{"id":309,"date":"2013-01-29T18:18:37","date_gmt":"2013-01-29T18:18:37","guid":{"rendered":"http:\/\/nextmovesoftware.com\/blog\/?p=309"},"modified":"2015-06-22T17:02:29","modified_gmt":"2015-06-22T16:02:29","slug":"bringing-sugars-to-opsin","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2013\/01\/29\/bringing-sugars-to-opsin\/","title":{"rendered":"Bringing sugars to OPSIN"},"content":{"rendered":"<p><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/cycleofsugarsupport.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-326 alignright\" alt=\"cycleofsugarsupport\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/cycleofsugarsupport.png\" width=\"386\" height=\"241\" srcset=\"https:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/cycleofsugarsupport.png 386w, https:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/cycleofsugarsupport-300x187.png 300w\" sizes=\"(max-width: 386px) 100vw, 386px\" \/><\/a>I&#8217;m pleased to announce the release of OPSIN 1.4.0. This new release brings significant improvements to OPSIN&#8217;s coverage of <a title=\"IUPAC Carbohydrate Nomenclature\" href=\"http:\/\/www.chem.qmul.ac.uk\/iupac\/2carb\/\" target=\"_blank\">carbohydrate nomenclature<\/a>. It also complements NextMove Software&#8217;s <a title=\"Sugar &amp; Splice\" href=\"http:\/\/nextmovesoftware.co.uk\/products\/SugarNSplice.html\">Sugar &amp; Splice <\/a>project that aims to make the conversion between carbohydrate and small molecule representations effortless.<\/p>\n<p>Below is the effect this improvement to OPSIN has had on the conversion of IUPAC names in ChEBI. (This is one of the data sets used in the <a href=\"http:\/\/pubs.acs.org\/doi\/full\/10.1021\/ci100384d\">OPSIN publication<\/a> [<a href=\"http:\/\/pubs.acs.org\/articlesonrequest\/AOR-PcYgSy87ettZWfqyvHmN\">free access<\/a>])<\/p>\n<figure id=\"attachment_334\" aria-describedby=\"caption-attachment-334\" style=\"width: 617px\" class=\"wp-caption alignnone\"><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/OPSIN1.4_chebisept2010.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-334\" alt=\"Number of names convertible to InChI on IUPAC names from ChEBI (Sept 2010)\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/OPSIN1.4_chebisept2010.png\" width=\"617\" height=\"398\" srcset=\"https:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/OPSIN1.4_chebisept2010.png 617w, https:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/OPSIN1.4_chebisept2010-300x193.png 300w\" sizes=\"(max-width: 617px) 100vw, 617px\" \/><\/a><figcaption id=\"caption-attachment-334\" class=\"wp-caption-text\">Number of names convertible to InChI on IUPAC names from ChEBI (Sept 2010)<\/figcaption><\/figure>\n<p>Examples of new nomenclature supported (pictures generated by the <a title=\"OPSIN web service\" href=\"http:\/\/opsin.ch.cam.ac.uk\/\">OPSIN web service<\/a>)<\/p>\n<table>\n<tbody>\n<tr>\n<td>\n<p><figure id=\"attachment_312\" aria-describedby=\"caption-attachment-312\" style=\"width: 225px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic-acid.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-312 \" alt=\"3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic acid\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic-acid.png\" width=\"225\" height=\"152\" \/><\/a><figcaption id=\"caption-attachment-312\" class=\"wp-caption-text\">3-Deoxy-alpha-D-manno-oct-2-ulopyranosonic acid<\/figcaption><\/figure><\/td>\n<td>\n<p><figure id=\"attachment_340\" aria-describedby=\"caption-attachment-340\" style=\"width: 291px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/beta-D-Fructofuranosyl-alpha-D-glucopyranoside.