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Parsing Chemistry

https://re.factorcode.org/2025/10/parsing-chemistry.html
27•kencausey•1w ago

Comments

whitten•1h ago
Does the SMILE (or Simplified Molecular Input Line Entry System) code have an EBNF definition ? https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Lin... Claims there is a context free grammar.
the__alchemist•1h ago
Note: There are two standardized formats for this called SMILES and SELFIES. SMILES is much better supported, but SELFIES is more robust. I'm integrating them into some bio and chem software I'm working on.

You can do things like look up, using PubChem's API, similar molecules etc to a SMILES string.

I believe most molecule editors can load and save SMILES.

dachrillz•1h ago
What about inchi? Isn’t that a common way of describing molecules as well?
the__alchemist•1h ago
Good point!
jugoetz•4m ago
SMILES and SELFIES are molecular graph representations and aren't meant to solve the "parse this sum formula" problem.

SELFIES are for genAI. If you ask a VAE to generate SMILES, it will spit out some strings that are invalid - can't happen with SELFIES, that is the one application where they are robust.

logifail•1h ago
Does this do structural formulae too?

Was thinking of InChI[0] but on Googling SMILES and SELFIES I found this[1] talk, this[2] paper and my goodness I've been down a few rabbit holes since...

[0] https://en.wikipedia.org/wiki/International_Chemical_Identif... [1] https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/18... [2] https://pubs.rsc.org/en/content/articlehtml/2022/dd/d1dd0001...

jugoetz•12m ago
No, in Python you can use rdkit (https://github.com/rdkit/rdkit) for that
toast_x•25m ago
this is insanely cool

The Shadows Lurking in the Equations

https://gods.art/articles/equation_shadows.html
69•calebm•1h ago•14 comments

An eBPF Loophole: Using XDP for Egress Traffic

https://loopholelabs.io/blog/xdp-for-egress-traffic
87•loopholelabs•23h ago•27 comments

Radiant Computer

https://radiant.computer
52•beardicus•2h ago•31 comments

Carice TC2 – An fully analog electric car

https://www.caricecars.com/
20•RubenvanE•1h ago•17 comments

A P2P Vision for QUIC (2024)

https://seemann.io/posts/2024-10-26---p2p-quic/
16•mooreds•1h ago•8 comments

Mr TIFF

https://inventingthefuture.ghost.io/mr-tiff/
837•speckx•16h ago•113 comments

iOS 26.2 to allow third-party app stores in Japan ahead of regulatory deadline

https://www.macrumors.com/2025/11/05/ios-26-2-third-party-app-stores-japan/
149•tosh•3h ago•88 comments

SPy: An interpreter and compiler for a fast statically typed variant of Python

https://antocuni.eu/2025/10/29/inside-spy-part-1-motivations-and-goals/
150•og_kalu•5d ago•61 comments

Learning from Failure to Tackle Hard Problems

https://blog.ml.cmu.edu/2025/10/27/learning-from-failure-to-tackle-extremely-hard-problems/
8•djoldman•5d ago•1 comments

Parsing Chemistry

https://re.factorcode.org/2025/10/parsing-chemistry.html
27•kencausey•1w ago•8 comments

Ask HN: My family business runs on a 1993-era text-based-UI (TUI). Anybody else?

33•urnicus•1h ago•14 comments

Founder in Residence at Woz (San Francisco)

1•bcollins34•3h ago

RISC-V takes first step toward international ISO/IEC standardization

https://riscv.org/blog/risc-v-jtc1-pas-submitter/
205•jrepinc•6d ago•76 comments

UPS plane crashes near Louisville airport

https://avherald.com/h?article=52f5748f&opt=0
242•jnsaff2•16h ago•214 comments

Hypothesis: Property-Based Testing for Python

https://hypothesis.readthedocs.io/en/latest/
173•lwhsiao•12h ago•99 comments

NY Smartphone Ban Has Made Lunch Loud Again

https://gothamist.com/news/ny-smartphone-ban-has-made-lunch-loud-again
56•hrldcpr•2h ago•26 comments

Bluetui – A TUI for managing Bluetooth on Linux

https://github.com/pythops/bluetui
217•birdculture•16h ago•77 comments

Blue Prince (1989)

https://novalis.org/blog/2025-10-27-blue-prince-1989.html
21•luu•1w ago•15 comments

Asus Announces October Availability of ProArt Display 8K PA32KCX

https://press.asus.com/news/press-releases/asus-proart-display-8k-pa32kcx-availability/
125•Roachma•1w ago•188 comments

Kosmos: An AI Scientist for Autonomous Discovery

https://arxiv.org/abs/2511.02824
17•belter•1h ago•0 comments

Intervaltree with Rust Back End

https://github.com/Athe-kunal/intervaltree_rs
36•athekunal•3d ago•11 comments

Apple’s Persona technology uses Gaussian splatting to create 3D facial scans

https://www.cnet.com/tech/computing/apple-talks-to-me-about-vision-pro-personas-where-is-our-virt...
180•dmarcos•5d ago•82 comments

Gnome Mutter Now "Completely Drops the Whole X11 Back End"

https://www.phoronix.com/news/GNOME-Mutter-Drops-X11
17•throwaway7489•1h ago•3 comments

Optimism Associated with Exceptional Longevity

https://www.pnas.org/doi/10.1073/pnas.1900712116
35•RickJWagner•2h ago•25 comments

Moving tables across PostgreSQL instances

https://ananthakumaran.in/2025/11/02/moving-tables-across-postgres-instances.html
48•ananthakumaran•3d ago•1 comments

I’m worried that they put co-pilot in Excel

https://simonwillison.net/2025/Nov/5/brenda/
245•isaacfrond•6h ago•172 comments

Grayskull: A tiny computer vision library in C for embedded systems, etc.

https://github.com/zserge/grayskull
146•gurjeet•17h ago•13 comments

Pg_lake: Postgres with Iceberg and data lake access

https://github.com/Snowflake-Labs/pg_lake
353•plaur782•23h ago•107 comments

The Microsoft SoftCard for the Apple II: Getting two processors to share memory

https://devblogs.microsoft.com/oldnewthing/20251104-00/?p=111758
77•zdw•12h ago•33 comments

Removing XSLT for a more secure browser

https://developer.chrome.com/docs/web-platform/deprecating-xslt
51•justin-reeves•1h ago•51 comments