Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-01

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All times shown according to UTC.

Time Nick Message
00:01 CIA-16 cdk: miguelrojasch * r9538 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (3 files in 2 dirs): New Rule validating the charge of the MolecularFormula
00:07 CIA-16 jmol: nicove * r8714 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
06:48 jbrefort joined #cdk
08:14 rojasm joined #cdk
08:51 CIA-16 cdk: miguelrojasch * r9539 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (3 files in 2 dirs): New class MolecularFormulaExpand. It express a MolecularFormula but not with a fixed occurrence of the IIsotopes. Necessary when you want to have the number of isotopes inside of a range.
09:11 CIA-16 cdk: miguelrojasch * r9540 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (3 files in 3 dirs): update Rules to MolecularFormulaExpand
09:22 egonw_ joined #cdk
09:31 egonw_ rojasm: jean-claude is posting m/z spectra.... http://usefulchem.wikispaces.com/​space/showimage/Exp148B-5-MS.JPG
09:32 rojasm hi egonw
09:32 egonw_ maybe we can do something with that...
09:33 rojasm yes
09:34 CIA-16 cdk: miguelrojasch * r9541 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (2 files in 2 dirs): New class which take account the Tolerance of a MolecularFormula and a experimental mass
09:36 rojasm egonw I created a new MolecularFormulaExpand which not have a number fix of Isotopes for a given MolecularFormula but a interval
09:36 rojasm so it reduces a lot of problems that I had for the rules
09:47 egonw_ saw the commit...
09:48 egonw_ but I don't understand why you it is needed
09:53 rojasm I didn't know how implemented some thing to say that a MolecularFormula with Isotopes between a range
09:53 egonw_ right, but why do you want to do that?
09:54 rojasm important for restrictions
09:54 rojasm and for the Tree spectral
09:54 rojasm which go up and down I need this information
09:55 rojasm not good idea?
09:55 egonw_ right... for restrictions...
09:55 egonw_ but there was already something for restrictions?
09:55 egonw_ was that not enough?
09:56 rojasm and to make simple the method MAssToFormulaTool
09:56 egonw_ don't see that link
09:56 egonw_ masstoformula does not return a MF with ranges on the isotopes...
09:57 rojasm but you need to put
09:57 rojasm you need to say the interval of isotopes which must look for
09:58 egonw_ yes
09:58 rojasm And now it was the method with setRestrictions with a class Restrictions which I think was a bit kaotisch
09:58 egonw_ ok, so you replaced Restriction with MFExtend?
09:58 rojasm And now With (MolecularFormulaExpand (may be the name is not total correct)
09:59 rojasm yes
09:59 egonw_ where does the name 'Extend' come from?
09:59 rojasm not exactly. setRestrictions(List<IRule>)
10:00 rojasm Extend or extansion or
10:00 egonw_ OK, I think I will have a look at the JUnit tests :)
10:00 egonw_ ic
10:00 egonw_ well, extension suggests to me it is all...
10:00 egonw_ what about MFRange ?
10:02 rojasm ok, sound good for me
10:02 egonw_ OK, do you have time for something else too?
10:03 egonw_ might we discuss LonePair and reaction stuff?
10:04 rojasm ja
10:05 rojasm of course
10:06 egonw_ some derived things, like charge/IP calculation is all partially broken...
10:06 egonw_ and I cannot get it working...
10:06 egonw_ it's quite complicated code...
10:06 egonw_ and quite impossible for me to see where things go wrong... or why
10:06 egonw_ I would very much like to use the new atom type perception code...
10:07 egonw_ so that I can see what happens on that level...
10:07 rojasm I can understand. I would say chaotic better
10:07 egonw_ and make sure, that bit goes right
10:07 egonw_ what are the most fundamental steps here?
10:07 egonw_ LonePair detection is one...
10:07 egonw_ gasteiger charges, IP, reactions all require this...
10:08 egonw_ what else?
10:08 rojasm I think it is all, but I look at
10:08 rojasm but the new implementation is not in trunk, still?
10:08 egonw_ OK, so far so good :)
10:09 egonw_ yes, it is...
10:09 egonw_ new atom typing is
10:09 egonw_ the IBond.Order patch is not
10:09 rojasm ok
10:09 egonw_ so, next, I would like to rewrite the LP tool...
10:10 egonw_ mom...
10:12 egonw_ OK, I have a branches/egonw/lpchecker
10:12 rojasm not problem. Could you say me some class test which I can start to say how the atom type is working now To have a idea!!
10:13 egonw_ well... I'll commit the code, and then you can check?
10:13 rojasm ok
10:13 egonw_ ok, got to go now...
10:13 egonw_ I will email when I updated the LPChecker to the new code...
10:14 egonw_ so that you can have a look at it...
10:15 rojasm ok, it is already in my package explorer
10:15 egonw_ ok, I will email when I need your feedback
10:15 egonw_ cu later
10:25 CIA-16 cdk: miguelrojasch * r9542 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (7 files in 4 dirs): rename the class MolecularFormulaExpand to MolecularFormulaRange
13:24 carsten joined #cdk
13:24 carsten egonw: ... density has been removed from elements.xml???
13:27 carsten egonw: I checked, densty.txt is in bodr
13:28 carsten yes, it has been removed in the elements.pl
13:28 carsten egonw: do you remember the reasons?
13:29 carsten egonw: there is no source given... I have that source now..
17:24 rojasm left #cdk
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20:32 CIA-16 cdk: miguelrojasch * r9543 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (7 files in 3 dirs): update MassToFormulaTool to MolecularFormulaRange
20:38 CIA-16 cdk: miguelrojasch * r9544 /branches/miguelrojasch/mf/src/org/opensc​ience/cdk/formula/MassToFormulaTool.java: cleaning
21:59 dleidert joined #cdk
22:03 rojasm left #cdk
22:55 CIA-16 jmol: hansonr * r8715 /trunk/Jmol/src/org/jmol/ (10 files in 5 dirs):
22:55 CIA-16 jmol: version=11.3.52_dev
22:55 CIA-16 jmol: # bug fix: quaternion not including chain designation
22:55 CIA-16 jmol: # bug fix: default connections include proper PDB CONECT records
22:55 CIA-16 jmol: # new feature: connect PDB # just does PDB CONECT connections
22:55 CIA-16 jmol: # new feature: connect PDB AUTO # PDB CONECT and autobonding

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