[WP4-EDIAQI] Canceled: EDIAQI WP4 regular meeting

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[WP4-EDIAQI] Canceled: EDIAQI WP4 regular meeting

BEGIN:VCALENDAR METHOD:CANCEL PRODID:Microsoft Exchange Server 2010 VERSION:2.0 BEGIN:VTIMEZONE TZID:W. Europe Standard Time BEGIN:STANDARD DTSTART:16010101T03 TZOFFSETFROM:+0200 TZOFFSETTO:+0100 RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=-1SU;BYMONTH=10 END:STANDARD BEGIN:DAYLIGHT

[WP4-EDIAQI] Canceled: EDIAQI WP4 regular meeting

BEGIN:VCALENDAR METHOD:CANCEL PRODID:Microsoft Exchange Server 2010 VERSION:2.0 BEGIN:VTIMEZONE TZID:W. Europe Standard Time BEGIN:STANDARD DTSTART:16010101T03 TZOFFSETFROM:+0200 TZOFFSETTO:+0100 RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=-1SU;BYMONTH=10 END:STANDARD BEGIN:DAYLIGHT

[WP4-EDIAQI] Canceled: EDIAQI WP4 regular meeting

BEGIN:VCALENDAR METHOD:CANCEL PRODID:Microsoft Exchange Server 2010 VERSION:2.0 BEGIN:VTIMEZONE TZID:W. Europe Standard Time BEGIN:STANDARD DTSTART:16010101T03 TZOFFSETFROM:+0200 TZOFFSETTO:+0100 RRULE:FREQ=YEARLY;INTERVAL=1;BYDAY=-1SU;BYMONTH=10 END:STANDARD BEGIN:DAYLIGHT

[WP4-EDIAQI] ediaqi WP4 updates [action needed]

Dear all Next week Thursday we have our regular WP4 meeting. I kindly ask the task leads to send me a slide or notes with updates. All pilots please send info to @kalle.ku...@taltech.ee @kalle.ku...@taltech.ee - T4.2 (overview of

[WP4-EDIAQI] wp4 meeting minutes and ppt

Dear all The WP4 monthly meeting materials are in the Lisbon council folder WP4 Meeting

[WP4-EDIAQI] Re: FW: wp4 regular meeting

Dear WP4 partners, I kindly ask to send your slides asap, I have only received 2 slides so far. Pilots and tasks – please see list below. Best Mario Lovrić From: Mario Lovrić Sent: Friday, 31 March 2023 19:17 To: wp4-ediaqi@lists.lisboncouncil.net; David Cemernek ; ju...@thinnect.com

[WP4-EDIAQI] Re: FW: wp4 regular meeting

.ku...@taltech.ee<mailto:kalle.ku...@taltech.ee> or @Ralf Martin Soe<mailto:ralf-martin@taltech.ee> Best Mario Lovrić From: Switters, Jon Sent: Wednesday, 22 March 2023 11:31 To: wp4-ediaqi@lists.lisboncouncil.net Cc: Mario Lovrić ; Francesco Mureddu Subject: Fwd: FW: wp4 regular me

[WP4-EDIAQI] FW: wp4 regular meeting

Dear all [Mario Lovrić] Apparently my e-mail didn't go through with some. Here it is again: The meeting notes are located in teams: WP4 Monthly Meetings.docx<https://lisboncouncil.sharepoint.com/:w:/r/sites/EDIAQI/Gedeelde%20documenten/General/4.%20Work%20Package%204%20-%20Monitor%20-%20Pil

[WP4-EDIAQI] EDIAQI WP4 regular meeting

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[WP4-EDIAQI] wp4 regular meeting

Dear all The meeting notes are located in teams: WP4 Monthly

[WP4-EDIAQI] EDIAQI WP4 [new] meeting

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[WP4-EDIAQI] [important] EDIAQI 1st WP4 Meeting

solve in small-group/1:1 meetings later if needed. Best Mario Lovrić -Original Appointment- From: Eva Sophie Paulusberger Sent: Monday, 13 February 2023 10:05 To: Eva Sophie Paulusberger; wp4-ediaqi@lists.lisboncouncil.net Cc: Mario Lovrić; de...@ascalia.io; Alessandro Battaglia

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

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 (lets call it file1)

[Rdkit-discuss] performance issues with PandasTools LoadSDF

2nd) 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 =

[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

/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., 0., 1., 0.], > [ 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 <mario.lovri...@gmail.com> > wrote: > >> C

Re: [Rdkit-discuss] edge matrix

hem import MolFromSmiles >> import numpy as np >> m = 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 >> >>

Re: [Rdkit-discuss] edge matrix

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 <mario.lovri...@gmail.com>: > >> Dear all, >> >> Does any

[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. -- Mario Lovrić

[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 <greg.land...@gmail.com> wrote: > > > On Fri, Sep 11, 2015 at 1:24 PM, Mario Lovrić <mario.lovri...@gmail.com> > wrote: > >> Hey, >> >> You mean in cmake? >> >> C:/RDkit

[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++.

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

commands below? > > -greg > > > On Fri, Sep 11, 2015 at 10:54 AM, Mario Lovrić <mario.lovri...@gmail.com> > wrote: > >> Hello, >> >> >> I have problems with RDkit installation on windows, after following the >> instructions. >> >>