[Rdkit-discuss] Windows and PandasTools again

2014-09-26 Thread Samo Turk 
Hi All,

While we are at PandasTools and Windows. If you use Anaconda on Windows and
Riccardo Vianello's excellent and convenient binstar package PandasTools
also returns an error because it looks for Salts.txt at the wrong place.
You can fix it by opening
WereEverYouHave\Anaconda\Lib\site-packages\rdkit\RDPaths.py and modifying
RDCodeDir and _share to:
RDCodeDir=os.path.dirname(__file__)
_share = os.path.join(r'WereEverYouHave/Anaconda/Library', r'share/RDKit')

Cheers,
Samo
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2014-09-26 Thread Markus Hartenfeller 

Hi Paul,

I had a similar problem and discussed it with Niko here on the list (around 7/8 
May 2013).

The solution was to update to Pandas 0.11 and use this call for displaying the 
table:

display(HTML(antibiotics.to_html(escape=False)))

, where 'antibiotics' ist the pandas dataframe.

I can send you the Email exchange in a separate Email to avoid spamming the 
list with redundant postings.

Cheers,
Markus


On 09/26/2014 09:26 AM, 
paul.czodrow...@merckgroup.com wrote:
Dear Riccardo,

upps, that did the job!
Thanks!

Bur I have another:

import os
from rdkit import RDConfig
sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')
frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
frame[['Molecule']].head(2)

==>
"



































   Molecule
0   





   

frame[['SMILES']].head(2)

"
  SMILES
0   CC1=CC(=O)C=CC1=O
1  c1ccc2sc(SSc3nc4c4s3)nc2c1
"



Cheers & Thanks,
Paul




From:Riccardo Vianello 

To:
paul.czodrow...@merckgroup.com,
Date:26.09.2014 09:13
Subject:Re: [Rdkit-discuss] Weird iPython PandasTools notebook look&feel




Hi Paul,

I'm not a regular pandas user, so this comment could be misplaced, but from 
this output:

On Fri, Sep 26, 2014 at 9:02 AM, 
mailto:paul.czodrow...@merckgroup.com>> wrote:

frame.info

rdkit-discuss@lists.sourceforge.net

2014-09-26 Thread Paul . Czodrowski 
Dear Riccardo,

upps, that did the job!
Thanks!

Bur I have another:
>>> import os
>>> from rdkit import RDConfig
>>> sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')
>>> frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
>>> frame[['Molecule']].head(2)
==>
"
   
Molecule
0  >> frame[['SMILES']].head(2)
"
   SMILES
0   CC1=CC(=O)C=CC1=O
1  c1ccc2sc(SSc3nc4c4s3)nc2c1
"



Cheers & Thanks,
Paul




From:   Riccardo Vianello 
To: paul.czodrow...@merckgroup.com, 
Date:   26.09.2014 09:13
Subject:Re: [Rdkit-discuss] Weird iPython PandasTools notebook 
look&feel



Hi Paul,

I'm not a regular pandas user, so this comment could be misplaced, but 
from this output:

On Fri, Sep 26, 2014 at 9:02 AM,  wrote:
>>> frame.info # doctest: +SKIP 
 

it looks like you might be looking at the textual representation of the 
frame.info method, instead of calling it and look at its output with 
frame.info(). Is this intended?

Best regards,
Riccardo



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2014-09-26 Thread Paul . Czodrowski 
Dear RDKitters,

on my new Windows laptop, I tried one of the PandasTools examples, which 
should give this output:
"
>>> sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')
>>> frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
>>> frame.info # doctest: +SKIP

Int64Index: 200 entries, 0 to 199
Data columns:
AMW   200  non-null values
CLOGP 200  non-null values
CP200  non-null values
CR200  non-null values
DAYLIGHT.FPG  200  non-null values
DAYLIGHT_CLOGP200  non-null values
FP200  non-null values
ID200  non-null values
ISM   200  non-null values
LIPINSKI_VIOLATIONS   200  non-null values
NUM_HACCEPTORS200  non-null values
NUM_HDONORS   200  non-null values
NUM_HETEROATOMS   200  non-null values
NUM_LIPINSKIHACCEPTORS200  non-null values
NUM_LIPINSKIHDONORS   200  non-null values
NUM_RINGS 200  non-null values
NUM_ROTATABLEBONDS200  non-null values
P130  non-null values
SMILES200  non-null values
Molecule  200  non-null values
dtypes: object(20)>
"

However, in my case, I end up in such an output (mostly truncated):
"
>>> frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
Patching pandas
>>> frame.info
 I changed this on my Windows laptop according to one hint from Paul 
Emsley.



Cheers & Thanks,
Paul


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