[Rdkit-discuss] draw molecule without rescaling or translating

ted to the width and height used in the MolDraw2D constructor, and I see that there are options fixedBondLength, fixedScale, as well as a setScale method. But I'm not clear on what values to set in these to set the rescaling to 1 and translation to 0. Tha

Re: [Rdkit-discuss] draw molecule without rescaling or translating

out making access > functions for. > I hope this helps. If not, please do get back to me either privately or > via the list. It would be useful for future development to find out how > you get on and what would have made it easier for you. > > Best, > Dave > > >

[Rdkit-discuss] c++ atomic lifetime

Everything I know about C++ I learned just so that I can write a link between an interpreted language and the rdkit, so there are definitely some gaps in my knowledge. What I'm trying to understand right now is the expected lifetime of an Atom pointer returned by a molecule, for instance by the ge

Re: [Rdkit-discuss] c++ atomic lifetime

wn these sorts of error, and many more besides. If you’re developing on > Linux, it’s good practice to use it on any code before you use that program > in earnest. > > Cheers, > Dave > > > On Thu, 27 Aug 2020 at 20:17, Jason Biggs wrote: > >> Everything I know about

Re: [Rdkit-discuss] c++ atomic lifetime

Jason Biggs On Fri, Aug 28, 2020 at 8:16 PM dmaziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > On 8/27/2020 8:48 PM, Jason Biggs wrote: > > > > I'm not very familiar with how the python interface works, is there a > > similar issue wit

Re: [Rdkit-discuss] Order of linking static libraries

I don't have this problem on mac/windows, but it came up on Linux. Rather than figure out which library or libraries to link twice I just use the idiom --start-group -llib1 -llib2 -llib3 --end-group Maybe that will help with your issue. Jason On Mon, Sep 14, 2020 at 10:46 AM topgunhaides

Re: [Rdkit-discuss] Counting Stereo centers in CPP. And [H] in SMILES string

On Wed, Sep 30, 2020 at 9:45 PM Steven Pak wrote: > Hello, > > I have been using RDKIT for some time now, and I could not get a certain > descriptor that would be super useful for my work. Every other descriptor > works fine, however, for some reason the following calculations always > gives me 0

Re: [Rdkit-discuss] SA_scores and QED scores questions?

Have you compared the output of debugMol from your from-smiles ROMol (from test2) versus the ROMol objects you get from the larger program? That can help to explain the differences, though not alway. Ja

[Rdkit-discuss] RWMol, ROMol, and static casting

I have learned what C++ I know in order to build a link to rdkit from my own system, so the following may be more of a general coding question than anything rdkit-specific. I am looking at the python wrappers, and I see many functions return a ROMol object by static casting the RWMol pointer to a

[Rdkit-discuss] sanitization converts "I(=O)(=O)[O-]" into "[O-][I+2]([O-])[O-]"

The RDKit will always convert iodate from the form on the left, with an expanded octet on iodine and a single negative charge, into the form on the right with all single bonds and a charge on every atom (image here https://i.stack.imgur.com/hq3St.png). This happens no matter how I import the molec

Re: [Rdkit-discuss] explicit H atoms

Jason Biggs On Tue, Mar 9, 2021 at 10:49 AM Maciek Wójcikowski wrote: > Hi Jean-Marc, > > I know you can draw them, but both SMILES and RDKit internally use two > bonds (up/down) directions to assign the bond stereo, which means that > there are not > Fortunately the RDKit

Re: [Rdkit-discuss] two molecules in mol object

Have you looked at GetMolFrags? if you define >m=MolFromSmiles('CCC.CC') then >rdmolops.GetMolFrags(m,asMols=True) returns two molecules, keeping any coordinates or non-computed properties in the process. Jason Biggs On Wed, Mar 10, 2021 at 9:42 AM Shani Zev wrote: &g

Re: [Rdkit-discuss] Error: free(): double free detected in tcache 2 (going from pickles to mol)

Jason Biggs On Thu, Dec 29, 2022 at 3:22 PM Jarod Younker wrote: > The code compiles fine, but I’m running into a memory deallocation issue > in ‘Dummy’ if I use ROMol derived from pickled strings: > > > > Error: free(): double free detected in tcache 2 > > > >

[Rdkit-discuss] How to assign stereochemistry from CIP code?

When creating a molecule, I can set a stereocenter by setting the chiralTag to be clockwise or counterclockwise, and get back the absolute chirality int atoms [5] = {7, 6, 6, 8, 9}; RDKit::RWMol *mol = new RDKit::RWMol(); for (int i : atoms) { RDKit::Atom atom(i); mol->addAtom(&atom); } mol->addBo

Re: [Rdkit-discuss] Extracting data of a standard structural formula

Peleg, I was doing something similar using the c++ function compute2DCoords, where you can give a coordinate map as the second argument. It looks like this is exposed in python, using the Compute2DCoords method ( http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#Compute2DCoords), s

Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.

RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETDG); RDKit::DGeomHelpers::EmbedMolecule(*mol, params); bool explicitOnly = false; bool addCoords = true; RDKit::MolOps::addHs(*mol, explicitOnly, addCoords); seems to work. Jason Biggs On Thu, Sep 7, 2017 at 10:49 AM, Dmitry Redkin

Re: [Rdkit-discuss] SMARTS pattern matching of canonical forms of aromatic molecules

or '-', but not ':' (they will also match '@' or '~', but that's beside the point here) As Peter mentions, by default if you read in a kekulized SMILES string, the mol you create will not be kekulized, but it sounds like you are intentionally kekulizi

Re: [Rdkit-discuss] how to output multiple Kekule structures

tch(Chem.MolFromSmarts('[c]=[c]-[c]')) > True So at the very least, you need to change the smarts strings to use [#6] instead of [C] Jason Biggs On Mon, Sep 11, 2017 at 2:53 PM, Paolo Tosco wrote: > Hi Jim, > > you can indeed enumerate all Kekulè st

Re: [Rdkit-discuss] bad inchi or parsing problem?

ifferent structures due to the specified charges. Is this a limitation of inchi, or do I need to rethink my ideas of what makes two chemical structures the same? Jason Biggs On Thu, Sep 14, 2017 at 12:38 PM, John Mayfield wrote: > InChI is an identifier and not a representation, you s

Re: [Rdkit-discuss] bad inchi or parsing problem?

Thanks to Curt, Markus, and John for helping me understand this. I knew that inchi had its limitations, but that didn't jump out at me here because there's no hydrogen migration between the different forms - not realizing these forms also qualify as tautomers. But So this is definitely a feature

Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?

if you don't care what type of atom it is, just that it's aromatic, you should use [a], so [a]1[a][a][a][a][a]1 would match any 6-membered aromatic ring Jason Biggs On Wed, Sep 20, 2017 at 7:57 PM, James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net>

[Rdkit-discuss] what if all explicit hydrogens were actual atoms

ter, https://sourceforge.net/p/rdkit/mailman/message/30200937/, but it looks like the branch mentioned there was abandoned. Jason Biggs -- Check out the vibrant tech community on one of the world's most enga

Re: [Rdkit-discuss] SMARTS for Joback and Reid method

">C=O (ring)","[$([#6X3H0](=[OX1]));!$([#6X3](=[#8X1])~[#8X2]);R]=O"}, {"Aldehyde","O=CH-","[CX3H1](=O)"}, {"CarboxylicAcid", "COOH", "[OX2H]-[C]=O"}, {"Ester", "-C(=O)O-", "[#6X3H0;!$([#6X3H

Re: [Rdkit-discuss] transformation of an atom or group of atoms by atom indices

Something along these lines? mol = Chem.MolFromSmiles('')emol = Chem.EditableMol(mol)emol.ReplaceAtom(3, Chem.Atom(1))mol = emol.GetMol() In [12]: Chem.MolToSmiles(mol) Out[12]: '[H]CCC' In [13]: Chem.MolToSmiles(Chem.RemoveHs(mol)) Out[13]: 'CCC' Jas

[Rdkit-discuss] bad coordinates for acetylenic hydrogens

CC#C)cc1'. I can write a hack on my end to look for this special case, but where in the drawing code does it decide where to place hydrogens? Jason Biggs -- Check out the vibrant tech community on one of the wo

Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

-4.82204677e-16, -7.5000e-01, 0.e+00], [ 4.36280422e-16, 7.5000e-01, 0.e+00]]) The above seems to happen with any terminal alkyne hydrogen. I will file an issue for this Jason Jason Biggs On Fri, Dec 1, 2017 at 4:59 AM, Malitha Kabir wrote: > Hi Jas

Re: [Rdkit-discuss] RDkit and Pubchem

JSON format, but you can have it return XML or plain text. If you want an SDF file, something like https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF?record_type=3d setting up a python function to query this shouldn't be difficult. Jason Biggs On Fri, Dec 1, 2017 at 12:

Re: [Rdkit-discuss] RDkit and Pubchem

rns a message stating so. Jason Jason Biggs On Fri, Dec 1, 2017 at 5:33 PM, Sundar wrote: > Hi Jason, > > This is great. I would really benefit from this. > At present I am looking for a way to download smiles or mol data of a few > compound which only have SIDs and CIDs. >

[Rdkit-discuss] SanitizeMol changing drawing

y produce the same pickle, pickle.dumps(m) == pickle.dumps(m2) True So why do they get treated differently by the drawing code? The only way to return m2 to its original state is to run AssignStereoChemistry with force = True. What variable is being thrown off by SanitizeMol? [image: Inl

