Re: [Rdkit-discuss] Does rdkit depend on pandas?

No. The main reason that the conda recipe includes pandas is for testing the pandas extension. We could probably remove it from the run-time dependency however and let the user install it in addition. In any case, feel free to remove pandas from the conda installation. Cheers, Brian On Tue

[Rdkit-discuss] format.py in Pandas 0.20.1 Has Moved

This may have already been addressed in the next release, but I wanted to be sure. It appears that Pandas was refactored in the 0.20.1 release in a way that breaks PandasTools: Python 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:25:24) [MSC v.1900 64 bit (AMD64)] on win32 Type

[Rdkit-discuss] Does rdkit depend on pandas?

Hi, I just upgraded rdkit from 2017.03.1 to 2017.03.2 using Conda. What I have noticed is that pandas are now installed during the installation of rdkit. Does rdkit depend on pandas now? Is it safe to remove it? If it works without pandas, maybe it makes sense to remove the dependency. Kind

Re: [Rdkit-discuss] In a pickle with pandas

Hi, Tim, PandasTools.RenderImagesInAllDataFrames(images=True)solve the problem. Here is a jupyter notebook example.rdkit 2020.03.2 pandas 1.0.3 -- Original -- From:"Tim Dudgeon"https://lists.sourceforge.net/lists/listinfo/rdk

[Rdkit-discuss] Pandas to Excel

Hi, Is it possible to export from a Pandas data frame to Excel, inserting the structures as images in the excel sheet? Cheers Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit

[Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Dear all, would it be possible to make RDKit package not depend on mkl (probably via numpy, pandas) and that it accepts pre-installed numpy and pandas for example from pip as sufficient? The background to this is simple. Intel MKL cripples performance on any AMD bases processor (4-5 times

Re: [Rdkit-discuss] format.py in Pandas 0.20.1 Has Moved

Hi Steve, Thanks for pointing this out. Brian fixed this on master a while ago ( https://github.com/rdkit/rdkit/pull/1410) and we will have the fix in the 2017.03.2 patch release (coming, hopefully, next week). Here's a quick demo that it actually works: In [2]: pandas.__version__ Out[2]: '0.20.1

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Hi Thomas, I'm not sure how to configure conda so that a pip-installed version of numpy and/or pandas is used, but you can use conda versions without MKL by installing the nomkl package. This conda command creates a functioning environment that does not have the MKL installed: conda create -n

[Rdkit-discuss] New version of PandasTools and Tutorial available

Dear all, a tutorial ipython notebook for using the RDKit/Pandas integration is now available on the wiki (http://code.google.com/p/rdkit/wiki/Tutorials - Using Pandas in combination with RDKit). There is also a new version of the PandasTools module in the rdkit trunk on GitHub. This fixes

Re: [Rdkit-discuss] In a pickle with pandas

 Probably not the reason, but there was an older version of pandas, 0.24 IIRC, that dinner render the molecules correctly. Can you perform calculations on the mol objects? On Mar 29, 2020, at 4:07 AM, Tim Dudgeon wrote:  I'm finding that if I create a pandas dataframe using

Re: [Rdkit-discuss] In a pickle with pandas

Strange. It's just started working now. I can't explain it. On 30/03/2020 08:30, Markus Heller wrote:  Probably not the reason, but there was an older version of pandas, 0.24 IIRC, that dinner render the molecules correctly. Can you perform calculations on the mol objects? On Mar 29

[Rdkit-discuss] RDKit Pandas iterate through all Descriptors for compounds in dataframe

Hi RDKit community,I would like to ask if it is possible to calculate (iterate over) all the available descriptors for a set of compounds loaded in a pandas dataframe.I have found a few examples doing the same with a "mols" list.T

[Rdkit-discuss] Adding molecules to pandas dataframe

Hi all, is it possible to manually add molecules to a pandas dataframe? I am reading a bunch of mol2 files, adding some properties (including some atom highlighting), then I'd like to add the resulting molecule to the dataframe in order to show its depiction along with the data. However, API docs

[Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule

: Etc But Pandas DF’s seem to being playing hard-ball. Any thoughts? Cheers, mike ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

