Greg Landrum
f1bbc319b5
Fixes #3531 ( #3545 )
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* Fixes #3531
* remove the new Br valences too
2020-11-08 07:17:37 +01:00
Greg Landrum
b86b2364c2
add new oxidation states for Cl, Br, I, Xe, Po, At ( #3486 )
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* add new oxidation states for Br, I, Xe, Po, At
Changes the allowed value 2->3 for I
* add Cl too
* update expected test results
2020-10-12 15:26:18 +02:00
Greg Landrum
47d8813358
Fixes #2784 ( #2787 )
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* Fixes #2784
* changes in response to review.
* clarifying comment
2019-11-15 07:53:42 -05:00
Greg Landrum
7ffd863c9b
A collection of bug fixes ( #2608 )
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* Fixes #2602
* Fixes #2605
* Remove vestigial isEarlyAtom() definition in Kekulize.cpp
* Fixes #2606
* Fixes #2607
adds allowed valence 2 for Sn and Pb
* Fixes #2610
* update in response to review
2019-08-15 04:53:23 +02:00
Francois Berenger
7ec8ec0bb9
Vdv radii from blue obelisk ( #2154 )
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* updated atomic radii to follow the Blue Obelisk Data Repository
Ubuntu package bodr version 10-1; radii are from file
/usr/share/bodr/elements.xml
* typo
* use 2.0 as default VDW radius instead of 1.7
for elements missing from the Blue Obelisk Data Repository
* Document the atomic_data
* update expected test results
* update java tests
* allow a bit more slop when comparing confs
For cross-platform stability
2019-05-29 09:23:27 +02:00
Greg Landrum
8d72034367
Add an allowed valence of 3 for Al ( #2425 )
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Fixes #2423
2019-05-09 10:49:14 -04:00
Greg Landrum
b1e255f470
Fixes #1668 ( #1669 )
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* Fixes #1668
* add test for the additional Bi valence
2017-12-21 05:45:24 +01:00
Greg Landrum
c21605dbea
SMILES lexer optimization/enhancement ( #1575 )
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* needs testing
* add some tests, update periodic table
* update isotope data from NIST
2017-09-17 09:12:53 -04:00
Greg Landrum
97916ef894
Fixes #1204 ( #1212 )
2016-12-19 12:50:28 -05:00
Greg Landrum
9f9f2cd2d2
support additional trans-uranic elements ( #1134 )
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* support additional trans-uranic elements
- update the atomic data and isotope lists
- update the SMILES and SMARTS parsers
* rebreak an input file
2016-11-03 11:48:31 -04:00
Greg Landrum
dee0215886
Fixes #694
2016-02-16 15:38:02 +01:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
672f8ea200
Fixes #510
2015-05-20 05:19:40 +02:00
Greg Landrum
04edaa3380
add Darmstadtium isotope support in honor of the UGM
2014-10-24 13:55:03 +02:00
Greg Landrum
3f90cecd9c
Fixes #164
2013-12-31 08:27:09 +01:00
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
6bdd87e1c5
fix and test sf.net issue 267;
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this removes default valence info from dummy atoms
2012-11-21 04:05:37 +00:00
Greg Landrum
16e2a04d2c
patch from Roger Sayle to improve valence handling of
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transition metals and lanthanides
2012-10-10 10:14:42 +00:00
Greg Landrum
b327ab5b23
get this building with MSVC++
2012-04-25 03:11:07 +00:00
Greg Landrum
162662186d
not working yet
2012-04-19 06:15:40 +00:00
Greg Landrum
24bbcec6fd
typo
2011-04-18 11:27:41 +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
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542
cleanups:
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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
0ff4b1646b
since there's not really a right answer about default valence for transition metals, we might as well be consistent
2009-03-30 07:15:46 +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
bc60f17b91
make the next step towards completing feature request (186217);
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display deprecation warnings for [X] dummies, output [*] by default
2008-04-06 10:41:14 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
