Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)

Dier Hans. That's nice work. I tried to install the module. But there was no __init__.py file in silicos_it folder. So, import was failed. Do you have any idea? Thanks. 2012年3月30日23:27 Hans De Winter h...@silicos-it.com: Hi - A RDKit-based implementation of the QED measure as described by

[Rdkit-discuss] pharmacophore align

Dear all. I have some questions about Pharmacophore. I want to align molecules that from SDF files, by Pharmacophore. At first, I set Pharmacophore by using EmbedPharmacophore() method. And checked molecules by EmbedPharmacophore() method. Then, generated 3D structures by EmbedPharmacophore()

Re: [Rdkit-discuss] pharmacophore align

that by useing feature.GetPos() method. I want to do same thing by using AtomIds. Sincerely. Taka 2012/7/20 Greg Landrum greg.land...@gmail.com: Dear Taka, On Thu, Jul 19, 2012 at 9:44 AM, Taka Seri serit...@gmail.com wrote: Dear all. I have some questions about Pharmacophore. I want to align

Re: [Rdkit-discuss] pharmacophore align

Dear Greg and rdkit-discuss members. Thank you for your kindness. Your messages are very helpful for me. Thanks. Taka 2012/7/22 Greg Landrum greg.land...@gmail.com: Dear Taka, On Sun, Jul 22, 2012 at 12:20 AM, Taka Seri serit...@gmail.com wrote: And I have one question. Can I get

[Rdkit-discuss] About PCA

Dear All. I want to do PCA with molecular fingerprint . So, I wrote following code. But, this code did not work . Does anyone have a suggestion? Thanks. Takayuki 1 from rdkit import Chem 2 from rdkit.Chem import AllChem 3 from rdkit.ML.Data import Stats 4 import numpy 5 import sys

Re: [Rdkit-discuss] About PCA

AM, Taka Seri serit...@gmail.com wrote: Dear All. I want to do PCA with molecular fingerprint . So, I wrote following code. But, this code did not work . Does anyone have a suggestion? Thanks. Takayuki 1 from rdkit import Chem 2 from rdkit.Chem import AllChem 3 from rdkit.ML.Data

Re: [Rdkit-discuss] About Building The Cartrige

Dear Greg. Thank you for your quick reply. Your advice is helpful for me. I tried rebuilding the .o files, then all tests were passed ! I'm very grateful to you. takayuki 2013/1/26 Greg Landrum greg.land...@gmail.com Dear Takayuki, On Sat, Jan 26, 2013 at 5:37 AM, Taka Seri serit

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

[Rdkit-discuss] Get Bond order

Dear All . I want to know how to get bond order of molecules. GetBondType method can get bond-type SINGLE, DOUBLE, TRIPLE , but can't get bond order. Are there any idea to solve it ? Thanks. Takayuki -- How

Re: [Rdkit-discuss] Get Bond order

Dear Greg. Thank you for your advice. I think your idea is nice! Thank you for your time and consideration. Takayuki 2013/6/9 Greg Landrum greg.land...@gmail.com Dear Takayuki, On Sat, Jun 8, 2013 at 10:05 AM, Taka Seri serit...@gmail.com wrote: I want to know how to get bond order

[Rdkit-discuss] Install RDKit2014.09.02 from homebrew

Dear All. I tried to update rdkit using homebrew. But update was failed, and I got following error. = Installing rdkit from rdkit/homebrew-rdkit == Downloading https://github.com/rdkit/rdkit/archive/Release_2014_09_2.tar.gz

Re: [Rdkit-discuss] aromatic ring that contain sulfur atom

]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE In [16]: print Chem.MolToSmiles(mol,True) COS1=CC=CC=C1 Does that make sense? -greg On Sat, Feb 28, 2015 at 3:11 PM, Taka Seri serit...@gmail.com wrote: Dear rdkitter. I have a question about aromatic rings. So, I want to change atoms in aromatic ring. For example code

[Rdkit-discuss] about MACCSkeys

Dear all, I have a question about MACCSkeys. I checked number of keys using MACCSkeys.smartsPatts, the result was 166. But when I calculated MACCSkeys-fingerprint, the length of fingerprint was 167bit. Why the bit length is not 166 bit ? In [1]: from rdkit import Chem In [2]: from rdkit.Chem

Re: [Rdkit-discuss] Clustering 1M molecules

Dear Jing, How about your trying using bayon ? https://code.google.com/p/bayon/ It's not function of RDKit, but I think the library can cluster molecules using ECFP4. Unfortunately, input file format of bayon is not distance matrix but easy to prepare the format. Best regards. Takayuki

