Re: [Rdkit-discuss] Unwanted explicit Hs

explaining your problem to others, helps finding the solution. Thomas Il giorno sab 29 apr 2023 alle ore 20:45 Wim Dehaen ha scritto: > THe reason for this is that it will prevent ambiguities due to > nonstandard, higher valences. Because of this, it is not possible to infer > the impl

[Rdkit-discuss] Unwanted explicit Hs

I am not a chemist, so it can be a silly question, but I am interested in the logic behind it, also because other libraries (like OpenBabel) behave differently. Why sometimes RDKit writes hydrogens explicitly? mol = rdkit.MolFromSmiles('CCS=O', sanitize=False) rdkit.MolToSmiles(mol) 'CC[SH]=O'

Re: [Rdkit-discuss] SMARTS: "NOT Hydrogen" wildcard?

Thank you Greg you made my day! For future references, "not hydrogen" is [!#1] (not [!#0]) Il giorno lun 30 gen 2023 alle ore 17:47 Greg Landrum < greg.land...@gmail.com> ha scritto: > Hi Thomas, > > * in SMARTS just means "any atom". > [!H], for histo

[Rdkit-discuss] SMARTS: "NOT Hydrogen" wildcard?

ady tried to replace the * with a [!H] (NOT hydrogen) with no luck. Thanks to anyone :) Thomas ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Get original SMILES from molecule

Is there a way to get the SMILES used to generate the molecule (NOT the canonical one)? If I generate a molecule from a SMILES, a call to GetAtoms() returns the atoms in the order of the input SMILES. I'd like to retrieve that SMILES, so I can play with it using the info from GetAtoms or

[Rdkit-discuss] rdkit and py2exe

it runs. With Pyinstaller it works out of the box, but the executables produced by pyinstaller are problematic for many other reasons (huge size, manifest file ignored, subprocess based, no multiple exe allowed...) Does anybody have a recent working recipe for the setup file? Thank you! Thomas

Re: [Rdkit-discuss] unsubscribe....

Il giorno ven 19 mar 2021 alle ore 18:55 Thomas ha scritto: > In my inbox I have 4 removal confirmation starting from 15th March > > Let's do it like this: I made a filter and a "rdkit" label in my gmail, so > my problem is sorted. PLS DO NOT REMOVE ME: you ne

Re: [Rdkit-discuss] unsubscribe....

In my inbox I have 4 removal confirmation starting from 15th March Let's do it like this: I made a filter and a "rdkit" label in my gmail, so my problem is sorted. PLS DO NOT REMOVE ME: you never know :) But the obvious reason why I was writing here, was to inform you about a possible

[Rdkit-discuss] unsubscribe....

Sorry to disturb you all, I'm trying to unsubscribe, I tried in many different ways with no success. Can anybody help me? I know that I can "spam" it, but then i guess that if more people have the same issue, soon or later Google servers will block the whole mailing list. Thank

Re: [Rdkit-discuss] SMARTS representing a fragment (with "unbonded" bonds)

ng. I seriously hope to sort this out with smarts without any graph approach... Thomas Il giorno ven 5 mar 2021 alle ore 18:08 Ivan Tubert-Brohman < ivan.tubert-broh...@schrodinger.com> ha scritto: > Hi Thomas, > > I believe what you want can be done using recursive SMARTS and > disco

[Rdkit-discuss] SMARTS representing a fragment (with "unbonded" bonds)

Is it possible to search for a fragment that is not a valid structure itself, but part of a structure? Problem: "Given a structure, and a decomposition of the structure, highlight each part with a different color" The decomposition is always in the form of 1 SMILES and n SMILES FRAGMENTS The

Re: [Rdkit-discuss] Drawing options: noCarbonSymbols = False

cookbook that requires importing ipython for that: is it really necessary? Thank you Il giorno gio 4 mar 2021 alle ore 06:52 Greg Landrum ha scritto: > Hi Thomas, > > noCarbonSymbols was an option for the old drawing code and is not > currently available in the new drawing code since it didn't seem t

