[Rdkit-discuss] PandasTools

2020-06-14 Thread Eduardo Mayo 
Hi RDKit users:
I have a couple of moleculas that must be load using the sanitize=False
flag. Then do a partial sanitization for make some calculations.
When I use PandaTools.LoadSDF the molecules with the sanitize trouble don't
load so I copy  PandaTools to my working folder and modified  it changing
the sanitize flag to false and add a line who partial sanitize the mol.
I was wondering if there other way to do that. If not I recommend change
the LoadSDF function to a more broad usability.
Best,
Eduardo
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[Rdkit-discuss] PandasTools LoadSDF: Different treatment of SMILES depending on presence of 'MOL' column?

2019-09-23 Thread Gustavo Seabra 
Hi all,

 

I'm trying to load a DrugBank library into a Pandas DataFrame, using two
different possibilities: creating or not a 'mol' column during load. In
principle I'm only interested in the SMILES, so creating the 'Mol' column
should not be necessary.

 

However, I noticed that the two procedures actually generate a different
number of molecules, and the SMILES are not necessarily the same: 

 

1.   Creating 'Mol' column: 2,410 molecules

2.   Not creating the 'Mol' column: 2,413 molecules

 

I assumed the difference would be due to some molecules which RDKit could
not generate the 'Mol' column for some reason and then just silently dropped
the molecules. So, I tried to find out the difference between the sets by:

 

>>>
drugbank.merge(drugbank_nomol,how='outer',on='SMILES',indicator=True).loc[
lambda x: x['_merge'] == 'right_only']

 

Which, assuming the SMILES are the same, *should* be 3, but it returns 1865
records (!) meaning the SMILES are mostly different between the sets.

 

Could someone help me figure out what is going on here?

 

To avoid attach files here, I put a test database and a Jupyter Notebook
with the example in here:

https://www.dropbox.com/s/v8kf7vzpmrjkidl/RDKit_test.zip?dl=0

 

Thanks a lot!

--

Gustavo Seabra

 

 

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Re: [Rdkit-discuss] PandasTools on Windows iPython notebook

2014-09-25 Thread Paul . Czodrowski 
height has been deprecated.

but, it works!

thanks, paul!!!


paul



From:   Paul Emsley 
To: rdkit-discuss@lists.sourceforge.net, 
Date:   25.09.2014 19:32
Subject:Re: [Rdkit-discuss] PandasTools on Windows iPython 
notebook



On 25/09/14 18:06, paul.czodrow...@merckgroup.com wrote:
Dear RDKitter, 

on my new Windows laptop, I run into this issue: 
" 
import pandas as pd 
import rdkit.Chem as Chem 
from rdkit.Chem import PandasTools 
" 
=> 
" 
ValueErrorTraceback (most recent call 
last)
 in ()
 1 import pandas as pd
 2 import rdkit.Chem as Chem
> 3 from rdkit.Chem import PandasTools
 4 #import os
 5 #from rdkit import RDConfig

C:\RDKit_2013_06_1\rdkit\Chem\PandasTools.py in ()
87   import pandas as pd
88   if 'display.width' in  pd.core.config._registered_options:
---> 89 pd.set_option('display.width',1000)
90   if 'display.height' in  pd.core.config._registered_options:
91 pd.set_option('display.height',1000)

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in __call__(self, *args, **kwds)
   215 
   216 def __call__(self, *args, **kwds):
--> 217 return self.__func__(*args, **kwds)
   218 
   219 @property

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in _set_option(*args, **kwargs)
   116 o = _get_registered_option(key)
   117 if o and o.validator:
--> 118 o.validator(v)
   119 
   120 # walk the nested dict

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in inner(x)
   780 def inner(x):
   781 if not isinstance(x, _type):
--> 782 raise ValueError("Value must be an instance of %s" % 
type_repr)
   783 
   784 return inner

ValueError: Value must be an instance of | 
" 

Is this familiar to anyone? 

