lp://qastaging/jmol/old-trunk

Branch merges

This import branch has no branches proposed for merge into it.

No branches dependent on this one.

Related source package recipes

No recipes using this branch. (?)

Create packaging recipe

Related snap packages

Related bugs

Related blueprints

20110114 maxb Approved

15114. By hansonr on 2015-07-12

15113. By hansonr on 2015-07-11

bug fix: format("%5.-5i") broken -- only shows right four digits if # digits is 5.

15112. By hansonr on 2015-07-11

format("%5.-5i") broken -- only shows right four digits if # digits is 5.

15111. By hansonr on 2015-07-11

Jmol.___JmolVersion="14.3.15_2015.07.09"

bug fix: write PDB broken for systems with multiple (14.3.12)

15110. By hansonr on 2015-07-11

Jmol.___JmolVersion="14.3.15_2015.07.09"

bug fix: write PDB broken for systems with multiple (14.3.12)

15109. By hansonr on 2015-07-10

Jmol.___JmolVersion="14.3.15_2015.07.09"

bug fix: load "xxx" 1 {10 10 10} does not recognize lattice information when model number is given (broken in 07.07)

15108. By hansonr on 2015-07-09

Jmol.___JmolVersion="14.3.15_2015.07.08c"

bug fix: load files "xxx.png|xxxx" "xxx.png|zzzz" not read from state properly
bug fix: polyhedra not saved in state property
bug fix: moving atoms with 4x4 matrix not saved in state
bug fix: moving of an atom having a polyhedron fails to move the polyhedron as well

new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
  -- asMap = TRUE (default false) indicates you want an atom
     correlation map indicating positions in smiles2 corresponding to smiles1
  -- allMappings = TRUE (default false) indicates you want
     all mappings, not just the first found
  -- returns a number, -1, 0, n>0 when asMap is false (allMappings ignored)
  -- returns int[] when allMappings is false
  -- returns int[][] when allMappings is true
  -- example:
    var s1 = atom1.polyhedron.getProperty("SMILES")
    var coords = atom2.polyhedron.getProperty("vertices")
    var s2 = atom2.polyhedron.getProperty("SMILES")
    var coords2 = atom2.polyhedron.getProperty("vertices")
    var map12 = s2.find("SMILES", s1, true, false)
    var coords2Mapped = []
    for (var i in map12) coords2Mapped.push(coords2[i + 1])
    coords2 = coords2Mapped
    var mat = compare(coords1, coords2)
    select {1.1}
    rotateselected @mat

15107. By hansonr on 2015-07-08

M4.round(f); change in return from SmilesMatcher.find from bs[][] to int[][]

15106. By hansonr on 2015-07-08

Jmol.___JmolVersion="14.3.15_2015.07.08"

new feature: smiles2.find("SMILES",smiles1, asMap, allMappings)
  -- asMap = TRUE (default false) indicates you want an atom
     correlation map indicating positions in smiles2 corresponding to smiles1
  -- allMappings = TRUE (default false) indicates you want
     all mappings, not just the first found
  -- returns a number, -1, 0, n>0 when asMap is false (allMappings ignored)
  -- returns int[] when allMappings is false
  -- returns int[][] when allMappings is true
  -- example:
    var s1 = atom1.polyhedron.getProperty("SMILES")
    var coords = atom2.polyhedron.getProperty("vertices")
    var s2 = atom2.polyhedron.getProperty("SMILES")
    var coords2 = atom2.polyhedron.getProperty("vertices")
    var map12 = s2.find("SMILES", s1, true, false)
    var coords2Mapped = []
    for (var i in map12) coords2Mapped.push(coords2[i + 1])
    coords2 = coords2Mapped
    var mat = compare(coords1, coords2)
    select {1.1}
    rotateselected @mat

bug fix: moving of an atom having a polyhedron fails to move the polyhedron as well

15105. By hansonr on 2015-07-07

Jmol.___JmolVersion="14.3.15_2015.07.07c"

bug fix: x.getProperty("[select name where composition[1] == 0.5]")
 -- the [ there is tripping us up. True, ..1 could be used instead as well.