTOOLS_DIR=/usr/local/src/avalontools/SourceDistribution -DRDK_BUILD_AVALON_SUPPORT=ON Best, -greg -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] New module for RDKit - PANDAS integration
Dear all, We developed a new module ( rdkit.Chem.PandasTools.py ) that allows for using RDKit molecule objects directly in pandas dataframes. Pandas (http://pandas.pydata.org/) is a python library that offers table-like datacontainers, which are incredibly useful for anything related to data mining. Moreover, it integrates nicely with the ipython notebook producing rendered HTML tables for the dataframes. The RDKit integration allows to have molecule-type columns and functionality to perform substructure-based row filtering directly on the pandas table. Additionally, if a dataframe is exported as HTML or shown within an ipython notebook, the molecules in the table are rendered as 2D structures. The new module is available in the current SF trunk and contains a doctest header that provides examples of how to use it. I hope some of you find that interesting. As always, bug reports, comments, ideas... are very much appreciated. Best, Nikolas -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] New module for RDKit - PANDAS integration
I think Nikolas is being a bit modest... the Pandas integration is
pretty cool. :-)
Here's an example of using it from the IPython prompt (it's better in
the notebook, but that doesn't paste so nicely into email)
Loading an SD file:
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import PandasTools
In [3]: import pandas as pd
In [4]: df =
PandasTools.LoadSDF('hERG_inhibition_dataset.sdf',includeFingerprints=True)
In [5]: df
Out[5]:
class 'pandas.core.frame.DataFrame'
Int64Index: 242 entries, 0 to 241
Data columns:
ACTIVITY_CLASS242 non-null values
CompoundName 242 non-null values
ID242 non-null values
MDLPublicKeys 242 non-null values
SMILES242 non-null values
pIC50 242 non-null values
ROMol 242 non-null values
dtypes: object(7)
And doing a substructure search:
In [6]: N3s = df[df['ROMol']=Chem.MolFromSmiles('N(C)(C)C')]
In [7]: N3s
Out[7]:
class 'pandas.core.frame.DataFrame'
Int64Index: 177 entries, 0 to 239
Data columns:
ACTIVITY_CLASS177 non-null values
CompoundName 177 non-null values
ID177 non-null values
MDLPublicKeys 177 non-null values
SMILES177 non-null values
pIC50 177 non-null values
ROMol 177 non-null values
dtypes: object(7)
Because I used the includeFingerprints argument, that actually did
the search using a substructure fingerprint to speed things up. This
is using the avalon fingerprint at the moment, but that will change
between now and the release so as to not add an additional dependency.
-greg
On Fri, Apr 19, 2013 at 11:56 AM, Nikolas Fechner niko...@fechner.cc wrote:
Dear all,
We developed a new module ( rdkit.Chem.PandasTools.py ) that allows for
using RDKit molecule objects directly in pandas dataframes. Pandas
(http://pandas.pydata.org/) is a python library that offers table-like
datacontainers, which are incredibly useful for anything related to data
mining. Moreover, it integrates nicely with the ipython notebook producing
rendered HTML tables for the dataframes. The RDKit integration allows to
have molecule-type columns and functionality to perform substructure-based
row filtering directly on the pandas table. Additionally, if a dataframe is
exported as HTML or shown within an ipython notebook, the molecules in the
table are rendered as 2D structures.
The new module is available in the current SF trunk and contains a doctest
header that provides examples of how to use it.
I hope some of you find that interesting. As always, bug reports, comments,
ideas... are very much appreciated.
Best,
Nikolas
--
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
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Rdkit-discuss mailing list
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--
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