Hi RDKit Gurus, I've followed the docs and created a molecule column in my Pandas dataframe. However, I do not seem to be able to do molecular operations on the column. For example, if you had a SMILES column, how would you calculate heavy atom count and append this result to a new column

Re: [Rdkit-discuss] Friday pandas q

the core DataFrame class of pandas to disable the HTML escaping, which is enabled by default in pandas, so this methods affects ALL dataframes. Seeing HTML code in a dataframe is an indicator that something around this pandas patching was not done.The method is called inside

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

not sure how to configure conda so that a pip-installed version of numpy and/or pandas is used, but you can use conda versions without MKL by installing the nomkl package. This conda command creates a functioning environment that does not have the MKL installed: conda create -n no_mkl python=3.7

Re: [Rdkit-discuss] pythonTestDirChem test failing

On Mon, Jun 17, 2013 at 4:08 PM, Michał Nowotka mmm...@gmail.com wrote: I'm trying to understand your advice? Should I check if I have pandas installed and uninstall it? Or installing pandas will help me with testing? sorry, I was confusing. I could reproduce an error that occurs

[Rdkit-discuss] Friday pandas q

Question to rdkit pandas users (pandaskitters?): I managed to have the mol_send(m) object in a pandas frame: [image: Inline images 1] if I do this: data['mol'].map(str).map(Chem.Mol) I get the mol in base64 PNG: [image: Inline images 2] How do I display the column as rendered images (and keep

[Rdkit-discuss] Calculating Chem.MolFromSmiles using vectorization

Hello, This might be trivial python question but I am stuck in calculating the Chem.MolFromSmiles: My smiles strings are in a pandas DataFrame (df) with SMILES column (df.SMILES) and I have been calculating the mols (df_mol) by Pandas apply function as below: df_mol = df.SMILES.apply( lambda x

Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule

Hello Mike, you could create a function with your if else structure and use apply on the pandas dataframe. For example, if you have a SMILES column in your df: def addMol(smiles): if Chem.MolFromSmiles(smiles) is None: Etc return None # or whatever you

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

r 31, 2019 2:17 AM To: 'RDKit Discuss' Subject: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule Hi RDKit Gurus, I've followed the docs and created a molecule column in my Pandas dataframe. However, I do not seem to be able to do molecular operations on

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

What I'm failing to understand here is what you want to do. Do you want the rows with molecules that failed to parse to remain in the DataFrame? If not you can just remove them (there's probably a simpler way to do this, but Pandas never fails to surprise me): filtered_df = df[df['ROMol'].astype

Re: [Rdkit-discuss] pythonTestDirChem test failing

Hi Michał, Is pandas available in your test environment? I could reproduce a similar problem on my own linux box, but it's apparently due to an oversight in the PandasTools module that can raise an exception when pandas is not imported. The interested output could be similar to the following: 77

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

Sorry I missed that you were on windows. It looks like you can probably carefully construct an environment manually using the '--no-deps' argument to "conda install" I created and activated a python 3.7 environment on windows, installed pandas and numpy from pip, and then did: con

[Rdkit-discuss] ?????? How to sort a list of mol objects

Hi, I've tested the code below, and found out that put mol objects into pandas is just straightforward. [code] #SMILES string list into mol objects, and then into dataframe import pandas as pd from rdkit import Chem smiles = ['c1c1', 'c1c1O', 'c1cc(O)ccc1O'] mols

[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

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 = ValueError Traceback (most recent call last) ipython-input-6-52de9e808c94in

Re: [Rdkit-discuss] Pandas

Search and add similarity to resulting data frame > On 27 Nov 2016, at 07:55, Greg Landrum wrote: > > > You don't know if what could be done as a single line? > > -greg --

Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule

Jensen ; RDKit Discuss Subject: Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule Hello Mike, you could create a function with your if else structure and use apply on the pandas dataframe. For example, if you have a SMILES column in your df: def addMol

