lp:jmol/old-trunk

Created by Nicolas Vervelle and last modified
Get this branch:
bzr branch lp:jmol/old-trunk

Branch merges

Related bugs

Related blueprints

Branch information

Owner:
Nicolas Vervelle
Project:
Jmol
Status:
Mature

Import details

Import Status: Failed

This branch is an import of the Subversion branch from https://jmol.svn.sourceforge.net/svnroot/jmol/trunk/Jmol/.

The import has been suspended because it failed 5 or more times in succession.

Last successful import was .

Import started on neumayer and finished taking 2 minutes — see the log
Import started on pear and finished taking 2 minutes — see the log
Import started on pear and finished taking 2 minutes — see the log
Import started on pear and finished taking 2 minutes — see the log

Whiteboard

20110114 maxb Approved

Recent revisions

15114. By hansonr
15113. By hansonr

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

15112. By hansonr

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

15111. By hansonr

Jmol.___JmolVersion="14.3.15_2015.07.09"

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

15110. By hansonr

Jmol.___JmolVersion="14.3.15_2015.07.09"

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

15109. By hansonr

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

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

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

15106. By hansonr

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

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.

Branch metadata

Branch format:
Branch format 7
Repository format:
Bazaar repository format 2a (needs bzr 1.16 or later)
This branch contains Public information 
Everyone can see this information.

Subscribers