Re: [Rdkit-discuss] SanitizeMol changing drawing

code and replacing > the use of CIP ranks with the atom ranking generated by Nadine's > canonicalization code > > -greg > > > On Wed, Dec 13, 2017 at 10:38 PM, Jason Biggs > wrote: > >> using the recent release, >> >> >> m = Chem.Mol

[Rdkit-discuss] strange linker error using VC++

I'm trying to use the rdkit as a library in another project, and am having trouble getting it to build on windows. I can get the code to compile on mac and linux, but it fails for windows, both 32-big and 64-bit varieties. I don't know how specific this is to the rdkit, but I have zero experience

Re: [Rdkit-discuss] strange linker error using VC++

(smi); > RDKit::ROMol molCopy(*mol); > delete mol; > std::string res = RDKit::MolToSmiles(molCopy); > > Cheers, > p. > > > On 11/01/2018 02:33, Jason Biggs wrote: > > I'm trying to use the rdkit as a library in another project, and am having > trouble

Re: [Rdkit-discuss] How to convert numpy array to rdkit fingerprint object?

(bv1.GetBit(i)) False True True True False True False True False True True True False True True True True True False False Jason Biggs On Thu, Jan 11, 2018 at 9:30 AM, Michał Nowotka wrote: > Hi, > > Imagine I have two numpy arrays containing zeros and ones (or bools) > effec

[Rdkit-discuss] RDKit and Mathematica

ge but uses an RDKit::ROMol as the underlying structure. As we find bugs, we will report them, and when we implement functionality that that isn't available in the RDKit, I'm hoping to add back to the community here. Best wishes, Jason Biggs PS - I find it to be surreal, but my boss has take

[Rdkit-discuss] mol file parsing, 3D or 2D

Two question about mol file conformer reading: Looking through the .mol files included for testing, and chose "Code/GraphMol/Depictor/test_data/7UPJ_spread.mol" at random. When I read in this file using the RDKit::MolFileToMol function, and then query its conformer's is3D() method, it returns tru

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

he jar in the External folder and write python wrappers. Jason Biggs On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum wrote: > Dear all, > > We've been invited again to participate in the OpenChemistry application > for Google Summer of Code. > > In order to participate we

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

Thanks for the detailed reply > > The fact that this isn't happening for you indicates that you are reading > the molecules in without sanitizing them - the mol file parser calls > assignStereochemistry() by default if you sanitize. Are you sure that you > should be disabling sanitization? > > I

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

On Wed, Jan 17, 2018 at 10:12 AM, Dimitri Maziuk wrote: > On 2018-01-16 22:46, Greg Landrum wrote: > > It might be worth thinking about adding an option to the aromaticity >> perception code to maintain the original bond types and just set the >> "isAromatic" flag on the bonds. >> > > This is how

Re: [Rdkit-discuss] edge matrix

{0, 1, 0, 0, 0}, {1, 0, 1, 1, 0}, {0, 1, 0, 0, 0}, {0, 1, 0, 0, 1}, {0, 0, 0, 1, 0}}; graph = AdjacencyGraph[adjacencyMatrix]; lineGraph = LineGraph[graph]; AdjacencyMatrix[lineGraph] // MatrixForm [image: Inline image 1] Jason Biggs On Wed, Jan 17, 2018 at 10:21 AM, Marta Stępniewska-Dziub

[Rdkit-discuss] cmake error building master

Trying to build on Scientific Linux release 6.9, and I'm getting boost serialization errors, both on the recent release branch and on master In file included from > base/Boost/include/boost/numeric/ublas/vector.hpp:21:0, > from base/Boost/include/boost/numeric/ublas/matrix.hpp:18

Re: [Rdkit-discuss] cmake error building master

f I manually download the maeparser, the coordgenlibs, and the rapidjson files and put them in External/ then it works fine. Thanks, Jason Jason Biggs On Thu, Apr 19, 2018 at 12:42 PM, Greg Landrum wrote: > Which version of boost is that? > > On Thu, 19 Apr 2018 at 19:34, Jason Biggs

[Rdkit-discuss] EmbedMolecule ignoring double-bond ring stereochemistry

I don't know if this is a duplicate of https://github.com/rdkit/rdkit/issues/435 I notice that ring double-bond stereo gets quietly ignored by the embedding code. Trying to make cis and trans cyclododecene (choosing a large ring to minimize any strain), and they both come out cis. Using the SMIL

[Rdkit-discuss] A couple of questions about CoordGen in RDKit

I recently switched to the 2018_03_1 release, and I am trying out the new 2D coordinate generating functions. The diagrams look good, but I can't seem to figure out what the role of the template file is. I find that I can set the templateFileDir parameter either to a real directory with the templ

