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Release_2020_03
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13 Commits

Author SHA1 Message Date
Manan Goel
f3a6db2a02 This commit fixes the bug "segmenation fault/core dump when chargePar… (#3029) 
* This commit fixes the bug "segmenation fault/core dump when chargeParent is run with skip_standardize set to true" mentioned in #2970

* Fixed memory leaks in MolStandardize and deleted variables which aren't required
 2020-03-24 07:48:38 +01:00
shrey183
00c6a7e370 Possible fix for issue #2965 (#3001) 
* fixed issue #2965

* added test case for issue #2965

* fixed formatting and added comment.
 2020-03-14 14:28:17 +01:00
Greg Landrum
f2841ecf42 Fixes #2792 (#2793) 2019-11-20 16:26:35 +01:00
Greg Landrum
c09fb2f3f4 fragments need to match bond counts too (#2768) 2019-11-14 13:57:22 +01:00
Greg Landrum
cb55f6b979 Fixes #2749 (#2750) 
* Switch to using numTotalHs() instead of numExplicitHs()

* Fixes #2749

* changes in response to review
 2019-10-31 07:24:34 -04:00
Greg Landrum
02cff7dfe4 Fix #2722 and #2721 (#2723) 
* Fixes #2722

* Fixes and tests #2721
 2019-10-17 11:35:32 -04:00
Greg Landrum
b87c629e10 fix a problem with normalize, ringinfo, and fragments (#2685) 2019-10-03 15:28:33 +02:00
Greg Landrum
7ffd863c9b A collection of bug fixes (#2608) 
* Fixes #2602

* Fixes #2605

* Remove vestigial isEarlyAtom() definition in Kekulize.cpp

* Fixes #2606

* Fixes #2607

adds allowed valence 2 for Sn and Pb

* Fixes #2610

* update in response to review
 2019-08-15 04:53:23 +02:00
Greg Landrum
3ce2016039 Fixes #2452 (#2507) 2019-06-24 23:07:19 -04:00
Greg Landrum
d0c8c3cf8f Fixes #2411 and #2414 (#2412) 
* clang-tidy-7 pass

* Fixes #2411

* Fixes #2414
 2019-04-19 21:51:41 -04:00
Greg Landrum
941d7abb5f Fixes #2392 (#2393) 
* Fixes #2392

* update release notes
 2019-04-06 07:16:55 -04:00
Greg Landrum
1d01874678 improvements to the Uncharge functionality (#2374) 
* modify the uncharger to be use a canonical atom ordering

* add doCanonical cleanup parameter
make canonical ordering the default
document the change

* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.

* expose the new parameter to python

* changes in response to review
 2019-03-29 21:02:55 -04:00
Greg Landrum
55fb9034a6 Add a skip_all_if_match option to the FragmentRemover (#2338) 
* add SKIP_IF_ALL_MATCH argument to FragmentRemover
    Refactor FragmentRemover::remove() to make it more efficient

* implement and test SKIP_IF_ALL_MATCH

* expose the extra option to Python

* add info to logger
 2019-03-14 09:32:08 -04:00