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[Jmol-commits] SF.net SVN: jmol: [8558] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2007-11-03 03:57:16
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Revision: 8558
http://jmol.svn.sourceforge.net/jmol/?rev=8558&view=rev
Author: hansonr
Date: 2007-11-02 20:56:59 -0700 (Fri, 02 Nov 2007)
Log Message:
-----------
version=11.3.40 VERSION # new feature: Ramachandran/Model commands switch between plot and model
# -- one Ramachandran plot per model
# -- axes labels and special hover label for Ramachandran plots
# -- Ramachandran saved in state
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/Bond.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/shape/HoverRenderer.java
trunk/Jmol/src/org/jmol/shapespecial/Draw.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -826,15 +826,19 @@
*/
public String getInfo() {
- return getIdentity();
- }
+ return getIdentity(true);
+ }
String getInfoXYZ(boolean withScreens) {
- return getIdentity() + " " + x + " " + y + " " + z
+ return getIdentity(true) + " " + x + " " + y + " " + z
+ (withScreens ? " ### " + screenX + " " + screenY + " " + screenZ : "");
}
- public String getIdentity() {
+ private String getIdentityXYZ() {
+ return getIdentity(false) + " " + x + " " + y + " " + z;
+ }
+
+ private String getIdentity(boolean allInfo) {
StringBuffer info = new StringBuffer();
String group3 = getGroup3();
String seqcodeString = getSeqcodeString();
@@ -850,6 +854,8 @@
info.append(":");
info.append(chainID);
}
+ if (!allInfo)
+ return info.toString();
String atomName = getAtomNameOrNull();
if (atomName != null) {
if (info.length() > 0)
@@ -1124,6 +1130,7 @@
case 'D': atom inDex (was "X")
case 'e': element symbol
case 'E': insErtion code
+ case 'f': phi
case 'g': selected group index (for testing)
case 'i': atom number
case 'I': Ionic radius
@@ -1134,6 +1141,7 @@
case 'n': group3
case 'N': molecule Number
case 'o': symmetry operator set
+ case 'p': psi
case 'P': Partial charge
case 'q': occupancy 0-100%
case 'Q': occupancy 0.00 - 1.00
@@ -1148,6 +1156,7 @@
case 'V': van der Waals
case 'x': x coord
case 'X': fractional X coord
+ case 'W': identity - with X,Y,Z
case 'y': y coord
case 'Y': fractional Y coord
case 'z': z coord
@@ -1221,6 +1230,12 @@
case 'P':
floatT = getPartialCharge();
break;
+ case 'f':
+ floatT = getGroupPhi();
+ break;
+ case 'p':
+ floatT = getGroupPsi();
+ break;
case 'v':
ch = (ich < strFormat.length() ? strFormat.charAt(ich++) : '\0');
switch (ch) {
@@ -1285,8 +1300,11 @@
strT = "" + getResno();
break;
case 'U':
- strT = getIdentity();
+ strT = getIdentity(true);
break;
+ case 'W':
+ strT = getIdentityXYZ();
+ break;
case 'u':
floatT = getSurfaceDistance100() / 100f;
break;
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -434,7 +434,7 @@
float d = points[j].distance(atom) - envelopeRadius;
if (d < 0 && Logger.isActiveLevel(Logger.LEVEL_DEBUG))
Logger.debug("draw d" + j + " " + Escape.escape(points[j])
- + " \"" + d + " ? " + atom.getIdentity() + "\"");
+ + " \"" + d + " ? " + atom.getInfo() + "\"");
dMin = Math.min(d, dMin);
}
int d = surfaceDistance100s[i] = (int) (dMin * 100);
@@ -789,7 +789,7 @@
for (int i = 0; i < atomCount; i++)
if (t.get(i)) {
s.append(i + 1).append(" ").append(atoms[i].getElementSymbol())
- .append(" ").append(atoms[i].getIdentity().replace(' ', '_')).append(" ");
+ .append(" ").append(atoms[i].getInfo().replace(' ', '_')).append(" ");
switch (type) {
case TAINT_COORD:
dataLabel = "coord set";
@@ -1170,7 +1170,7 @@
z.normalize();
if (Logger.isActiveLevel(Logger.LEVEL_DEBUG)) {
- Logger.debug(atom.getIdentity() + " nBonds=" + nBonds + " " + hybridization);
+ Logger.debug(atom.getInfo() + " nBonds=" + nBonds + " " + hybridization);
}
if (hybridizationCompatible) {
