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

2017-02-21 Thread Thomas Evangelidis
February 2017 at 07:35, Greg Landrum <greg.land...@gmail.com> wrote: > > > On Mon, Feb 20, 2017 at 6:17 PM, Thomas Evangelidis <teva...@gmail.com> > wrote: > >> >> Thank you for your useful hints. All the compounds that I want to align >> are supp

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

2017-02-20 Thread Thomas Evangelidis
, 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: >

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

2017-02-20 Thread Thomas Evangelidis
​ 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

2017-02-20 Thread Thomas Evangelidis
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 >>

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

2017-02-19 Thread Thomas Evangelidis
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

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

2017-02-22 Thread Thomas Evangelidis
OK, I am almost there! First, I tried the AllChem.ConstrainedEmbed(qmol, core) function to generate conformers, where core was a mol object created from the MCS with 3D coordinates copied from template's MCS. But is seems that this functions works only when core is an intact molecule, because I

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

2017-03-01 Thread Thomas Evangelidis
Hi Greg, Actually this question is relevant to my recent thread about aligning MCS of 2 compounds. As also seen in the code I have posted in my last email, I first generate N conformers of each query compound and then optimize them using distance restraints in order to superimpose their MCS with

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

2016-10-27 Thread Thomas Evangelidis
gt; A python implementation of this would be a good topic for Friday's UGM > hackathon, we can see if anyone finds it interesting enough to work on. > > -greg > > > On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis <teva...@gmail.com> > wrote: > >> H

[Rdkit-discuss] installation issues

2016-10-19 Thread Thomas Evangelidis
Greetings everyone, I use Ubuntu 14.04.4 LTS and first I tried to install RDkit through Conda. After getting a strange segmentation fault when invoking USRCAT functions that imported scipy, I managed to fix it by installing accelerate libraries: conda install accelerate However, in order to

[Rdkit-discuss] reading multiple conformers from file

2016-10-24 Thread Thomas Evangelidis
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

2016-10-21 Thread Thomas Evangelidis
version of Python and that you PYTHONPATH is not set. > > -greg > > > _________ > From: Thomas Evangelidis <teva...@gmail.com> > Sent: Wednesday, October 19, 2016 8:10 AM > Subject: [Rdkit-discuss] installation issues > To: <rdkit-discuss@lists.

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

2016-12-14 Thread Thomas Evangelidis
-- == 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 website: https://sites.google.com/site

[Rdkit-discuss] numpy array to bit vector

2017-03-16 Thread Thomas Evangelidis
-- == 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 website: https

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

2017-03-17 Thread Thomas Evangelidis
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), >>

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

2017-08-14 Thread Thomas Evangelidis
gt; > > On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis <teva...@gmail.com> > wrote: > >> Hello everyone, >> >> I am a new user of RDkit and I was looking in the documentation for an >> easy way to load multiple conformers from a structure file like .sdf.

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

2017-08-15 Thread Thomas Evangelidis
!??) 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

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

2017-05-19 Thread Thomas Evangelidis
-- == 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 teva...@gmail.com website: https://sites.google.com/site

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

2017-05-20 Thread Thomas Evangelidis
ther poor since it was >> adapted for screening millions of compounds in short time scales. >> >> I would appreciate any advice. >> >> best, >> Thomas >> >> >> -- >> >>

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

2017-11-01 Thread Thomas Evangelidis
u think that this is the source of the problem? You can download the structures (also attached) from this link: https://www.dropbox.com/s/pp9srlkemweboaf/failed_compounds.sdf.gz?dl=0 thanks in advance Thomas -- ========== Dr Thoma

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

2018-02-22 Thread Thomas Evangelidis
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

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

2018-08-31 Thread Thomas Evangelidis
_ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- == Dr Thomas Evangelidis R

Re: [Rdkit-discuss] RDK5 fingerprint

2018-10-04 Thread Thomas Evangelidis
gt; > > On Thu, Oct 4, 2018 at 11:22 AM Thomas Evangelidis > wrote: > >> Dear RDKit community, >> >> I need some advice regarding the usage of RDK5 fingerprints for machine >> learning. I have a big training set (2200 molecules) and a small test set >> (130

Re: [Rdkit-discuss] RDK5 fingerprint

2018-10-04 Thread Thomas Evangelidis
risk > of bit collisions in folded fingerprints. > If you increase the fpSize to 8192, won't you reduce the risk of bit collisions? > > Am 04.10.2018 um 19:56 schrieb Thomas Evangelidis: > > Hi Nils, > > > > In general, yes, but there are still cases where RDK5 gives

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

2018-10-10 Thread Thomas Evangelidis
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

[Rdkit-discuss] online sdf to mol2 converter

2018-09-24 Thread Thomas Evangelidis
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

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

2019-04-13 Thread Thomas Evangelidis
. 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

2019-04-09 Thread Thomas Evangelidis
__ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https:

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

2019-11-14 Thread Thomas Evangelidis
d isn't the slowest thing I came up with): >>> def np_to_bv(fv): >>> bv = DataStructs.ExplicitBitVect(len(fv)) >>> for i,v in enumerate(fv): >>> if v: >>> bv.SetBit(i) >>>return bv >>> >>> -greg >>> &

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

2019-11-14 Thread Thomas Evangelidis
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

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

2019-11-22 Thread Thomas Evangelidis
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] How to pass atomic charge as atom invariant to ECFP?

2019-11-27 Thread Thomas Evangelidis
ts >> >> >> And then generate the fingerprint like this: >> >> >> fp = AllChem.GetMorganFingerprint(mol, radius=3, >> invariants=generateAtomInvariant(mol)) >> >> >> -- == Dr. Thomas Eva

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

2019-12-01 Thread Thomas Evangelidis
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?

2019-12-02 Thread Thomas Evangelidis
Dne po 2. 12. 2019 4:45 PM uživatel Greg Landrum napsal: > [Adding the mailing list back on] > Oops, sorry about that. > But if you add partial charges (a floating point number) then essentially > every atom is going to end up with its own invariant. That's unlikely to > end well. > > I

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

2020-08-31 Thread Thomas Evangelidis
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] result discrepancy between SubstructLibrary, PatternFingerprint comparison and HasSubstructMatch

2020-08-31 Thread Thomas Evangelidis
ld, at the very > least, generate an error when you try to do this), but it's easy enough to > fix in your code: just stop specifying the length of the pattern > fingerprints. > > Best, > -greg > > > > On Mon, Aug 31, 2020 at 3:57 PM Thomas Evangelidis > wrote: >