Paolo Tosco
d16b312ee6
- Completely revised coordinate ownership
...
- Implemented Python wrappers
- prepared relevant test cases
2016-04-24 23:30:25 +01:00
Paolo Tosco
a5de000c5c
- fixed int/unsigned int
2016-04-16 20:41:40 +01:00
Paolo Tosco
b35538599f
- Added AMBER trajectory reader and relevant tests
2016-04-16 20:28:45 +01:00
Paolo Tosco
9d5e56fcd2
- added a test for testAddConformersFromTrajectory()
...
- added some documentation
2016-04-14 23:45:24 +01:00
Paolo Tosco
584b77ea18
- work in progress on the Trajectory branch
2016-04-14 20:04:58 +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
Brian Kelley
fb84c9f0b7
Switches to URANGE_CHECK when appropriate
2015-10-18 21:14:02 -04:00
Brian Kelley
daa7e62258
Fixes signed conversion issues (use rdcast)
2015-10-18 15:16:38 -04:00
Greg Landrum
b78bb40ca5
Fixes #384
2015-03-30 07:20:24 +02:00
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
Nadine Schneider
0bbf3ec79b
Add function to test if UpdatePropertyCache is necessary
2014-12-19 13:59:42 +01:00
Greg Landrum
b5b6fac181
minor optimization
2014-02-08 04:32:02 +01:00
Greg Landrum
387406f657
ongoing optimization work
2014-02-05 04:22:59 +01:00
Greg Landrum
8076fefc17
add MatchingAtomIterator to C++
2013-12-16 05:24:19 +01:00
Greg Landrum
9dca8636b7
Fixes #175
2013-12-07 08:26:58 +01:00
Greg Landrum
7a586e9391
further robustification of the computed properties
2013-12-07 07:24:22 +01:00
Greg Landrum
b5fe1f3f8c
add return vals for getProps on ROMol, Atom, and Bond;
...
use a variable to store computed prop names
2013-07-20 06:07:19 -04:00
Greg Landrum
8d9fd053b2
fix and test issue 256;
...
this is a change that affects backwards compatibility.
2012-10-08 03:18:05 +00:00
Greg Landrum
a9e2447b28
another checkpoint; this seems to be working for the lipinksi and crippen descriptors
2012-02-25 05:38:09 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
4f0321acc7
cleanup
2010-12-29 07:10:10 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
...
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
116c036c07
doc updates for writers to indicate that "-" writes to stdout;
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rename computedProps property to __computedProps
2010-09-19 13:13:10 +00:00
Greg Landrum
214f1c5c20
primarily minor code cleanups.
2010-05-26 18:27:40 +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
...
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
8867db464f
check that self bonds are not added
2008-07-16 04:00:54 +00:00
Greg Landrum
95b86eb371
"fix" issue1993296
2008-06-16 05:52:30 +00:00
Greg Landrum
9c7f33a5c8
merge changes from QuerySerialization_6March2008 branch, revs 555:563, into the trunk;
2008-03-12 06:11:39 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
...
The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
6aeeca797d
fix a small memory leak
2008-01-26 04:34:45 +00:00
Greg Landrum
430a83bd96
merge in the jamfiles from the bjam branch;
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various and sundry minor code cleanups;
this probably does not yet build on windows... that is next
2007-11-23 15:55:30 +00:00
Greg Landrum
1b0ccef933
minor cleanups
2007-10-13 09:27:37 +00:00
Greg Landrum
4e7d182fcc
Support editable molecules in Python.
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This is Feature Request #1764162
http://sourceforge.net/tracker/index.php?func=detail&aid=1764162&group_id=160139&atid=814653
This implementation has been tested on Windows
2007-07-31 05:30:11 +00:00
Greg Landrum
1378a5c934
small cleanups
2006-12-17 14:58:54 +00:00
Greg Landrum
6615ae5a01
SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue.
...
Conformer.cpp: make sure we don't ask for space for zero atoms.
Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.
molopstest.cpp: bad smiles corrected in one test.exe
ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)
Wrap/MolOps.cpp: docs for replacesubstructs.
2006-09-18 05:21:39 +00:00
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
