From: <ha...@us...> - 2008-03-01 17:39:57
|
Revision: 9037 http://jmol.svn.sourceforge.net/jmol/?rev=9037&view=rev Author: hansonr Date: 2008-03-01 09:39:54 -0800 (Sat, 01 Mar 2008) Log Message: ----------- 11.5.11 version Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelset/Atom.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java =================================================================== --- trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-03-01 17:22:36 UTC (rev 9036) +++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2008-03-01 17:39:54 UTC (rev 9037) @@ -218,20 +218,20 @@ } else if (size == -1001) // ionic size = (getBondingMar() * 2); else if (size == -100) { // simple van der waals - size = (int)(getVanderwaalsRadiusFloat() * 2000); + size = getVanderwaalsMad(); } else if (size < 0) { size = -size; if (size > 200) size = 200; size = // we are going from a radius to a diameter - (int)(size / 100f * getVanderwaalsMar() * 2); + (int)(size / 100f * getVanderwaalsMad()); } else if (size >= 10000) { // radiusAngstroms = vdw + x, where size = (x*2)*1000 + 10000 // and vdwMar = vdw * 1000 // we want mad = diameterAngstroms * 1000 = (radiusAngstroms *2)*1000 // = (vdw * 2 * 1000) + x * 2 * 1000 // = vdwMar * 2 + (size - 10000) - size = size - 10000 + getVanderwaalsMar() * 2; + size = size - 10000 + getVanderwaalsMad(); } return (short)size; } @@ -367,8 +367,10 @@ return (dimension == 0 ? x : (dimension == 1 ? y : z)); } - short getVanderwaalsMar() { - return JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 128]; + int getVanderwaalsMad() { + return (Float.isNaN(userDefinedVanDerWaalRadius) + ? JmolConstants.vanderwaalsMars[atomicAndIsotopeNumber % 128] * 2 + : (int)(userDefinedVanDerWaalRadius * 2000f)); } public float getVanderwaalsRadiusFloat() { Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-03-01 17:22:36 UTC (rev 9036) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-03-01 17:39:54 UTC (rev 9037) @@ -1,4 +1,4 @@ -version=11.5.11 HOLD +version=11.5.11 # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propertyDataField # bug fix: functions, save/restore state were disabled by bug in 1.5.8 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |