Jmol Code

missing apache GZip tools in Jmol.jar and JSmol

Jmol.___JmolVersion="14.20.3"

bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
bug fix: MOL file reading where isotope is indicated in atom line and V item
bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along with isotope difference

20% speed improvement

casting issue with _M.molData

better spiro testing

Jmol.___JmolVersion="14.20.2" // 2017.07.09

bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828 lines)
bug fix: write SDF and write MOL do not set atom parity field
bug fix: JavaScript JSmol broken for chirality due to bug in Clazz.clone(obj)

bug fix: Upgrade of natural abundance average masses (no significant changes here):

// all numbers except radionuclides from:
// Atomic weights of the elements 2013 (IUPAC Technical Report)
// Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul De Bièvre,
// Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss, Thomas Walczyk,
// Thomas Prohaska Published Online: 2016-02-24 | DOI: https://doi.org/10.1515/pac-2015-0305
// https://www.degruyter.com/view/j/pac.2016.88.issue-3/pac-2015-0305/pac-2015-0305.xml

/* 1 H */ 1.008f, 4.002f,
/* 2 Li */ 6.9675f, 9.012f, 10.8135f, 12.0106f, 14.006f, 15.999f, 18.998f, 20.1797f,
/* 3 Na */ 22.989f, 24.307f, 26.981f, 28.084f, 30.973f, 32.059f, 35.4515f, 39.948f,
/* 4 K */ 39.0983f, 40.078f, 44.955f, 47.867f, 50.9415f, 51.9961f, 54.938f, 55.845f, 58.933f, 58.6934f, 63.546f, 65.38f, 69.723f, 72.63f, 74.921f, 78.971f, 79.904f, 83.798f,
/* 5 Rb */ 85.4678f, 87.62f, 88.905f, 91.224f, 92.906f, 95.95f, 98.91f, 101.07f, 102.905f, 106.42f, 107.8682f, 112.414f, 114.818f, 118.71f, 121.76f, 127.6f, 126.904f, 131.293f,
/* 6 Cs, Ba, actinides */132.905f, 137.327f, 138.905f, 140.116f, 140.907f, 144.242f, 144.9f, 150.36f, 151.964f, 157.25f, 158.925f, 162.5f, 164.93f, 167.259f, 168.934f, 173.054f, 174.9668f,
/* 6 Hf */ 178.49f,180.947f,183.84f,186.207f,190.23f,192.217f,195.084f,196.966f,200.592f,204.3835f,207.2f,208.98f,210f, 210f, 222f,
/* 7 Fr, Ra, lanthanides */ 223f, 226.03f, 227.03f, 232.0377f, 231.035f, 238.028f, 237.05f, 239.1f, 243.1f, 247.1f, 247.1f, 252.1f, 252.1f, 257.1f, 256.1f, 259.1f, 260.1f,
/* 7 Rf - Mt */ 261f, 262f, 263f, 262f, 265f, 268f

Jmol.___JmolVersion="14.20.2" // 2017.07.08

bug fix: CIPChirality adding presort for Rules 4a and 4c (test12.mol; 828 lines)
bug fix: write SDF and write MOL do not set atom parity field
bug fix: JavaScript JSmol broken for chirality due to bug in Clazz.clone(obj)

adds SDF write/read of jmol_atom_names

* 7/7/17 Jmol 14.20.1 minor coding efficiencies (833 lines)

minor logic simplification 836 lines

Jmol.___JmolVersion="14.20.2"

bug fix: write SDF and write MOL do not set atom parity field
bug fix: JavaScript JSmol broken for chirality due to bug in Clazz.clone(obj)