Re: [Rdkit-discuss] Chem.PandasTools
Dear Grégori, when storing the image into a new data frame: MMP_reaction = Chem.rdChemReactions.ReactionFromSmarts([*:1][H][*:1]C) newnew_df = pd.DataFrame(columns=['fig'],index=[1] ) newnew_df['fig'].ix[1] = Draw.ReactionToImage(MMP_reaction) apparently, the image can be stored in a data frame, but in the ipython notebook it is displayed as PIL image Cheers Thanks so far (in particular for the impressive speed in response!), Paul Hi Paul, You first have to read the MMP into a reaction object (Chem.ReactionFromSmarts). Greg On Friday, May 9, 2014, paul.czodrow...@merckgroup.com wrote: Dear Gregori Samo, thanks for your hints. I just tried running Draw.ReactionToImage([*:1][H][*:1]C) = AttributeError: 'str' object has no attribute 'GetNumReactantTemplates' BTW, how would I finally add a picture to a Pandas data frame? Cheers, 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.PandasTools
Hi, You can create new object that stores MMP and has default pandas and ipython representation as base64 encoded png. This usually works for me, but I'm not sure why in this case it works only for ipython representation and not for pandas.. The code: # codecell import pandas as pd import rdkit.Chem as Chem from rdkit.Chem import PandasTools from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole # codecell from base64 import b64encode from StringIO import StringIO class Reaction(): def __init__(self, reaction=None): self.reaction = reaction def _repr_html_(self): sio = StringIO() Draw.ReactionToImage(self.reaction).save(sio,format='PNG') s = b64encode(sio.getvalue()) return 'img src=data:image/png;base64,%s/' %s def __str__(self): sio = StringIO() Draw.ReactionToImage(self.reaction).save(sio,format='PNG') s = b64encode(sio.getvalue()) return 'img src=data:image/png;base64,%s/' %s # codecell MMP_reaction = Chem.rdChemReactions.ReactionFromSmarts([*:1][H][*:1]C) # codecell mmp = Reaction(MMP_reaction) # codecell mmp # codecell newnew_df = pd.DataFrame(columns=['fig'],index=[1] ) newnew_df['fig'].ix[1] = mmp # codecell newnew_df # codecell Regards, Samo On Fri, May 9, 2014 at 8:19 AM, paul.czodrow...@merckgroup.com wrote: Dear Grégori, when storing the image into a new data frame: MMP_reaction = Chem.rdChemReactions.ReactionFromSmarts([*:1][H][*:1]C) newnew_df = pd.DataFrame(columns=['fig'],index=[1] ) newnew_df['fig'].ix[1] = Draw.ReactionToImage(MMP_reaction) apparently, the image can be stored in a data frame, but in the ipython notebook it is displayed as PIL image Cheers Thanks so far (in particular for the impressive speed in response!), Paul Hi Paul, You first have to read the MMP into a reaction object (Chem.ReactionFromSmarts). Greg On Friday, May 9, 2014, paul.czodrow...@merckgroup.com wrote: Dear Gregori Samo, thanks for your hints. I just tried running Draw.ReactionToImage([*:1][H][*:1]C) = AttributeError: 'str' object has no attribute 'GetNumReactantTemplates' BTW, how would I finally add a picture to a Pandas data frame? Cheers, 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.PandasTools
Hi, I'm not sure if it will work but you can try: df['new'] = df['Transformation'].map(showLine_MMP) Regards, Samo On Thu, May 8, 2014 at 4:31 PM, paul.czodrow...@merckgroup.com wrote: Dear RDKitters, I started to play around with the great Chem.PandasTool contribution provided by Nicholas and Samo. Given such a data frame: Transformation npairs 1 [*:1][H][*:1]C5 how do I depict the molecular transformation in the dataframe? I guess that I somehow have to integrate this function def showLine_MMP(in_string): f = in_string.split(\t) LHS = Chem.MolFromSmiles(f[0].split()[0]) RHS = Chem.MolFromSmiles(f[0].split()[1]) mols.append(LHS) mols.append(RHS) return Draw.MolsToGridImage(mols,molsPerRow=2) but I'm not sure how to accomplish this. 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.PandasTools
Hi Paul, The Draw modules also contains a ReactionToImage function; Your MMP can be read as a reaction. Hope this helps further! Grégori Date: Thu, 8 May 2014 16:31:32 +0200 From: paul.czodrow...@merckgroup.com Subject: [Rdkit-discuss] Chem.PandasTools To: rdkit-discuss@lists.sourceforge.net Message-ID: ofc0c168e1.8dc7f4cf-onc1257cd2.004f2cec-c1257cd2.004fc...@merck.de Content-Type: text/plain; charset=US-ASCII Dear RDKitters, I started to play around with the great Chem.PandasTool contribution provided by Nicholas and Samo. Given such a data frame: Transformation npairs 1 [*:1][H][*:1]C5 how do I depict the molecular transformation in the dataframe? I guess that I somehow have to integrate this function def showLine_MMP(in_string): f = in_string.split(\t) LHS = Chem.MolFromSmiles(f[0].split()[0]) RHS = Chem.MolFromSmiles(f[0].split()[1]) mols.append(LHS) mols.append(RHS) return Draw.MolsToGridImage(mols,molsPerRow=2) but I'm not sure how to accomplish this. 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.PandasTools
Dear Gregori Samo, thanks for your hints. I just tried running Draw.ReactionToImage([*:1][H][*:1]C) = AttributeError: 'str' object has no attribute 'GetNumReactantTemplates' BTW, how would I finally add a picture to a Pandas data frame? Cheers, Paul Hi Paul, The Draw modules also contains a ReactionToImage function; Your MMP can be read as a reaction. Hope this helps further! Grégori 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Chem.PandasTools
Hi Paul, You first have to read the MMP into a reaction object (Chem.ReactionFromSmarts). Greg On Friday, May 9, 2014, paul.czodrow...@merckgroup.com wrote: Dear Gregori Samo, thanks for your hints. I just tried running Draw.ReactionToImage([*:1][H][*:1]C) = AttributeError: 'str' object has no attribute 'GetNumReactantTemplates' BTW, how would I finally add a picture to a Pandas data frame? Cheers, Paul Hi Paul, The Draw modules also contains a ReactionToImage function; Your MMP can be read as a reaction. Hope this helps further! Grégori 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, Spanish and Portuguese versions of this disclaimer. -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