Re: [Rdkit-discuss] about MACCSkeys

Dear Andrew, Thank you for your quick reply. I understood it. It was helpful information for me! Best regards, Takayuki 2015年8月1日(土) 16:01 Andrew Dalke da...@dalkescientific.com: Dear Takayuki, On Aug 1, 2015, at 3:54 AM, Taka Seri wrote: Why the [MACCSkeys] bit length is not 166 bit

Re: [Rdkit-discuss] Change font size in SVG image

the normal size > drawer.DrawMolecule(mol) > drawer.FinishDrawing() > svg = drawer.GetDrawingText() > > > I hope this helps, > -greg > > > On Fri, Sep 11, 2015 at 11:20 PM, Taka Seri <serit...@gmail.com> wrote: > >> Dear all, >> I want to change atom f

Re: [Rdkit-discuss] Attribute Error about PandasTools

itching back to pandas > 0.18.0 seems to fix the error, thus going back to pandas 0.18.0 is > certainly the easiest option. > However, I guess if the changed import path is the only problem with > 0.18.1 this could probably easily be fixed in PandasTools directly. > > Kind re

[Rdkit-discuss] Attribute Error about PandasTools

Dier RDKitters, I want to handle sdf as DataFrame. But when I read molecule from SDF using PandasTools, I got following Error. from rdkit import Chem from rdkit.Chem import PandasTools df = PandasTools.LoadSDF("testset.sdf") df --> 131 formatter =

Re: [Rdkit-discuss] highlight substructure with Draw.MolsToGridImage

Dear Francesco, I think you can highlight each molecules using highlightAtomLists option. I wrote an example. Following code was written in IPython notebook. ''' from rdkit import Chem from rdkit.Chem import rdBase from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole from rdkit

Re: [Rdkit-discuss] Question about Run Reaction

年2月6日(土) 23:01 Michal Krompiec <michal.kromp...@gmail.com>: > Hi Taka, > You have to call SanitizeMol() on the product(s) explicitely. The error is > caused by the reactants not being 'sanitized'. > Best wishes, > Michal > > > On Saturday, 6 February 2016, Taka Seri <serit.

[Rdkit-discuss] Question about Run Reaction

Dear RDKitters, I have question about rdkit reaction function. I want to generate molecules using several reaction steps. I referred rdkit blog post, and wrote following code. But second step of reaction caused error. I could not difference about mol and mol2 object. I wonder if anyone could help

[Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

Dear rdkitters, I want to analyse and build prediction model about reaction or matched molecular pair ( molecular transformations ). I found new function named CreateDifferenceFingerprintForReaction. So, I tried to use the function to do it. But I confused following result. I defined three

Re: [Rdkit-discuss] Question about CreateDifferenceFingerprintForReaction

rxfp3 = buildReactionFP(rxn3,maxSize=1,fpType='Morgan') > > > tc12 = DataStructs.TanimotoSimilarity(rxfp1, rxfp2) > tc13 = DataStructs.TanimotoSimilarity(rxfp1, rxfp3) > tc23 = DataStructs.TanimotoSimilarity(rxfp2, rxfp3) > > print(tc12,tc13,tc23) > > >> (1.0

Re: [Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

Dear Andrew, I installed following version of mmpdb with new version of rdkit. And it worked fine! I appreciate your work. Kind regards, Takayuki On Apr 27, 2018, at 00:20, Andrew Dalke wrote: > Please try out: > http://dalkescientific.com/mmpdb-2.1b1.tar.gz > > or

Re: [Rdkit-discuss] How can I count the substructures with RDKit?

Dear Shojiro, To count the number of on bits, you can use GetNumOnBits. http://www.rdkit.org/Python_Docs/rdkit.DataStructs.cDataStructs.ExplicitBitVect-class.html#GetNumOnBits from rdkit import Chem from rdkit.Chem import AllChem mol = Chem.MolFromSmiles('O1ccnccc1') maccsfp =

Re: [Rdkit-discuss] Ipc descriptor values too large for float32

Hi Christoph, I think same topic was discussed in github issue. You can use Use avg=True option to avoid the problem. I hope the URL would be help for you. https://github.com/rdkit/rdkit/issues/1527 Best regards, Taka 2019年4月5日(金) 18:37 Christoph Hillisch : > Hello all, > > I use RDKit to

Re: [Rdkit-discuss] Drawing quality image with PandasTools.FrameToGridImage

Hi Diallo, I could reproduce it. It seems MolsToGridimage method throws error when the function get pandas Series and useSVG=True. I can get svg image when I converted the series to list. Like the below. df is Data frame which has rdkit mol object. from IPython.display import SVG

Re: [Rdkit-discuss] rotate a conformer around an axis?

