Wednesday, October 21, 2009

Maintaining patches is fixing patches

Today I had a question about having to fix patches against upstream changes because those patches were not included upstream yet is not very productive.

However, it is a prominent part of maintaining a code base. In the past 9 year, I and many others have been reworking a lot of CDK code because of API changes and bug fixes in deeper parts of the CDK library. At least half of the work I have done for the CDK is doing this kind of fixing of downstream code. This is never trivial, and it is never productive. Well, depends somewhat on your definition of productivity.

Whether productive or not, it is just something that needs to happen. Additionally, it is not something you can prevent. I guess one can call this a fact of life. Doesn't make it nice work. Not at all. And most of my frustration with the CDK library is the lack of documentation and unit testing, which makes such fixing of downstream code hard. This means that the person best suited to do this job, is the one who wrote the patch in the first place. The person who made the comment I mentioned earlier is seeing this from very up close now.

Code Quality
I very much understand his feeling of being unproductive when updating patches; been there, done that. He (that I can disclose) is absolutely right. With all the quality assurance functionality I have set up in the past for the CDK, nicely integrated in Rajarshi's Nightly script, I hope to make it easier for people to write proper maintainable patches. Often these reports are, however, again about doing tasks which make you feel unproductive. But I can assure you that writing such tools quality assurance tools, like the OpenJavaDocCheck I worked on this weekend, makes you feel even less productive.

Sometimes making a library better maintainable, includes reworking the design. Almost always this take serious effort, and potentially introduce new bugs. At the same time, it always fixes a lot of older bugs and at the same time, of redesigned properly, makes it much easier to fix other bugs and allow more functionality to be implemented.

But again, this requires rewriting of downstream patches too. And the one doing the redesign will always get comments about this requiring to make unproductive code updates downstream. I have seen this on several occasions in the CDK, such as my rewrite of the atom typing functionality in the CDK. (And don't get any KDE4 developer started on that topic ;) Another fact of life, I guess.

Tuesday, October 20, 2009

CrossRef writes up RSS usage recommendations

CrossTech announced that a CrossRef working group has written a best practices for the use of RSS feeds by publishers. Nice introduction for anyone who is creating RSS feeds. Only comment I could make, is the lack of other modules. For example, a Chemistry module has been proposed by us 5 years ago already (DOI:10.1021/ci034244p) and about which I blogged on several occasions.

Below is the CMLRSS feed of Chemical blogspace.

Of course, publishers can take advantage of such modules, using the XML Namespaces technology. The best practices uses that for a Dublin Core and a PRISM extension. The here discussed CML extension is another one, but the point is, that you can basically plug in any module.

Saturday, October 17, 2009

Work in Progress: an Open DocCheck replacement

While it is still very much in progress, I have already made more progress than I had hoped for. The JavaDoc Doclet API is actually not too difficult to use, though my use will very likely improve more later. The CDK has been using Sun's DocCheck utility for testing the library's JavaDoc quality, but the reports never really satisfied me. Moreover, the most recent version is ancient and because it is closed source, no one can continue on those efforts. DocCheck is MIA.

Instead, PMD is given nice overviews of what it believes to be wrong with the CDK, and also provides a decent XML format which allows extraction of information, which is used by, for example, SuperNightly as showed yesterday in PMD 2.4.5 installed in the CDK 1.2.x branch.

I have been pondering about it for a long time now, but writing a JavaDoc checking library is hardly core cheminformatics research; at least, you would not get funding for it, despite everyone always complaining about good documentation. Alas.

Last week, I was reviewing some more code, and again saw the very common error of the missing period at the end of the first sentence in JavaDoc. This one is sort of important for proper JavaDoc documentation generation, but the complexity of the current DocCheck reporting, people are not familiar enough with it. Being tired of having to repeat myself, I decided to address the problen, but creating better Nightly error reporting for the CDK JavaDoc.

So, I started OpenJavaDocCheck, or ojdcheck. As mentioned, I have made quite promising progress, and the current version provides the ability to write custom tests (which I plan to use for validating content of CDK taglet content), and create XML as well as XHTML which can be saved to any file. To give you a glimps of where things are going, here's a screenshot of the current XHTML output:

The current list of tests is really small, and consists of a single test:
  • test if each class and method has JavaDoc

Friday, October 16, 2009

PMD 2.4.5 installed in the CDK 1.2.x branch

Today I installed PMD 4.2.5 in the CDK 1.2.x branch which contains mostly bug fixes compared to the 4.2.2 version we had earlier. Several of these include false positives: warnings which were not really problems, but tests going bad.

