Nadine Schneider
0bbf3ec79b
Add function to test if UpdatePropertyCache is necessary
2014-12-19 13:59:42 +01:00
Greg Landrum
c26cbc26cb
switch to using references to smart pointers for the Match functions;
...
really ought to re-examine when/how we are passing smart pointers
around in general, but that is a bigger job.
Ref: http://herbsutter.com/2013/06/05/gotw-91-solution-smart-pointer-parameters/
2014-05-10 06:21:27 +02:00
Greg Landrum
9f4471f872
more on #204
...
A few other cleanups
2014-02-06 06:43:28 +01:00
Greg Landrum
924fc373ef
Fixes #165
2013-12-31 07:52:08 +01:00
Greg Landrum
eec7c1c089
make sure there is ring info available
2013-12-03 04:12:46 +01:00
Greg Landrum
53ea3259c9
small SSS optimization
2013-12-02 06:21:32 +01:00
Greg Landrum
46b80e92a6
Merge branch 'mmpa_update_14Aug2013'
2013-09-18 01:56:15 +02:00
Greg Landrum
585385a166
remove extraneous print
2013-08-23 07:31:21 +02:00
Greg Landrum
7e1843a2c5
initial set of tests in
2013-08-09 14:07:20 +02:00
Greg Landrum
3c835f61bb
initial pass
2013-08-09 10:14:33 +02:00
Greg Landrum
a4734bbd43
start using the alternate getProp form
2013-07-20 07:26:06 -04:00
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
50bc499c20
fix for sf.net bug 274
2012-12-15 03:29:03 +00:00
Greg Landrum
175338d061
fix sf.net issue261: add isotope information to debugMol()
2012-12-04 05:40:55 +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
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
e38ef02346
initial pass at changing atom-atom matching behavior;
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fix for issue 3495370
2012-03-02 07:20:16 +00:00
Greg Landrum
813f4863ed
fix and test Issue 3480481
2012-02-18 05:34:34 +00:00
Greg Landrum
29312e73e1
minor updates
2012-01-03 07:50:53 +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
052ec66542
cleanups:
...
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
2010-09-08 04:25:57 +00:00
Greg Landrum
1d7168f0ab
cleanup
2010-06-03 15:49:32 +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
0f469bd5c4
fix and test issue 2381580
2008-12-05 14:32:39 +00:00
Greg Landrum
6d3a9f6fb3
Check in a bunch of changes to fix radical handling.
...
These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +00:00
Greg Landrum
023f7b4f0f
Merge changes from the iterative chirality branch:
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https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.
Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
2008-09-19 09:40:15 +00:00
Greg Landrum
cd97b8035b
refactor the new radical-handling code to add a getNumRadicalElectrons()
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method to Atom
2008-09-04 18:09:54 +00:00
Greg Landrum
57be4a92ef
This is a fix for sf.net issue 1968930:
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http://sourceforge.net/tracker/index.php?func=detail&aid=1968930&group_id=160139&atid=814650
In order to fix the problem, the value of the query function for atomMass queries
is being multiplied by a constant factor (currently 1000) before converting
to an int. This allows distinguishing between things like [CH4] (where the
C has mass 12.011) and [12CH4] (where the C has mass 12.000).
2008-08-13 04:56:48 +00:00
Greg Landrum
41fa5fa7b0
The force argument to getExplicitValence and getImplicitValence wasn't doing anything
2008-06-12 05:44:57 +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
a6c1a64d1a
remove some compiler warnings
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rearrange the argument ordering for the Dice similarity stuff so
that it can be invoked the same as the other similarity metrics.
2008-04-24 19:03:34 +00:00
Greg Landrum
eb3d720010
Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences
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http://sourceforge.net/tracker/index.php?func=detail&aid=1942657&group_id=160139&atid=814650
This was handled by adding error/consistency checking to Atom.calcExplicitValence()
This includes another pretty big scale modification:
the allowed valence list for atoms (in atomic_data.cpp) can now contain a -1 at the end. If this is the case, the atom will tolerate valences above the ones listed.
This is done to allow "flexible" atoms (i.e. transition metals and the like) to accept arbitrary coordination numbers without generating errors.
2008-04-17 05:09:02 +00:00
Greg Landrum
1036921809
better handling of dummies in matching
2008-04-16 15:41:22 +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
430a83bd96
merge in the jamfiles from the bjam branch;
...
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
9bd4c59606
substantial optimization of SD/mol file parsing;some reformattig
2007-03-20 21:06:37 +00:00
Santosh Putta
58189509d1
Atom no long contains a d_pos data member - conformations are supposed to take care of atom positions
2006-10-19 23:37:02 +00:00
Greg Landrum
7041ae233e
handle the NoImplicit flag properly
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update aromaticity to require unsaturation at single-atom donors
test the above two things
This is not necessarily completely stable, but all current tests pass
(once obvious changes have been made). We will just have to see where
the aromaticity changes cause trouble going forward.
2006-09-19 20:20:09 +00:00
Greg Landrum
a890611a22
merge back in changes from ChemTransforms (r30:51);
...
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
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
