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
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +02:00
Greg Landrum
9e4ceef1bd
Fixes #206 but more testing is definitely required
2014-01-28 06:44:43 +01:00
Greg Landrum
0a421d8aa5
Fixes #182
2013-12-31 07:11:31 +01:00
Greg Landrum
60a68669da
remove more clang warnings
2013-12-02 04:46:46 +01:00
Greg Landrum
b4f2ec374e
Fixes : #61
2013-07-04 18:00:09 +02:00
Greg Landrum
dccf20b8c7
Fixes #45
2013-06-08 06:01:54 +02:00
Greg Landrum
9ff479838c
fix and test issue 264
2012-11-17 06:49:38 +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
5c2a3f12ce
fix and test issue 257
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Note that unknown bond types are now written to SMILES as "~" characters.
The smiles parser has been modified to recognize these.
2012-10-12 08:58:38 +00:00
Greg Landrum
42e140e0c0
make sure that a nonzero atom list is passed to MolFragmentToSmiles
2012-09-27 17:50:35 +00:00
Greg Landrum
854dde8097
fix and test issue 253
2012-09-21 12:32:35 +00:00
Greg Landrum
af502c43cb
add another precondition
2012-09-19 07:12:58 +00:00
Greg Landrum
3277a2ede1
cleanup
2012-07-09 05:19:03 +00:00
Greg Landrum
0f3b84cd28
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
Greg Landrum
086cbd769c
fix a bug in MolFragmentToSmiles() without canonicalization
2012-05-23 04:37:03 +00:00
Greg Landrum
efc76f5bd5
clean up an uninitialized variable that was causing problems on the mac
2012-05-20 06:11:48 +00:00
Greg Landrum
c293dc23da
initial version of MolFragmentToSmiles
2012-05-19 03:50:31 +00:00
Greg Landrum
7495b6248f
cleanup + tests for issue 3526815
2012-05-18 09:09:04 +00:00
Greg Landrum
cfc14230e1
fix issues 3525799 and 3526810
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this changes some canonical SMILES
and removes support for "[Xa]" dummy atoms in SMILES
2012-05-18 05:56:45 +00:00
Greg Landrum
8ffcfd7149
fix and test issue 35525671
2012-05-11 07:13:45 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
de2126b641
optimization work
2012-04-15 06:19:22 +00:00
Greg Landrum
3520c441cb
add allBondsExplicit argument for SMILES writing
2012-03-26 03:12:37 +00:00
Greg Landrum
d9949b6765
fixes and tests for sf.net issues 3496759, 3496799, and 3496800
2012-03-04 15:37:50 +00:00
Greg Landrum
c807c6b064
make the non-canonical smiles writing actually work
2011-12-04 05:28:58 +00:00
Greg Landrum
9316758cec
improved handling of isotope specifications (still definitely not optimal)
2011-07-01 03:42:35 +00:00
Greg Landrum
dd15020a0f
remove use of a static variable that was causing problems with thread safety while writing smiles
2011-06-29 02:21:01 +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
d6741adc22
make some types more explicit in MolOps.h (easier SWIG wrapping)
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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
28747ea745
checkin some fragment and fingerprint changes. these are not yet well tested
2011-01-14 06:24:03 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
c6c7af1e6a
fix and test issue 3152751
2011-01-07 05:04:26 +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
e977a642f6
add support for writing non-canonical SMILES;
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add support for atom-mapping information in plain SMILES
2010-12-20 03:59:56 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
2805355f34
First pass at the rewrite:
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this gets rid of all the "preceding atom" code and passes all tests on linux
builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +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
fc6c2b2f9a
fixes to issues 2196817 and 2208994
2008-10-30 06:56:39 +00:00
Greg Landrum
6d3a9f6fb3
Check in a bunch of changes to fix radical handling.
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These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +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
c9eb4e91e1
merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008
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This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
2008-07-05 07:42:38 +00:00
Greg Landrum
b0dcc08a1a
make this a bit more robust to roundoff
2008-05-06 03:39:10 +00:00
Greg Landrum
eb3d720010
Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences
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http://sourceforge.net/tracker/index.php?func=detail&aid=1942657&group_id=160139&atid=814650
This was handled by adding error/consistency checking to Atom.calcExplicitValence()
This includes another pretty big scale modification:
the allowed valence list for atoms (in atomic_data.cpp) can now contain a -1 at the end. If this is the case, the atom will tolerate valences above the ones listed.
This is done to allow "flexible" atoms (i.e. transition metals and the like) to accept arbitrary coordination numbers without generating errors.
2008-04-17 05:09:02 +00:00
Greg Landrum
e6ccdd9b91
improve handling of Hs on smiles output (connected to sf.net
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bug 1942220
2008-04-16 05:54:05 +00:00
Greg Landrum
75cd5eb0e8
this is partial progress towards feature request 1902466 :
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translate more query information into SMARTS
https://sourceforge.net/tracker/index.php?func=detail&aid=1902466&group_id=160139&atid=814653
This commit adds support for ring bond counts
and unsaturation queries.
2008-03-04 05:34:49 +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
