Camelia, the Perl 6 bug

IRC log for #cdk, 2010-05-24

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All times shown according to UTC.

Time Nick Message
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09:22 Gpox In a test for the cdk (specificly the GeometryToolsTest) new AtomContianer() is used to setup the molecule is this the correct way of doing it in a test?
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09:55 egonw Gpox: new AtomContainer() in unit tests is fine
09:55 egonw (did not see the question until just now)
09:55 Gpox ok
09:55 * Gpox prepares patch
09:56 egonw cool
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10:00 egonw s9asad: can you check the PMD tests... there are some unused imports and a few new issue, regarding not using the CDK interfaces... can you please check?
10:01 egonw for master, that is...
10:01 egonw and you module
10:01 s9asad Ok
10:02 CIA-2 cdk: mark_rynbeek * r15545 /jchempaint/trunk/yguard.jar: Not allowed to distrubute yguard
10:05 egonw oh no
10:05 egonw that doesn't look good... let's hope they will not require is to remove it from the SVN history too :(
10:05 egonw that doesn't look good... let's hope they will not require Us to remove it from the SVN history too :(
10:09 s9asad org.openscience.cdk.smsd.tools.​ExtAtomContainerManipulator329 Use instanceof against interfaces not implementations
10:09 s9asad I am using this
10:10 s9asad */
10:10 s9asad @TestMethod("testPercieveAt​omTypesAndConfigureAtoms")
10:10 s9asad public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer container) throws CDKException {
10:10 s9asad CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstan​ce(container.getBuilder());
10:10 s9asad for (IAtom atom : container.atoms()) {
10:10 s9asad if (!(atom instanceof PseudoAtom)) {
10:10 s9asad IAtomType matched = matcher.findMatchingAtomType(container, atom);
10:10 s9asad if (matched != null) {
10:10 s9asad AtomTypeManipulator.configure(atom, matched);
10:10 s9asad }
10:10 s9asad }
10:10 s9asad }
10:10 s9asad }
10:10 egonw if (!(atom instanceof PseudoAtom)) {
10:10 egonw that should be:
10:10 egonw if (!(atom instanceof IPseudoAtom)) {
10:10 egonw using the interface, not the implementation
10:10 s9asad hmm
10:10 s9asad correct
10:10 egonw pretty cool, not? :)
10:11 egonw but what I still need to do is:
10:11 egonw 1. write a XSLT stylesheet to create HTML for the tests
10:11 egonw 2. upload to the CDK SF homepage
10:11 egonw 3. add the link
10:11 egonw so, apologies for missing explanation with example
10:11 egonw please refer to pmd/cdkinterfaces.xml for now
10:18 CIA-2 cdk: mark_rynbeek * r15546 /jchempaint/tags/3.0.1/yguard.jar: Not allowed to distribute yguard
10:18 CIA-2 cdk: mark_rynbeek * r15547 /jchempaint/tags/3.1.1/yguard.jar: not allowed to distribute yguard.jar
10:36 s9asad http://sourceforge.net/tracker/?func=detail&amp​;aid=3006363&group_id=20024&atid=320024
10:37 zarah s9asad's link is also http://tinyurl.com/3aztjyo
10:37 s9asad Here are the changes :-)
10:37 s9asad its really cool!
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14:11 egonw hi maclean
14:11 maclean hi
14:11 zarah oh hai maclean
14:17 maclean egonw: I am starting to make the changes necessary for signatures to sort atoms by atom number, which may also make sorting by mass number possible.
14:17 maclean (I think you mentioned needing isotopes to be distinguishable)
14:17 egonw the CIP algorithm does
14:18 egonw but then again... that also needs cis/trans isomerism
14:18 maclean hm...
14:18 maclean mm....mmm....
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14:22 egonw bbl
14:27 maclean Wikipedia : "Usually, trans isomers are more stable than the cis isomers. This is partly due to their shape; the straighter shape of the trans isomer leads to hydrogen intermolecular forces that make the isomer more stable[http://en.wikipedia.org/wik​i/Wikipedia:Citation_needed]."
14:27 zarah maclean's link is also http://tinyurl.com/39fwka
14:28 maclean gah. didn't want that link. oh  well.
14:31 maclean "To handle a molecule containing one or more cycles, one must first expand it into a tree (called a hierarchical digraph by the authors) "
14:32 maclean Why would you call a tree a 'hierarchical digraph'? What a weird name.
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18:30 CIA-48 cdk: Rajarshi Guha master * r3043c17 / (5 files in 5 dirs):
18:30 CIA-48 cdk: Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality
18:30 CIA-48 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/cblhxI
19:17 CIA-48 cdk: Syed Asad Rahman master * re36a2a1 / (6 files in 6 dirs):
19:17 CIA-48 cdk: fixed PMD errors on Use instanceof against interfaces not implementations and few more Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>
19:17 CIA-48 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/9TBhrp
20:25 CIA-48 cdk: Rajarshi Guha master * rd80628e / (2 files in 2 dirs):
20:25 CIA-48 cdk: Renamed the ligancy classes to use the term tetrahedral since they implicitly encode for tetrahedral chirality
20:25 CIA-48 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/8Ysbxn
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