Re: [Rdkit-discuss] A couple of questions about CoordGen in RDKit

the library that implements them. Would it be wrong to call the rdkit method "DistanceGeometry"? What is the main distinction between the two methods? Best, Jason (the image from Nicola's email didn't come through to me, showing the example with template on the bottom, with

Re: [Rdkit-discuss] (no subject)

, 0.]]) > > Chem.rdMolAlign.AlignMol(mol2,mol, atomMap = ((0,0),(1,1))) > >> 0.005493118189962501 > > mol2.GetConformer(0).GetPositions() > >> array([[ 3.10580323, -0.07674776, -0.45975102], >>[ 1.75185317, 0.36881027, 0.04161089]]) > >

[Rdkit-discuss] GETAWAY descriptor returning non-numeric values

I don't know enough about the GETAWAY descriptor to know if this is to be expected. >>>m = Chem.MolFromSmiles('CC=O') >>>m2=Chem.AddHs(m) >>>AllChem.EmbedMolecule(m2,randomSeed = 1234) >>>(Chem.rdMolDescriptors.CalcGETAWAY(m2))[85:90] [0.207, 0.008, 0.027, nan, 0.0] Is this a bug? If not, is i

Re: [Rdkit-discuss] InChI to Mol to InChi

ss in the mailing list?) Jason Biggs On Mon, Dec 17, 2018 at 7:24 AM JEAN-MARC NUZILLARD < jm.nuzill...@univ-reims.fr> wrote: > Dear all, > > I tried to transform an InChI into a Mol and back to InChi. > > The following code: > > inchi1 = > > "InChI=1S/C20

Re: [Rdkit-discuss] InChI to Mol to InChi

he 3D bond stereo but the smiles doesn't until you remove and re-detect the stereo? Does the InChI code go to the 3D structure when present and ignore stereo information in the mol object? Jason Biggs On Tue, Dec 18, 2018 at 12:14 PM Christos Kannas wrote: > Hi Jean-Marc, > > Th

[Rdkit-discuss] MMFF changing molecule

ng the MMFFMolProperties object using that copy (which can then be discarded). Is there a better workaround? Jason Biggs ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] MMFF changing molecule

(4,), (5,), (14,)) > > Chem.SetAromaticity(m2) > > m2.GetSubstructMatches(Chem.MolFromSmarts('a')) > > ((1,), (2,), (3,), (4,), (5,), (7,), (8,), (9,), (10,), (12,), (13,), (14,)) > > > Cheers, > p. > > On 02/05/19 20:31, Jason Biggs w

Re: [Rdkit-discuss] Why this doesn't work? HasStructMatch function

Change your pattern to use ~ as an unspecified bond instead of - for a single bond: >m=Chem.MolFromSmiles('CN(C(C=CC=C1)=C1C2=O)C3=C2C=CC=C3') >s=Chem.MolFromSmarts('c1c1~[#6](~c2c2)=[#8]') >m.HasSubstructMatch(s) True Jason On Tue, Feb 19, 2019 at 4:42 PM Li, Xiaobo [xiaoboli] < xia

Re: [Rdkit-discuss] Smarts conversion help

On Tue, Mar 26, 2019 at 8:22 PM Patrick Walters wrote: > HI Xiaobo, > > There's an explicit hydrogen in the SMARTS that shouldn't be there. I > also wouldn't include the single bonds around the ring closures. > To be fair, that explicit hydrogen was in the original SMILES string, so it is reaso

[Rdkit-discuss] AdditionalOutput from FingerprintGenerator

I am taking a look at the FingerprintGenerator class and I really like this unified interface for these four types of fingerprints. I have very limited experience with the fingerprint code before the generator API was introduced. What I'm not sure about is how to get information about the atoms/e

Re: [Rdkit-discuss] AdditionalOutput from FingerprintGenerator

ular bits in the Morgan or RDKit fingerprints using the new API? Jason Biggs On Fri, Mar 13, 2020 at 10:20 AM Greg Landrum wrote: > Hi Jason, > > At the moment there's nothing available here except what's in the C++ > tests. This part of the code didn't end up being c

Re: [Rdkit-discuss] AdditionalOutput from FingerprintGenerator

nerator.cpp#L99 > > I will take a look and see if it's possible to get these into the next > release. In the meantime, if you want that info it looks like you'll need > to use the older fingerprinting functions. > > -greg > > On Fri, Mar 13, 2020 at 11:10 PM Jason Big

Re: [Rdkit-discuss] Get the Exact Mass from a Molecular Formula field

You can get the most common isotope mass from the periodic table. Here is a small modification to the code you linked, https://gist.github.com/jasondbiggs/cadc261ed00a08054ad5c4a85cccd9d4 Jason Biggs On Mon, Mar 23, 2020 at 9:21 AM Pierre-Marie Allard < pierre-marie.all...@unige.ch>