![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/box99.png\"/)
Early March I reported about Konstantin's JChemPaint-based\nchemistry plugin for OpenOffice, but there is (friendly)\ncompetition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software,\nunfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty\ncool. Another big difference is that Microsoft gave the Chem4Word a big grant, and Konstantin does not have such funding, AFAIK, and\nrelies on community support.
\nNow, Chem4Word was released earlier this month, as announced by Joe,\nand I just heard from Jim about it now being opensourced\n(and Peter blogged it too). Congratulations to all involved in the development!\nThe Chem4Word project page indicates the actual license: Apache 2.0.\nGood choice!
\nNow, I said that a limitation of the plugin is that it requires proprietary software to run. This is why you will not quickly see my\nuse it. Well, this is even why you do not see any screenshot! However, this should not spoil the news. This is for two reasons:
\nAnd that's, to me, the biggest news: if the organic chemists start using this plug-in, this will be a big win for Open Data. I am sure this is the hidden agenda of an unorthodox move of our fellow Blue Obelisk community members.
","doi":"https://doi.org/10.59350/m4x3w-52604","guid":"https://doi.org/10.59350/m4x3w-52604","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1272067200,"rid":"ka7q4-fm952","summary":"Early March I reported about Konstantin's JChemPaint-based chemistry plugin for OpenOffice, but there is (friendly) competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool.","title":"Chem4Word goes Apache 2.0","updated_at":1784492185,"url":"https://chem-bla-ics.linkedchemistry.info/2010/04/24/chem4word-goes-apache-20.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"\u00a0
\n
I recently wrote about a project for a (partial) CIP implementation.\nThis implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES\nand as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding. Actually,\na few years ago Jonathan Brecher wrote up the IUPAC recommendation for the use of the wedge bond for chirality specification\n(doi:10.1351/pac200678101897), with 74 pages of rules and examples, like the following (copyright by\nauthors or journal; I'm claiming fair use):
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/wedgeChirality.png\"/)
So, using wedges leaves plenty of room for incorrectly specifying the stereochemistry. Therefore, we decided to go for SMILES, even though Noel\nrecently showed that processing stereochemistry in SMILES is not trivial\neither. The SMILES I am currently using:
\nBr[C@@H](Cl)IBr[C@H](Cl)IBr[C@@]([H])(Cl)IBr[C@]([H])(Cl)I[C@]12(OC1)NCN2C[C@H](O)[C@H](O)CNC([C@H](O)C)ClI1.Cl2.Br3.[C@]123CCCI'm looking for more corner cases\u2026 please leave them as comments.
","doi":"https://doi.org/10.59350/n8f2y-adq94","guid":"https://doi.org/10.59350/n8f2y-adq94","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273276800,"reference":[{"id":"https://doi.org/10.1351/pac200678101897","unstructured":"Brecher, J. (2006). Graphical representation of stereochemical configuration (IUPAC Recommendations 2006). Pure and Applied Chemistry, 78(10), 1897\u20131970."}],"rid":"w128f-cwv89","summary":"I recently wrote about a project for a (partial) CIP implementation. This implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES and as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding.","tags":["Cdk","Iupac"],"title":"CIP rules #2: parsing @ and @@ from SMILES","updated_at":1784492182,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/08/cip-rules-2-parsing-and-from-smiles.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Below should show up the wave (that is, if you have a Google Wave account), about a piece I am writing\nfor a course on PhD Supervision I am following. The aim is to dig up old standards and how they apply to Web 2.0 technologies, including wikis,\nwaves, blogs, source code repositories etc.
\nUpdate: there seems to be some problems even for those who have a wave account to load the wave. Not sure why that is happening. I'm using the\nMadoqua robot; should I be using something else?
\nUpdate: this technology is long gone, and I replaced the whitespace with displaying the underlying HTML as a code block:
\n<div id=\"wave1\" style=\"width: 500px; height: 420px;\"></div>\n\n<script type=\"text/javascript\">\n var wave = new WavePanel('https://wave.google.com/wave/');\n wave.setUIConfig('white', 'black', 'Arial', '13px');\n wave.loadWave('googlewave.com!w+2gYDmL7eA');\n wave.init(document.getElementById('wave1'));\n</script>\nThe workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch,\nand goes to the commit page on GitHub, and hovers over the line numbers and clicks the 'Add comment' button and leaves a comment;\nthe reviewer informs the author, and the author updates his patch.
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/githubCodeReview.png\"/)
BTW, this screenshot is for a paper I am writing \nabout the use of blogs and source code repositories in chem- and bioinformatics education.