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

h all pandas versions above 0.25.0, So I guess for now the easiest fix is to downgrade pandas. Or you can use this method which seemed to work for me: from IPython.display import HTML HTML(df.to_html()) I haven’t managed to downgrade pandas on Colab (almost certainly a Colab issue) but the

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

Hi, Pandas apply function will work too. AddMoleculeColumnToFrame(DF, "Smiles") at first. Default setting, rdkit mol object will be added "ROMol" column in your dataframe. https://www.rdkit.org/docs/source/rdkit.Chem.PandasTools.html Then call apply function to apply a

Re: [Rdkit-discuss] Pandas to Excel

Hi Both, Many thanks for your rapid response, much appreciated. Cheers Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Attribute Error about PandasTools

Dier Niko, Thank you for your quick reply. I tried to use pandas 0.18.0 and I work fine. ;-) Best regards, Takayuki 2016年6月2日(木) 3:13 Nikolas Fechner <m...@fechner.cc>: > Hi Takayuki, > It seems that the respective piece of the pandas API got restructured for > 0.18.1 and t

Re: [Rdkit-discuss] Generating Fingerprints from Smiles or Mol

Hi Greg, Thanks so much for taking the time to help! I didn't realize the size limit recommendation for pandas so maybe that's why I don't see much of it. I often work on much larger scale and was investigating moving from KNIME to RDKit on Linux for that reason. The curve is just steep right

Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule

can address the rows where mol is ‘None’ … From: Mike Mazanetz Sent: Thursday, October 31, 2019 8:54 AM To: 'Fiorella Ruggiu' Cc: 'RDKit Discuss' Subject: Re: [Rdkit-discuss] failed mols in converting SMILES to Pandas dataframe Molecule Hi Fio, Thanks for the tips. I’ve found that I need

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

Yes, I can confirm that this is a problem caused by changes in Pandas v0.25.x Now we just need to figure out what those changes are and how to work around them. Here's a github issue to track the problem: https://github.com/rdkit/rdkit/issues/2673 -greg On Tue, Nov 5, 2019 at 12:21 PM Jan

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

From: Taka Seri Sent: 31 October 2019 10:15 To: Jan Halborg Jensen Cc: Mike Mazanetz ; RDKit Discuss Subject: Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule Hi, Pandas apply function will work too. AddMoleculeColumnToFrame(DF, "S

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

[Rdkit-discuss] PandasTools on Windows iPython notebook

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) ipython-input-6-52de9e808c94 in module() 1 import pandas as pd

Re: [Rdkit-discuss] Generating Fingerprints from Smiles or Mol

On Fri, Jan 4, 2019 at 1:59 PM Jason Ochoada wrote: > > Thanks so much for taking the time to help! I didn't realize the size > limit recommendation for pandas so maybe that's why I don't see much of it. > Yeah, Pandas is designed to keep the entire dataframe in memory. This

Re: [Rdkit-discuss] Generating Fingerprints from Smiles or Mol

Awesome! Thanks for all the help! Jason On Sat, Jan 5, 2019, 1:21 AM Greg Landrum wrote: > > > On Fri, Jan 4, 2019 at 1:59 PM Jason Ochoada wrote: > >> >> Thanks so much for taking the time to help! I didn't realize the size >> limit recommendation for pandas s

[Rdkit-discuss] rdkit mol objects from sql

Hi RDKitters, I must have seen this in an ipython notebook but can't find it right now: If I have a table of rdkit mols generated by the cartridge, is there a way to retrieve them using a psycopg2 connection within python - ideally inside a pandas dataframe? I've got this snippet: import pandas

[Rdkit-discuss] GetSubstructMatch in pandas

do the same in a loop inside a method of a class, and send the output to a pandas dataframe, the match is not highlighted when visualizing the dataframe. Even more weird, if a store the molecule (after having applied GetSubstructMatch on it) in a class field (e.g. self.test), and then I do

[Rdkit-discuss] warnings when exporting pandas tables with molecules to hdf

Hi all, I am working on some molecules in a pandas DataFrame and have to export them to a hdf file. This works just fine but I get a warning about Performance due to mixed types. (1) Why are RDKIT Mol objects causing this warning in the first place? Am I doing something wrong? Please