[Rdkit-discuss] Drawing options: noCarbonSymbols = False

) drawer.drawOptions().noCarbonSymbols = False but again no luck. I tried also to modify the MolDrawOptions object options = drawer.drawOptions() but there is nothing about "noCarbonSymbol"... Can anybody address me on the right path? Much apprecia

[Rdkit-discuss] rdkit-cartridge: Inserting new molecules

duplicates all the data (and even more wasteful with ctab file). Is it possible to not duplicate the data and be able to insert smiles/ctab directly? Best Regards, Thomas ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge

[Rdkit-discuss] Jupyter Notebook Structure image size

Hi all, how can I change the default structure image size in Jupyter notebook for a - single molecule? - molecules in a pandastools dataframe? default size is way too large for my taste (takes up too much screen space) Best Regards, Thomas

Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

Hi Brian, commercial tools usually use the term "reaction-based enumeration" or "reaction-based library design". Best Regards, Thomas Von: Bennion, Brian via Rdkit-discuss Gesendet: Freitag, 25. September 2020 07:19 An: RDKit Discuss Bet

[Rdkit-discuss] TIL: Mol objects having varying attributes depending on rdkit imports

this problem, you will now hopefully find this information via search and be able to solve it much faster than I was. best regards, Thomas ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit

Re: [Rdkit-discuss] result discrepancy between SubstructLibrary, PatternFingerprint comparison and HasSubstructMatch

lines below returned an error. fps.AddFingerprint( fps.MakeFingerprint(mol2, fpSize=4096) ) fps.AddFingerprint( fps.MakeFingerprint(mol2, nBits=4096) ) For the time being, I will use 2048 bits but it would be good to be able to control it in the future. Best wishes, Thomas On Mon, 31 Aug 2020

[Rdkit-discuss] result discrepancy between SubstructLibrary, PatternFingerprint comparison and HasSubstructMatch

acilitate linking or extension. What is wrong in this case and the results do not agree? Am I not using SubstructLibrary correctly? I thank you in advance. Thomas -- ====== Dr. Thomas Evangelidis Research Scientist IOCB -

Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers

ecifically, I'm looking for a way to access rdkit.Chem.MolStandardize.rdMolStandardize from Java. I could not find any matching Java class nor function. Is this functionality supported via the Java wrappers ? Thanks & Regards, Thomas On Wed, Apr 22, 2020 at 11:55 AM Tim Dudgeon wrote:

[Rdkit-discuss] Problems building RDKit + JavaWrappers

to /home/thomas/git/rdkit and set env variables RDBASE=/home/thomas/git/rdkit LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/ Using this 'cmake' command cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON .. I get OK looking output except for CMake Warning

Re: [Rdkit-discuss] RDkit in Python vs. on PostgreSQL?

what this would be used for as obviously this approach doesn't scale at all and you would need some form of storing the fingerprints also on spark. Also if your goal is to do similarity searches with lots of fingerprints I suggest you have a look at ChemFP. Best Regards, Thomas

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

ts size I assume it works. So I suggest to add the bondLineWidth as option to above method. Best Regards, Thomas Von: Thomas Strunz Gesendet: Donnerstag, 13. Februar 2020 09:09 An: rdkit-discuss@lists.sourceforge.net Betreff: [Rdkit-discuss] RDKit Cartridge mol

[Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

of this function? I tried stuff like below: mol_to_svg(mol, 'Test', 150, 100, '{"bondLineWidth": 1, "legendFontSize": 0.5}') There is no error but the "JSON" options are not applied. The image always looks the same with for my taste too thick

Re: [Rdkit-discuss] How does rdkit cartridge work?

screenout step. Best Regards, Thomas Von: Greg Landrum Gesendet: Samstag, 25. Januar 2020 06:11 An: Chicago Ji Cc: rdkit-discuss Betreff: Re: [Rdkit-discuss] How does rdkit cartridge work? Hi Changge, On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji mailto:chica