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-340    \" alt=\"beta-D-Fructofuranosyl alpha-D-glucopyranoside\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/beta-D-Fructofuranosyl-alpha-D-glucopyranoside.png\" width=\"291\" height=\"167\" \/><\/a><figcaption id=\"caption-attachment-340\" class=\"wp-caption-text\">beta-D-Fructofuranosyl alpha-D-glucopyranoside<\/figcaption><\/figure><\/td>\n<\/tr>\n<tr>\n<td>\n<p><figure id=\"attachment_313\" aria-describedby=\"caption-attachment-313\" style=\"width: 254px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/Methyl-234-tri-O-acetyl-alpha-D-glucopyranosyluronate-bromide.png\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-313  \" alt=\"Methyl 2,3,4-tri-O-acetyl-alpha-D-glucopyranosyluronate bromide\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/Methyl-234-tri-O-acetyl-alpha-D-glucopyranosyluronate-bromide.png\" width=\"254\" height=\"196\" \/><\/a><figcaption id=\"caption-attachment-313\" class=\"wp-caption-text\">Methyl 2,3,4-tri-O-acetyl-alpha-D-glucopyranosyluronate bromide<\/figcaption><\/figure><\/td>\n<td>\n<p><figure id=\"attachment_339\" aria-describedby=\"caption-attachment-339\" style=\"width: 279px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/3-O-beta-D-galactosyl-sn-glycerol-.png\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-339   \" alt=\"3-O-beta-D-galactosyl-sn-glycerol\" src=\"\/\/nextmovesoftware.com\/blog\/wp-content\/uploads\/2013\/01\/3-O-beta-D-galactosyl-sn-glycerol-.png\" width=\"279\" height=\"172\" \/><\/a><figcaption id=\"caption-attachment-339\" class=\"wp-caption-text\">3-O-beta-D-galactosyl-sn-glycerol<\/figcaption><\/figure><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>OPSIN 1.4.0 is available from <a title=\"OPSIN download page\" href=\" https:\/\/bitbucket.org\/dan2097\/opsin\/downloads\" target=\"_blank\">Bitbucket<\/a> and Maven Central. The full release notes are below:<\/p>\n<ul>\n<li>Added support for dialdoses,diketoses,ketoaldoses,alditols,aldonic acids,uronic acids,aldaric acids,glycosides,oligosacchardides, named systematically or from trivial stems, in cyclic or acyclic form<\/li>\n<li>Added support for ketoses named using dehydro<\/li>\n<li>Added support for anhydro<\/li>\n<li>Added more trivial carbohydrate names<\/li>\n<li>Added support for sn-glcyerol<\/li>\n<li>Improved heuristics for phospho substitution<\/li>\n<li>Added hydrazido and anilate suffixes<\/li>\n<li>Allowed more functional class nomenclature to apply to amino acids<\/li>\n<li>Added support for inverting CAS names with substituted functional terms e.g. Acetaldehyde, O-methyloxime<\/li>\n<li>Double substitution of a deoxy chiral centre now uses the CIP rules to decide which substituent replaced the hydroxy group<\/li>\n<li>Unicode right arrows, superscripts and the soft hyphen are now recognised<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>I&#8217;m pleased to announce the release of OPSIN 1.4.0. This new release brings significant improvements to OPSIN&#8217;s coverage of carbohydrate nomenclature. It also complements NextMove Software&#8217;s Sugar &amp; Splice project that aims to make the conversion between carbohydrate and small molecule representations effortless. Below is the effect this improvement to OPSIN has had on the &hellip; <a href=\"https:\/\/nextmovesoftware.com\/blog\/2013\/01\/29\/bringing-sugars-to-opsin\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Bringing sugars to OPSIN<\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/309"}],"collection":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/comments?post=309"}],"version-history":[{"count":30,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/309\/revisions"}],"predecessor-version":[{"id":1463,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/309\/revisions\/1463"}],"wp:attachment":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/media?parent=309"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/categories?post=309"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/tags?post=309"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}