Nadine Schneider
0cf0dd37ce
Bugfix in SmilesWrite and some additional tests for getMolFrags function
2015-04-16 10:53:20 +02:00
Nadine Schneider
0132cc72e9
Merge branch 'newCanon' into master3
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Conflicts:
Code/GraphMol/SmilesParse/test.cpp
2015-04-10 10:25:47 +02:00
Nadine Schneider
ca4bcca6ae
Include atom-mapping numbers if present in the canonicalization
2015-04-10 09:47:16 +02:00
Greg Landrum
c134974d3a
support empty SMILES and SMARTS strings
2015-04-02 11:11:09 +02:00
Nadine Schneider
7ddff9c71c
Some performance fixes
2015-03-20 18:19:08 +01:00
Nadine Schneider
465c7cb4c6
new_canon: Delete numRingMember invariant
2015-02-12 18:06:27 +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
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
48c5d0d6ff
At this point all C++ tests pass
2015-01-03 06:42:54 +00:00
Greg Landrum
22eb598012
SMILES tests now pass with the exception of:
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- the issue 1844617 test
- the fragment smiles generation tests (commented out at the bottom, there is still implementation work to do for these)
2014-12-30 07:21:25 +00:00
Greg Landrum
76b3efb449
Fixes #389
2014-11-20 03:45:43 +01:00
Greg Landrum
28b22837af
Fixes #378
2014-11-10 04:54:32 +01:00
Greg Landrum
ff872cdba7
add test for #378
2014-11-09 11:47:46 +01:00
Greg Landrum
a94ce46a43
smiles tests now pass as well
2014-08-27 22:32:49 +02:00
Greg Landrum
23076b1cdb
Fixes #298
2014-07-23 05:31:16 +02:00
Greg Landrum
0839cf41ad
Fixes #210
2014-02-03 05:25:27 +01:00
Greg Landrum
9e4ceef1bd
Fixes #206 but more testing is definitely required
2014-01-28 06:44:43 +01:00
Greg Landrum
47afcc1f53
remove some debugging printing
2013-12-31 07:12:40 +01:00
Greg Landrum
0a421d8aa5
Fixes #182
2013-12-31 07:11:31 +01:00
Greg Landrum
158c9b9e45
Fixes #136
2013-10-21 05:55:42 +02:00
Greg Landrum
dccf20b8c7
Fixes #45
2013-06-08 06:01:54 +02:00
Greg Landrum
e9d8cb1b99
fix and test github issue 12
2013-03-19 04:44:24 +00:00
Greg Landrum
ca5edda7fb
fix and test problems with reading aromatic Si from smiles
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(github issue 5)
2013-02-14 03:59:44 +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
854dde8097
fix and test issue 253
2012-09-21 12:32:35 +00:00
Greg Landrum
14e396c26d
refactoring the SMILES parser to make it more efficient
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NOTE: this changes the ordering of bonds in molecules with branches.
2012-08-28 04:01:49 +00:00
Greg Landrum
f2d9755a65
at this point all tests pass
2012-06-29 03:40:28 +00:00
Greg Landrum
55ae9a6e26
start fixing some tests (note: this is not done)
2012-06-29 02:42:27 +00:00
Greg Landrum
0f3b84cd28
backup commit; we are not quite there yet
2012-06-26 06:15:08 +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
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
700d60c94d
left out some tests
2012-05-19 04:34:45 +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
a39187a528
fix and test issue 3526814
2012-05-16 05:29:34 +00:00
Greg Landrum
e77cfcf336
fix and test issue 3525776
2012-05-11 13:02:07 +00:00
Greg Landrum
8ffcfd7149
fix and test issue 35525671
2012-05-11 07:13:45 +00:00
Greg Landrum
f2bc7f77d2
fix and test issue 3525669
2012-05-11 06:42:08 +00:00
Greg Landrum
54f861e5ee
fix and test issue 3525668
2012-05-11 06:36:08 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
3520c441cb
add allBondsExplicit argument for SMILES writing
2012-03-26 03:12:37 +00:00
Greg Landrum
813f4863ed
fix and test Issue 3480481
2012-02-18 05:34:34 +00:00
Greg Landrum
d47f423009
support [HH]
2011-12-20 04:12:07 +00:00
Greg Landrum
9316758cec
improved handling of isotope specifications (still definitely not optimal)
2011-07-01 03:42:35 +00:00
Greg Landrum
faab610321
add string replacements to smiles and smarts parsers
2011-05-22 10:45:14 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
