Nadine Schneider
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624dd72ad6
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new canon: fix in special symmetry invariant
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2015-11-06 18:05:04 +01:00 |
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Nadine Schneider
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0cf0dd37ce
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Bugfix in SmilesWrite and some additional tests for getMolFrags function
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2015-04-16 10:53:20 +02:00 |
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Nadine Schneider
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0b8b6a3690
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Some performance fixes for the new canonicalization
- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
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2015-04-15 18:42:29 +02:00 |
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Nadine Schneider
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0132cc72e9
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Merge branch 'newCanon' into master3
Conflicts:
Code/GraphMol/SmilesParse/test.cpp
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2015-04-10 10:25:47 +02:00 |
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Nadine Schneider
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b4c230c7d0
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new_canon: move hanoiSort to a seperate file
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2015-04-10 09:47:17 +02:00 |
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Nadine Schneider
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ca4bcca6ae
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Include atom-mapping numbers if present in the canonicalization
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2015-04-10 09:47:16 +02:00 |
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Nadine Schneider
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69ceace885
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Bugfix in SpecialChiralityAtomCompareFunctor and additional tests
Conflicts:
Code/GraphMol/hanoitest.cpp
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2015-04-10 09:47:09 +02:00 |
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Nadine Schneider
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7e59908121
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SmilesWrite: introduce new function for fragments
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2015-03-20 16:38:23 +01:00 |
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Nadine Schneider
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e013399bb9
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Bugfixes and new invariant for chiralAtoms
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2015-03-06 15:47:08 +01:00 |
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Nadine Schneider
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0d90e31c46
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New canon: new atom invariant also including neighbors
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2015-02-12 18:08:03 +01:00 |
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Nadine Schneider
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465c7cb4c6
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new_canon: Delete numRingMember invariant
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2015-02-12 18:06:27 +01:00 |
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Nadine Schneider
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66fe6cf10f
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update and new canon tests
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2015-02-12 13:05:59 +01:00 |
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Nadine Schneider
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d82f30f5d4
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Optimization canon
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2015-02-02 12:53:19 +01:00 |
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Greg Landrum
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38cab28eb6
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add a couple fullerenes as renumbering tests
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2015-01-28 01:26:15 +01:00 |
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Greg Landrum
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002d6f7cb0
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minor optimization
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2015-01-16 14:26:22 +01:00 |
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Greg Landrum
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27c6c61d9b
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At this point the hanoiTests pass and all 140K ZNP compounds pass the 50x torture test.
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2015-01-16 05:08:36 +01:00 |
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Greg Landrum
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baf26c053c
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not fixed; still lots of debugging printing; backup commit
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2015-01-09 06:33:49 +01:00 |
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Greg Landrum
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1f4c2e915c
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fix a nasty canonicalization problem:
need to be sure to sort neighbors by their ranks in a *decreasing* order
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2015-01-07 20:46:08 +01:00 |
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Greg Landrum
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756404a0b0
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re-enable some tests
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2015-01-05 09:25:51 +01:00 |
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Greg Landrum
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48c5d0d6ff
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At this point all C++ tests pass
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2015-01-03 06:42:54 +00:00 |
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Greg Landrum
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5a3e65fd30
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at least the basics of stereochemistry are working
all hanoitest.cpp tests passing
chiralityTest.cpp failes still, so we are not done yet
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2014-12-23 08:05:47 +00:00 |
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Greg Landrum
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ab0f1dcf60
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rename to new_canon (probably should come up with a better name, but this will do for now)
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2014-12-22 07:56:26 +00:00 |
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Greg Landrum
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cad05ca184
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get rid of RankAtoms.cpp and
move the remaining functionality from RankAtoms.h into the new file
RDGeneral/Ranking.h
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2014-12-22 07:35:58 +00:00 |
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Greg Landrum
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d11deb813b
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all hanoitest.cpp tests pass at this point.
The challenging dummy-atom case is commented out.
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2014-12-22 06:47:15 +00:00 |
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Greg Landrum
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b286d4e601
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better error reporting; but still not working
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2014-08-27 04:05:45 +02:00 |
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Greg Landrum
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2f701327f2
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backup
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2014-08-25 05:50:50 +02:00 |
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Greg Landrum
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0d21cdc7c9
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backup commit
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2014-08-24 16:24:31 +02:00 |
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Greg Landrum
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643b927c25
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backup before messing with chirality
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2014-08-24 13:18:58 +02:00 |
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Greg Landrum
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329bf48b77
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fix a pathological symmetry case by modifying the atom invariants
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2014-08-24 10:51:35 +02:00 |
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Greg Landrum
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88ce84aa9c
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certainly should not be including the chiral tag itself in the comparison
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2014-08-23 09:46:35 +02:00 |
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Greg Landrum
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4a4d724466
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hanoi tests passing again
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2014-08-23 03:22:09 +02:00 |
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Greg Landrum
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f9906e055b
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add in a few more tests with ring stereo. These currently fail.
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2014-08-23 02:02:51 +02:00 |
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Greg Landrum
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3a9169d642
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bug fix from Roger
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2014-08-23 02:01:28 +02:00 |
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Greg Landrum
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101a5879d7
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focus the tests being run
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2014-08-08 09:16:01 +02:00 |
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Greg Landrum
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ee66d4e068
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backup commit
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2014-08-08 06:44:56 +02:00 |
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Greg Landrum
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e170195421
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backup commit; this does not completely work yet
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2014-08-03 08:01:58 +02:00 |
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Greg Landrum
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787d9d4c89
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some less successful experiments with the node changed optimization added, but commented out
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2014-07-31 04:34:25 +02:00 |
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Greg Landrum
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3edfafec87
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about ready to add and tests the node-changed optimization
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2014-07-30 03:34:39 +02:00 |
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Greg Landrum
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9906fd7842
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get ready for the node changed optimization
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2014-07-29 04:48:22 +02:00 |
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Greg Landrum
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a01f3fc042
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rename to rankMolAtoms; add breakTies option
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2014-07-27 07:44:34 +02:00 |
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Greg Landrum
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4d8041ead5
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everything works except the renumbering test
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2014-07-26 16:36:30 +02:00 |
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Greg Landrum
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5c3369805f
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makes it through all tests so far
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2014-07-26 15:56:38 +02:00 |
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Greg Landrum
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faf805f9cc
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get cleverer about atom comparison
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2014-07-26 08:38:23 +02:00 |
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Greg Landrum
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1bd244c28e
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steps towards having atoms compare themselves
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2014-07-26 04:11:03 +02:00 |
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Greg Landrum
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2b74d8c78f
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steps towards having atoms compare themselves
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2014-07-26 04:04:40 +02:00 |
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Greg Landrum
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c78effb0d4
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fix a misconception that was leading to the test1() failures
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2014-07-26 03:40:25 +02:00 |
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Greg Landrum
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c4b46e6677
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basic functionality done; basic testing done; time for larger-scale tests and performance comparison
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2014-07-25 05:52:10 +02:00 |
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Greg Landrum
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db06606454
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first pass at tie-breaking is working
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2014-07-25 05:15:34 +02:00 |
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Greg Landrum
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7b61ea6cd5
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another big step: now we have uniquification propagating through molecules.
Note that the Morgan-encoding step is definitely not optimal
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2014-07-25 05:02:51 +02:00 |
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Greg Landrum
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d3ab885b8a
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the random int vector test no longer passes, but we now have a lot of molecule stuff working (basic class assignment at least
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2014-07-24 14:17:04 +02:00 |
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