Re: [Rdkit-discuss] Adding molecules to pandas dataframe

demonstrating: https://gist.github.com/greglandrum/914ae66fd2f97addbbd472ae726567b1 -greg On Thu, Jul 25, 2019 at 4:45 PM Gianluca Sforna wrote: > Hi all, > is it possible to manually add molecules to a pandas dataframe? I am > reading a bunch of mol2 files, adding some properties (

Re: [Rdkit-discuss] Adding molecules to pandas dataframe

ecule"] = mols Best, Christos Christos Kannas Scientific Software Developer (Cheminformatics) On Thu, 25 Jul 2019 at 15:45, Gianluca Sforna wrote: > Hi all, > is it possible to manually add molecules to a pandas dataframe? I am > reading a bunch of mol2 files, adding some propert

Re: [Rdkit-discuss] Issue with SmilesMolSupplier using FreeSolv data

Hard to say without seeing the data, but could it be that the pandas data frame contains a bunch of molecules that are None? -greg On Tue, Oct 1, 2019 at 10:40 AM Guillaume GODIN < guillaume.go...@firmenich.com> wrote: > Dear All, > > > > I try this code on ‘Fre

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

Hi, Thanks for your response. The problem is that I’d like to chunk Pandas dataframes to different processors. And efficiently as possible, remove those rows which fail to be converted into RDKit Mols. What I find however, is that the entire process dies if the PandasTools fails

[Rdkit-discuss] Random (?) highlighting in pandas dataframe

Hi all, I have an issue with molecule rendering in a pandas dataframe. I read a csv file with SMILES strings and names into a dataframe, and add a mol column to the dataframe based on the SMILES. I then display the molecules in the dataframe like so: from IPython.display import HTML HTML

Re: [Rdkit-discuss] calculating molecular properties on a Pandas dataframe Molecule

Hi Mike This should work DF[‘HAC’] = [Chem.Lipinski.HeavyAtomCount(mol) for mol in DF[‘Molecule’]] Best regards, Jan On 31 Oct 2019, at 10.16, Mike Mazanetz mailto:mi...@novadatasolutions.co.uk>> wrote: Hi RDKit Gurus, I’ve followed the docs and created a molecule column in my

Re: [Rdkit-discuss] New module for RDKit - PANDAS integration

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

Re: [Rdkit-discuss] pythonTestDirChem test failing

Hi Riccardo, I'm trying to understand your advice? Should I check if I have pandas installed and uninstall it? Or installing pandas will help me with testing? Anyway, I think there are two things worth mentioning: 1. I'm compiling it on raspberry pi 2. Installation failed - sudo make install

Re: [Rdkit-discuss] Pandas dataframe manipulation

x.replace('>', '')}) http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_csv.html Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2016-03-11 11:12 GMT+01:00 Paul Czodrowski <paul.czodrow...@merckgroup.com>: > Dear RDKitter & Pandas-Dataframes h

[Rdkit-discuss] Tautomer database comparison

Hey, I am having problems displaying the Mol objects in a Pandas dataframes. The IPythonConsole is not drawing the Mol Objects in my dataframes. The Rdkit PandasTools module works good for me, when I am using the AddMoleculeColumnToFrame module. The Mol Objects were shown properly

Re: [Rdkit-discuss] How to sort a list of mol objects

Hi Paolo, Your previous reply already helped me. If I need to sort multiple properties, with different directions, What would the code be? Would it be easier to put mols into a pandas dataframe? If so, how to do it? Best regards Zhenting ---Original--- From: "Paolo Tosco&

[Rdkit-discuss] ModuleNotFoundError: No module named 'rdkit'

py39hfadf033_0conda-forge From this enviroment I can call pandas (for example) but not RDKIT. What is still not working? Best regards, Andrés ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo

Re: [Rdkit-discuss] Friday pandas q

= pd.DataFrame(d,columns=('molregno','pkl')) df2['romol']=df2.apply(lambda x:Chem.Mol(str(x['pkl'])),axis=1) PandasTools.RenderImagesInAllDataFrames() del df2['pkl'] df2.head(2) -greg On Fri, Oct 25, 2013 at 4:43 PM, George Papadatos gpapada...@gmail.comwrote: Question to rdkit pandas