The number of these false positives seems to be significant as the number of PMD violations for the CDK 1.2.x branch seems to have dropped about 1500! warnings :)

Thursday, October 15, 2009

SPARQL end points, Jena and bif:contains

I have been having fun with SPARQL in Bioclipse for a while now, and blogged at several occasions:
One thing I had not been able to work out, is that Virtuoso uses a (rather nice) bif:contains extension that support indexing. However, Jena would complain with:
com.hp.hpl.jena.query.QueryParseException: Line 1, column 31: Unresolved
prefixed name: bif:contains
Defining the prefix did not solve the problem either, but Ivan Mikhailov just replied to my post to the virtuoso-user mailing list providing the solution.

The solution is in the fact that bif: is in its own namespace, which makes it possible to replace bif:contains by its full reference <bif:contains>. I directly gave that a try in Bioclipse, and just succesfull ran this Bioclipse script snippet:
  "SELECT * WHERE {?s ?p ?o . ?o <bif:contains> \"aspirin\" .};"

Thanx, Ivan!

Friday, October 09, 2009

NMRShiftDB RDF #3: Bio2RDF

My might have seen my efforts to convert the NMRShiftDB data into RDF:
Peter Ansell has shortly after that copied the data into Bio2RDF, but I had not blogged about that yet. So, here goes. If you have not looked at Bio2RDF yet, this is a good time to do that. The structure of the exposed triples is not perfect, and I just realized I made a beginners mistake, to use a domain name in a namespace I have not control over (bad me). The Virtuoso6 faceted browser allows you to navigate the data in Bio2RDF by molecule (e.g. molecule 234):

And by spectrum too (e.g. spectrum 4735):

Thursday, October 08, 2009

Where are the CDK 1.3.1 and 1.2.4 releases ?!?

You might be wondering what is keeping the CDK 1.3.1 and 1.2.4 releases. And right you are. When we look at Supernightly, we get a clue (BTW, I hope the EBI nodes will join soon too):

Studying this table shows the reasons: there are too many regressions, too many failing unit tests. For example, 1.2.4 (while not yet released, called 1.2.3.git) has 50 new failing tests. Now, fair enough, this is mostly because of ioformats not being tested in 1.2.3 and most of the fails caused by a bug in the test, not in the code. But that still leaves 20 other failing tests. Mostly related to known bugs, and for some problems patches are actually available.

These last 22 we also see in the differences between 1.3.0 and 1.3.1 (while not yet released, called 1.3.0.git). That's because the ioformats modules is not tested in that branch either, pending a new merge with the cdk-1.2.x branch.

Wednesday, October 07, 2009 funded research to be OA as of 2010

Happy news from the Swedish Vetenskapsradet (via Coturnix): as of next 2010 all peer reviewed journal papers must be Open Access. I am not yet VR funded, but involved in a few VR grant applications. Not that that really matters, as I am happily publishing OA already.

Keeping my Bioclipse repositories in sync with upstream

Bioclipse is now split up over several Git repositories (and some additional stuff in even more repositories). This has all to do with each repository now having one person acting as point-of-access. This means that I have several repositories checked out, which I need to keep synchronized. Now, I am pretty sure there are many solutions (and suggestions very welcome!), but this is the Bash script I have just written to give me an overview of the state of my repositories, hoping it may be useful to others too:

PLUGINS=`ls -1`

        echo "***************************************************************** $PLUGIN"
        cd $PLUGIN; git fetch origin; git status; cd ..

Tuesday, October 06, 2009

CDK Molecules in RDF

Yesterday, I finally got around to starting a branch on adding RDF support to the CDK; in particular, write the CDK data model ontology in OWL and serialization to and from RDF using the ontology. The framework is now set up, but I have yet to formalize all bits and pieces of the CDK data model in classes and properties. Just as a preview, here is what a very basic bit of CDK model in RDF looks like (N3 format):
@prefix cdk:     <> .

      a       cdk:Atom ;
      cdk:symbol "C" .

      a       cdk:Molecule ;
      cdk:hasAtom  .
Still rather verbose, but very flexible. I have even been thinking of an XHTML+RDFa writer...

Thursday, October 01, 2009

Google Wave Invite: but you need to work on the CDK and the CDKitty robot

I just posted to below email to the cdk-user mailing list. Next Monday, I'll decide.
Hi all,

unless you have not read any news in the last two days, you will have
seen that Google is rolling out a second batch of Google Wave
accounts... I have one invite for someone who wants to co-develop the
CDKitty robot, which adds CDK-based functionality to Google Wave...

The code is at:

If you are interested in the account, please email me offline with:

* how you think you can contribute to the robot
* why you want to do that
* how much time you will have for it

The position is open to anyway, and consider your email an application
to the position :) (and, if you are a student, we could even try to
arrange Uppsala University credit points, if you can work 20 weeks
full time on it).

BTW, existing Google Wave users can invite the robot by adding

Processing the ChEBI MDL SD file with the CDK

Bioclipse has a bug report about browsing the ChEBI SD file in its moltable editor. Some entries make Bioclipse crash (as reported), or just very sluggish as with my Dell superlapcomputer :)

So, I processed the file with a pure CDK 1.2.3 with this small piece of Groovy script:
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.*;

iterator = new IteratingMDLReader(
  new File("ChEBI_complete.sdf").newReader(),
int i = 0;
boolean hasNext = true;
while (hasNext) {
  long startTime = System.currentTimeMillis();
  hasNext = iterator.hasNext();
  IMolecule mol =
  long endTime = System.currentTimeMillis();
  formula = MolecularFormulaManipulator.getMolecularFormula(mol)
  long time = endTime - startTime;
  if (time > 99)
    println i + ": " + MolecularFormulaManipulator.getString(formula) +
            " (" + endTime + "-" + startTime + "=" + time + " ms)"


This script times reading of all entries and reports all that entries take more than 100 ms to read (in the scripting environment). There are surprising results: H2O takes 50 seconds, phosphate 100 seconds. So, I am quite certain it must be the reading of the metadata, and not the connection table. But, this I will explore in more detail now, hoping to come up with a patch for the CDK to speed up reading of such entries.

The full list of timings:
1: C10H2 (1254375053450-1254375052356=1094 ms)                                           
152: C20HN7O6 (1254375054779-1254375054125=654 ms)                                       
592: C3HO3 (1254375056604-1254375055499=1105 ms)                                         
832: C9NO5 (1254375057016-1254375056823=193 ms)                                          
879: C20N4 (1254375057381-1254375057039=342 ms)                                          
1125: R (1254375058293-1254375057528=765 ms)                                             
1197: C20N7O6 (1254375058612-1254375058372=240 ms)                                       
1198: C5NO3 (1254375058714-1254375058613=101 ms)                                         
1243: C5NO4 (1254375063698-1254375058800=4898 ms)                                        
1272: C21N7O16P3S (1254375067185-1254375063856=3329 ms)                                  
1277: C23N7O17P3S (1254375067625-1254375067239=386 ms)                                   
1282: C3NO2S (1254375070673-1254375067650=3023 ms)                                       
1285: C3O3 (1254375071600-1254375070675=925 ms)                                          
1290: C2O2 (1254375071802-1254375071608=194 ms)                                          
1299: H2O (1254375122202-1254375071808=50394 ms)                                         
1300: H (1254375136668-1254375122202=14466 ms)                                           
1301: O2 (1254375145270-1254375136670=8600 ms)                                           
1335: C15N6O5S (1254375150683-1254375145319=5364 ms)                                     
1343: C10N5O13P3 (1254375298927-1254375150686=148241 ms)                                 
1349: C2NO2 (1254375301391-1254375298953=2438 ms)                                        
1351: C34N4O4 (1254375301659-1254375301396=263 ms)                                       
1509: C6NO2 (1254375302753-1254375302011=742 ms)                                         
1541: C19N7O6 (1254375303296-1254375302778=518 ms)                                       
1543: C20HN7O7 (1254375303441-1254375303312=129 ms)                                      
1609: C9N2O15P3 (1254375303740-1254375303558=182 ms)                                     
1631: CHO2 (1254375303975-1254375303837=138 ms)                                          
1632: C4O4 (1254375304127-1254375303976=151 ms)                                          
1711: C21N7O14P2 (1254375310174-1254375304245=5929 ms)                                   
1788: C6H3O9P (1254375310555-1254375310387=168 ms)                                       
1798: C10H2N2O3S (1254375310705-1254375310588=117 ms)                                    
1808: C6N3O2 (1254375312665-1254375310727=1938 ms)                                       
1823: C10N5O14P3 (1254375318534-1254375312781=5753 ms)                                   
1839: C5NO4 (1254375325988-1254375318583=7405 ms)                                        
1840: C3O3 (1254375326249-1254375325989=260 ms)                                          
1848: C10N5O7P (1254375336661-1254375326273=10388 ms)                                    
1862: C5NOSR2 (1254375337336-1254375336699=637 ms)                                       
1882: C3N2 (1254375337489-1254375337351=138 ms)                                          
1893: C6O9P (1254375337626-1254375337501=125 ms)                                         
1910: C3O6P (1254375337846-1254375337639=207 ms)                                         
1934: H3N (1254375349713-1254375337921=11792 ms)                                         
1977: O4S (1254375350045-1254375349902=143 ms)                                           
1984: CN2O (1254375350174-1254375350050=124 ms)                                          
2007: C5N (1254375350324-1254375350183=141 ms)                                           
2015: C5N5O (1254375350493-1254375350329=164 ms)                                         
2016: C2O (1254375350683-1254375350494=189 ms)                                           
2018: C27N9O15P2 (1254375351927-1254375350684=1243 ms)                                   
2020: H2O2 (1254375352124-1254375351928=196 ms)                                          
2036: C17N3O17P2 (1254375352309-1254375352196=113 ms)                                    
2095: C10N5O4 (1254375352578-1254375352394=184 ms)                                       
2137: C14HO4R (1254375353331-1254375352646=685 ms)                                       
2180: C3NO2 (1254375354199-1254375353469=730 ms)                                         
2184: C9NO5 (1254375354480-1254375354270=210 ms)                                         
2194: C6N4O2 (1254375356738-1254375354485=2253 ms)                                       
2201: C21N7O17P3 (1254375359838-1254375356748=3090 ms)                                   
2228: C6O2 (1254375360480-1254375359912=568 ms)                                          
2240: CO2 (1254375363324-1254375360485=2839 ms)                                          
2327: C5NO2S (1254375370536-1254375363612=6924 ms)                                       
2348: C14N6O5S (1254375371522-1254375370558=964 ms)                                      
2359: C9N2O9P (1254375372236-1254375371544=692 ms)                                       
2367: C9N2O6 (1254375373614-1254375372265=1349 ms)                                       
2370: C5N5 (1254375373975-1254375373615=360 ms)                                          
2404: C10N5O5 (1254375374360-1254375374108=252 ms)                                       
2413: C10N5O10P2 (1254375401639-1254375374373=27266 ms)                                  
