~nvervelle/jmol/old-trunk : changes

~nvervelle/jmol/old-trunk » Changes from revision 15114

From Revision 15114 to 15095

Rev	Summary	Authors	Date
15114		hansonr	8 years ago
15113	bug fix: format("%5.-5i") broken -- only shows right four ... bug fix: format("%5.-5i") broken -- only shows right four digits if # digits is 5.	hansonr	8 years ago
15112	format("%5.-5i") broken -- only shows right four digits if... format("%5.-5i") broken -- only shows right four digits if # digits is 5.	hansonr	8 years ago
15111	Jmol.___JmolVersion="14.3.15_2015.07.09" Jmol.___JmolVersion="14.3.15_2015.07.09" bug fix: write PDB broken for systems with multiple (14.3.12)	hansonr	8 years ago
15110	Jmol.___JmolVersion="14.3.15_2015.07.09" Jmol.___JmolVersion="14.3.15_2015.07.09" bug fix: write PDB broken for systems with multiple (14.3.12)	hansonr	8 years ago
15109	Jmol.___JmolVersion="14.3.15_2015.07.09" 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)	hansonr	8 years ago
15108	Jmol.___JmolVersion="14.3.15_2015.07.08c" 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	hansonr	8 years ago
15107	M4.round(f); change in return from SmilesMatcher.find from b... M4.round(f); change in return from SmilesMatcher.find from bs[][] to int[][]	hansonr	8 years ago
15106	Jmol.___JmolVersion="14.3.15_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	hansonr	8 years ago
15105	Jmol.___JmolVersion="14.3.15_2015.07.07c" 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.	hansonr	8 years ago
15104		hansonr	8 years ago
15103	Jmol.___JmolVersion="14.3.15_2015.07.07b" Jmol.___JmolVersion="14.3.15_2015.07.07b" bug fix: 2015.07.06 breaks text writing in JSmol bug fix: Crystal reader cannot handle TOTAL ENERGY CORRECTED... line	hansonr	8 years ago
15102	JSmol text writing broken in just-released Jmol 14.3.15 JSmol text writing broken in just-released Jmol 14.3.15	hansonr	8 years ago
15101	Jmol.___JmolVersion="14.3.15_2015.07.07" Jmol.___JmolVersion="14.3.15_2015.07.07" new feature: load xxx filter "latticeScaling=1.2" -- scales model based on a crystal lattice -- allows volume matching for crystal comparison bug fix: SMARTS processing with "." may not find substructure	hansonr	8 years ago
15100	Jmol.___JmolVersion="14.3.15_2015.07.03" Jmol.___JmolVersion="14.3.15_2015.07.03" bug fix: mmCIF reader does not recognize load MODEL ... bug fix: PDB reader should be reading load "" [1 3 4] as MODEL record numbers, not sequential numbers bug fix: load MODELS "" [1 3 4] does not work (although load "" [1 3 4], without with MODELS keyword, works) clarification: load "" 1 # loads the first model in a file when not PDB or mmCIF. load "" 1 # loads the model with MODEL 1 record for a PDB file. load "" 1 # loads the model with _atom_site.pdbx_PDB_model_num = 1 for an mmCIF file load "" [1] # same as load "" 1; brackets allow for more than one model, for instance [1 3 5] load MODELS ({1}) "" # always loads the SECOND model in a file	hansonr	8 years ago
15099	Jmol.___JmolVersion="14.3.15_2015.07.03" Jmol.___JmolVersion="14.3.15_2015.07.03" bug fix: mmCIF reader does not recognize load model bug fix: load MODELS "" [1 3 4] does not work	hansonr	8 years ago
15098	Jmol.___JmolVersion="14.3.15_2015.07.03" Jmol.___JmolVersion="14.3.15_2015.07.03" bug fix: mmCIF reader does not recognize load model	hansonr	8 years ago
15097	Jmol.___JmolVersion="14.3.15_2015.06.30" Jmol.___JmolVersion="14.3.15_2015.06.30" bug fix: POVRay and VRML exporters mishandle label backgrounds bug fix: exports not handling rockets correctly	hansonr	8 years ago
15096	Jmol.___JmolVersion="14.3.15_2015.06.19c" Jmol.___JmolVersion="14.3.15_2015.06.19c" bug fix: 1/{a b c} gives 0, not 1/length({a b c})	hansonr	8 years ago
15095	Jmol.___JmolVersion="14.3.15_2015.06.19b" Jmol.___JmolVersion="14.3.15_2015.06.19b" new feature: MACRO command -- runs predefined script, generally defining new functions of general use -- contributions welcome! -- will be expanded $ macro aflow running http://aflowlib.mems.duke.edu/users/jmolers/jmol/spt/AFLOW.spt aflowLoad(binaryAlloy) loaded aflowBinaries loaded aflowDualArray(binaryAlloy, a, b) loaded aflowDualWrite loaded aflowConvexHull(binaryAlloy) loaded aflowCheckBinary(binaryAlloy) loaded aflowGetPG(binaryAlloy, a, range1, range2,radius) loaded $ aflowLoad("AgAu") 294 models $ print aflowConvexHull { "Cb" : 0.0 "Hf_eV_VASP" : 0.0 "modelNumber" : 2 } { "Cb" : 0.25 "Hf_eV_VASP" : -0.0472733 "modelNumber" : 26 } { "Cb" : 0.5 "Hf_eV_VASP" : -0.085589 "modelNumber" : 180 } { "Cb" : 0.75 "Hf_eV_VASP" : -0.0463823 "modelNumber" : 25 } { "Cb" : 1.0 "Hf_eV_VASP" : 0.0 "modelNumber" : 260 } bug fix: AFLOW binary file reader can fail with certain VASP formats containing both in-line atom labels and atom elements prior to #elements line. (AlPd#5, for example)	hansonr	8 years ago

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