From: <ha...@us...> - 2008-04-20 12:41:54
|
Revision: 9290 http://jmol.svn.sourceforge.net/jmol/?rev=9290&view=rev Author: hansonr Date: 2008-04-20 05:41:48 -0700 (Sun, 20 Apr 2008) Log Message: ----------- version=11.5.30_dev # new feature: set sequenceRangePhysical -- range based on file (Jmol 11.4 and previous) -- NOW DEFAULT FALSE # setting false gives Rasmol-like behavior and just sets the range to be "resno >= a and resno <= b" Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Eval.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/viewer/StateManager.java trunk/Jmol/src/org/jmol/viewer/Viewer.java Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-04-20 12:22:52 UTC (rev 9289) +++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-04-20 12:41:48 UTC (rev 9290) @@ -1542,7 +1542,7 @@ rpn.addX(instruction.intValue); break; } - rpn.addX(getAtomBits(instruction.tok, getSeqCode(instruction))); + rpn.addX(getAtomBits(Token.spec_seqcode, getSeqCode(instruction))); break; case Token.spec_seqcode_range: if (isInMath) { @@ -1551,17 +1551,23 @@ rpn.addX(code[++pc].intValue); break; } - if (viewer.getBooleanProperty("sequenceRangeRasmol")) { + if (viewer.getBooleanProperty("sequenceRangePhysical")) { + rpn.addX(getAtomBits(Token.spec_seqcode_range, new int[] { + getSeqCode(instruction), getSeqCode(code[++pc]) })); + } else { + int seqcode = getSeqCode(instruction); + int inscode = Group.getInsertionCodeValue(seqcode); BitSet bs = comparatorInstruction(Token.resno, null, Token.opGE, - Group.getSequenceNumber(getSeqCode(instruction)), 0); - int seqcode2 = getSeqCode(code[++pc]); - if (seqcode2 != Integer.MAX_VALUE) // not just "select 3-" + Group.getSequenceNumber(seqcode), 0); + seqcode = getSeqCode(code[++pc]); + if (seqcode != Integer.MAX_VALUE) { // not just "select 3-" bs.and(comparatorInstruction(Token.resno, null, Token.opLE, - Group.getSequenceNumber(seqcode2), 0)); + Group.getSequenceNumber(seqcode), 0)); + inscode = Group.getInsertionCodeValue(seqcode); + } + if (inscode != 0) + bs.and(getAtomBits(Token.spec_seqcode, inscode)); rpn.addX(bs); - } else { - rpn.addX(getAtomBits(instruction.tok, new int[] { - getSeqCode(instruction), getSeqCode(code[++pc]) })); } break; case Token.cell: Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-04-20 12:22:52 UTC (rev 9289) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-04-20 12:41:48 UTC (rev 9290) @@ -8,8 +8,8 @@ # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored. # bug fix: state for draw arrow in multimodel context delivers wrong coordinates # -# new feature: set sequenceRangeRasmol -- ignores ^ insertion codes in sequence code ranges -# and just sets the range to be "resno >= a and resno <= b" +# new feature: set sequenceRangePhysical -- range based on file (Jmol 11.4 and previous) -- NOW DEFAULT FALSE +# setting false gives Rasmol-like behavior and just sets the range to be "resno >= a and resno <= b" # new feature: ellipsoid ball rendering tied to "set wireframerotation" option # new feature: set ellipsoidAxisDiameter x.y # Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-04-20 12:22:52 UTC (rev 9289) +++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-04-20 12:41:48 UTC (rev 9290) @@ -129,7 +129,6 @@ viewer.setStringProperty("defaultColorScheme", "Jmol"); viewer.setBooleanProperty("axesOrientationRasmol", false); viewer.setBooleanProperty("zeroBasedXyzRasmol", false); - viewer.setBooleanProperty("sequenceRangeRasmol", false); viewer.setDefaultVdw("Jmol"); } @@ -138,7 +137,6 @@ viewer.setStringProperty("defaultColorScheme", "RasMol"); viewer.setBooleanProperty("axesOrientationRasmol", true); viewer.setBooleanProperty("zeroBasedXyzRasmol", true); - viewer.setBooleanProperty("sequenceRangeRasmol", true); viewer.setIntProperty("percentVdwAtom", 0); viewer.setIntProperty("bondRadiusMilliAngstroms", 1); viewer.setDefaultVdw("Rasmol"); @@ -602,7 +600,7 @@ boolean measurementLabels = true; int pickingSpinRate = 10; String propertyColorScheme = "roygb"; - boolean sequenceRangeRasmol = false; + boolean sequenceRangePhysical = false; float solventProbeRadius = 1.2f; int scriptDelay = 0; boolean statusReporting = true; @@ -1141,7 +1139,7 @@ setParameterValue("selectionHalos",false); setParameterValue("selectHetero",rasmolHeteroSetting); setParameterValue("selectHydrogen",rasmolHydrogenSetting); - setParameterValue("sequenceRangeRasmol", sequenceRangeRasmol); + setParameterValue("sequenceRangePhysical", sequenceRangePhysical); setParameterValue("sheetSmoothing",sheetSmoothing); setParameterValue("showaxes",false); setParameterValue("showboundbox",false); Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-04-20 12:22:52 UTC (rev 9289) +++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-04-20 12:41:48 UTC (rev 9290) @@ -4492,7 +4492,7 @@ boolean doRepaint = true; while (true) { //11.5.30 - // sequenceRangeRasmol" just handled as getBooleanProperty() + // sequenceRangePhysical" just handled as getBooleanProperty() // ellipsoidAxes" just handled as getBooleanProperty() // ellipsoidArcs" just handled as getBooleanProperty() // ellipsoidDots" just handled as getBooleanProperty() This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |