Re: [Rdkit-discuss] Unwanted explicit Hs

;CCS=O' Sometimes, just 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 p

[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' T

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 histori

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

s there a way? I've already 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 GetBonds.

[Rdkit-discuss] rdkit and py2exe

mport 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! T

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

ed 4 times 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

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 problem.

[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. T

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

ious... kind of captcha thing. 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 r

[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 "smil

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

our 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 si

[Rdkit-discuss] Drawing options: noCarbonSymbols = False

, 100) 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 app

[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

have 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/list

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

ctor size. Both 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 M

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

in this case) that can facilitate 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 Resear

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

by the wrappers. Specifically, 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 11:5

[Rdkit-discuss] Problems building RDKit + JavaWrappers

es 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

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, T

Re: [Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

(0.5) which got silently ignored. But with a proper value in points 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.s

[Rdkit-discuss] RDKit Cartridge mol_to_svg parameters

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 fo

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

fingerprint for the 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 Chic

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

nd VM (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. J

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

ifferences. 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

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

The difference here is smaller but VMs also take >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:

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

he virtual 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 R

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

the > different 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 mor

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

default ECFP atom invariants, while with user-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. Th

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

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

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

ase would just suffice to add this extra line in generateAtomInvariant() function? descriptors.append(a.GetProp('partial charge')) Could someone please answer my question below? On Fri, 22 Nov 2019 at 15:38, Thomas Evangelidis wrote: > Greetings, > > Could someone please clar

[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

u, Nov 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

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

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

nsorflow-gpu 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 r

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

nomkl. 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,

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

. Can this be 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] distinguishing macrocyclic molecules

better definition. Could anyone give me some hints on how to program this? I thank you in advance. Thomas 1. Yudin AK (2015) Macrocycles: lessons from the distant past, recent developments, and future directions. Chem Sci 6:30–49. 2. Marsault E, Peterson ML (2011) Macrocycles are great cycles

[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] Structure-Based Drug Design

se you need protein and ligand force field parameter files and that's where my script will come in handy. I am also looking forward to seeing more SBDD integration to RDKit and I am happy to contribute code. With best regards, Thomas Evangelidis -- ====

Re: [Rdkit-discuss] [Question] Ok to switch to conda-forge for RDKit builds?

2018.03.4.0-py36h71b666b_1 rdkit --> 2018.03.4-py36ha4bbe77_0 conda-forge ------ Cheers, Thomas On Thu, Oct 18, 2018 at 4:43 PM Greg Landrum wrote: > > > > On Thu, Oct 18, 2018 at 2:21 PM Eric Jonas wrote: >

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

ining 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 Eva

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

ourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- == 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] 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 increas

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,

[Rdkit-discuss] RDK5 fingerprint

and corresponding bond paths as values. Defaults to empty. Thanks in advance. Thomas -- == Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <

[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 of

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

t 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

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

V.y)) #shrink 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

[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 on

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

([H])(C(=O)[O-])C([H])([H])[H] ps = rxn21.RunReactants((llac,)) print('l2 >> r2') print('Sub ', Chem.MolToSmiles(llac)) print('Prod', Chem.MolToSmiles(ps[0][0])) # l2 >> r2 # Sub  [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H] # Prod [H]O[C@]([H])(C(=O)[O-])C([H])

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

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

.GetBondWithIdx(0) print(qb.HasQuery()) # True print(qb.GetBondDir()) # ENDUPRIGHT print('SMARTS:', qb.GetSmarts()) # SMARTS: - Any tip and help are welcome, thank you by advance, Best wishes, Thomas -- Ch

[Rdkit-discuss] Inversion of chirality using reaction SMARTS

int('Prod', Chem.MolToSmiles(ps[0][0])) # Sub [H]O[C@]([H])(C(=O)[O-])C([H])([H])[H] # 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

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

nts, but I 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...@ph

[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-doctor

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 wrote: > Hi Thomas, > > You're right, reading multiple conformations out of an SDF does seem like > on

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

ly 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 wrote: > Hi Thomas, > > There i

[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

gt;> >> *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

[Rdkit-discuss] comparing the valence after superimposition

the aligned molecules written in the sdf file have the same valence as in the original sdf file (e.g. the atoms in the non-planar rings are still aromatic)? Can I do that by comparing the canonical SMILES of the original molecule with the canonical SMILES of the aligned? thanks Thomas

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

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 Land

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

threshold approach. Do you think that this is the right way to go? Thanks in advance. Thomas -- == Thomas Evangelidis Research Specialist CEITEC - Central European Institute of Technology Masaryk University Kamenice 5/A35

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

d most 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 on

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

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

>> 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 >> >> On Mon, F

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

onfID, 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 wrote: > Dear all, > > I

[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

in advance 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...

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 wrote: > Hi Thomas, > > The first thing I would check is that you are actually running the system > version of Python and that you PYTHO

[Rdkit-discuss] installation issues

-xr-x 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 t

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

, 27 Jun 2014 08:20:56 +0200 Subject: Re: [Rdkit-discuss] 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 wrote: thanks for your quick reply. This helped to improve the

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

gards, 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(

Re: [Rdkit-discuss] Q2 2010 Release

Greg Landrum schrieb: > Dear Thomas, > > I'm uploading a python 2.5 build to the sourceforge and google code > repositories now. Great! > Sorry that took so long, No problem - and thanks for it. Thomas --

Re: [Rdkit-discuss] Q2 2010 Release

se let me know if anyone needs a python 2.5 release) will be on > the sourceforge downloads page: If it isn't too much work for you I would very much appreciate a python 2.5 windows binary. -- Thanks, Thomas --

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? -- Thank

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

Greg Landrum schrieb: > Dear Thomas, > > On Thu, Apr 29, 2010 at 4:05 PM, Thomas Heller 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

[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 ;-( -- Than

[Rdkit-discuss] Buglets in the last release

#x27;Wrong amount of data for image') rdkit\Chem\Draw\__init__.py contains an unneeded 'import cairo' statement on line 58 which prevents this function from working when cairo is not installed. Otherwise I'm fascinated by the smiles re