Here's a guess: 

Try changing 1000 to 20 (2 billion) in PandaTools.py 

Paul.
 



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Re: [Rdkit-discuss] PandasTools on Windows iPython notebook

2014-09-25 Thread Paul Emsley 

On 25/09/14 18:06, paul.czodrow...@merckgroup.com wrote:

Dear RDKitter,

on my new Windows laptop, I run into this issue:
"
import pandas as pd
import rdkit.Chem as Chem
from rdkit.Chem import PandasTools
"
=>
"
ValueError Traceback (most recent call last)
in ()
 1importpandas aspd
 2importrdkit.Chem asChem
> 3fromrdkit.Chem importPandasTools
 4#import os
 5#from rdkit import RDConfig

C:\RDKit_2013_06_1\rdkit\Chem\PandasTools.pyin ()
87importpandas aspd
88if'display.width'in pd.core.config._registered_options:
---> 89pd.set_option('display.width',1000)
90if'display.height'in pd.core.config._registered_options:
91pd.set_option('display.height',1000)

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.pyin 
__call__(self, *args, **kwds)

   215
   216def__call__(self,*args,**kwds):
--> 217returnself.__func__(*args,**kwds)
   218
   219@property

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.pyin 
_set_option(*args, **kwargs)

   116o =_get_registered_option(key)
   117ifo ando.validator:
--> 118o.validator(v)
   119
   120# walk the nested dict

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.pyin 
inner(x)

   780definner(x):
   781ifnotisinstance(x,_type):
--> 782raiseValueError("Value must be an instance of %s"%type_repr)
   783
   784returninner

ValueError: Value must be an instance of |
"

Is this familiar to anyone?


Here's a guess:

Try changing 1000 to 20 (2 billion) in PandaTools.py

Paul.





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[Rdkit-discuss] PandasTools on Windows iPython notebook

2014-09-25 Thread Paul . Czodrowski 
Dear RDKitter,

on my new Windows laptop, I run into this issue:
"
import pandas as pd
import rdkit.Chem as Chem
from rdkit.Chem import PandasTools
"
=>
"
ValueErrorTraceback (most recent call 
last)
 in ()
  1 import pandas as pd
  2 import rdkit.Chem as Chem
> 3 from rdkit.Chem import PandasTools
  4 #import os
  5 #from rdkit import RDConfig

C:\RDKit_2013_06_1\rdkit\Chem\PandasTools.py in ()
 87   import pandas as pd
 88   if 'display.width' in  pd.core.config._registered_options:
---> 89 pd.set_option('display.width',1000)
 90   if 'display.height' in  pd.core.config._registered_options:
 91 pd.set_option('display.height',1000)

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in __call__(self, *args, **kwds)
215 
216 def __call__(self, *args, **kwds):
--> 217 return self.__func__(*args, **kwds)
218 
219 @property

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in _set_option(*args, **kwargs)
116 o = _get_registered_option(key)
117 if o and o.validator:
--> 118 o.validator(v)
119 
120 # walk the nested dict

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in inner(x)
780 def inner(x):
781 if not isinstance(x, _type):
--> 782 raise ValueError("Value must be an instance of %s" % 
type_repr)
783 
784 return inner

ValueError: Value must be an instance of | 
"

Is this familiar to anyone?


Cheers & Thanks,
Paul


This message and any attachment are confidential and may be privileged or 
otherwise protected from disclosure. If you are not the intended recipient, you 
must not copy this message or attachment or disclose the contents to any other 
person. If you have received this transmission in error, please notify the 
sender immediately and delete the message and any attachment from your system. 
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept 
liability for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any unauthorized 
changes of the content of this message and any attachment thereto. Merck KGaA, 
Darmstadt, Germany and any of its subsidiaries do not guarantee that this 
message is free of viruses and does not accept liability for any damages caused 
by any virus transmitted therewith.

Click http://www.merckgroup.com/disclaimer to access the German, French, 
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