Greg Landrum
de2126b641
optimization work
2012-04-15 06:19:22 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542
cleanups:
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remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
b78abe26d6
fix and test sf.net issue 2787221
2009-05-05 12:54:41 +00:00
Greg Landrum
e05580e495
This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties
...
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
2009-02-11 20:19:25 +00:00
Greg Landrum
c0e1ffdc65
fix and test Issue2313979
2008-12-02 08:50:51 +00:00
Greg Landrum
cb6982e9e0
not done, this is a backup commit
2008-12-02 07:01:46 +00:00
Greg Landrum
fc6c2b2f9a
fixes to issues 2196817 and 2208994
2008-10-30 06:56:39 +00:00
Greg Landrum
6d3a9f6fb3
Check in a bunch of changes to fix radical handling.
...
These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +00:00
Greg Landrum
cd97b8035b
refactor the new radical-handling code to add a getNumRadicalElectrons()
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method to Atom
2008-09-04 18:09:54 +00:00
Greg Landrum
4702ed3e20
partial fixes (not thoroughly tested, needing more cleanup) for bug 2091839; this mainly has to do with fixing the treatment of radicals
2008-09-04 13:02:07 +00:00
Greg Landrum
3729140375
additional tests for sf.net bug 1934360.
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fix and test bug 1940646.
a bit of refactoring of the aromaticity code
2008-04-12 13:49:04 +00:00
Greg Landrum
820749851b
clean up the keulization code a bit; more can be done here
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initial fix and test for sf.net bug 1934360. more tests needed,
so this is basically a backup commit
2008-04-11 19:49:31 +00:00
Greg Landrum
5400bafb7d
support Se and Te as potentially aromatic atoms
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(sf.net bug 1932365, http://sourceforge.net/tracker/index.php?func=detail&aid=1932365&group_id=160139&atid=814650 )
2008-04-06 06:11:58 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
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The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
8b4accb050
improve support for dummy atoms
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this was sf.net feature request 1868217:
https://sourceforge.net/tracker/index.php?func=detail&aid=1868217&group_id=160139&atid=814653
2008-01-10 06:39:33 +00:00
Greg Landrum
7041ae233e
handle the NoImplicit flag properly
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update aromaticity to require unsaturation at single-atom donors
test the above two things
This is not necessarily completely stable, but all current tests pass
(once obvious changes have been made). We will just have to see where
the aromaticity changes cause trouble going forward.
2006-09-19 20:20:09 +00:00
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