Re: [Rdkit-discuss] GetSubstructMatch in pandas

Dear Isidro, I can’t test at the moment, but as I understand it so far I would guess the reason for the behaviour is two-fold. First, the substructure search in the pandas data frame just checks wether the substructure is present by calling the HasSubstructMatch method from the molecule object

[Rdkit-discuss] Pandas dataframe manipulation

Dear RDKitter & Pandas-Dataframes heavy users, please find below a question concerning the conversion of pandas dataframes: df = pd.DataFrame({"item": ["a", "b", "c", "d", "e"], "row1": [1,2,3,">2",5],

Re: [Rdkit-discuss] Generating Fingerprints from Smiles or Mol

Hi Jason, This gist shows how to generate fingerprints for the molecules in a pandas dataframe and then use them to do similarity searches: https://gist.github.com/greglandrum/045ccf8009fde91fc985864e70ee72a1 This is a reasonably efficient way of working with a smallish (<10K) num

Re: [Rdkit-discuss] Random (?) highlighting in pandas dataframe

: November 13, 2019 5:01 PM To: rdkit-discuss (rdkit-discuss@lists.sourceforge.net) Subject: [Rdkit-discuss] Random (?) highlighting in pandas dataframe   Hi all, I have an issue with molecule rendering in a pandas dataframe.  I read a csv file with SMILES strings and names into a dataframe

[Rdkit-discuss] Try to reproduce a code working in January

ValueErrorTraceback (most recent call last) in 1 frame = frame[["ROMol", "Smiles", "Core", "R1", "R2", "R3"]] > 2 frame['Core']=frame['Core']

Re: [Rdkit-discuss] Using SmilesMolSuplier with CSV containing quotemarks

I figured as much, and I guess in my case the pandas side will be useful enough for this, thanks. On Mon, 10 Jan 2022 at 14:05, Greg Landrum wrote: > Hi James, > > The RDKit does not have a full-featured CSV parser, writing such a thing > is a non-trivial task. If you need to sup

Re: [Rdkit-discuss] Pandas to Excel

rce/rdkit.Chem.PandasTools.html#rdkit.Chem.PandasTools.SaveXlsxFromFrame> Saves pandas DataFrame as a xlsx file with embedded images. molCol can be either a single column label or a list of column labels. It maps numpy data types to excel cell types: int, float -> number datetime -> datetime object ->

Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows)

- freetype - eigen - rdkit - ipykernel - pip: - pandas I suspect just installing from this yml won't work as some of these libs have unlisted dependencies while for rdkit you want no deps. So below the exact non-optimized order of commands used: conda create -n rdkit_openblas python=3.7 conda

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

, 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) ipython-input-6-52de9e808c94

Re: [Rdkit-discuss] pandas / sd-tags

Hi Paul, I am not sure if it is easily doable to get the pandas read_table function to handle sd-files. However, there is some basic functionality for this already built-in in the PandasTools module. If you check the docktest header there is a small example. Basically, frame

[Rdkit-discuss] error using pandas render images in dataframe

If I add mol to pandas dataframe and try to visualize in table format using from rdkit.Chem.Draw import IPythonConsole and either PandasTools.RenderImagesInAllDataFrames(images=True) or PandasTools.ChangeMoleculeRendering(frame) I get the following error

Re: [Rdkit-discuss] Pandas

://pypi.python.org/pypi/chemfp/1.0 In my copious spare time, I've been trying to think of ways to embed this directly in a pandas dataframe however, using them side by side is certainly doable. Cheers, Brian On Wed, Nov 23, 2016 at 10:06 AM, Peter Gedeck <peter.ged...@gmail.com> wrote: > Is it

Re: [Rdkit-discuss] Random (?) highlighting in pandas dataframe

Sent: November 13, 2019 5:01 PM > > To: rdkit-discuss (rdkit-discuss@lists.sourceforge.net) < > rdkit-discuss@lists.sourceforge.net> > > Subject: [Rdkit-discuss] Random (?) highlighting in pandas dataframe > > > > > Hi all, > > > > I have an i

