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24 Commits

Author SHA1 Message Date
Francois Berenger
7ec8ec0bb9 Vdv radii from blue obelisk (#2154) 
* 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) 
Fixes #2423
 2019-05-09 10:49:14 -04:00
Greg Landrum
b1e255f470 Fixes #1668 (#1669) 
* 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) 
* 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) 
* 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; 
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 
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: 
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 
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); 
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