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

(Lubuntu 16.04) takes 2.5s. While the difference again is roughly 50%, I'm hesitant as here we really are not comparing apples to apples as windows uses Intel mkl vs openblas on linux. Best Regards, Thomas Von: Jan Holst Jensen Gesendet: Freitag, 24. Januar 2020

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

It's confusing to me as the performance difference is so consitent and apparent but I would assume if this was normal people would have noticed a long time ago?Yet I can't find anything about it. Or does everyone run their code native? Best Regards, Thomas Von: Maciek W

Re: [Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

>50% more time. So there seems to be a consistent large performance impact in VMs. Of course the VM will be a bit slower but not by that much? What am I missing? Other experiences? Best Regards, Thomas Von: Greg Landrum Gesendet: Montag, 16. Dezember 2019 17:1

[Rdkit-discuss] Observations about RDKit performance: PatternFingerprinter, Windows, Linux and Virtual machines

machine aspect is kind of troubling because I would assume many real-world applications are deployed as VM and hence might suffer from this too? I don't have a well defined question but more interested in other users experience especially regarding the virtualization. Best Regards, Thomas

Re: [Rdkit-discuss] How to pass atomic charge as atom invariant to ECFP?

rent hashing schemes for the atom invariants. If you really want to > track down what's going on, you'll have to figure out which molecules are > different and share those. > > I will get back to this thread in due time with more information about these

Re: [Rdkit-discuss] How to pass atomic charge as atom invariant to ECFP?

r-defined invariants are much less (795) and the performance of the ML model is significantly different. Could someone point out what I am doing wrong? ~Thomas -- ====== Dr. Thomas Evangelidis Research Scientist IOC

Re: [Rdkit-discuss] How to pass atomic charge as atom invariant to ECFP?

ts >> >> >> And then generate the fingerprint like this: >> >> >> fp = AllChem.GetMorganFingerprint(mol, radius=3, >> invariants=generateAtomInvariant(mol)) >> >> >> -- == Dr. Thomas Eva

[Rdkit-discuss] How to pass atomic charge as atom invariant to ECFP?

ffice to add this extra line in generateAtomInvariant() function? descriptors.append(a.GetFormalCharge()) I thank you in advance. Thomas -- ====== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and

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

, Thomas ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] numpy array to bit vector

v 14, 2019 at 4:35 PM Maciek Wójcikowski > wrote: > >> Hi Thomas, >> >> You could also use SetBitsFromList() method: >> >>> bv.SetBitsFromList(np.where(ar)[0].tolist()) >>> >> >> >> Pozdrawiam, | Best regards, >> Maciek Wój

Re: [Rdkit-discuss] numpy array to bit vector

ow do I do it? fv1 = numpy.array([1,1,0,0,1,0,1]) fv2 = numpy.array([0,1,1,0,1,0,0]) Thanks in advance. Thomas -- == Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of

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

compatible with openblas. There are probably more such issues but I guess still better than getting everything but rdkit from pypi. Best Regards, Thomas Von: Peter St. John Gesendet: Dienstag, 12. November 2019 16:25 An: Greg Landrum Cc: Thomas Strunz ; rdk

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

on top not sure how that will work. Plus updating this env is probably also big problem. So for me this is temporary workaround but not really a permanent long term solution (and as far as I can tell mostly an issue of conda and windows and not rdkit) Best regards, Thomas

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

. best regards, Thomas Von: Greg Landrum Gesendet: Dienstag, 12. November 2019 10:13 An: Thomas Strunz Cc: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Anaconda installation without hard dependency on Intel MKl (windows) Hi Thomas, I'm

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

changed so that when installing rdkit it accepts numpy and pandas install from pypi? thanks for any help. Best regards, Thomas ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] How to fragment a molecule as in Morgan fingerprints?

