Greg Landrum
0ddfa00147
update to assertEqual (no reason to dig the python3 hole any deeper
2014-07-01 06:20:21 +02:00
Greg Landrum
f4da8d91d8
support completeRingsOnly and ringMatchesRingOnly from Python
2014-07-01 06:19:40 +02:00
Greg Landrum
c9b91cd744
code formatting changes (indentation and untabify)
2014-07-01 05:48:51 +02:00
Greg Landrum
38d9f00f84
merge
2014-06-28 15:02:52 +02:00
Greg Landrum
150c963630
fix a build problem
2014-06-28 15:01:13 +02:00
Greg Landrum
d4fc8d6d18
typo fix
2014-06-27 08:46:27 +02:00
Greg Landrum
5ed406a901
Merge remote-tracking branch 'origin/master' into fmcs_port_21Feb2014
2014-06-27 08:09:10 +02:00
Greg Landrum
2389ab4859
Merge remote-tracking branch 'origin/fmcs_port_21Feb2014' into fmcs_port_21Feb2014
2014-06-27 08:03:54 +02:00
Alexander Savelyev
21b2ea4a68
improve prune() heuristic. the search speed was increased. mem leaks fixed
2014-06-26 19:05:55 +04:00
Greg Landrum
eb15c98f97
clean up some leaks in one of the tests
2014-06-23 21:14:54 +02:00
Greg Landrum
8905d71f7f
Merge remote-tracking branch 'origin/fmcs_port_21Feb2014' into fmcs_port_21Feb2014
2014-06-20 14:06:38 +02:00
Alexander Savelyev
f9245ec8ac
fix multiple atoms and bonds SMARTS for anyCompare
2014-06-20 13:31:12 +04:00
Greg Landrum
d5bb6b2d70
add isotope match test
2014-06-12 02:07:58 -04:00
Greg Landrum
c67b71a4f6
stop matching SMARTS
2014-06-11 11:42:00 -04:00
Greg Landrum
189de60e45
get build working on the mac and python tests running
2014-06-11 11:04:54 -04:00
Alexander Savelyev
98e052bc8c
bug with isotopes was fixed
2014-06-11 17:38:20 +04:00
Greg Landrum
07e9356c1e
Merge remote-tracking branch 'origin' into fmcs_port_21Feb2014
2014-06-09 23:45:20 +02:00
Greg Landrum
ae0388cfba
start to support atom and bond comparators
2014-06-09 23:43:44 +02:00
Greg Landrum
c6deb3f492
add some real python tests
2014-06-09 22:58:21 +02:00
f
009885306d
seg fault was fixed
2014-06-02 19:17:39 +04:00
ptosco
ba4a48ce05
- fixed a bug in Code/ForceField/MMFF/testMMFFForceField.cpp
...
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
which caused misassignment of atom types in CYGUAN01 upon shuffling
the order of atoms in the validation SDF files
- added checks for acos and asin function parameters to be within
a (-1, 1) range
2014-06-01 16:23:03 +01:00
f
be1a2dde81
query optimisation was implemented. Memory leak was fixed. Verbose cosmetic
2014-05-30 15:02:53 +04:00
Greg Landrum
f94ed4a1f5
get queries from SMARTS into CTABs more reasonably
2014-05-26 09:02:08 +02:00
Greg Landrum
665872cb39
Fixes #268
2014-05-25 06:55:30 +02:00
Greg Landrum
6b26036f6a
Fixes #269
2014-05-23 08:26:26 +02:00
Greg Landrum
684f451352
Fixes #266
2014-05-22 17:34:06 +02:00
Greg Landrum
1567ec4462
add getFullDescription() to Query;
...
Fixes #287
2014-05-22 15:18:07 +02:00
Greg Landrum
4665bbb9cf
remove a compiler warning
2014-05-13 03:47:41 -04:00
Greg Landrum
a979cde58f
merge in changes from trunk
2014-05-13 03:34:36 -04:00
Savelyev Alexander
604ee4c675
bug with empty MCS was fixed. MT stub
2014-05-12 21:39:55 +04:00
Greg Landrum
d8c523352c
fix a profoundly stupid mistake from an earlier commit
2014-05-10 07:43:30 +02:00
Greg Landrum
c26cbc26cb
switch to using references to smart pointers for the Match functions;
...
really ought to re-examine when/how we are passing smart pointers
around in general, but that is a bigger job.
Ref: http://herbsutter.com/2013/06/05/gotw-91-solution-smart-pointer-parameters/
2014-05-10 06:21:27 +02:00
Greg Landrum
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +02:00
Greg Landrum
7306903ef7
use boost::flyweight to ensure thread-safe construction of the pattern fingerprint queries
2014-05-08 04:27:06 +02:00
Greg Landrum
118306d1f9
expose useQueryQueryMatch info to python;
...
Fixes #258
2014-05-07 06:04:38 +02:00
Greg Landrum
34ab68ca2a
introduce QueryBond::QueryMatch, as with QueryAtoms;
...
all tests passing;
performance tests still needed
2014-05-07 05:29:25 +02:00
Greg Landrum
12a97b3bd2
fixes the bug, but probably drastically drops the screenout rate
2014-05-06 03:25:20 +02:00
Greg Landrum
ab1f936425
Fixes #256
2014-05-05 05:44:36 +02:00
Greg Landrum
302b84960b
improve docs;
...
cleanup some compiler warnings;
add parseQueryDefText()
2014-05-03 06:45:35 +02:00
Alexander Savelyev
ddba1b3650
fast match was implemented for FMCS. cosmetic changes
2014-04-29 15:34:21 +04:00
Greg Landrum
9f11a37753
test multi-threaded use of the pattern fingerprint; this passes on the mac, but I am skeptical about it
2014-04-28 11:53:43 +02:00
Greg Landrum
699588fe0f
Fixes #252
2014-04-25 07:21:10 +02:00
Greg Landrum
40d19aad14
Fixes #251
2014-04-21 06:28:39 +02:00
Greg Landrum
5fefd6469e
merge
2014-04-16 08:58:36 +02:00
Greg Landrum
a310f3bff5
Fixes #249
2014-04-16 08:58:03 +02:00
ptosco
13bb831dd5
- removed a few spurious, though non harmful, "const" keywords from
...
Code/ForceField/MMFF/Params.h, Code/ForceField/UFF/Params.h,
Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
and Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h (I realized
their uselessness thanks to a warning issued by Intel C++ compiler)
- refactored O3A code
- added the possibility to set weighted constraints on selected
atom pairs
- added an option to carry out local-only optimization
2014-04-15 22:13:54 +01:00
ptosco
5b2f6763a5
- Added the std::fstream::binary flag in testMMFFForceField.cpp
...
whose absence might cause intermittent problem in parsing the
logs on Windows due to tellg/seekg not correctly handling CR/LF
- Fixed the code for assigning the HOCN MMFF94 atom type
(thanks to Toby Wright for reporting this)
- Added a missing copyright notice in testMMFFForceField.h
2014-04-14 23:57:22 +01:00
Greg Landrum
94116bc416
next changes from Alex
2014-04-14 16:22:50 +02:00
Greg Landrum
9ff19390e8
re-enable the threshold test
2014-04-14 12:42:08 +02:00
Greg Landrum
9d734e7b74
next round of updates from Alex
2014-04-14 12:32:18 +02:00
