Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-06

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All times shown according to UTC.

Time Nick Message
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07:50 CIA-31 cdk: miguelrojasch * r8889 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs):
07:50 CIA-31 cdk: Implemented a method which determine the molecular formula given a accurate mass.
07:50 CIA-31 cdk: It is not implemented still the validation if the molecular formula can have existence.
07:53 CIA-31 cdk: miguelrojasch * r8890 /trunk/cdk/src/org/openscience​/cdk/test/MstandardTests.java: add test corresponding to MassToFormulaToolTest
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09:55 CIA-31 cdk: miguelrojasch * r8891 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Controlling the occurrences for each elemental element
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13:03 rojasm egonw around?
13:10 egonw yes
13:10 egonw but talking to three persons in total now
13:10 rojasm ups
13:10 rojasm no worry
13:10 egonw all via IRC
13:11 egonw so, managable
13:11 rojasm we speak later then
13:11 rojasm it is about how to validate if a molecular formula is existable
13:11 rojasm like c2h11
13:15 egonw there is code in the deterministic structure generator for that...
13:16 egonw we could consider factoring that out...
13:16 egonw but not easy...
13:16 rojasm ok, that was more or lest the question
13:16 rojasm if we could use some code of cdk
13:18 egonw don't think there is anything other than that, but certainly not sure about that
13:18 rojasm other question sould we remove the code from the applet?
13:18 rojasm I didn't use it
13:19 egonw yes, please do
13:19 rojasm other question: does cdk define what ist MolecularFormula
13:19 rojasm makes sence to create a class for that
13:19 egonw yes, have been thinking about that too...
13:20 egonw MFAnalyser could make good use of that...
13:20 * egonw is getting a cup of coffee
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13:49 olas egonw: around?
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13:51 olas Anyone knows of preferred programming languages in chemo/bioinformatics?
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13:55 dleidert olas: maybe you can ask/look on bioinformatics.org for a first overview (you normally can search for project langiuages in the project tags)
13:55 olas sounds like a start
13:55 olas thx
13:56 dleidert so with this search on project tags you might be able to check freshmeat.net and sf.net too
13:56 olas right...
13:56 olas have not really seen a comparison out there but maybe it exists
13:56 dleidert just an idea - I really don't know, if this workes in the way you need it
13:57 olas http://www.bioinformaticszen.com/2007/03/bioi​nformatics-which-programming-language-to-use/
13:57 lambdabot2 Title: Bioinformatics Zen � Bioinformatics : which programming language to use?, http://tinyurl.com/2h7h6t
13:57 olas found that one
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14:36 CIA-31 jmol: hansonr * r8207 /trunk/Jmol/src/org/jmol/ (7 files in 3 dirs): (log message trimmed)
14:36 CIA-31 jmol: version=11.3.16_dev # new feature: byElement and byResidue color schemes allow
14:36 CIA-31 jmol: # customized element and residue coloring schemes.
14:36 CIA-31 jmol: # built-in include: byElement_Jmol, byElement_Rasmol,
14:36 CIA-31 jmol: # byResidue_Jmol (shapely) and byResidue_Rasmol (amino)
14:36 CIA-31 jmol: # with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol
14:36 CIA-31 jmol: # color atoms "byresidue_Jmol"
14:39 CIA-31 jmol: hansonr * r8208 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
14:39 CIA-31 jmol: version=11.3.16
14:39 CIA-31 jmol: # new feature: byElement and byResidue color schemes allow
14:39 CIA-31 jmol: # customized element and residue coloring schemes.
14:39 CIA-31 jmol: # built-in include: byElement_Jmol, byElement_Rasmol,
14:39 CIA-31 jmol: # byResidue_Jmol (shapely) and byResidue_Rasmol (amino)
14:39 CIA-31 jmol: # with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol
14:50 CIA-31 jmol: hansonr * r8209 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:
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15:07 CIA-31 cdk: miguelrojasch * r8892 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs):
15:07 CIA-31 cdk: Implemented validation of the molecular formula according the corollary 3.4 from http://www.sccj.net/publicat​ions/JCCJ/v3n3/a01/text.html.
15:07 CIA-31 cdk: Now, the method obtain only formulas that can have existence.
15:07 lambdabot2 Title: Journal of Computer Chemistry, Japan, Vol. 3, No. 3 (2004)
15:08 rojasm egonw: implemented the validation.
15:08 rojasm Only I need to calculate for molecular formulas that have charge
15:14 rojasm Now for example comparing with the results of the apple from Rzepa. He obtained for the mass 44.0032 the follown molecular formula (CO2, N2O, CH2NO, N3H2, CH4N2, C2H6N). Contrary I obtain only (CO2, N2O, CH4N2)
15:14 rojasm I think it is correct right?
15:15 rojasm egonw: sorry question
15:15 rojasm how can I write a molecular formula with charge
15:15 rojasm is it possible?
15:15 rojasm like C2H5+
15:17 rojasm somebody knows if it is possible to write a molecular formula with charge!!!!
15:27 egonw no idea...
15:27 egonw good question...
15:32 rojasm ok, on the time I will give the results as C2H5[+]
15:32 rojasm do you think it is ok
15:35 egonw then make it [C2H5]+
15:36 rojasm if the charge is 2
15:36 egonw then make it [C2H5]2+
15:36 rojasm perfect
15:59 CIA-31 cdk: miguelrojasch * r8893 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): implemented the molecular formula validation for mass with charge.
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18:29 CIA-31 jmol: nicove * r8210 /trunk/Jmol-FAH/projects/p3656.xyz.gz: Folding@Home
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