if (hybridization == "")
Modified: trunk/Jmol/src/org/jmol/modelset/Bond.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Bond.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/Bond.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -96,8 +96,8 @@
}
public String getIdentity() {
- return (index + 1) + " "+ order + " " + atom1.getIdentity() + " -- "
- + atom2.getIdentity();
+ return (index + 1) + " "+ order + " " + atom1.getInfo() + " -- "
+ + atom2.getInfo();
}
public String formatLabel(String strFormat, int[] indices) {
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -81,19 +81,15 @@
int moleculeCount;
int nAltLocs;
int nInsertions;
+ int ramachandranFrame;
+ int quaternionFrame = -1;
+ int dataSourceFrame = -1;
+
boolean isPDB = false;
String jmolData; // from a PDB remark "Jmol PDB-encoded data"
String jmolDataType;
- boolean isJmolDataFrame() {
- return (jmolData != null);
- }
-
- String getJmolDataFrameType() {
- return jmolDataType;
- }
-
private int chainCount = 0;
private Chain[] chains = new Chain[8];
private int bioPolymerCount = 0;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -45,6 +45,7 @@
import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Parser;
+import org.jmol.util.TextFormat;
import org.jmol.viewer.JmolConstants;
import org.jmol.viewer.Token;
@@ -651,22 +652,21 @@
/* ONLY from one model
*
*/
- private String getPdbData(String type, char ctype, BitSet bsAtoms,
+ private String getPdbData(String type, char ctype, int modelIndex,
boolean isDerivative) {
- StringBuffer pdbATOM = new StringBuffer();
StringBuffer pdbCONECT = new StringBuffer();
- int firstAtom = BitSetUtil.firstSetBit(bsAtoms);
- if (firstAtom < 0)
- return null;
- int modelIndex = atoms[firstAtom].modelIndex;
if (isJmolDataFrame(modelIndex))
- return null;
+ modelIndex = viewer.getJmolDataSourceFrame(modelIndex);
+ if (modelIndex < 0)
+ return "";
int nPoly = models[modelIndex].getBioPolymerCount();
+ StringBuffer pdbATOM = new StringBuffer();
+ BitSet bsAtoms = getModelAtomBitSet(modelIndex);
for (int p = 0; p < nPoly; p++)
models[modelIndex].getPdbData(ctype, isDerivative, bsAtoms, pdbATOM,
pdbCONECT);
pdbATOM.append(pdbCONECT);
- return pdbATOM.toString();
+ return getProteinStructureState(bsAtoms) + pdbATOM.toString();
}
/* **********************
@@ -675,13 +675,13 @@
*
*****************************/
- public String getPdbData(String type, BitSet bsAtoms) {
+ public String getPdbData(int modelIndex, String type) {
char ctype = (type.length() > 11 && type.indexOf("quaternion ") >= 0 ? type
.charAt(11) : 'r');
- String s = getPdbData(type, ctype, bsAtoms, (type.indexOf(" deriv") >= 0));
- if (s == null)
- return null;
- String remark = "REMARK 999 Jmol PDB-encoded data: " + type
+ String s = getPdbData(type, ctype, modelIndex, (type.indexOf(" deriv") >= 0));
+ if (s.length() == 0)
+ return "";
+ String remark = "REMARK 6 Jmol PDB-encoded data: " + type
+ " data(x,y,z,charge)=";
switch (ctype) {
case 'w':
@@ -721,28 +721,31 @@
}
public boolean isJmolDataFrame(int modelIndex) {
- return (modelIndex >= 0 && modelIndex < modelCount && models[modelIndex]
- .isJmolDataFrame());
+ return (modelIndex >= 0 && modelIndex < modelCount && models[modelIndex].jmolData != null);
}
- protected Hashtable htJmolData = new Hashtable();
-
- public void setPtJmolDataFrame(String type, int modelIndex) {
- htJmolData.put(type, new Integer(modelIndex));
+ public void setJmolDataFrame(String type, int modelIndex, int modelDataIndex) {
+ if (type.equals("ramachandan"))
+ models[modelIndex].ramachandranFrame = modelDataIndex;
+ else
+ models[modelIndex].quaternionFrame = modelDataIndex;
+ models[modelDataIndex].dataSourceFrame = modelIndex;
}
- public int getPtJmolDataFrame(String type) {
- Integer iModel = (Integer) htJmolData.get(type);