2454: C5O5 (1254375401831-1254375401688=143 ms)                                          
2455: C5NO2S (1254375407807-1254375401832=5975 ms)                                       
2470: C11N2O2 (1254375408251-1254375407815=436 ms)                                       
2494: C4NO3 (1254375409200-1254375408373=827 ms)                                         
2499: C5O10P2R (1254375412153-1254375409297=2856 ms)                                     
2525: C4HO7P (1254375412777-1254375412293=484 ms)                                        
2526: C4N2 (1254375414071-1254375412777=1294 ms)                                         
2534: C21N7O14P2 (1254375417657-1254375414091=3566 ms)                                   
2581: C3NO2 (1254375422072-1254375417745=4327 ms)                                        
2638: C4NO4 (1254375424772-1254375422244=2528 ms)                                        
2680: C5O14P3 (1254375426347-1254375424831=1516 ms)                                      
2683: C3NO3 (1254375433063-1254375426353=6710 ms)                                        
2702: C3HO6P (1254375433192-1254375433079=113 ms)                                        
2749: C4N2O3 (1254375434106-1254375433445=661 ms)                                        
2755: C10N4O8P (1254375434417-1254375434113=304 ms)                                      
2756: C5NO2 (1254375436750-1254375434418=2332 ms)                                        
2779: C4NO2S (1254375437847-1254375436759=1088 ms)                                       
2803: C5N4 (1254375438991-1254375437968=1023 ms)                                         
2832: C9NO2 (1254375439226-1254375439026=200 ms)                                         
2844: C8HNO3 (1254375440463-1254375439238=1225 ms)                                       
2856: C5O13P3R (1254375441336-1254375440497=839 ms)                                      
2863: C10O6 (1254375442424-1254375441348=1076 ms)                                        
2873: C10N5O8P (1254375442560-1254375442433=127 ms)                                      
2898: C3HO3 (1254375443712-1254375442655=1057 ms)                                        
2925: C8H4NO6 (1254375443886-1254375443729=157 ms)                                       
3025: CO3 (1254375444508-1254375444131=377 ms)                                           
3031: C10N5O11P2 (1254375444810-1254375444601=209 ms)                                    
3038: C3NO2S (1254375449012-1254375444836=4176 ms)                                       
3042: C4N2O2 (1254375449224-1254375449066=158 ms)                                        
3060: C6O2 (1254375449433-1254375449274=159 ms)                                          
3083: C17N4O9P (1254375450751-1254375449465=1286 ms)                                     
3088: C34FeN4O4 (1254375452873-1254375450848=2025 ms)                                    
3111: C9N2O12P2 (1254375454560-1254375452939=1621 ms)                                    
3119: CNO5P (1254375454774-1254375454563=211 ms)                                         
3122: C9N3O14P3 (1254375454972-1254375454778=194 ms)                                     
3184: C3O3 (1254375455362-1254375455053=309 ms)                                          
3213: CO (1254375455489-1254375455375=114 ms)                                            
3216: C3HO7P (1254375455662-1254375455490=172 ms)                                        
3223: C9N2O6 (1254375455850-1254375455737=113 ms)                                        
3239: C3NO3 (1254375458116-1254375455868=2248 ms)                                        
3296: C9NO3 (1254375459575-1254375458250=1325 ms)                                        
3306: S3R (1254375464014-1254375459596=4418 ms)                                          
3313: C6O6 (1254375464701-1254375464016=685 ms)                                          
3348: C14HO4 (1254375465102-1254375464766=336 ms)                                        
3360: C12O11 (1254375465830-1254375465193=637 ms)                                        
3364: N2 (1254375475917-1254375465872=10045 ms)                                          
3371: C21N7O17P3 (1254375479243-1254375475920=3323 ms)                                   
3377: C6N2O2 (1254375481175-1254375479306=1869 ms)                                       
3379: C3O6P (1254375482278-1254375481176=1102 ms)                                        
3390: O10P3 (1254375484356-1254375482286=2070 ms)                                        
3403: C5N2O3 (1254375486975-1254375484451=2524 ms)                                       
3499: C9NO3 (1254375487745-1254375487074=671 ms)                                         
3502: C5O8P (1254375489044-1254375487747=1297 ms)                                        
3532: C55MgN4O5 (1254375489206-1254375489097=109 ms)                                     
3537: C5NO4 (1254375494872-1254375489209=5663 ms)                                        
3546: Fe (1254375507646-1254375494892=12754 ms)                                          
3554: C5N2O2 (1254375507934-1254375507650=284 ms)                                        
3566: H2 (1254375508526-1254375508033=493 ms)                                            
3576: C12ClN4O7P2S (1254375508737-1254375508548=189 ms)                                  
3577: Mn (1254375511113-1254375508738=2375 ms)                                           
3582: C11NO6P (1254375511249-1254375511120=129 ms)                                       
3628: O7P2 (1254375554180-1254375511388=42792 ms)                                        
3633: O4P (1254375659461-1254375554183=105278 ms)                                        