","doi":"https://doi.org/10.59350/9h2g1-n3717","guid":"https://doi.org/10.59350/9h2g1-n3717","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273449600,"rid":"6hhvy-mt418","summary":"The workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch, and goes to the commit page on GitHub, and hovers over the line numbers and clicks the 'Add comment' button and leaves a comment; the reviewer informs the author, and the author updates his patch.","tags":["Cdk","Github"],"title":"GitHub simplifies code review and leaving comments","updated_at":1784492180,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/10/github-simplifies-code-review-and.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Triggered by posts in the past three \ndays, I though about writing up a short\ntutorial on how to perform code review for existing code on GitHub. Therefore, this applied to\nCDK and Bioclipse source code, many but will work for any project hosted\nin GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the\nprocedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics\nrepository.
\nClick on the images to get a higher resolution version.
\nUse the GitHub web interface to browse your way towards the source code of the class you want to review. For example,\nthe SmartsMatchingHelper.java:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview1.png\"/)
Next step is to perform some code reviewing. For example, we might want to ask something about how parseProperty() works:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview2.png\"/)
Now, this page on GitHub does not provide the means to leave comments; instead, you comment on commits.
\nGit has a blame option (also called annotate)\nwhich will show you for each line who last changed that line. The GitHub web page makes this functionality available with the\n'blame' link just above the first line of the source code:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview3.png\"/)
This link will lead us to a page with a new column on the left side showing commit hashes, name of the commit author,\nand the first few characters of the commit message. For example, the\nweb page\nbits relevant to code we want to comment on, looks like:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview4.png\"/)
This shows us that commit 3ce78ba5\nis the one we are interested in:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview5.png\"/)
In the web page with the appropriate commit looked in the previous step, you scroll down to the line you want to comment on.\nIf you hover over that line, a blue comment bubble will show up on the left side:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview6.png\"/)
Clicking that blue comment icon, you get a dialog where you can enter your comment:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview7.png\"/)
The 'Add Line Note' button confirms and saves your comment:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview8.png\"/)
The next step would be to inform the commit author. GitHub actually helps here, and should send a message,\nlike this one:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/codeReview9.png\"/)
But it would certainly not hurt of you filed a bug report or sent an email.
\nNow, I should only convert this into a screencast\u2026
","doi":"https://doi.org/10.59350/nfcyx-jxj82","guid":"https://doi.org/10.59350/nfcyx-jxj82","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273449600,"rid":"vrsz7-ftc23","summary":"Triggered by posts in the past three days, I though about writing up a short tutorial on how to perform code review for existing code on GitHub. Therefore, this applied to CDK and Bioclipse source code, many but will work for any project hosted in GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the procedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics repository.","tags":["Cdk","Bioclipse","Github"],"title":"How to use GitHub for [CDK|Bioclipse] code review","updated_at":1784492178,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/10/how-to-use-github-for-cdkbioclipse-code.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Yeah, it's my turn. Standing on the shoulders of ChemJobber,\nAzmanam, and\nScienceBase, here's list of things I like about chemistry.\nTo put things into perspective first, a bit, I note that ChemJobber and Azmanam focused on wet-lab chemistry, and David on fancy\nmolecules. Now, I am a theoretical chemist, and was thinking on what to orient the things I like, and on how general to make them.\nThis meme is not easy, you now. But here goes:
\nChemical graph theory is one of the common theoretical models chemists work with to make sense of chemical properties.\nI like it because the graph theory is fairly straightforward, but chemistry adds enough color (literally!) to create a\nnice complexity that kept the cheminformatics field going strong for more than 50 years now :) For example, how to adapt\nthe theory to deal with mutli-atom bonds :)
\nThe NMRShiftDB is an Open Data repository for annotated NMR spectra. The fun here is to\nadd NMR spectra of rare nuclei .\nDon't you just love a\nmolecule with NMR shifts for all atoms?
\nMetabolomics is the research field that studies the small molecules of life. Plant metabolomics is particularly fun.\nTens of thousands of molecules, and a lot of metabolite identification to be done, and much more. Lot's of cool stuff\nto do here, and I am trying to secure funding for it. This is\nwhat I blogged about metabolomics before. What about\nhis nice secondary metabolite (source:\nWikipedia, CC0):
\n![\"\"](\"https://upload.wikimedia.org/wikipedia/commons/e/e4/Discodermolide_Structure.png\"/)
Atom types is another theoretical model for chemistry. Atom typing \nis one of the underlying technologies of force fields, which are used\nin many, many fields in chemistry. Now, force fields typically take only a subset of atom types. New atom types, consequently, need\nto be added. One such new atom type was the hexavalent carbon. Rare, very rare, but\njust the amount of complexity I like about chemistry.
\n\nKohonen maps, or self-organizing maps (SOM), are a machine learning\nmethod that have interesting visualization features. They have numerous applications, and also in chemistry. The group\nwhere I did my PhD developed a supervised SOM, which I used them to classify crystal structures\n(doi:10.1021/cg060872y). Another of my favorites is the\nreaction classification by Aires-de-Sousa et al. \nusing unsupervised SOMs.
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/som_thesis_image.png\"/)
People who know me personally, know that I like tasting things. That also makes me have to worry about overweight.\nTaste is to a large extend governed by cooking, and the Maillard reaction\nplays an important role here. If you like to learn more about the chemistry of cooking, checkout these\ntwo blogs.
\nCb is a new element on the world wide web. Well, not so new anymore, and the full name is likely more familiar:\nChemical blogspace. This social web application brings together blogging chemists\nworld wide. Oh, and this meme is picked up nicely:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/chemMeme.png\"/)
No, not the database, but the nice graphical article abstracts in chemistry journals. ChemFeeds\ngets is all together. BTW, there remains very much to be done about improving publishing chemistry.\nI\nblogged\nabout \nthat\nrepeatedly .
\nOrganometallics is, like metabolomics, a really\ninteresting area, with lots of complexities (pun intended :). Actually, I am not even aware of a\norganometallics/metabolomics mashup. Anyone with some nice pointers? I have not blogged about it much,\nand the one time \nI did was in relation\nto chemical graph theory.
\nBurning things. Nothing more to say about that, I guess. Well, perhaps. Chemists like burning things;\nothers might too, but chemists at least. Blowing up things too. When I was a student, I had a very\nfriendly colleague who liked blowing up things and made TNT himself and took that to university too\n(stabilized, mind you :). Cool!
\nAnyway, while googling for something to spice up this tenth item, I ran into this book:\nCaveman Chemistry: 28 Projects, from the Creation of Fire to the Production of Plastics.\nThe prologue nicely writes up that you need to sparkle\nsome fire in education to get the students enlightened:
\n\n\nI teach chemistry at Hampden-Sydney College, a small liberal-arts college in central Virginia. The students\nhere, by and large, do not come equipped with insatiable curiosity about my discipline and experience has\nconvinced me that the profession of professing has more to do with motivation than with explanation; a student\nwho is not curious will resist even the most valiant attempts at compulsory education; conversely, inquiring\nminds want to know. A great deal of my time, then, has been spent devising tricks, gimmicks, schemes and plots\nfor leading stubborn horses to water, knowing full well that I can't make them think.
\n
Now, that leaves me with tagging a few further blogs to tag to continue the meme. The meme is spreading fast,\nso I hope I do not tag someone who already is tagged. Jean-Claude,\nPeter, Noel,\nRich, Antony, would you mind letting us know your\nten favourite chemistry things?
","doi":"https://doi.org/10.59350/be00d-tn533","guid":"https://doi.org/10.59350/be00d-tn533","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273708800,"reference":[{"id":"https://doi.org/10.1021/cg060872y","unstructured":"Willighagen, E. L., Wehrens, R., Melssen, W., de Gelder, R.& Buydens, L. M. C. (2007). Supervised Self-Organizing Maps in Crystal Property and Structure Prediction. Crystal Growth & Design, 7(9), 1738\u20131745."}],"rid":"k2113-tjf27","summary":"Yeah, it's my turn. Standing on the shoulders of ChemJobber, Azmanam, and ScienceBase, here's list of things I like about chemistry. To put things into perspective first, a bit, I note that ChemJobber and Azmanam focused on wet-lab chemistry, and David on fancy molecules. Now, I am a theoretical chemist, and was thinking on what to orient the things I like, and on how general to make them. This meme is not easy, you now.","tags":["Chemistry"],"title":"My favourite chemistry things","updated_at":1784492177,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/13/my-favourite-chemistry-things.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"It has been a while since I gave an update on the ACS-RDF session in Boston .\nThings are settling in, and it seems there will be three sessions, each with an approximate theme. Each session will have five talks, of which one will be extended, where the speaker will be invited to set the context of the theme. Full programs will follow, but find the current sessions wordles below:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/wordle.cinf003.png\"/)
![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/wordle.cinf0031.png\"/)
![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/wordle.cinf0032.png\"/)
Rajarshi is at the EBI (or at least was yesterday), talking about his\nrcdk package (his excellent slides).\nOne slide is about how to create a new atom; he mentions not to use new Atom() but the\nDefaultChemObjectBuilder\ninstead (slide 73). I do not entire agree with the message given.
\nThe slide seems to favour the DefaultChemObjectBuilder, but there like are more suitable builders for a particular application.\nCurrently, I am aware of two alternative builders: the DebugChemObjectBuilder, and the NoNotificationChemObjectBuilder.
\nThe reason the CDK has a builder pattern is the following. It is cleaner to write against interfaces than against\nimplementations, because it allows alternative implementations. I just listed all three provided by the CDK library itself,\nbut other implementations may exists too; they might have a completely different data model, e.g. fully CMLDOM-based, or\nfully SQL-based. By programming against interfaces, changing the implementation becomes easy.
\nNow, by using new Atom() you choose a particular implementation (in this case, the one around the DefaultChemObjectBuilder.\nHowever, you like the user to pick the implementation. This is why the CDK library itself uses builders all over the place:\nit assumes a IChemObjectBuilder is predefined and that is used.
For example:
\n![CC0](\"http://en.wikipedia.org/wiki/File:Discodermolide_Structure.png\"){kind=link}
IChemObjectBuilder builder = new DefaultChemObjectBuilder();\nIMolecule molecule = builder.newMolecule();\nIAtom atom = builder.newAtom();\nmolecule.addAtom(atom);\nIf your method actually has an IChemObject as input, it can retrieve the builder from there:
\npublic IMolecule addToMolecule(IAtom atom) {\n IChemObjectBuilder builder = atom.getBuilder();\n IMolecule molecule = builder.newMolecule();\n molecule.addAtom(atom);\n}\nThis latter situation is what exists most in the CDK library, actually. In some cases, this is not the case, and sometimes\nyou may need to pass an IChemObjectBuilder to a constructor. This is, for example, the case with the constructor of the\nSmilesParser.
Now, reconsider the first code example. By defining a builder only once, and reusing that builder in the rest of your code,\nyou only have to change one line to use a different implementation. For example, the DebugChemObjectBuilder that sends\ndebug messages for each set and get call to one of the data classes. I used this in the past, and solved several nasty bugs\nwith this; just by seeing in what order data was set and read. And I only needed to change one single line of code for that.
","doi":"https://doi.org/10.59350/1bedv-rsy83","guid":"https://doi.org/10.59350/1bedv-rsy83","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273881600,"rid":"hj6w8-eqj34","summary":"Rajarshi is at the EBI (or at least was yesterday), talking about his rcdk package (his excellent slides). One slide is about how to create a new atom; he mentions not to use new Atom() but the DefaultChemObjectBuilder instead (slide 73). I do not entire agree with the message given.","tags":["Cdk","Java"],"title":"Cleaner CDK Code #5: develop against interfaces","updated_at":1784492173,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/15/cleaner-cdk-code-5-developer-against.html","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"content_html":"Peter informed about the CKAN 1.0 release.\nI browsed the 27 chemistry packages, and saw for example BODR show up:
\n![\"\"](\"https://chem-bla-ics.linkedchemistry.info/assets/images/ckan.png\"/)
The database of packages is community based, and you can simply log in with an OpenID. This allows me to updated some\noutdated and add missing information.
\nAs mentioned, the list contains 27 packages, out of a total of almost 1000. So, not so much chemistry there yet, but that's\nsomething we are getting used to. Worse even, is that of these 27, only a small subset is Open. These are identified,\nI think, by the blue bar on the left of the packages in the above screenshot. Even then, many of these are labeled\npublic domain, which we know is not very practicaly. This is why the CC0 waiver\nexists.
\nBut it at least allows us to create overviews of the available downloadable data. The system is very easy to use. Well done!
","doi":"https://doi.org/10.59350/3dt2a-bm621","guid":"https://doi.org/10.59350/3dt2a-bm621","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1274400000,"rid":"naczg-cxt29","summary":"Peter informed about the CKAN 1.0 release.","tags":["Opendata","Chemistry"],"title":"CKAN 1.0: A major contribution to Open Knowledge","updated_at":1784492171,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/21/ckan-10-major-contribution-to-open.html","version":"v1"}}],"items":[{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Early March I reported about Konstantin's JChemPaint-based\nchemistry plugin for OpenOffice, but there is (friendly)\ncompetition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software,\nunfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty\ncool. Another big difference is that Microsoft gave the Chem4Word a big grant, and Konstantin does not have such funding, AFAIK, and\nrelies on community support.
\nNow, Chem4Word was released earlier this month, as announced by Joe,\nand I just heard from Jim about it now being opensourced\n(and Peter blogged it too). Congratulations to all involved in the development!\nThe Chem4Word project page indicates the actual license: Apache 2.0.\nGood choice!
\nNow, I said that a limitation of the plugin is that it requires proprietary software to run. This is why you will not quickly see my\nuse it. Well, this is even why you do not see any screenshot! However, this should not spoil the news. This is for two reasons:
\nAnd that's, to me, the biggest news: if the organic chemists start using this plug-in, this will be a big win for Open Data. I am sure this is the hidden agenda of an unorthodox move of our fellow Blue Obelisk community members.
","doi":"https://doi.org/10.59350/m4x3w-52604","guid":"https://doi.org/10.59350/m4x3w-52604","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1272067200,"rid":"ka7q4-fm952","summary":"Early March I reported about Konstantin's JChemPaint-based chemistry plugin for OpenOffice, but there is (friendly) competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool.","title":"Chem4Word goes Apache 2.0","updated_at":1784492185,"url":"https://chem-bla-ics.linkedchemistry.info/2010/04/24/chem4word-goes-apache-20.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"\u00a0
\n
I recently wrote about a project for a (partial) CIP implementation.\nThis implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES\nand as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding. Actually,\na few years ago Jonathan Brecher wrote up the IUPAC recommendation for the use of the wedge bond for chirality specification\n(doi:10.1351/pac200678101897), with 74 pages of rules and examples, like the following (copyright by\nauthors or journal; I'm claiming fair use):
\n
So, using wedges leaves plenty of room for incorrectly specifying the stereochemistry. Therefore, we decided to go for SMILES, even though Noel\nrecently showed that processing stereochemistry in SMILES is not trivial\neither. The SMILES I am currently using:
\nBr[C@@H](Cl)IBr[C@H](Cl)IBr[C@@]([H])(Cl)IBr[C@]([H])(Cl)I[C@]12(OC1)NCN2C[C@H](O)[C@H](O)CNC([C@H](O)C)ClI1.Cl2.Br3.[C@]123CCCI'm looking for more corner cases\u2026 please leave them as comments.
","doi":"https://doi.org/10.59350/n8f2y-adq94","guid":"https://doi.org/10.59350/n8f2y-adq94","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273276800,"reference":[{"id":"https://doi.org/10.1351/pac200678101897","unstructured":"Brecher, J. (2006). Graphical representation of stereochemical configuration (IUPAC Recommendations 2006). Pure and Applied Chemistry, 78(10), 1897\u20131970."}],"rid":"w128f-cwv89","summary":"I recently wrote about a project for a (partial) CIP implementation. This implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES and as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding.","tags":["Cdk","Iupac"],"title":"CIP rules #2: parsing @ and @@ from SMILES","updated_at":1784492182,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/08/cip-rules-2-parsing-and-from-smiles.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Below should show up the wave (that is, if you have a Google Wave account), about a piece I am writing\nfor a course on PhD Supervision I am following. The aim is to dig up old standards and how they apply to Web 2.0 technologies, including wikis,\nwaves, blogs, source code repositories etc.
\nUpdate: there seems to be some problems even for those who have a wave account to load the wave. Not sure why that is happening. I'm using the\nMadoqua robot; should I be using something else?
\nUpdate: this technology is long gone, and I replaced the whitespace with displaying the underlying HTML as a code block:
\n<div id=\"wave1\" style=\"width: 500px; height: 420px;\"></div>\n\n<script type=\"text/javascript\">\n var wave = new WavePanel('https://wave.google.com/wave/');\n wave.setUIConfig('white', 'black', 'Arial', '13px');\n wave.loadWave('googlewave.com!w+2gYDmL7eA');\n wave.init(document.getElementById('wave1'));\n</script>\nThe workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch,\nand goes to the commit page on GitHub, and hovers over the line numbers and clicks the 'Add comment' button and leaves a comment;\nthe reviewer informs the author, and the author updates his patch.
\n
BTW, this screenshot is for a paper I am writing \nabout the use of blogs and source code repositories in chem- and bioinformatics education.
","doi":"https://doi.org/10.59350/9h2g1-n3717","guid":"https://doi.org/10.59350/9h2g1-n3717","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273449600,"rid":"6hhvy-mt418","summary":"The workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch, and goes to the commit page on GitHub, and hovers over the line numbers and clicks the 'Add comment' button and leaves a comment; the reviewer informs the author, and the author updates his patch.","tags":["Cdk","Github"],"title":"GitHub simplifies code review and leaving comments","updated_at":1784492180,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/10/github-simplifies-code-review-and.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Triggered by posts in the past three \ndays, I though about writing up a short\ntutorial on how to perform code review for existing code on GitHub. Therefore, this applied to\nCDK and Bioclipse source code, many but will work for any project hosted\nin GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the\nprocedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics\nrepository.
\nClick on the images to get a higher resolution version.
\nUse the GitHub web interface to browse your way towards the source code of the class you want to review. For example,\nthe SmartsMatchingHelper.java:
\n
Next step is to perform some code reviewing. For example, we might want to ask something about how parseProperty() works:
\n
Now, this page on GitHub does not provide the means to leave comments; instead, you comment on commits.
\nGit has a blame option (also called annotate)\nwhich will show you for each line who last changed that line. The GitHub web page makes this functionality available with the\n'blame' link just above the first line of the source code:
\n
This link will lead us to a page with a new column on the left side showing commit hashes, name of the commit author,\nand the first few characters of the commit message. For example, the\nweb page\nbits relevant to code we want to comment on, looks like:
\n
This shows us that commit 3ce78ba5\nis the one we are interested in:
\n
In the web page with the appropriate commit looked in the previous step, you scroll down to the line you want to comment on.\nIf you hover over that line, a blue comment bubble will show up on the left side:
\n
Clicking that blue comment icon, you get a dialog where you can enter your comment:
\n
The 'Add Line Note' button confirms and saves your comment:
\n
The next step would be to inform the commit author. GitHub actually helps here, and should send a message,\nlike this one:
\n
But it would certainly not hurt of you filed a bug report or sent an email.
\nNow, I should only convert this into a screencast\u2026
","doi":"https://doi.org/10.59350/nfcyx-jxj82","guid":"https://doi.org/10.59350/nfcyx-jxj82","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273449600,"rid":"vrsz7-ftc23","summary":"Triggered by posts in the past three days, I though about writing up a short tutorial on how to perform code review for existing code on GitHub. Therefore, this applied to CDK and Bioclipse source code, many but will work for any project hosted in GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the procedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics repository.","tags":["Cdk","Bioclipse","Github"],"title":"How to use GitHub for [CDK|Bioclipse] code review","updated_at":1784492178,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/10/how-to-use-github-for-cdkbioclipse-code.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"Yeah, it's my turn. Standing on the shoulders of ChemJobber,\nAzmanam, and\nScienceBase, here's list of things I like about chemistry.\nTo put things into perspective first, a bit, I note that ChemJobber and Azmanam focused on wet-lab chemistry, and David on fancy\nmolecules. Now, I am a theoretical chemist, and was thinking on what to orient the things I like, and on how general to make them.\nThis meme is not easy, you now. But here goes:
\nChemical graph theory is one of the common theoretical models chemists work with to make sense of chemical properties.\nI like it because the graph theory is fairly straightforward, but chemistry adds enough color (literally!) to create a\nnice complexity that kept the cheminformatics field going strong for more than 50 years now :) For example, how to adapt\nthe theory to deal with mutli-atom bonds :)
\nThe NMRShiftDB is an Open Data repository for annotated NMR spectra. The fun here is to\nadd NMR spectra of rare nuclei .\nDon't you just love a\nmolecule with NMR shifts for all atoms?
\nMetabolomics is the research field that studies the small molecules of life. Plant metabolomics is particularly fun.\nTens of thousands of molecules, and a lot of metabolite identification to be done, and much more. Lot's of cool stuff\nto do here, and I am trying to secure funding for it. This is\nwhat I blogged about metabolomics before. What about\nhis nice secondary metabolite (source:\nWikipedia, CC0):
\n
Atom types is another theoretical model for chemistry. Atom typing \nis one of the underlying technologies of force fields, which are used\nin many, many fields in chemistry. Now, force fields typically take only a subset of atom types. New atom types, consequently, need\nto be added. One such new atom type was the hexavalent carbon. Rare, very rare, but\njust the amount of complexity I like about chemistry.
\n\nKohonen maps, or self-organizing maps (SOM), are a machine learning\nmethod that have interesting visualization features. They have numerous applications, and also in chemistry. The group\nwhere I did my PhD developed a supervised SOM, which I used them to classify crystal structures\n(doi:10.1021/cg060872y). Another of my favorites is the\nreaction classification by Aires-de-Sousa et al. \nusing unsupervised SOMs.
\n
People who know me personally, know that I like tasting things. That also makes me have to worry about overweight.\nTaste is to a large extend governed by cooking, and the Maillard reaction\nplays an important role here. If you like to learn more about the chemistry of cooking, checkout these\ntwo blogs.
\nCb is a new element on the world wide web. Well, not so new anymore, and the full name is likely more familiar:\nChemical blogspace. This social web application brings together blogging chemists\nworld wide. Oh, and this meme is picked up nicely:
\n
No, not the database, but the nice graphical article abstracts in chemistry journals. ChemFeeds\ngets is all together. BTW, there remains very much to be done about improving publishing chemistry.\nI\nblogged\nabout \nthat\nrepeatedly .
\nOrganometallics is, like metabolomics, a really\ninteresting area, with lots of complexities (pun intended :). Actually, I am not even aware of a\norganometallics/metabolomics mashup. Anyone with some nice pointers? I have not blogged about it much,\nand the one time \nI did was in relation\nto chemical graph theory.
\nBurning things. Nothing more to say about that, I guess. Well, perhaps. Chemists like burning things;\nothers might too, but chemists at least. Blowing up things too. When I was a student, I had a very\nfriendly colleague who liked blowing up things and made TNT himself and took that to university too\n(stabilized, mind you :). Cool!
\nAnyway, while googling for something to spice up this tenth item, I ran into this book:\nCaveman Chemistry: 28 Projects, from the Creation of Fire to the Production of Plastics.\nThe prologue nicely writes up that you need to sparkle\nsome fire in education to get the students enlightened:
\n\n\nI teach chemistry at Hampden-Sydney College, a small liberal-arts college in central Virginia. The students\nhere, by and large, do not come equipped with insatiable curiosity about my discipline and experience has\nconvinced me that the profession of professing has more to do with motivation than with explanation; a student\nwho is not curious will resist even the most valiant attempts at compulsory education; conversely, inquiring\nminds want to know. A great deal of my time, then, has been spent devising tricks, gimmicks, schemes and plots\nfor leading stubborn horses to water, knowing full well that I can't make them think.
\n
Now, that leaves me with tagging a few further blogs to tag to continue the meme. The meme is spreading fast,\nso I hope I do not tag someone who already is tagged. Jean-Claude,\nPeter, Noel,\nRich, Antony, would you mind letting us know your\nten favourite chemistry things?
","doi":"https://doi.org/10.59350/be00d-tn533","guid":"https://doi.org/10.59350/be00d-tn533","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273708800,"reference":[{"id":"https://doi.org/10.1021/cg060872y","unstructured":"Willighagen, E. L., Wehrens, R., Melssen, W., de Gelder, R.& Buydens, L. M. C. (2007). Supervised Self-Organizing Maps in Crystal Property and Structure Prediction. Crystal Growth & Design, 7(9), 1738\u20131745."}],"rid":"k2113-tjf27","summary":"Yeah, it's my turn. Standing on the shoulders of ChemJobber, Azmanam, and ScienceBase, here's list of things I like about chemistry. To put things into perspective first, a bit, I note that ChemJobber and Azmanam focused on wet-lab chemistry, and David on fancy molecules. Now, I am a theoretical chemist, and was thinking on what to orient the things I like, and on how general to make them. This meme is not easy, you now.","tags":["Chemistry"],"title":"My favourite chemistry things","updated_at":1784492177,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/13/my-favourite-chemistry-things.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"blog":{"authors":[{"name":"Egon Willighagen"}],"community_id":"7f57028e-9d03-489c-b3b4-3d60de06bc9e","created":1710288000,"current_feed_url":"https://chem-bla-ics.linkedchemistry.info/feed.json","description":"Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.","doi":"https://doi.org/10.59350/chem_bla_ics","favicon":"https://rogue-scholar.org/api/communities/7f57028e-9d03-489c-b3b4-3d60de06bc9e/logo","feed_format":"application/feed+json","feed_url":"https://chem-bla-ics.linkedchemistry.info/archive.json","filter":null,"generator":"Jekyll","home_page_url":"https://chem-bla-ics.linkedchemistry.info","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"chem_bla_ics","status":"active","subfield":"1606","title":"chem-bla-ics","updated":1748131200,"use_api":true},"blog_name":"chem-bla-ics","blog_slug":"chem_bla_ics","content_html":"It has been a while since I gave an update on the ACS-RDF session in Boston .\nThings are settling in, and it seems there will be three sessions, each with an approximate theme. Each session will have five talks, of which one will be extended, where the speaker will be invited to set the context of the theme. Full programs will follow, but find the current sessions wordles below:
\n
Rajarshi is at the EBI (or at least was yesterday), talking about his\nrcdk package (his excellent slides).\nOne slide is about how to create a new atom; he mentions not to use new Atom() but the\nDefaultChemObjectBuilder\ninstead (slide 73). I do not entire agree with the message given.
\nThe slide seems to favour the DefaultChemObjectBuilder, but there like are more suitable builders for a particular application.\nCurrently, I am aware of two alternative builders: the DebugChemObjectBuilder, and the NoNotificationChemObjectBuilder.
\nThe reason the CDK has a builder pattern is the following. It is cleaner to write against interfaces than against\nimplementations, because it allows alternative implementations. I just listed all three provided by the CDK library itself,\nbut other implementations may exists too; they might have a completely different data model, e.g. fully CMLDOM-based, or\nfully SQL-based. By programming against interfaces, changing the implementation becomes easy.
\nNow, by using new Atom() you choose a particular implementation (in this case, the one around the DefaultChemObjectBuilder.\nHowever, you like the user to pick the implementation. This is why the CDK library itself uses builders all over the place:\nit assumes a IChemObjectBuilder is predefined and that is used.
For example:
\nIChemObjectBuilder builder = new DefaultChemObjectBuilder();\nIMolecule molecule = builder.newMolecule();\nIAtom atom = builder.newAtom();\nmolecule.addAtom(atom);\nIf your method actually has an IChemObject as input, it can retrieve the builder from there:
\npublic IMolecule addToMolecule(IAtom atom) {\n IChemObjectBuilder builder = atom.getBuilder();\n IMolecule molecule = builder.newMolecule();\n molecule.addAtom(atom);\n}\nThis latter situation is what exists most in the CDK library, actually. In some cases, this is not the case, and sometimes\nyou may need to pass an IChemObjectBuilder to a constructor. This is, for example, the case with the constructor of the\nSmilesParser.
Now, reconsider the first code example. By defining a builder only once, and reusing that builder in the rest of your code,\nyou only have to change one line to use a different implementation. For example, the DebugChemObjectBuilder that sends\ndebug messages for each set and get call to one of the data classes. I used this in the past, and solved several nasty bugs\nwith this; just by seeing in what order data was set and read. And I only needed to change one single line of code for that.
","doi":"https://doi.org/10.59350/1bedv-rsy83","guid":"https://doi.org/10.59350/1bedv-rsy83","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1273881600,"rid":"hj6w8-eqj34","summary":"Rajarshi is at the EBI (or at least was yesterday), talking about his rcdk package (his excellent slides). One slide is about how to create a new atom; he mentions not to use new Atom() but the DefaultChemObjectBuilder instead (slide 73). I do not entire agree with the message given.","tags":["Cdk","Java"],"title":"Cleaner CDK Code #5: develop against interfaces","updated_at":1784492173,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/15/cleaner-cdk-code-5-developer-against.html","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/048a87296","name":"Uppsala University"}],"contributor_roles":[],"family":"Willighagen","given":"Egon","url":"https://orcid.org/0000-0001-7542-0286"}],"content_html":"Peter informed about the CKAN 1.0 release.\nI browsed the 27 chemistry packages, and saw for example BODR show up:
\n
The database of packages is community based, and you can simply log in with an OpenID. This allows me to updated some\noutdated and add missing information.
\nAs mentioned, the list contains 27 packages, out of a total of almost 1000. So, not so much chemistry there yet, but that's\nsomething we are getting used to. Worse even, is that of these 27, only a small subset is Open. These are identified,\nI think, by the blue bar on the left of the packages in the above screenshot. Even then, many of these are labeled\npublic domain, which we know is not very practicaly. This is why the CC0 waiver\nexists.
\nBut it at least allows us to create overviews of the available downloadable data. The system is very easy to use. Well done!
","doi":"https://doi.org/10.59350/3dt2a-bm621","guid":"https://doi.org/10.59350/3dt2a-bm621","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1274400000,"rid":"naczg-cxt29","summary":"Peter informed about the CKAN 1.0 release.","tags":["Opendata","Chemistry"],"title":"CKAN 1.0: A major contribution to Open Knowledge","updated_at":1784492171,"url":"https://chem-bla-ics.linkedchemistry.info/2010/05/21/ckan-10-major-contribution-to-open.html","version":"v1"}],"out_of":50849,"page":1,"per_page":10,"total-results":50849}