Hi Mchal, TransformConformer can rotate molecule with given rotation matrix I think. I rotate mol by using the method. Following code rotates molecule around x, y, z axis. https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb Unfortunately molecule will not

Re: [Rdkit-discuss] conda install rdkit

Dear Paul, Current version of rdkit is provided for python3.6 and 2.7 from anaconda "rdkit" and "conda-forge" channel. https://anaconda.org/rdkit/rdkit/files?version=2018.09.1.0 https://anaconda.org/conda-forge/rdkit/files?version=2018.09.1 i recommend you to make python3.6 environment for using

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

Hi Guillaume, I confirmed the issue. RemoveHs does not work to invalid molecule. So I updated my code example and uploaded gist. Could you please check new version of my code? https://gist.github.com/iwatobipen/77269b8a10eafe0e0cba8de5c1cae6ec Any comments or suggestions will be appreciated.

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 calculation function

Re: [Rdkit-discuss] Drawing the sum of reactive molecules

Hi Pablo, How about call ReactionFromSmarts with useSmiles = True? With the option, RDKit can render the reaction from smiles instead of smarts. https://www.rdkit.org/docs/source/rdkit.Chem.rdChemReactions.html Kind regards, Taka 2020年2月7日(金) 23:00 Pablo Ramos : > Dear all, > > > > I am trying

Re: [Rdkit-discuss] How to protect atoms in specified location

Dear Shaozhen, RDKit can render molecule with atom index, So you can check the indexes and identify which atoms should be protected. An example to visualize molecule with atom index is below. https://gist.github.com/iwatobipen/7001d81080756fea46968d1966c36f59 I hope it helps you. Thanks, Taka

Re: [Rdkit-discuss] The RDKit and GSoC 2020

Dear Steve, Greg and All, Recently I moved from clab to Binder to make cloud env with python. However I'll try to make my code more compact and share it. Thanks for following my blog post. ;) https://iwatobipen.wordpress.com/ Best regards, Taka (tiwtter account / iwatobipen) 2020年3月16日(月)

Re: [Rdkit-discuss] Restraining torsions whilst generating conformers

Dear Bruce, How about to use the defined core which has your desired torsions? Here are examples to generate restricted conformers with user defined cores. https://www.discngine.com/blog/2019/6/6/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock

Re: [Rdkit-discuss] Restraining torsions whilst generating conformers

> macrocycle to remain flexible. If this was only a single part of the > macrocycle the ConstrainedEmbed method would work but I need to > simultaneously restrain several parts of the ring that are connected by > flexible regions. > > Cheers, > Bruce > > On Sun, 26 Apr 2020 at 0

Re: [Rdkit-discuss] conda install rdkit

Hi Ling, How about trying to use conda update command? $ conda activate my-rdkit-env $ conda update rdkit Thanks, Taka 2020年10月11日(日) 7:48 Ling Chan : > Dear colleagues, > > I am trying to install RDKit using conda. According to the manual at >

Re: [Rdkit-discuss] Num .Of Benzene rings and Substitents

Dear Raghu, Hello, How about using GetSubstructMatches method to get query structures? Here is an example to detect phenyl rings and count matches. https://gist.github.com/iwatobipen/7e922c761a0326493a5115fb615badf5 And also I think IFG code in Contrib seems useful for you. Kind regards, Taka

Re: [Rdkit-discuss] Get conformers as independent mols?

Dear Gustavo, As Omar described, you can get each conformer with confId. Here is an example for rendering multiple confromers with py3Dmol. https://gist.github.com/iwatobipen/1fbf30ed6c21a4016ec4885c7fd614ed I hope this will help you. Thanks, Taka 2021年1月8日(金) 8:48 Omar H94 : > Dear

Re: [Rdkit-discuss] Pandas to Excel

Hi Chris, I think you can do it with SaveXlsxFromFrame. http://rdkit.org/docs/source/rdkit.Chem.PandasTools.html#SaveXlsxFromFrame rdkit.Chem.PandasTools.SaveXlsxFromFrame(*frame*, *outFile*, *molCol='ROMol'*, *size=(300, 300)*, *formats=None*)¶