Arch Linux

poopship21

Member

Registered: 2009-05-13

Posts: 177

chemical structure rendering [SOLVED]

does anyone know of an X-based tool which allows chemical structures to be drawn from an in-line-structure (ALS) argument?

by ALS i mean the format described here:
http://pubs.acs.org.proxy.lib.ohio-stat … /ci7004687

TIA

Last edited by poopship21 (2009-11-26 16:36:24)

majiq

Member

Registered: 2009-03-06

Posts: 259

Re: chemical structure rendering [SOLVED]

I don't know about the specific file format (especially since the link you gave requires a login), but there are several chemical structure drawing programs available. Search for chem in the AUR and try some of those, maybe? Or google "linux chemical drawing" possibly?

skottish

Forum Fellow

From: Here

Registered: 2006-06-16

Posts: 7,942

Re: chemical structure rendering [SOLVED]

I'm was a bit curious and found this. Maybe something here is the AUR already:

http://www.redbrick.dcu.ie/~noel/linux4chemistry/

sctincman

Member

From: CO (USA)

Registered: 2009-04-08

Posts: 85

Re: chemical structure rendering [SOLVED]

The link you posted prompted me for a login Couldn't find anything via google either...

Chemist myself here, but have never heard of ALS :x

However, wrt to chem drawing programs I prefer bkchem (in the aur) which supports import by SMILES (another type of line notation) and InChI. Also, bkchem being in python is easily extensible that way, but also has it's own plugin system, so shouldn't be too hard to add support if absolutely necessary (and decent with python...)

Hope this helps

poopship21

Member

Registered: 2009-05-13

Posts: 177

Re: chemical structure rendering [SOLVED]

hi friends, two BIG apologies: 1) sorry, when i read at home i surf through a web proxy which gives me access to library subscriptions.  2) its SLN not ALS.  why that acronym was stuck in my head i dont know,

here is the link to the public abstract: http://pubs.acs.org/doi/abs/10.1021/ci7004687

incidentaly i was amused with the notation for cyclic structures since it is reminiscent of the in-line back referencing used by at least one regex syntax

poopship21

Member

Registered: 2009-05-13

Posts: 177

Re: chemical structure rendering [SOLVED]

in any case, libraries for SLN parsing and structure drawing are available, which is sufficient for generating simple apps.