Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
210f2951e0
Silences warnings in tests
2015-10-18 21:20:11 -04:00
Brian Kelley
54311dff9c
Suppresses warnings in tests
2015-10-18 16:09:58 -04:00
Greg Landrum
1a6fafdec3
Fixes #610
2015-09-09 18:39:56 +02:00
Greg Landrum
07c9c10e26
Fixes #608
2015-09-08 09:52:06 +02:00
Brian Kelley
48a7549773
Travis Tests could not find the mol file
2015-04-06 10:07:11 -04:00
Brian Kelley
85e2e94d20
Fix MolFile Atom Line List Writer
...
Only the first element in the atom one was being
written correctly, the remainder were not being
padded correctly and could not be round tripped.
2015-04-05 20:47:02 -04:00
Greg Landrum
220e2bbdcf
add few more atom.getProp tests
2015-02-28 06:38:21 +01:00
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
5b7b3b3d3d
fix problem with Atom->needsUpdatePropertyCache() and noImplicit
2014-12-29 08:00:40 +00:00
Nadine Schneider
0bbf3ec79b
Add function to test if UpdatePropertyCache is necessary
2014-12-19 13:59:42 +01:00
Greg Landrum
c91b5b5ee1
Fixes #176
2013-12-07 03:18:40 +01:00
Greg Landrum
7b805988f1
rename AtomPeptideMonomerInfo->AtomPDBMonomerInfo;
...
remove element and charge fields
2013-08-20 17:07:37 +02:00
Greg Landrum
7e1843a2c5
initial set of tests in
2013-08-09 14:07:20 +02:00
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
b4f2ec374e
Fixes : #61
2013-07-04 18:00:09 +02:00
Greg Landrum
586e91ba96
Fixes #59
2013-07-04 05:53:16 +02:00
Greg Landrum
d768875648
add RWMol.clear()
2013-05-01 07:51:03 +00:00
Greg Landrum
be669050a6
fix and test sf.net issue284
2013-01-31 04:03:04 +00:00
Greg Landrum
3f6d82a4d1
start to take a swing at the locale problem; this still needs testing on non-linux
2012-12-12 03:24:54 +00:00
Greg Landrum
3aa651d167
fix and test sf.net issue 269
2012-11-23 06:52:30 +00:00
Greg Landrum
6bdd87e1c5
fix and test sf.net issue 267;
...
this removes default valence info from dummy atoms
2012-11-21 04:05:37 +00:00
Greg Landrum
1b328e3789
fix and test for issue 264
2012-11-12 14:54:18 +00:00
Greg Landrum
16e2a04d2c
patch from Roger Sayle to improve valence handling of
...
transition metals and lanthanides
2012-10-10 10:14:42 +00:00
Greg Landrum
37c342046a
add isotopic mass information; add molecular formula calculation; add isotopic mass calculator; expose additional descriptors to java
2011-04-18 10:11:09 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +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;
...
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
fc2804e4c6
initial pass at fixes and a test for issue 2840217
2009-08-21 18:18:22 +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
0f469bd5c4
fix and test issue 2381580
2008-12-05 14:32:39 +00:00
Greg Landrum
7c1aa77c2e
remove a compiler warning in smiles.ll;
...
initial version of implementation of feature request 2047386; This all still needs some more testing
2008-08-12 05:52:25 +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
148a3a87c4
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
Greg Landrum
4ea82818a6
switch away from using the old, unsupported boost::log stuff.
...
This "lookalike" implementation is much cruder than the real thing and does not really support
enabling and disabling logs, or associating them with files, but those components were not being
particularly used in the RDKit anyway.
2008-04-06 09:12:02 +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