3647: C12N4OS (1254375659706-1254375659481=225 ms)                                       
3664: C8HNO6P (1254375661230-1254375659713=1517 ms)                                      
3665: C9N4O8P (1254375661450-1254375661231=219 ms)                                       
3679: Mg (1254375679426-1254375661513=17913 ms)                                          
3859: C20N7O6 (1254375679768-1254375679522=246 ms)                                       
3860: C19N7O6 (1254375680069-1254375679769=300 ms)                                       
4026: Ca (1254375681849-1254375680582=1267 ms)                                           
4029: CNOR (1254375682983-1254375681850=1133 ms)                                         
4031: COR2 (1254375686384-1254375682984=3400 ms)                                         
4038: Cl (1254375686610-1254375686387=223 ms)                                            
4099: F (1254375687012-1254375686767=245 ms)                                             
4138: H (1254375722496-1254375687100=35396 ms)                                           
4163: C6NO2 (1254375722805-1254375722566=239 ms)                                         
4166: C6N2O2 (1254375724837-1254375722807=2030 ms)                                       
4167: Mg (1254375746423-1254375724838=21585 ms)                                          
4229: O (1254375754305-1254375746586=7719 ms)                                            
4254: H3O4P (1254375771602-1254375754367=17235 ms)                                       
4263: K (1254375771850-1254375771608=242 ms)                                             
4265: C5NO2 (1254375772195-1254375771852=343 ms)                                         
4297: Na (1254375772801-1254375772310=491 ms)                                            
4311: C4O3R (1254375773107-1254375772835=272 ms)                                         
4313: S (1254375795116-1254375773109=22007 ms)                                           
4356: Zn (1254375814849-1254375795263=19586 ms)                                          
4424: C5O5 (1254375818351-1254375814892=3459 ms)                                         
4453: C2 (1254375818489-1254375818369=120 ms)                                            
4482: C6N3O2 (1254375819699-1254375818525=1174 ms)                                       
4494: C (1254375821009-1254375819706=1303 ms)                                            
4519: Co (1254375821358-1254375821068=290 ms)                                            
4670: C11N2O2 (1254375821817-1254375821583=234 ms)                                       
4677: C4H2O4 (1254375822301-1254375821824=477 ms)                                        
4801: Ni (1254375822605-1254375822450=155 ms)                                            
4912: C5N2O3 (1254375823778-1254375822655=1123 ms)                                       
5060: C5O5 (1254375824119-1254375823908=211 ms)                                          
5111: C6O6 (1254375824420-1254375824212=208 ms)                                          
5143: Cu (1254375824613-1254375824502=111 ms)                                            
5357: C6N4O2 (1254375826277-1254375824919=1358 ms)                                       
5368: C9NO5 (1254375826504-1254375826289=215 ms)                                         
5369: Fe (1254375826620-1254375826505=115 ms)                                            
5380: C3HO6P (1254375827340-1254375826635=705 ms)                                        
5398: Na (1254375827949-1254375827359=590 ms)                                            
5400: K (1254375828174-1254375827951=223 ms)                                             
5402: Zn (1254375844116-1254375828175=15941 ms)                                          
5404: Ca (1254375845806-1254375844117=1689 ms)                                           
5438: HO (1254375846125-1254375845836=289 ms)                                            
5538: CH3 (1254375847891-1254375846233=1658 ms)                                          
5548: Ca (1254375861972-1254375847928=14044 ms)                                          
5560: H2N (1254375866398-1254375861980=4418 ms)                                          
5693: C10O6 (1254375867526-1254375866499=1027 ms)                                        
5814: O7P2 (1254375910579-1254375867608=42971 ms)                                        
5869: C2NOR2 (1254375914124-1254375910633=3491 ms)                                       
5871: C3NOSR2 (1254375914574-1254375914161=413 ms)                                       
5873: C6N4OR2 (1254375916764-1254375914575=2189 ms)                                      
5875: C11N2OR2 (1254375917143-1254375916766=377 ms)                                      
5877: C4NO3R2 (1254375917710-1254375917145=565 ms)                                       
5885: C6N2OR2 (1254375919573-1254375917716=1857 ms)                                      
5889: C5NO3R2 (1254375920901-1254375919576=1325 ms)                                      
5895: C6N3OR2 (1254375922306-1254375920904=1402 ms)                                      
5900: C5NO4 (1254375925689-1254375922310=3379 ms)                                        
5902: C5NO4 (1254375930626-1254375925693=4933 ms)                                        
5903: C5NO4 (1254375933920-1254375930626=3294 ms)                                        
5906: C4NO4 (1254375934593-1254375933924=669 ms)                                         
5907: C4NO4 (1254375935274-1254375934594=680 ms)                                         
5909: C4NO4 (1254375936451-1254375935274=1177 ms)                                        
5911: C9NOR2 (1254375936575-1254375936453=122 ms)                                        
5913: C3NO2R2 (1254375940197-1254375936577=3620 ms)                                      
5914: C3NOSeR2 (1254375940307-1254375940197=110 ms)                                      
5920: C6NOR2 (1254375940705-1254375940311=394 ms)                                        
5925: C5N2O2R2 (1254375942662-1254375940737=1925 ms)                                     
5926: C4NO2R2 (1254375943012-1254375942662=350 ms)                                       
5939: C4O4 (1254375943199-1254375943061=138 ms)                                          
5993: C2O2 (1254375943413-1254375943287=126 ms)                                          
6082: Zn (1254375958993-1254375943449=15544 ms)                                          
6453: C10N5O13P3 (1254376116554-1254375959193=157361 ms)                                 
6574: CHO2 (1254376116903-1254376116743=160 ms)                                          
6706: C5O5 (1254376117248-1254376117131=117 ms)                                          
7032: C3O4 (1254376117689-1254376117435=254 ms)                                          
7104: C5NO3R2 (1254376118481-1254376117843=638 ms)                                       
7252: C5NOSR2 (1254376118731-1254376118630=101 ms)                                       
7411: C3O3 (1254376120056-1254376119011=1045 ms)                                         
7465: CR (1254376121752-1254376120212=1540 ms)                                           
7627: CNO (1254376122089-1254376121887=202 ms)                                           
7741: C12ClN4OS (1254376122320-1254376122156=164 ms)                                     
7858: CO2R (1254376122547-1254376122436=111 ms)                                          
7891: Fe4S4 (1254376122844-1254376122585=259 ms)                                         
8178: Mn (1254376124399-1254376122960=1439 ms)                                           
8338: C4NO2 (1254376124643-1254376124480=163 ms)                                         
9219: C4NO6P (1254376127494-1254376124951=2543 ms)                                       
9234: C9N3O14P3 (1254376127605-1254376127498=107 ms)                                     
9235: C10N5O14P3 (1254376132596-1254376127605=4991 ms)                                   
9305: C3NO6P (1254376143823-1254376132629=11194 ms)                                      
9311: C6O6 (1254376144017-1254376143825=192 ms)                                          
9402: C5NOSR (1254376144332-1254376144214=118 ms)                                        
9427: C4O2R2 (1254376144645-1254376144419=226 ms)                                        
10281: O10P3 (1254376146646-1254376144942=1704 ms)                                       
10308: C2OR (1254376148204-1254376146659=1545 ms)                                        
10453: CHOR (1254376148682-1254376148321=361 ms)                                         
10506: HOR (1254376149933-1254376148793=1140 ms)                                         
10589: C21N7O17P3 (1254376150485-1254376150182=303 ms)                                   
10602: C5N2O2R (1254376150727-1254376150503=224 ms)                                      
10604: C5N2OR2 (1254376150946-1254376150728=218 ms)                                      
10614: C5N2O2 (1254376151170-1254376150949=221 ms)                                       
10617: C5N2OR (1254376151389-1254376151171=218 ms)                                       
10641: C3O6P (1254376152229-1254376151404=825 ms)                                        
10656: C16OR (1254376152505-1254376152235=270 ms)                                        
10688: C5O5 (1254376155565-1254376152582=2983 ms)                                        
10690: C3NO5PR2 (1254376166856-1254376155566=11290 ms)                                   
10729: C12N4O7P2S (1254376167090-1254376166889=201 ms)                                   
10748: C3NOR2 (1254376171309-1254376167097=4212 ms)                                      
10756: C34O4 (1254376172041-1254376171320=721 ms)                                        
10760: C9N2O15P3 (1254376172162-1254376172045=117 ms)                                    
10786: OR (1254376172419-1254376172169=250 ms)                                           
10828: C2NO2R (1254376173256-1254376172429=827 ms)                                       
10830: C2NOR (1254376174784-1254376173258=1526 ms)                                       
10883: C9NO2R2 (1254376175110-1254376174827=283 ms)                                      
10899: NR (1254376202420-1254376175114=27306 ms)                                         
10902: C2O (1254376203938-1254376202454=1484 ms)                                         
10914: C9NO5 (1254376204203-1254376203942=261 ms)                                        
11203: C6O6 (1254376204716-1254376204522=194 ms)                                         
11226: C4HO7P (1254376205190-1254376204732=458 ms)                                       
11680: C5NO2SR (1254376205649-1254376205392=257 ms)                                      
11681: C5NOSR (1254376205900-1254376205650=250 ms)                                       
11916: H (1254376206483-1254376206109=374 ms)                                            
12216: C5NOR2 (1254376208374-1254376206750=1624 ms)                                      
12217: C4N2O2R2 (1254376209040-1254376208375=665 ms)                                     
12680: COSR2 (1254376209601-1254376209314=287 ms)                                        
13478: C25HN2O19 (1254376210152-1254376209951=201 ms)                                    
13662: C5O8P (1254376210482-1254376210379=103 ms)