Greg Landrum
b0f140a55c
Fixes #511
2016-03-29 16:56:15 +02:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
403a3d6b7c
Suppresses Boost warnings
2015-10-18 13:41:03 -04:00
Brian Kelley
6ebbeb3bd3
Major conversion of std::string API to const std::string &
2015-09-25 15:15:59 -04:00
Greg Landrum
97d8b8a7db
this was a similar bug to #584
2015-08-27 10:13:46 +02:00
Nadine Schneider
5d963846b8
merge
2015-04-10 09:44:18 +02:00
Nadine Schneider
7e59908121
SmilesWrite: introduce new function for fragments
2015-03-20 16:38:23 +01:00
Riccardo Vianello
7c346d7c2e
Code/RDBoost/Exceptions.h moved to Code/RDGeneral
2015-03-16 22:31:48 +01:00
Greg Landrum
7fa02f748b
Fixes #430
2015-02-04 13:45:47 +01:00
Greg Landrum
2fbea33612
Fixes #429
2015-02-04 10:20:13 +01:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
...
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
2015-01-15 12:23:29 -05:00
Greg Landrum
3f23c91eba
did not have the version for breakSomeBonds() quite right
2014-11-22 10:42:17 +01:00
Greg Landrum
1725e22cca
allow tracking the number of cuts made by the fragmentation code on a per-atom basis
2014-11-22 07:57:39 +01:00
Greg Landrum
2187437649
fix a couple typos
2014-07-07 15:57:27 +02:00
Greg Landrum
288feb7a8a
support partial fragmentation on bonds;
...
Fixes #288
2014-07-02 05:47:02 +02:00
Greg Landrum
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +02:00
Greg Landrum
302b84960b
improve docs;
...
cleanup some compiler warnings;
add parseQueryDefText()
2014-05-03 06:45:35 +02:00
Greg Landrum
d7971cc40c
Fixes #171
2013-12-06 06:54:31 +01:00
Greg Landrum
4ace62f019
remove more clang warnings
2013-12-02 05:10:23 +01:00
Greg Landrum
6c354852d1
small cleanups
2013-11-07 10:57:18 +01:00
Greg Landrum
6d936e9d31
Merge branch 'master' of https://github.com/rdkit/rdkit
2013-11-02 07:23:31 +01:00
Greg Landrum
95c6c7f261
fragmentOnBonds() fix
2013-11-02 07:17:42 +01:00
Greg Landrum
afb9f1ddfa
add fragmentOnBonds() to python API
...
Fixes #142
2013-10-30 04:59:29 +01:00
Greg Landrum
70f2829524
do not include _static versions for test links. This breaks on windows
2013-03-22 05:18:35 +00:00
Greg Landrum
5a340dd454
Fix a typo
2013-03-01 06:53:17 +00:00
Greg Landrum
c595c29cb2
add missing headers for "make install"
...
fixes github issue 2
2013-02-05 04:57:59 +00:00
Greg Landrum
ea42bf5465
BRICS-related bug fixes
2013-02-05 04:56:10 +00:00
Greg Landrum
89398a10c2
make sure computed props get cleared
2013-01-31 04:54:28 +00:00
Greg Landrum
84d6ddb3f3
add fragmentOnBRICSBonds()
2013-01-30 06:31:06 +00:00
Greg Landrum
fa2b82b606
breaking all BRICS bonds now works
2013-01-29 16:22:27 +00:00
Greg Landrum
00655e7bd6
backup commit; may not build
2013-01-29 06:28:31 +00:00
Greg Landrum
052b87564c
add one more test for issue 275
2013-01-09 13:12:27 +00:00
Greg Landrum
03ef0e6f1b
Add support for merging recursive queries on the C++ side
...
(contribution from Sereina Riniker)
A pure Python version of this was in the tutorial material from the RDKit UGM.
2013-01-08 15:13:01 +00:00
Greg Landrum
68e370d581
initial pass at a fix for sf.net issu275
2012-12-18 17:16:06 +00:00
Greg Landrum
bef74c1c81
initial support for reading query files. Python wrapper still needs to be done.
2012-12-17 10:28:35 +00:00
Greg Landrum
57572918de
add initial support for addRecursiveQueries to ChemTransforms.
...
active and tested in C++ and python, in the SWIG wrapper but untested.
still needs linux and windows builds.
2012-12-17 09:06:02 +00:00
Greg Landrum
cfaea83d7d
optimizations for molecule construction
2012-08-27 04:52:27 +00:00
Greg Landrum
93f6445e01
minor cleanup to RWMol::insertMol; add combineMols to ChemTransforms
2012-07-10 04:00:46 +00:00
Greg Landrum
2e5b33e2fd
fix and test issue 3537675
2012-07-02 03:07:02 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
...
there are still some problems with double bonds
2012-06-11 03:21:30 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
a99ad44859
clean up some compiler warnings
2011-12-31 15:58:57 +00:00
Greg Landrum
3b751bad46
fix and test issue 3453144
2011-12-13 04:56:56 +00:00
Greg Landrum
3ba11316b2
initial pass at requiring core-dummy matches in replaceCore; remove an extra header import from MolOps.cpp
2011-03-28 06:13:48 +00:00
Greg Landrum
633be739b0
- fix an edge case with disconnected molecules in the MurckoDecompose code.
...
- test that empty results are handled properly in MurckoDecompose.
2011-03-04 06:37:26 +00:00
Greg Landrum
f3a570fe29
add the test file
2011-03-04 05:23:13 +00:00
Greg Landrum
e1e1e5929d
fix assignment of dummy positions in replaceCore
2011-03-03 05:02:13 +00:00
Greg Landrum
d6741adc22
make some types more explicit in MolOps.h (easier SWIG wrapping)
...
support finding non-specfied chiral centers
remove vestigial GetFragmentSmiles() function
additional flexibility in AllChem.TransformMol()
2011-02-24 08:00:39 +00:00
Greg Landrum
4ca59a1987
clean up conformer handling in ChemTransforms
2011-02-22 06:16:23 +00:00
Greg Landrum
e2521dccbc
add murcko decomposition;
...
be sure pathToSubmol copies over coordinates
2011-02-21 06:43:53 +00:00