- if (iModel == null)
- return -1;
- return iModel.intValue();
+ public int getJmolDataFrameIndex(int modelIndex, String type) {
+ return (type.equals("ramachandan") ? models[modelIndex].ramachandranFrame
+ : models[modelIndex].quaternionFrame);
}
+
public String getJmolDataFrameType(int modelIndex) {
- return (modelIndex >= 0 && modelIndex < modelCount ? models[modelIndex]
- .getJmolDataFrameType() : "modelSet");
+ return (modelIndex >= 0 && modelIndex < modelCount ? models[modelIndex].jmolDataType : "modelSet");
}
+ public int getJmolDataSourceFrame(int modelIndex) {
+ return (modelIndex >= 0 && modelIndex < modelCount ? models[modelIndex].dataSourceFrame : -1);
+ }
+
private String pdbHeader;
/*
final static String[] pdbRecords = { "ATOM ", "HELIX ", "SHEET ", "TURN ",
@@ -1397,47 +1400,109 @@
}
//////////// state definition ///////////
-
-
- protected String getProteinStructureState() {
+
+ protected String getProteinStructureState(BitSet bsAtoms) {
BitSet bs = null;
StringBuffer cmd = new StringBuffer();
+ StringBuffer sbTurn = new StringBuffer();
+ StringBuffer sbHelix = new StringBuffer();
+ StringBuffer sbSheet = new StringBuffer();
int itype = 0;
int id = 0;
int iLastAtom = 0;
int lastId = -1;
int res1 = 0;
int res2 = 0;
+ String group1 = "";
+ String group2 = "";
int n = 0;
- for (int i = 0; i <= atomCount; i++) {
- id = Integer.MIN_VALUE;
- if (i == atomCount
- || (id = atoms[i].getProteinStructureID()) != lastId) {
- if (bs != null) {
- n++;
- cmd.append(" structure ")
- .append(JmolConstants.getProteinStructureName(itype))
- .append(" ").append(Escape.escape(bs))
- .append(" \t# model=").append(getModelName(-1 - atoms[iLastAtom].modelIndex))
- .append(" & (").append(res1).append(" - ").append(res2).append(");\n");
- bs = null;
+ int nHelix = 0;
+ int nTurn = 0;
+ int nSheet = 0;
+ for (int i = 0; i <= atomCount; i++)
+ if (bsAtoms == null || bsAtoms.get(i)) {
+ id = Integer.MIN_VALUE;
+ if (i == atomCount || (id = atoms[i].getProteinStructureID()) != lastId) {
+ if (bs != null) {
+ if (itype != JmolConstants.PROTEIN_STRUCTURE_HELIX
+ && itype != JmolConstants.PROTEIN_STRUCTURE_TURN
+ && itype != JmolConstants.PROTEIN_STRUCTURE_SHEET) {
+ bs = null;
+ continue;
+ }
+ n++;
+ if (bsAtoms == null) {
+ cmd.append(" structure ").append(
+ JmolConstants.getProteinStructureName(itype)).append(" ")
+ .append(Escape.escape(bs)).append(" \t# model=").append(
+ getModelName(-1 - atoms[iLastAtom].modelIndex)).append(
+ " & (").append(res1).append(" - ").append(res2).append(
+ ");\n");
+ } else {
+ String str;
+ int nx;
+ String sid;
+ StringBuffer sb;
+ switch (itype) {
+ case JmolConstants.PROTEIN_STRUCTURE_HELIX:
+ nx = ++nHelix;
+ sid = "H" + nx;
+ str = "HELIX %3N %3ID %3GROUPA %4RESA %3GROUPB %4RESB\n";
+ sb = sbHelix;
+ break;
+ case JmolConstants.PROTEIN_STRUCTURE_SHEET:
+ nx = ++nSheet;
+ sid = "S" + nx;
+ str = "SHEET %3N %3ID 2 %3GROUPA %4RESA %3GROUPB %4RESB\n";
+ sb = sbSheet;
+ break;
+ case JmolConstants.PROTEIN_STRUCTURE_TURN:
+ default:
+ nx = ++nTurn;
+ sid = "T" + nx;
+ str = "TURN %3N %3ID %3GROUPA %4RESA %3GROUPB %4RESB\n";
+ sb = sbTurn;
+ break;
+ }
+ str = TextFormat.formatString(str, "N", nx);
+ str = TextFormat.formatString(str, "ID", sid);
+ str = TextFormat.formatString(str, "GROUPA", group1);
+ str = TextFormat.formatString(str, "RESA", res1);
+ str = TextFormat.formatString(str, "GROUPB", group2);
+ str = TextFormat.formatString(str, "RESB", res2);
+ sb.append(str);
+
+ /*
+ HELIX 1 H1 ILE 7 PRO 19 1 3/10 CONFORMATION RES 17,19 1CRN 55
+ HELIX 2 H2 GLU 23 THR 30 1 DISTORTED 3/10 AT RES 30 1CRN 56
+ SHEET 1 S1 2 THR 1 CYS 4 0 1CRNA 4
+ SHEET 2 S1 2 CYS 32 ILE 35 -1 1CRN 58
+ TURN 1 T1 PRO 41 TYR 44 1CRN 59
+ */
+ }
+ bs = null;
+ }
+ if (id == Integer.MIN_VALUE ||
+ bsAtoms != null
+ && (Float.isNaN(atoms[i].getGroupPhi()) || Float.isNaN(atoms[i].getGroupPsi())))
+ continue;
+ res1 = atoms[i].getResno();
+ group1 = atoms[i].getGroup3();
}
- if (id == Integer.MIN_VALUE)
- continue;
- res1 = atoms[i].getResno();
+ if (bs == null) {
+ bs = new BitSet();
+ }
+ itype = atoms[i].getProteinStructureType();
+ bs.set(i);
+ lastId = id;
+ res2 = atoms[i].getResno();
+ group2 = atoms[i].getGroup3();
+ iLastAtom = i;
}
- if (bs == null) {
- bs = new BitSet();
- }
- itype = atoms[i].getProteinStructureType();
- bs.set(i);
- lastId = id;
- res2 = atoms[i].getResno();
- iLastAtom = i;
- }
if (n > 0)
cmd.append("\n");
- return cmd.toString();
+ return (bsAtoms == null ? cmd.toString() : sbHelix.append(sbSheet).append(
+ sbTurn).append(cmd).toString());
}
public String getModelInfoAsString() {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -128,7 +128,6 @@
someModelsHaveUnitcells |= mergeModelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveUnitcells");
someModelsHaveFractionalCoordinates |= mergeModelSet.getModelSetAuxiliaryInfoBoolean("someModelsHaveFractionalCoordinates");
someModelsHaveAromaticBonds |= mergeModelSet.someModelsHaveAromaticBonds;
- htJmolData = mergeModelSet.htJmolData;
}
initializeBuild(nAtoms);
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -378,12 +378,13 @@
private Vector stateScripts = new Vector();
private int thisStateModel = 0;
- public void addStateScript(String script) {
+ public void addStateScript(String script, boolean addFrameNumber) {
int iModel = viewer.getCurrentModelIndex();
if (thisStateModel != iModel) {
thisStateModel = iModel;
- script = "frame " + (iModel < 0 ? "" + iModel : getModelName(-1 - iModel))
- + ";\n" + script;
+ if (addFrameNumber)
+ script = " frame " + (iModel < 0 ? "" + iModel : getModelName(-1 - iModel))
+ + ";\n" + script;
}
stateScripts.addElement(script);
}
@@ -422,7 +423,7 @@
setModelVisibility();
- commands.append(getProteinStructureState());
+ commands.append(getProteinStructureState(null));
for (int i = 0; i < JmolConstants.SHAPE_MAX; ++i) {
Shape shape = shapes[i];
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -101,7 +101,7 @@
setStructure(new Helix((AlphaPolymer) bioPolymer, monomerIndex, 1));
break;
case JmolConstants.PROTEIN_STRUCTURE_SHEET:
- setStructure(new Sheet((AminoPolymer) bioPolymer, monomerIndex, 1));
+ setStructure(new Sheet((AlphaPolymer) bioPolymer, monomerIndex, 1));
break;
case JmolConstants.PROTEIN_STRUCTURE_TURN:
setStructure(new Turn((AlphaPolymer) bioPolymer, monomerIndex, 1));
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -548,7 +548,17 @@
Monomer monomer = p.monomers[m];
if (bsAtoms.get(monomer.getLeadAtomIndex())) {
Atom a = monomer.getLeadAtom();
- if (ctype != 'r') {
+ if (isRamachandran) {
+ x = monomer.getPhi();
+ y = monomer.getPsi();
+ z = monomer.getOmega();
+ if (z < -90)
+ z += 360;
+ z -= 180;
+ if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
+ continue;
+ w = a.getPartialCharge();
+ } else {
Quaternion q = a.getQuaternion();
if (q == null) {
qlast = null;
@@ -594,16 +604,6 @@
w = q.q1;
break;
}
- } else {
- x = monomer.getPhi();
- y = monomer.getPsi();
- z = monomer.getOmega();
- if (z < -90)
- z += 360;
- z -= 180;
- if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
- continue;
- w = a.getPartialCharge();
}
pdbATOM.append(a.formatLabel("ATOM %5i %-3a%1A%3n %1c%4R%1E "));
pdbATOM.append(TextFormat.formatString("%8.3x", "x", x * factor));
Modified: trunk/Jmol/src/org/jmol/shape/HoverRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/HoverRenderer.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/shape/HoverRenderer.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -36,7 +36,7 @@
String label = (hover.atomFormats != null
&& hover.atomFormats[hover.atomIndex] != null ?
