Nadine Schneider
0cf0dd37ce
Bugfix in SmilesWrite and some additional tests for getMolFrags function
2015-04-16 10:53:20 +02:00
Nadine Schneider
0b8b6a3690
Some performance fixes for the new canonicalization
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- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
2015-04-15 18:42:29 +02:00
Nadine Schneider
0132cc72e9
Merge branch 'newCanon' into master3
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Conflicts:
Code/GraphMol/SmilesParse/test.cpp
2015-04-10 10:25:47 +02:00
Nadine Schneider
b4c230c7d0
new_canon: move hanoiSort to a seperate file
2015-04-10 09:47:17 +02:00
Nadine Schneider
ca4bcca6ae
Include atom-mapping numbers if present in the canonicalization
2015-04-10 09:47:16 +02:00
Nadine Schneider
69ceace885
Bugfix in SpecialChiralityAtomCompareFunctor and additional tests
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Conflicts:
Code/GraphMol/hanoitest.cpp
2015-04-10 09:47:09 +02:00
Nadine Schneider
7e59908121
SmilesWrite: introduce new function for fragments
2015-03-20 16:38:23 +01:00
Nadine Schneider
e013399bb9
Bugfixes and new invariant for chiralAtoms
2015-03-06 15:47:08 +01:00
Nadine Schneider
0d90e31c46
New canon: new atom invariant also including neighbors
2015-02-12 18:08:03 +01:00
Nadine Schneider
465c7cb4c6
new_canon: Delete numRingMember invariant
2015-02-12 18:06:27 +01:00
Nadine Schneider
66fe6cf10f
update and new canon tests
2015-02-12 13:05:59 +01:00
Nadine Schneider
d82f30f5d4
Optimization canon
2015-02-02 12:53:19 +01:00
Greg Landrum
38cab28eb6
add a couple fullerenes as renumbering tests
2015-01-28 01:26:15 +01:00
Greg Landrum
002d6f7cb0
minor optimization
2015-01-16 14:26:22 +01:00
Greg Landrum
27c6c61d9b
At this point the hanoiTests pass and all 140K ZNP compounds pass the 50x torture test.
2015-01-16 05:08:36 +01:00
Greg Landrum
baf26c053c
not fixed; still lots of debugging printing; backup commit
2015-01-09 06:33:49 +01:00
Greg Landrum
1f4c2e915c
fix a nasty canonicalization problem:
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need to be sure to sort neighbors by their ranks in a *decreasing* order
2015-01-07 20:46:08 +01:00
Greg Landrum
756404a0b0
re-enable some tests
2015-01-05 09:25:51 +01:00
Greg Landrum
48c5d0d6ff
At this point all C++ tests pass
2015-01-03 06:42:54 +00:00
Greg Landrum
5a3e65fd30
at least the basics of stereochemistry are working
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all hanoitest.cpp tests passing
chiralityTest.cpp failes still, so we are not done yet
2014-12-23 08:05:47 +00:00
Greg Landrum
ab0f1dcf60
rename to new_canon (probably should come up with a better name, but this will do for now)
2014-12-22 07:56:26 +00:00
Greg Landrum
cad05ca184
get rid of RankAtoms.cpp and
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move the remaining functionality from RankAtoms.h into the new file
RDGeneral/Ranking.h
2014-12-22 07:35:58 +00:00
Greg Landrum
d11deb813b
all hanoitest.cpp tests pass at this point.
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The challenging dummy-atom case is commented out.
2014-12-22 06:47:15 +00:00
Greg Landrum
b286d4e601
better error reporting; but still not working
2014-08-27 04:05:45 +02:00
Greg Landrum
2f701327f2
backup
2014-08-25 05:50:50 +02:00
Greg Landrum
0d21cdc7c9
backup commit
2014-08-24 16:24:31 +02:00
Greg Landrum
643b927c25
backup before messing with chirality
2014-08-24 13:18:58 +02:00
Greg Landrum
329bf48b77
fix a pathological symmetry case by modifying the atom invariants
2014-08-24 10:51:35 +02:00
Greg Landrum
88ce84aa9c
certainly should not be including the chiral tag itself in the comparison
2014-08-23 09:46:35 +02:00
Greg Landrum
4a4d724466
hanoi tests passing again
2014-08-23 03:22:09 +02:00
Greg Landrum
f9906e055b
add in a few more tests with ring stereo. These currently fail.
2014-08-23 02:02:51 +02:00
Greg Landrum
3a9169d642
bug fix from Roger
2014-08-23 02:01:28 +02:00
Greg Landrum
101a5879d7
focus the tests being run
2014-08-08 09:16:01 +02:00
Greg Landrum
ee66d4e068
backup commit
2014-08-08 06:44:56 +02:00
Greg Landrum
e170195421
backup commit; this does not completely work yet
2014-08-03 08:01:58 +02:00
Greg Landrum
787d9d4c89
some less successful experiments with the node changed optimization added, but commented out
2014-07-31 04:34:25 +02:00
Greg Landrum
3edfafec87
about ready to add and tests the node-changed optimization
2014-07-30 03:34:39 +02:00
Greg Landrum
9906fd7842
get ready for the node changed optimization
2014-07-29 04:48:22 +02:00
Greg Landrum
a01f3fc042
rename to rankMolAtoms; add breakTies option
2014-07-27 07:44:34 +02:00
Greg Landrum
4d8041ead5
everything works except the renumbering test
2014-07-26 16:36:30 +02:00
Greg Landrum
5c3369805f
makes it through all tests so far
2014-07-26 15:56:38 +02:00
Greg Landrum
faf805f9cc
get cleverer about atom comparison
2014-07-26 08:38:23 +02:00
Greg Landrum
1bd244c28e
steps towards having atoms compare themselves
2014-07-26 04:11:03 +02:00
Greg Landrum
2b74d8c78f
steps towards having atoms compare themselves
2014-07-26 04:04:40 +02:00
Greg Landrum
c78effb0d4
fix a misconception that was leading to the test1() failures
2014-07-26 03:40:25 +02:00
Greg Landrum
c4b46e6677
basic functionality done; basic testing done; time for larger-scale tests and performance comparison
2014-07-25 05:52:10 +02:00
Greg Landrum
db06606454
first pass at tie-breaking is working
2014-07-25 05:15:34 +02:00
Greg Landrum
7b61ea6cd5
another big step: now we have uniquification propagating through molecules.
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Note that the Morgan-encoding step is definitely not optimal
2014-07-25 05:02:51 +02:00
Greg Landrum
d3ab885b8a
the random int vector test no longer passes, but we now have a lot of molecule stuff working (basic class assignment at least
2014-07-24 14:17:04 +02:00
Greg Landrum
172bc897a8
At this point the Hanoi sort works.
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The most highly optimized version still infinite loops in my test cases, so it is #if 0'ed out.
Starting to move on to actually doing the partition assignment and refinement, but it's good to get this backup commit in first.
2014-07-24 10:47:44 +02:00