. Thanks in advance. Thomas -- == Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>

Re: [Rdkit-discuss] Which method to prefer for computing 2D coordinates

Hello Lukas, I am also struggling with 2D coordinate generation quite a long time as well as what criteria to use for choosing the most appropriate. Therefore, I would be very interest to use your code for 2D coordinate selection. With best regards, Thomas PS: very nice notebook Jose. I also

Re: [Rdkit-discuss] Fingerprint collision and machine learning

samples to go up to bitvector length 8192 without overfitting the networks, although that will make the training much slower. On Wed, 10 Oct 2018 at 14:15, Michal Krompiec wrote: > Hi Thomas, > Radius 2, 2048 bits, 5200 data points. > > On Wed, 10 Oct 2018 at 13:13, Thomas Evangeli

Re: [Rdkit-discuss] RDK5 fingerprint

On Thu, 4 Oct 2018 at 20:48, Nils Weskamp wrote: > Hi Thomas, > > my understanding was always that RDK5 corresponds to maxPath = 5. I'm > not sure if significantly longer path lengths (e.g. 12) actually > "increase the amount of information" since they also increase the

Re: [Rdkit-discuss] RDK5 fingerprint

Hi Nils, In general, yes, but there are still cases where RDK5 gives better ML models that ECFP or FCFP (i.e. the HSP90 dataset from D3R GC2015). In the end, I combine them all. Anyway, we are out of topic and I am afraid I won't get an answer to my original question. Thomas On Thu, 4 Oct

[Rdkit-discuss] online sdf to mol2 converter

ar 99 46 96 1 100 47 48 ar 101 47 97 1 102 48 98 1 @SUBSTRUCTURE 1 UNK 1 GROUP 0 0 ROOT -- == Dr Thomas Evangelidis Research Scientist IOCB - Institute

Re: [Rdkit-discuss] descriptors beyond rotatable bond count and possible correlations with entropy

html best, Thomas On Tue, 28 Aug 2018 at 02:22, James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > RDkit users, > > Is there a RDkit descriptor (or code) to determine the largest number > of contiguous > rotatable bonds in a small molecule?

[Rdkit-discuss] Parallelize Butina clustering

and I would like to share the code. Would be the rdkit contrib folder the right place for these kind of work?  Cheers, Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites

Re: [Rdkit-discuss] New Drawing code: Fixed sized molecules

to fit if w > image_width or h > image_height: rw = w/image_width rh = h/image_height ratio = max(rw,rh) w = int(w/ratio) h = int(h/ratio) return (w, h, minV, maxV) Best Regards,

[Rdkit-discuss] New Drawing code: Fixed sized molecules

When using the "new" drawing code according to http://rdkit.blogspot.com/2015/02/new-drawing-code.html I also want to be able to control the size of the molecule (not image) so if for example I have to depict multiple molecules smaller

Re: [Rdkit-discuss] Inversion of chirality using reaction SMARTS

# Sub  [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H] # Prod [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H] Best wishes, Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http:/

Re: [Rdkit-discuss] [Rdkit-announce] RDKit 2018.03.2 release

Hi Drew, You have conda 4.3, which might be too old, and/or is missing the new Anaconda "main" channel. Try "conda update conda", or if that doesn't do the trick, try installing a fresh copy of Miniconda. Cheers, Thomas > On Jun 9, 2018, at 11:39 AM, Drew Gibson via

[Rdkit-discuss] Output EZ configuration in SMARTS (python)

Dir()) # ENDUPRIGHT print('SMARTS:', qb.GetSmarts()) # SMARTS: - Any tip and help are welcome, thank you by advance, Best wishes, Thomas -- Check out the vibrant tech community on one of the world's most engaging tech

[Rdkit-discuss] Inversion of chirality using reaction SMARTS

# Prod [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H] Did I make a mistake somewhere, or is there something additional to do in order to make inversion of chirality working in all cases? I am using the last stable conda version of rdkit (2018.03.2.0). Thank you by advance for any clue, Best wi

