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
...
- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
2015-04-15 18:42:29 +02:00
Nadine Schneider
267e4b9f0e
Fix in SmilesWrite
2015-04-10 09:47:15 +02:00
Nadine Schneider
7ddff9c71c
Some performance fixes
2015-03-20 18:19:08 +01:00
Nadine Schneider
7e59908121
SmilesWrite: introduce new function for fragments
2015-03-20 16:38:23 +01:00
Nadine Schneider
140dc2d938
Bugfix: consider doIsomericSmiles flag in canonicalizeFragment
2015-03-20 16:38:23 +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
a0a02b4a99
merge on master
2015-02-03 16:41:46 +01:00
Greg Landrum
e6cc6cc171
optimize GetBondSmiles()
2015-02-02 22:56:14 +01:00
Greg Landrum
117696847d
optimize GetAtomSmiles()
2015-02-02 22:51:57 +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.
...
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
6ea9029577
fragment smiles construction added. NOTE that bond symbols are no longer used in the canonicalization
2015-01-04 08:32:28 +01:00
Greg Landrum
746c07561e
merge with origin
2015-01-04 05:01:47 +01:00
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
bc96ccdf1b
Merge with master
2014-12-21 07:36:24 +01:00
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
76b3efb449
Fixes #389
2014-11-20 03:45:43 +01:00
Greg Landrum
7fb24da423
merge with master
2014-09-21 21:06:40 +02:00
Greg Landrum
a94ce46a43
smiles tests now pass as well
2014-08-27 22:32:49 +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
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:
...
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
...
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
...
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
