Re: [Rdkit-discuss] Conformer getPositions to return numpy array

Thanks this is great, just found it when needed again after those few years ;-) On 29 August 2014 at 19:35, Greg Landrum wrote: > Hi Jan, > > On Friday, August 29, 2014, Jan Domanski wrote: > >> Hi there, >> >> I'm trying to wrap the very handy method getPo

[Rdkit-discuss] Using CUDA inside of rdkit (and a shameless plug)

Hi there, In case somebody is interested in getting CUDA code to work with and talk to rdkit (with a python wrapper and all), here is a little example: http://jandomanski.blogspot.com/2014/08/rocs-like-shape-overlap-in-rdkit.html This may be useful for doing Gaussian volume overlaps on the GPU (

[Rdkit-discuss] Conformer getPositions to return numpy array

Hi there, I'm trying to wrap the very handy method getPositions from rdkit/Code/GraphMol/Wrap/Conformer.cpp to return coordinates of a conformer as a numpy array. So far I was able to return a tuple of tuples, as below PyObject *convertPoint(RDGeom::Point3D &point){ PyObject *res = PyTuple

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

wrote: > > On Fri, May 16, 2014 at 2:22 PM, Jan Domanski wrote: > >> Yup, David you're correct I think the code is in but Paolo guessed the >> intentions of my question. >> >> I appreciate the point about amides (and other planar groups) in >> unconstrained mi

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

ps://github.com/rdkit/rdkit/pull/261 > > -David > > > On Fri, May 16, 2014 at 1:51 PM, Jan Domanski wrote: > >> The reply from Paolo was amazing and quick. I'm looking at this after a >> week and one questions comes to mind: Is there a reason this can't work out

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

The reply from Paolo was amazing and quick. I'm looking at this after a week and one questions comes to mind: Is there a reason this can't work out of the box? On 11 May 2014 23:08, Jan Domanski wrote: > Awesome, this was lightning speed Paolo - many thanks! > > - Jan >

Re: [Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

code! > > Cheers, > Paolo > > > On 05/10/2014 04:28 PM, Jan Domanski wrote: > > Hi there, > > Attached is a crystal_ligand.mol2 for the ACE target from DUDE. I'd like > to generate a number of conformers for this ligand. The trick is it has 2 > amide bo

[Rdkit-discuss] DihedralConstraint in MMFF minimize - keeping amides planar

Hi there, Attached is a crystal_ligand.mol2 for the ACE target from DUDE. I'd like to generate a number of conformers for this ligand. The trick is it has 2 amide bonds that I'd like to keep planar. As far as I can see neither MMFF nor UFF will keep those planar by default, at least not for this i

Re: [Rdkit-discuss] autodock vina pdbqt file to mol2

Hi all, Many thanks for all the responses, Greg's suggestion did the trick! - Jan On 10 May 2014 05:32, TJ O'Donnell wrote: > Babel can read and write both pdbqt and mol2 files. I'm not sure how the > atom ordering might be accomplished though. > > TJ > On May

Re: [Rdkit-discuss] autodock vina pdbqt file to mol2

profile on > LinkedIn]<http://cy.linkedin.com/in/christoskannas> > > > On 9 May 2014 20:17, Jan Domanski wrote: > >> Hi guys, >> >> I'm really stuck here: I have some output from autodock vina in a rather >> obscure pdbqt format. It's a lit

Re: [Rdkit-discuss] Similarity of daylight and daylight-like fingerprint

Many thanks Greg - that's the slides that I've been looking for! ;-) - Jan On 4 May 2014 17:04, Greg Landrum wrote: > Hi Jan, > > On Sun, May 4, 2014 at 5:19 PM, Jan Domanski wrote: > >> >> Some time ago I remember finding a presentation that showed

[Rdkit-discuss] Similarity of daylight and daylight-like fingerprint

Hi, Some time ago I remember finding a presentation that showed similarity between the original daylight and the daylight-like fingerprint calculated in rdkit. I think it was a scatter plot of some sort, where the two fingeprints were calculated for a set of molecules. The question that I'm tryin

Re: [Rdkit-discuss] Randomize atom order of an rdkit molecule

Awesome, many thanks Greg - Jan On 15 March 2014 00:15, Greg Landrum wrote: > Hi Jan, > > On Sat, Mar 15, 2014 at 2:17 AM, Jan Domanski wrote: > >> Hi, >> >> I've been reading this paper by Feher, where he shows undesirable >> dependence of doc

[Rdkit-discuss] Randomize atom order of an rdkit molecule

Hi, I've been reading this paper by Feher, where he shows undesirable dependence of docking score on atom order in input ligands (keeping coordinates of the atoms in the input unchanged, just moving them around). http://pubs.acs.org/doi/pdf/10.1021/ci200598m I wonder if there is a way to permute

Re: [Rdkit-discuss] Rotatable bonds, amide bonds and SMARTS

2014 17:38, S.L. Chan wrote: > Hello Jan, > > This has been discussed not long ago: > > > http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03671.html > > Your second Smarts string is the "Chemaxon Smarts" in this discussion. > There may

[Rdkit-discuss] Rotate a rotatable bond

Hi all, Say I have a molecule and the molecule has a bunch of bonds. Some of them are rotatable and I would like to use rdkit to rotate them. Given atoms B and C, connected by a rotatable bond and with 2 flanking atoms A and D, I would like to get/set the dihedral A-B-C-D, such that the A-B part

Re: [Rdkit-discuss] ROMol getConformer returning the copy of a conformer

Thanks Paul! That was a very silly assignment by reference question - coming from python-land this is unexpected ;) Thanks again, Jan -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the

[Rdkit-discuss] ROMol getConformer returning the copy of a conformer

Hi, I'm trying to trivially modify the coordinates of the 0th atom of the 0th conformer in a (3D) ROMol called m. To do that I need to get the conformer: RDKit::ROMol m = ...; RDKit::Conformer conf = m.getConformer(-1); int idx = 0; // Get coordinates of 0th atom double x = conf.getAtomPos(idx)