Brian Kelley
71a0ae32b2
Adds replaceCore function that takes a matchVect ( #1013 )
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* Adds replaceCore function that takes a matchVect
* Fixes error reporting, adds tests
* Switches PRECONDITION to ValueError exceptions
* Fixes MatchVectType annoyance in swig. Don't know why this is necessary.
* Silences warnings
* Adds working doctests and better explanations.
2016-08-17 04:40:59 +02:00
Brian Kelley
fe7d4fefb3
Dev/chemtransforms chirality ( #1006 )
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* Adds useChirality to replaceCore, fixes atom ordering
n.b. when replaceDummies==False and labelByIndex==True
the indices used are the indices of the dummy atom,
previously they were the atoms the dummy was connected
to.
* Adds useChirality to the remaining functions in ChemTransforms
* Adds a mess o tests
* Fixes labelByIndex=false ordering for dummies
* Removes debugging statements
2016-08-09 04:41:36 +02:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
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
Riccardo Vianello
7c346d7c2e
Code/RDBoost/Exceptions.h moved to Code/RDGeneral
2015-03-16 22:31:48 +01:00
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
302b84960b
improve docs;
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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
5a340dd454
Fix a typo
2013-03-01 06:53:17 +00:00
Greg Landrum
00655e7bd6
backup commit; may not build
2013-01-29 06:28:31 +00:00
Greg Landrum
03ef0e6f1b
Add support for merging recursive queries on the C++ side
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(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.
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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
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.
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- test that empty results are handled properly in MurckoDecompose.
2011-03-04 06:37:26 +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)
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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
4ca59a1987
clean up conformer handling in ChemTransforms
2011-02-22 06:16:23 +00:00
Greg Landrum
e2521dccbc
add murcko decomposition;
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be sure pathToSubmol copies over coordinates
2011-02-21 06:43:53 +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
57cd641e50
in replaceCore: support labelling dummies with the index of the corresponding atom in the core
2008-11-06 09:10:38 +00:00
Greg Landrum
b36e6a911f
fix a drawing bug
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update release notes and docs
implement the new dummy atom stuff in ChemTransforms
expose lists of atom rings and bond rings from RingInfo
2008-05-14 20:20:52 +00:00
Greg Landrum
1d40302dcb
This builds and tests correctly with msvc8. Linux and msvc7 tests are still required.
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The primary changes consist of cleaning up edge cases that lead to memory errors (under VC8 with debugging turned out)
2008-02-16 05:25:53 +00:00
Greg Landrum
5b550374cb
fix problems with chirality and replaceCore
2008-01-30 15:39:46 +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
3e6cb74075
cleanup and documentation changes
2007-11-14 06:09:52 +00:00
Greg Landrum
5da5c9f7a6
add support for not removing dummies out from the core
2007-10-24 16:36:17 +00:00
Greg Landrum
9fb74bee78
this is not done yet
2007-07-31 16:53:08 +00:00
Greg Landrum
a890611a22
merge back in changes from ChemTransforms (r30:51);
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the makefile for linux is still missing (I have one, I just need to retrieve it)
but otherwise this is in pretty good shape.
err, I think so at least.
2006-09-15 16:44:38 +00:00