[Rdkit-discuss] date of RDKit User Group Meeting 2018

would. thanks, Thomas -- == Dr Thomas Evangelidis Post-doctoral Researcher CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35/2S049, 62500 Brno, Czech Republic email: tev...@pharm.uoa.gr

[Rdkit-discuss] IMPORTANT: minimization fails within bad direction in linearSearch

Greetings, I am trying to optimize the geometry of some of the molecules from the current D3R challenge (hence the "IMPORTANT" tag in the title), but RDKit returns this error: Invariant Violation bad direction in linearSearch Violation occurred on line 231 in file /home/thoma

Re: [Rdkit-discuss] reading multiple conformers from file

!??) molnames_list.append(molname) if get_molnames: return molname_SMILES_conformersMol_multidict, molnames_list else: > return molname_SMILES_conformersMol_multidict -- == Dr Thomas Evangelidis Post-doctoral Research

Re: [Rdkit-discuss] reading multiple conformers from file

Hello, I was just wondering, has there been any progress on the multi-conformer sdf file reader since last year? best Thomas On 27 October 2016 at 05:20, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Thomas, > > You're right, reading multiple conformations out of an SDF

Re: [Rdkit-discuss] shape descriptor expressed as array of numbers

in this case. So before I start writing something of my own, I would like to know if there is something similar already available. Can the 3D descriptors from DRAGON be expressed as arrays of numbers? best Thomas On 20 May 2017 at 07:56, Greg Landrum <greg.land...@gmail.com> wrote: >

[Rdkit-discuss] shape descriptor expressed as array of numbers

) algorithm which encodes shape information into 12 floating point numbers, but the shape information that it provides is rather poor since it was adapted for screening millions of compounds in short time scales. I would appreciate any advice. best, Thomas

Re: [Rdkit-discuss] numpy array to bit vector

division* >> >> *mol1 = Chem.MolFromSmiles('CCO')* >> *mol2 = Chem.MolFromSmiles('CCC')* >> >> *fp1 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol1, 8), >> dtype='bool')* >> *fp2 = np.array(AllChem.GetMorganFingerprintAsBitVect(mol2, 8), >>

[Rdkit-discuss] numpy array to bit vector

Hello, I created a numpyarray from a molecule using the following function: AllChem.GetMorganFingerprintAsBitVect() Now I would like to convert back to bit vector the numpy array, in order to calculate the Tanimoto similarity of two compounds. Is this possible? thanks Thomas

Re: [Rdkit-discuss] how to exclude conformers with wrong geometries

j,k) must not both belong to a ring > from Chem.rdMolTransforms.SetBondLength() > ValueError: bond (i,j) must not belong to a ring > How can I reset the bondlengths, angles and dihedrals of the aromatic rings to their initial values? thanks Thomas On 23 February 2017 at 20:52, Greg

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

t importantly (!!!), RDKit fails to generate conformers for many ligands. The error I get is: [16:29:30] Could not triangle bounds smooth molecule. > WARNING: No conformations generated for molecule erk36 > What does this mean? Am I using an old version of RDKit (2015.03.1, the one in

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

the crystal ligand with the biggest MCS (excluding hydrogens). 4) Like 3) but considering only the scaffolds of the query and the crystal ligands. If someone had experience the same problem and could recommend which way works best or suggest any better way I would be very grateful. Thomas On 21

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

st >> >> This might not be what you want, but we had good success with similar >> methods and virtual screening, especially when using multiple co-crystal >> active sites. I can send you a reference link if this interests you >> >> Cheers, >> Brian >>

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

​ Greg and Brian, Thank you for your useful hints. All the compounds that I want to align are supposed to belong to the same analogue series so they should shave a common substructure with substantial size. What I want to emulate is the "core restrained docking" with glide, where you specify the

