I write software for cheminformatics. You may know me from chemfp, mmpdb, fmcs, VMD, and other tools. Born in Miami, FL, I now live in Trollhättan, Sweden. Come and visit our historic lock system!
I have withdrawn my submission to the Journal of #Cheminformatics due to poor response by the editors for concerns I raised about possible ethical violations, and due to Springer denying my request for fee waiver, which I made in the submission process, on the grounds that it was made too late and should have been part of the submission process. I got this notification last week, three months after submission, and after two rounds of peer review.
I do not recommend people publish in J.Cheminf.
The answer is 42. When the pattern CD4H0X4(-)(-)-*) matches an atom, there are 24 possible ways for it to match (that's 4! = 4 * 3 * 2 * 1 because there are 4 places for the first *, 3 for the second, etc.).
RDKit's GetSubstructMatches by default matches at most maxMatches=1000 times.
1000/24 = 41.666...
Changing maxMatches to 2000 finds all 50 expected matches.
This means RDKit's recursive SMARTS matcher does all matches, rather than stop at first match.
@Unixbigot @me_ FWIW, from 1st ed. 1987,
A UNIX file system uses 1024-byte blocks and 16-bit disk addresses. The i-node holds 8 disk addresses for data blocks, one single indirect block address, and one double-indirect block address. What is the maximum file size? Think carefully.
Three different protection mechanisms that we have discusses are capabilities, access control lists, and the UNIX rwx bit. For each of the following protection problems, tell me [...] which can be used ...
The #cheminformatics fingerprint tool #chemfp version 5.1b1 is out! https://chemfp.com/
The big feature is integration of the new "superimposed" count simulation method to RDKit byte fingerprint generation.
Use it if you want Tanimoto similarity of count fingerprints, but don't want to toss out all of your existing byte fingerprint tools for similarity search, clustering, etc. nor take a big performance loss.
Instead, use superimposed and get a ~0.95 recall using "normal" byte fps.
My wife is on a sociology class trip to Rome. I suggested she install #OrganicMaps to get around. She found it easy to install and download the Rome map for offline use.
When the got to the hostel, turns out they were delivered to the wrong building. The right was 1 km away. Easy walk, no need for a roaming plan. When they are told to meet at a given plaza after lunch? Done.
Some of her classmates don't have working data on their phones. They like her map, but oddly haven't installed the app??
EState atom typing is 30% faster with the new SMARTS extension.
old time: 15.32 (EState atom typing with recursive SMARTS) new time: 10.59 (EState atom typing with my new notation) other time: 18.38 (Python startup/overhead and parse time)
Nicer to read too, for orbital configuration patterns. Compare:
[PX3#-3H2] [PX3#-3H1] [PX3#-3H0] [PX4#-3#=1H0]
vs
I and others have highlighted problems in the survey. No wonder mostly new Python programmers answer it.
need to agree to a 10 page legal document
which say you pay a fine if you discuss the survey before publication!
biased towards professional software developers, ie, the target audience of JetBrains, not "the Python community"
the prize is a $100 card from anti-labor, pro-Trump Amazon
The PSF account has never replied to any comment.
Read also https://discuss.python.org/t/your-python-your-voice-join-the-python-developers-survey-2026/105883/23
I've been an emacs user since the early 1990s.
My introduction to Unix-like systems was with Minux in 1990, where the class used elvis.
I then became one of those "I know just enough vi to compile emacs" people, on IRIX.
Today is the first time I've used TRAMP (the Transparent Remote Access, Multi-Protocol), so I could edit files on a remote computer using the emacs on my laptop.
Usually I just ssh in and use emacs locally as text-only.
I guess I decided to be adventurous today. :)
@molecule With my modifications to the RDKit SMARTS matcher:
mol = Chem.MolFromSmiles("FS(F)(F)(F)(F)N(S(F)(F)(F)(F)(F))S(F)(F)(F)(F)(F)") pat = Chem.MolFromSmarts("[$(d6()()()()*)]") print(len(mol.GetSubstructMatches(pat))) 2 pat = Chem.MolFromSmarts("[d6#-6]") print(len(mol.GetSubstructMatches(pat))) 3
Har bekräftat att #SocialDemokraterna i stan vill spara pengar med att minska möljigheten för att kunna åka kollektivt för folk som inte har bankkort eller app. Den kommer att påverka några
- äldre
- hemlösa
- nya immigranter & besökare från flera länder
- ungdomar
- flyktingar
- svenskar på USA:s "specially designated national" lista
samt
- de med höga krav på integritet, som skulle åka anonymt
- de som bojkottar USA och vill inte vara beronde på USA för sitt vardagligt liv
S omfamnar USA.
En vecka efter gökotta hörde jag en gök!
Ännu bättre, gök gal i väst.
Fröken västergök är bästergök
USA kallar "radically pro-transgender" folk som terrorister.
USA har stängt av internet och bankkort tjänster till svenskar som de stämplade som terrorister.
När kommer USA att stänga av Apple/ Google/ Microsoft/ Visa/MasterCard till transmänniskor i Sverige?
Och sen .. abortdoktorer? Forskare om amerikanska brott mot folkrätten?
app + kontantfri => USA få mer kraft över alla som bor i Sverige.
@aartaka Yes. I know traditional Polynesian navigation included many methods to help infer island location further than 8 miles away, and out of line of sight, like observing:
But note how position uncertainty and visual confusion lead to the name "False Bay", https://en.wikipedia.org/wiki/False_Bay
Jag ringde #Västtrafik och fick bekräftelse att i framtiden kommer de två lösningarna att betala kontant att vara: 1) pappersbilljet, som måste köps när butiken eller ombud har öppet, och är kan inte förköps, och 2) periodkort, som är mycket dyrare för oss som sällan åker.
De har inga planer för #hemlösa, #flyktningar, nya #immigranter, besökare, ungdomar, osv som saknar bankkonto och betalkort och måste använda kontant för att åka kollektivt! (t.ex, till/från sjukhuset)
Vsg och skicka vidare!
My Cat® feature phone fares poorly in the post-3G world. After 6 months of intermittent connectivity, I bit the bullet and got a new phone, a Mudita Kompakt.
Technically it's Android, but no Google, web browser, or app store in sight. Excellent battery life - looks like 10% battery loss/day at my use level.
For the first time in a long time I felt happy after reading the terms&conditions! Easy to read and doesn't confuse consent with permission for surveillance capitalism.
Planen e att göra Pilgrimsleden mellan Göteborg o Vänersborg. Ca. 14 mil. Ha börjat träna. 6 km idag, varav 3 km i skogen med upp-och-ner.
Förhoppningsvis kommer jag att klara hela Edsvidsleden (14 km) på en gång, inom flera veckor. Sen bytter jag till den stora ryggsäcken och mer vikt.
