Jekyll2026-06-07T16:43:55+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/openbabel.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenOSRA: GPL-ed molecule drawing to SMILES convertor2007-07-20T00:10:00+00:002007-07-20T00:10:00+00:00https://chem-bla-ics.linkedchemistry.info/2007/07/20/osra-gpl-ed-molecule-drawing-to-smilesIgor wrote a message to the CCL mailing list about OSRA:

We would like to announce a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES.

OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and generate the SMILES representation of the molecular structure images encountered within that document.

The email does not give any information on the fail rate, but the demo they provide via the webinterface does show some minor glitches (the bromine is not recognized):

The source reuses OpenBabel and uses the GPL license. The value equal to that of text mining tools like OSCAR3 , and together they sounds like the Jordan and Pippen of mining chemical literature.

]]>Egon WillighagenInChI’s in LaTex and CDK News2006-03-31T00:00:00+00:002006-03-31T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2006/03/31/inchis-in-latex-and-cdk-newsAn InChI (or see the FAQ) is a line notation for a molecular structure that was recently developed by the NIST and the IUPAC. Principally they can be applied to protein too (see below), but because proteins would give lenghty InChI’s and are quite well defined in terms of connectivity anyway, those can better be described by their amino acid sequence.

The March 2006 issue of CDK News, the Chemistry Development Kit project newsletter, will be released later today, and had, for the second time, the requirment that authors provide InChI’s for molecular structures mentioned in the articles. Different from the previous issue is how InChI’s are marked up in LaTeX. I’ve setup a \inchi{} for this that automatically creates a Google search query as link behind the InChI:

\newcommand{
  \inchi}[1]{\href{http://www.google.com/search?q=#1}
                  {\normalfont\texttt{InChI=#1}
            }
}

Now, googling for InChI’s only works if one removes the InChI= part of the InChI. As an example I will show how it works for methane. The InChI for this compound is InChI=1/CH4/h1H4, so in LaTex one enters \inchi{1/CH4/h1H4}. This will create a link like: InChI=1/CH4/h1H4.

BTW, if you are interested in InChI’s for proteins, here is the InChI for 1CRN, created with OpenBabel:

InChI=1/C202H439N55O64S6/c1-28-92(12)149-188(308)237-127-84-323-324-
85-128(176(296)225-114(46-37-63-212-202(209)210)165(285)232-122(69-89(6)7)195(315)253-64-38-
47-132(253)179(299)215-80-143(274)241-158(107(27)265)199(319)257-68-42-51-136(257)182(302)226-
115(60-61-144(275)276)164(284)218-100(20)162(282)244-149)236-187(307)148(91(10)11)242-172(292)
120(74-138(204)269)229-168(288)117(70-108-43-34-33-35-44-108)228-169(289)119(73-137(203)268)
230-173(293)124(81-258)234-166(286)113(45-36-62-211-201(207)208)224-159(279)99(19)221-186(306)
147(90(8)9)243-189(309)150(93(13)29-2)245-174(294)125(82-259)235-183(303)135-50-41-66-255(135)
196(316)130-87-326-322-83-126(223-142(273)79-216-185(305)154(103(23)261)251-171(291)118(72-
110-54-58-112(267)59-55-110)231-192(312)155(104(24)262)250-163(283)101(21)220-175(127)295)178
(298)246-151(94(14)30-3)190(310)247-152(95(15)31-4)191(311)248-153(96(16)32-5)198(318)256-67-
40-49-134(256)181(301)213-77-140(271)217-97(17)161(281)249-156(105(25)263)194(314)240-131
(88-327-325-86-129(177(297)239-130)238-193(313)157(106(26)264)252-184(304)146(206)102(22)260)197
(317)254-65-39-48-133(254)180(300)214-78-141(272)222-121(76-145(277)278)170(290)227-116(71-
109-52-56-111(266)57-53-109)167(287)219-98(18)160(280)233-123(200(320)321)75-139(205)270/h89-
202,211-252,258-321H,28-88,203-210H2,1-27H3/t92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102+,
103+,104+,105+,106+,107+,109-,110-,111+,112+,113-,114-,115-,116-,117-,118-,119-,120-,121-,122-,
123-,124-,125-,126-,127-,128-,129-,130-,131-,132-,133-,134-,135-,136-,137?,138-,139-,140-,141+,
142-,143+,146-,147-,148-,149-,150-,151-,152-,153-,154-,155-,156-,157-,158-,159+,160?,161-,162?,
163-,164-,165?,166+,167?,168+,169+,170+,171-,172+,173+,174+,175?,176-,177?,178+,179+,180-,
181?,182-,183+,184?,185+,186+,187-,188-,189-,190+,191?,192-,193?,194-,195-,196-,197-,198-,199-/m0/s1
]]>Egon Willighagen