Brian Kelley
2debdfde0d
Adds RDAny (smaller generic holder) Updates all used dictionaries ( #896 )
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* Adds RDAny (smaller generic holder) Updates all used dictionaries
This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.
* Removes code duplication
* Converts CHECK_INVARIANT to TEST_ASSERT
* Fixes DoubleTag issue
* Adds Bool to DoubleMagic implementation
* Removes reference to property pickler
2016-05-29 17:04:21 +01:00
kelley
5dbec2fe85
Adds rdcasts where appropriate
2015-11-29 17:52:27 -05:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7
post review
2015-11-14 08:08:14 +01:00
Brian Kelley
5f59333a56
Silences unused parameters
2015-10-18 14:02:29 -04:00
Brian Kelley
a146c3826a
Remove unused variables/functions and register keyword
2015-10-18 10:01:00 -04:00
Nadine Schneider
5d963846b8
merge
2015-04-10 09:44:18 +02:00
Nadine Schneider
140dc2d938
Bugfix: consider doIsomericSmiles flag in canonicalizeFragment
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
Nadine Schneider
e013399bb9
Bugfixes and new invariant for chiralAtoms
2015-03-06 15:47:08 +01:00
Nadine Schneider
489d06cfca
Constify atom ranks in smiles construction
2015-02-12 08:59:28 +01:00
Nadine Schneider
47dbaf2304
Fix: ring stereo chemistry was swapped incorrectly
2015-02-11 18:21:15 +01:00
Greg Landrum
6d7b2b0914
merge with master
2015-01-22 06:30:51 -05:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
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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
3193f88709
merged with trunk; this builds but it has not been tested at all
2014-11-30 06:33:56 +01:00
Greg Landrum
9830b0e8fd
some code cleanup
2014-08-27 22:47:08 +02:00
Greg Landrum
a94ce46a43
smiles tests now pass as well
2014-08-27 22:32:49 +02:00
Greg Landrum
b2a6fd1373
backup
2014-08-27 04:18:00 +02:00
Greg Landrum
e170195421
backup commit; this does not completely work yet
2014-08-03 08:01:58 +02:00
Greg Landrum
23076b1cdb
Fixes #298
2014-07-23 05:31:16 +02:00
Greg Landrum
75be63fd6b
merge with trunk
2014-02-09 05:00:18 +01:00
Greg Landrum
64366007e1
more C++ style cleanups
2014-01-01 17:16:25 +01:00
Greg Landrum
3b0c72c4bf
initial pass at ZBO support.
...
does not yet handle the HYD and ZCH lines
2013-11-30 06:58:03 +01:00
Greg Landrum
a4734bbd43
start using the alternate getProp form
2013-07-20 07:26:06 -04:00
Greg Landrum
f467bdad9a
fix problem caused by github-8 fix
2013-03-14 06:23:13 +00:00
Greg Landrum
24e269f8ac
I *think* that this fixes sf.net issue 40:
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the long-standing problem with ring stereochemistry and canonicalization
2012-11-02 06:33:11 +00:00
Greg Landrum
f2d9755a65
at this point all tests pass
2012-06-29 03:40:28 +00:00
Greg Landrum
6157345dde
this version passes the ZINC natural-products torture test
2012-06-28 06:45:42 +00:00
Greg Landrum
0f3b84cd28
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
Greg Landrum
ee43d3e8f8
another step forward
2012-06-13 05:20:39 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
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there are still some problems with double bonds
2012-06-11 03:21:30 +00:00
Greg Landrum
c293dc23da
initial version of MolFragmentToSmiles
2012-05-19 03:50:31 +00:00
Greg Landrum
de2126b641
optimization work
2012-04-15 06:19:22 +00:00
Greg Landrum
2ffaa92cf7
fix and test issue3228150;
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note that as part of these changes MolToSmiles and MolToSmarts no longer have
side effects on the original molecule.
2011-03-26 06:51:50 +00:00
Greg Landrum
5592e31464
initial fix and tests for issue 3154208
2011-01-10 07:11:44 +00:00
Greg Landrum
f4a0012bc6
fix a residual problem with ring stereochem
2011-01-04 04:45:42 +00:00
Greg Landrum
5891b5edc8
further work on bug 3139534
2010-12-28 15:43:20 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
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this needs a ton more testing, but it is worth getting a "working" version in
2010-12-28 10:38:14 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542
cleanups:
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remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
d23bdac363
fix and test sf.net issue 3018558
2010-06-20 03:46:58 +00:00
Greg Landrum
96adbc11ea
remove the deprecated assign{Atom,Bond}ChiralCodes functions
2009-08-02 15:33:08 +00:00
Greg Landrum
e05580e495
This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties
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instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
2009-02-11 20:19:25 +00:00
Greg Landrum
9ac8b25d4b
make ring stereochemistry in output SMILES at least correct (if not canonical);
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move the incorrectness warning to the SMILES writer
2008-12-06 06:51:52 +00:00
Greg Landrum
7d8e37a521
add ringStereoWarning prop when questionable ring stereochem is observed
2008-12-02 17:50:32 +00:00
Greg Landrum
eef831c2bf
fix and test issue 2316677; there probably should be a hand-crafted test for this as well, but that is going to be tricky
2008-11-20 05:55:46 +00:00
Greg Landrum
255b21ff49
fix a couple compiler warnings
2008-10-19 05:34:42 +00:00
Greg Landrum
023f7b4f0f
Merge changes from the iterative chirality branch:
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https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.
Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
2008-09-19 09:40:15 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
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The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