Re: [Rdkit-discuss] aligning maximum common substructure of 2 molecules

, refCid=0, reflect=True) AllChem.TransformMol(qmol, bestRMSDTrans[1], confId=bestconfID, keepConfs=False) and then I write the qmol in an sdf file. But when I visualize it the qmol is far from the refmol! On 20 February 2017 at 02:33, Thomas Evangelidis <teva...@gmail.com> wrote: >

[Rdkit-discuss] aligning maximum common substructure of 2 molecules

automatic way to find it on the fly while aligning the 2 molecules. -- == Thomas Evangelidis Research Specialist CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35/1S081, 62500 Brno, Czech Republic

[Rdkit-discuss] best free protein-ligand structure interaction fingerprint API

I am sorry for being off-topic. I would like to ask if anyone can suggest me any good python API that calculates protein-ligand structure interaction fingerprints as bit arrays. Preferably open source so I can incorporate it into my own code. thanks Thomas

Re: [Rdkit-discuss] reading multiple conformers from file

Hello Greg, Is the canonical SMILES string always unique for every isomer and tautomerization state of a molecule? If yes, then I have already written a function to load multiple molecules and their conformers, which I can share it here. best Thomas PS: thanks to David for pointing this out

[Rdkit-discuss] reading multiple conformers from file

Thomas -- == Thomas Evangelidis Research Specialist CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35/1S081, 62500 Brno, Czech Republic email: tev...@pharm.uoa.gr teva...@gmail.com

Re: [Rdkit-discuss] installation issues

Thank you Greg, It was that simple! export PYTHONPATH=/usr/lib/python2.7/dist-packages/:$PYTHONPATH On 20 October 2016 at 14:40, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Thomas, > > The first thing I would check is that you are actually running the system >

[Rdkit-discuss] installation issues

2 root root4096 ott 19 00:34 utils > drwxr-xr-x 3 root root4096 ott 19 00:34 VLib Thanks in advance for any advice. Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slas

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

] 3D alignment in Python: align conformers of 2 molecules To: beginn...@hotmail.de CC: rdkit-discuss@lists.sourceforge.net On Fri, Jun 27, 2014 at 7:57 AM, Thomas Strunz beginn...@hotmail.de wrote: thanks for your quick reply. This helped to improve the alignment. I'm glad to hear it! How

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Hi Greg, thanks for your quick reply. This helped to improve the alignment. How can I reproduce the alignment done in with the Open3DAlign Node in Python? Is it possible at all? Best Regards, Thomas From: greg.land...@gmail.com Date: Fri, 27 Jun 2014 05:10:42 +0200 Subject: Re: [Rdkit

[Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

, Thomas refCids = generateConformers(refMol, numConformers) mcs = MCS.FindMCS([refMol,mol], ringMatchesRingOnly=matchesRingOnly) if mcs.completed == 1 and mcs.numAtoms 0: core = Chem.MolFromSmarts(mcs.smarts) logger.info('MCS: %s

Re: [Rdkit-discuss] Error depicting a smiles string

Greg Landrum schrieb: Dear Thomas, I checked in the fix for this problem this morning. Great. Will you make a binary release as well, or should I try to compile it myself? -- Thanks, Thomas

Re: [Rdkit-discuss] Error depicting a smiles string

Greg Landrum schrieb: Dear Thomas, On Thu, Apr 29, 2010 at 4:05 PM, Thomas Heller thel...@ctypes.org wrote: I get errors when trying to depict this smiles string: OC(=O)[C@@H]1CCCN1 It is from the wikipedia entry for Proline: http://en.wikipedia.org/wiki/Proline As it turns out rdkit

[Rdkit-discuss] Error depicting a smiles string

Hi Greg, I get errors when trying to depict this smiles string: OC(=O)[C@@H]1CCCN1 It is from the wikipedia entry for Proline: http://en.wikipedia.org/wiki/Proline As it turns out rdkit is passing 'nan' as coordinates to all the drawing functions ;-( -- Thanks, Thomas