Re: [Rdkit-discuss] Try to reproduce a code working in January

- > > ValueErrorTraceback (most recent call > last) > > in > > * 1* frame = frame[["ROMol", "Smiles", "Core", "R1", "R2"

[Rdkit-discuss] MDS using RDKit, SciKit and Pandas

Hi RDKitters, This is not a question, more like an FYI. Inspired by Noel's related post: http://baoilleach.blogspot.co.uk/2014/01/convert-distance-matrix-to-2d.html, I've put together an iPython Notebook example that performs MDS on a bunch of ChEMBL compounds (i.e. visualises their chemical

[Rdkit-discuss] Is RDKit able to generate a Bag of Bonds Matrix?

Dear colleagues, I hope this message finds you all very well. I'm planning on using RDKit to read my Pandas DataFrame containing organometallic structures. Since the work deal strictly with geometric parameters that I'm feeding to a Neural Network I'd like to describe the molecules using Bag

[Rdkit-discuss] Generating Molecular Graphs with RDKit

Dear colleagues, I’m doing my Ph.D. in Inorganic Chemistry and part of the job is creating a large database that will be fed into a pandas dataframe in the Mol V3000 format to keep information about bond types and charges on the complexes. The dataframe will be used in machine learning

[Rdkit-discuss] Molecules not rendere in Dataframe

Hi, In a Jupyter notebook, the following code does not show renderings of the molecules in a Pandas dataframe: from rdkit import Chem from rdkit.Chem import PandasTools from rdkit.Chem.Draw import MolsToGridImage from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import rdDepictor

[Rdkit-discuss] Problem using AddMoleculeColumnToFrame on Google Colab

Colab. But could it also be that a new version of Pandas is causing the problem? Here’s the link to the notebook and a screenshot. Any help is appreciated. Best regards, Jan https://colab.research.google.com/drive/1nQPmdEbYQgVsFr7c44yRd3wpXPEsJar3 [cid:02DC0D56-42F8-4639-B923-9C38D0661AAD

Re: [Rdkit-discuss] Issue with PandaTools Export to Excel

Answer to myself... Le 27/10/2022 à 00:54, Stéphane Téletchéa a écrit : Any idea if I'm doing something wrong? Yes I was using "frame" and not "antibiotics"... The update about pandas concat instead of "append" stands :-) Do I need to submit a git pull reques

Re: [Rdkit-discuss] pandas / sd-tags

that happens when there are too many columns to fit the set display width. This can be adjusted as described here using also the describe problem: http://stackoverflow.com/questions/11707586/python-pandas-widen-output-display Alternatively, if you are using the iPython notebook, there is also

Re: [Rdkit-discuss] rdkit mol objects from sql

generated by the cartridge, is there a way to retrieve them using a psycopg2 connection within python - ideally inside a pandas dataframe? I've got this snippet: import pandas as pd import psycopg2 conn = psycopg2.connect(port=5432 user=chembl dbname=chembl_17) data = pd.read_sql(sql, conn

Re: [Rdkit-discuss] rdkit mol objects from sql

have a table of rdkit mols generated by the cartridge, is there a way to retrieve them using a psycopg2 connection within python - ideally inside a pandas dataframe? I've got this snippet: import pandas as pd import psycopg2 conn = psycopg2.connect(port=5432 user=chembl dbname=chembl_17

[Rdkit-discuss] Export pandas DataFrame to xlsx with molecule images

Hi rdkiters, Due to popular demand I started to work on a function to export pandas DataFrame to xlsx with molecule images embedded. Because of the xlsx specifics the code is not optimal. The most annoying thing about this implementation is that it has to write all images to the hard drive

Re: [Rdkit-discuss] still Attribute Error with PandasTools ...

