Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-30

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All times shown according to UTC.

Time Nick Message
01:39 CIA-16 jmol: hansonr * r8543 /trunk/Jmol/src/org/jmol/ (8 files in 3 dirs):
01:39 CIA-16 jmol: version=11.3.40_dev
01:39 CIA-16 jmol: # new feature: point3f in array():
01:39 CIA-16 jmol: # xlist = array({1,2,3}, {1,1,0});print xlist[1]+{1 0 0};
01:39 CIA-16 jmol: # bug fix: draw @{x - {1 0 0}}
01:39 CIA-16 jmol: # bug fix: antialias with set picking draw
06:52 egonw joined #cdk
07:30 jbrefort joined #cdk
07:39 rojasm joined #cdk
07:39 egonw hi rojasm
07:39 rojasm moin
07:39 rojasm moin egonw
07:39 egonw rojasm: I'm working a bit on charged atom types...
07:39 egonw making some progress...
07:39 egonw working my way through those you have in the reaction tests
07:39 rojasm :)
07:40 rojasm I finish the molecular formula object. And some functions to generate and validate them
07:40 egonw oh cool
07:40 egonw CDK News article?
07:40 rojasm according the isotopes pattern as well
07:40 rojasm I was thinking about that
07:41 rojasm but it should be necessary to compare with a database
07:41 rojasm how good is
07:41 rojasm like it did Tobias kind
07:41 egonw one or two NIST specs?
07:41 rojasm I thought with all of them
07:41 egonw yeah, you could ask him one or two
07:41 rojasm extract exact mass
07:42 egonw btw, we're still on for Fridya, right?
07:42 rojasm generate the molecular formula and compare with the real
07:42 rojasm yes
07:42 egonw good
07:42 rojasm for me is perfect
07:42 egonw same here
07:42 CIA-16 jmol: nicove * r8544 /trunk/Jmol-FAH/projects/p3903.xyz.gz: Folding@Home
07:45 egonw OK, will have a meeting very soon now...
07:45 egonw bbl
07:45 rojasm :)
07:52 egonw cu later
07:52 CIA-16 cdk: egonw * r9256 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added C.plus.planar [C+]H3, and two more JUnit tests, and some better perception of charged atom types
09:27 * egonw is going to reinstall Ubuntu, but now 32bits...
09:27 egonw I'm done with all those OutOfMemory crashes...
09:27 egonw 64bit is not stable enough for me :(
09:42 rojasm left #cdk
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09:56 jpansanel moin
10:17 egonw joined #cdk
10:17 egonw moin
10:17 * egonw is back in the 32bits world...
10:17 egonw and his systems runs much faster
10:59 egonw rojasm: OK, failing JUnit tests for 'reaction' in trunk/ is down to 8 tests and was 17
11:00 egonw lunch time
12:27 CIA-16 cdk: egonw * r9257 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added perception of more charged carbon atom types
14:01 jonalv joined #cdk
14:07 CIA-16 blueobelisk: rajarshi * r152 /userscripts/trunk/3DStructureView.user.js: Added some text for the update message
14:29 CIA-16 blueobelisk: baoilleach * r153 /userscripts/trunk/3DStructureView.user.js: Corrected typo, and bumped up version to enforce update...
15:05 CIA-16 cdk: egonw * r9258 /trunk/cdk/tools/nightly.py: Fixed two other sources of W3C broken link errors: 301 (moved permanently) for cia.vc, and missing '/' for dir causing a 301 too
16:01 CIA-16 cdk: egonw * r9259 /trunk/cdk/src/org/openscience/cdk/test/sm​iles/smarts/parser/SMARTSSearchTest.java: Unsafe to use global parameters in JUnit tests.
16:02 CIA-16 cdk: egonw * r9260 /trunk/cdk/src/org/openscience​/cdk/smiles/SmilesParser.java: Don't fail on weird chemistry: it's SMILES, you may expect undefined chemistry
16:03 CIA-16 cdk: egonw * r9261 /trunk/cdk/src/org/openscience/c​dk/tools/CDKHydrogenAdder.java: If the atom type is 'dummy' aka 'X': simply set implicit hydrogen count to zero
16:04 CIA-16 cdk: egonw * r9262 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added a few missing atom types (closes #1820873 and #1820874)
16:22 CIA-16 cdk: egonw * r9263 /trunk/cdk/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java: Fixed SMILES, 'c1cccn1' is not a valid SMILES.
16:59 CIA-16 cdk: egonw * r9264 /trunk/cdk/src/org/openscience​/cdk/smiles/SmilesParser.java: Cleaned up code: no bond order perception
17:06 CIA-16 cdk: rajarshi * r9265 /trunk/cdk/tools/nightly.py: Moved the smarts module to stable on the report page
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17:28 CIA-16 cdk: rajarshi * r9266 /trunk/cdk/build.xml: Removed compilation steps for the old SMARTS parser
17:29 CIA-16 cdk: rajarshi * r9267 /trunk/cdk/src/org/openscience/cd​k/smiles/smarts/SMARTSParser.jj: Removed the old (JavaCC) smarts parser
17:32 CIA-16 cdk: rajarshi * r9268 /trunk/cdk/src/org/openscie​nce/cdk/test/smiles/smarts/ (ParserTest.java SMARTSSearchTest.java): Removed the old (JavaCC) smarts parser tests
17:50 rojasm joined #cdk
18:31 CIA-16 cdk: miguelrojasch * r9269 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): added in AtomContainerManipulator the functionality getTotalExactMass, getTotalNaturalAbundance and tests
18:33 CIA-16 jmol: hansonr * r8545 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs):
18:33 CIA-16 jmol: version=11.3.40_dev
18:33 CIA-16 jmol: # new feature: model-based parallel array calculations:
18:33 CIA-16 jmol: # x = {atomno=3}.split() # a list, one element for each model
18:33 CIA-16 jmol: # draw @{x.xyz.sub({1 0 0})} # a set of points, one per model
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18:49 CIA-16 cdk: miguelrojasch * r9270 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Natural abundance relatived to 100
21:05 CIA-16 jmol: nicove * r8546 /trunk/Jmol-FAH/src/org/jmol/fah/ (Jmol-FAH.properties checkxyz/Check.java): Folding@Home
22:02 rojasm left #cdk
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