Re: [Rdkit-discuss] performance issues with PandasTools LoadSDF

andrum wrote: > Hi Mario, > > how big is the file? > did you *add* properties to it or just modify existing values? > > -greg > > > On Fri, May 15, 2020 at 11:34 AM Mario Lovrić > wrote: > >> Dear all, >> >> >> I have loaded a SDF file (le

[Rdkit-discuss] performance issues with PandasTools LoadSDF

nd) file2 is impossible to load again, it is eating up my CPU and RAM like crazy file1 is usually loaded within 30 seconds Any recommendations there? Is there something I didnt consider? Thanks -- Mario Lovrić ___ Rdkit-discuss mailing list R

Re: [Rdkit-discuss] SMILES to graphs

After the adjacency matrix from rdkit you can do a lot with the networkx python library. On Wed, 17 Jul 2019, 10:00 Jan Halborg Jensen, wrote: > You can get an adjacency matrix with the function GetAdjacencyMatrix: > > mol = Chem.GetMolFromSmiles(‘C’) > am = Chem.rdmolops.GetAdjacencyMatri

[Rdkit-discuss] any paper on fingerprint pre-selection/feature selection?

Dear all, Is there any paper discussing some sort of pre-selection/feature selection with fingerprints? Any rule of thumb? E.g. dont keep fingeprints if less than 5% hits? Thanks -- Mario Lovrić ___ Rdkit-discuss mailing list Rdkit-discuss

[Rdkit-discuss] idea for a general discussion thread

pecialized and pleasant to discuss with. And there are no anonymous "reputation" chasers here. Let me know your thoughts on this. Thanks -- Mario Lovrić ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforg

[Rdkit-discuss] citation for the daylight fingerprint

ool01/course/basics/fp.html Thanks -- Mario Lovrić ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Fingerprints standardization and cleaning

Dear all, What is your experience in preparing a compound set for fingerprint generation, do you follow the same procedures as for descriptors (remove salts, remove metals etc)? Does anyone have a cleaning procedure to recommend? Thank you in advance. -- Mario Lovrić

[Rdkit-discuss] remove salts + neutralize

)C(F)(F)F)c2)n[nH]1 The minuses appear front of the "c"s. I guess it is considered as bonds everywhere. When canonicalizing them in RDKit they dont change, but OpenBabel does for example. Fc1ccc(c(c1)c1(c1)c1n[nH]c(n1)C(=O)N)OCC(C(F)(F)F)(F)F Might it cause problems anywhere?

Re: [Rdkit-discuss] edge matrix

; [ 1., 1., 0., 1.], > [ 0., 0., 1., 0.]]) > > Hope this helps - but I'm way out of my depth here! > > Best regards, > Chris > > > On 17 January 2018 at 16:57, Mario Lovrić > wrote: > >> Correct, I am looking for a rdkit-hidden-option

Re: [Rdkit-discuss] edge matrix

MolFromSmiles('CC(C)CC') >> n = m.GetNumAtoms() >> E = np.zeros((n, n)) >> for b in m.GetBonds(): >> i = b.GetBeginAtomIdx() >> j = b.GetEndAtomIdx() >> E[[i,j], [j,i]] = 1 >> >> >> Hope this helps, >> Ma

Re: [Rdkit-discuss] edge matrix

n, n)) > for b in m.GetBonds(): > i = b.GetBeginAtomIdx() > j = b.GetEndAtomIdx() > E[[i,j], [j,i]] = 1 > > > Hope this helps, > Marta SD > > > > 2018-01-17 16:31 GMT+01:00 Mario Lovrić : > >> Dear all, >> >> Does any one have an idea how to

[Rdkit-discuss] edge matrix

Dear all, Does any one have an idea how to get an edge matrix (graph theory) out of Rdkit, I digged deep but didnt find anything. F.example for: 'CC(C)CC' it would be: array([[0, 1, 1, 0], [1, 0, 1, 0], [1, 1, 0, 1], [0, 0, 1, 0]]) Thanks. -- Ma

[Rdkit-discuss] MATLAB vs. RDKit/Python

Dear all, Has anyone done some comparison of MATLAB and Python in cheminformatics? Are there any equivalents to RDKit for MATLAB? I am preparing for a conference, I know for sure there will be many MATLAB fans :) Thanks -- Mario Lovrić

Re: [Rdkit-discuss] RDKit - cmake - installation problem

Thanks a lot. Works! On Fri, Sep 11, 2015 at 1:28 PM, Greg Landrum wrote: > > > On Fri, Sep 11, 2015 at 1:24 PM, Mario Lovrić > wrote: > >> Hey, >> >> You mean in cmake? >> >> C:/RDkit/build - for the build >> C:/RDkit/rdkit - for the s

Re: [Rdkit-discuss] RDKit - cmake - installation problem

> > On Fri, Sep 11, 2015 at 10:54 AM, Mario Lovrić > wrote: > >> Hello, >> >> >> I have problems with RDkit installation on windows, after following the >> instructions. >> >> There is a discussion on this already, it seems that is was solved

[Rdkit-discuss] RDKit - cmake - installation problem

Hello, I have problems with RDkit installation on windows, after following the instructions. There is a discussion on this already, it seems that is was solved by correcting the paths. Please help me finding the mistake. I used cmake, boost, python 2.7.10 and mingw for compiling (gcc, g++. exe)