Hi Andreas, Can you please send the full error message so that it shows the line numbers, as well as the output of: conda list | grep pandas that will help diagnose the problem. -greg On Fri, Jun 3, 2016 at 4:44 PM, Andreas Schulz <aschul...@web.de> wrote: > Hi, > today I s

Re: [Rdkit-discuss] Pandas

sure Chris won't mind and the real Pandas experts may have a better answer than me.] On Wed, Nov 23, 2016 at 9:51 AM, Chris Swain <sw...@mac.com> wrote: I quite like storing molecules and associated data in a data frame and I’ve see that it is possible to use rdkit for substructure searching

Re: [Rdkit-discuss] Pandas

s concerned I’m asking something blindingly obvious ;-) Chris On 23 Nov 2016, at 12:36, Greg Landrum <greg.land...@gmail.com> wrote: [including rdkit-discuss, because it's relevant there and I'm pretty sure Chris won't mind and the real Pandas experts may have a better answer than me.] On

[Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

tried changing the PandasTools.molSize but it didn't help. Here is my code: from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import PandasTools import pandas as pd from IPython.core.display import display, HTML # Normal inline display of molecule is fine

Re: [Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

e: > > from rdkit import Chem > from rdkit.Chem.Draw import IPythonConsole > from rdkit.Chem import PandasTools > import pandas as pd > from IPython.core.display import display, HTML > > # Normal inline display of molecule is fine > Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')

Re: [Rdkit-discuss] [Rdkit-announce] [Announcement] 7th RDKit UGM in Cambridge UK

is meant for someone who has some programming experience but has not worked with Python before. It will cover the basics of the language (variables, for loops, defining functions), with examples based on the RDKit. The students will work in an IPython notebook, and the exercises will also touch

[Rdkit-discuss] Generating Fingerprints from Smiles or Mol

Hi Everyone! I'm a newbie making the shift from RDKit in KNIME to working with the full package. I have been working (hacking) my through the tutorials I could find pandas, Jupyter, RDKit etc. I'm using RDKit in the anaconda 3 environment. I'm struggling to figure out how to do what I imagine

Re: [Rdkit-discuss] warnings when exporting pandas tables with molecules to hdf

`pickle` module to serialize it. On Fri, Feb 15, 2019 at 6:35 AM Jose Manuel Gally < jose.manuel.ga...@gmail.com> wrote: > Hi all, > > I am working on some molecules in a pandas DataFrame and have to export > them to a hdf file. > > This works just fine but I get a warni

Re: [Rdkit-discuss] Adding molecules to pandas dataframe

https://gist.github.com/greglandrum/914ae66fd2f97addbbd472ae726567b1 > > -greg > > > On Thu, Jul 25, 2019 at 4:45 PM Gianluca Sforna wrote: >> >> Hi all, >> is it possible to manually add molecules to a pandas dataframe? I am >> reading a bunch of mol2 files, adding some properties (includ

Re: [Rdkit-discuss] Using SmilesMolSuplier with CSV containing quotemarks

Hi James, The RDKit does not have a full-featured CSV parser, writing such a thing is a non-trivial task. If you need to support general CSV, I'd suggest using pandas or python's builtin csv module... it seems like overkill, but dealing with all the oddness that can show up in CSVs is really

Re: [Rdkit-discuss] Pandas dataframe manipulation

axis=0) Paul Von: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl] Gesendet: Freitag, 11. März 2016 12:29 An: Paul Czodrowski <paul.czodrow...@merckgroup.com> Cc: rdkit <rdkit-discuss@lists.sourceforge.net> Betreff: Re: [Rdkit-discuss] Pandas dataframe manipulation Hi Paul

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

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

Re: [Rdkit-discuss] New module for RDKit - PANDAS integration

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

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

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

Re: [Rdkit-discuss] pandas / sd-tags

? Cheers big thanks again, Paul Hi Paul, I am not sure if it is easily doable to get the pandas read_table function to handle sd-files. However, there is some basic functionality for this already built-in in the PandasTools module. If you check the docktest header there is a small

[Rdkit-discuss] Weird iPython PandasTools notebook lookfeel

(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True) Patching pandas frame.info bound method DataFrame.info ofAMW CLOGPCP CR DAYLIGHT.FPG DAYLIGHT_CLOGP FP ID

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