atom.formatLabel(hover.atomFormats[hover.atomIndex])
- : hover.labelFormat != null ? atom.formatLabel(hover.labelFormat)
+ : hover.labelFormat != null ? atom.formatLabel(fixLabel(atom, hover.labelFormat))
: null);
if (label == null)
return;
@@ -52,4 +52,11 @@
text.render(g3d, antialias);
}
}
+
+ String fixLabel(Atom atom, String label) {
+ if (label == null)
+ return null;
+ return (viewer.isJmolDataFrame(atom.getModelIndex())
+ && label.equals("%U") ?"%W" : label);
+ }
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -915,7 +915,7 @@
if (mesh.diameter > 0)
str.append(" diameter ").append(mesh.diameter);
int nVertices = mesh.drawVertexCount > 0 ? mesh.drawVertexCount
- : mesh.drawVertexCounts[0];
+ : mesh.drawVertexCounts[iModel >= 0 ? iModel : 0];
switch (mesh.drawTypes == null ? mesh.drawType : mesh.drawTypes[iModel]) {
case JmolConstants.DRAW_ARROW:
str.append(" ARROW");
@@ -936,6 +936,8 @@
if (mesh.modelIndex < 0 && !mesh.isFixed) {
for (int i = 0; i < modelCount; i++)
if (isPolygonDisplayable(mesh, i)) {
+ if (nVertices == 0)
+ nVertices = mesh.drawVertexCounts[i];
str.append(" [ " + i);
str.append(getVertexList(mesh, i, nVertices));
str.append(" ] ");
@@ -952,7 +954,9 @@
}
static boolean isPolygonDisplayable(Mesh mesh, int i) {
- return (mesh.polygonIndexes[i] != null && mesh.polygonIndexes[i].length > 0);
+ return (i < mesh.polygonIndexes.length
+ && mesh.polygonIndexes[i] != null
+ && mesh.polygonIndexes[i].length > 0);
}
private static String getVertexList(Mesh mesh, int iModel, int nVertices) {
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -3871,7 +3871,7 @@
for (int i = statementLength; --i >= 0;)
code[i] = statement[i];
variables.put("!" + variable.substring(8), code);
- viewer.addStateScript(thisCommand);
+ viewer.addStateScript(thisCommand, false);
} else {
assignBitsetVariable(variable, bs);
}
@@ -4162,49 +4162,45 @@
}
if (isSyntaxCheck) //just in case we later add parameter options to this
return;
- BitSet bs = viewer.getSelectedAtoms();
- int firstAtom = BitSetUtil.firstSetBit(bs);
- if (firstAtom < 0)
- return;
//for now, just one frame visible
- int modelIndex = viewer.getAtomModelIndex(firstAtom);
- int ptDataFrame = viewer.getPtJmolDataFrame(type + ":" + modelIndex);
+ int modelIndex = viewer.getCurrentModelIndex();
+ if (modelIndex < 0)
+ multipleModelsNotOK(type);
+ int ptDataFrame = viewer.getJmolDataFrameIndex(modelIndex, type);
if (ptDataFrame > 0) {
- viewer.setCurrentModelIndex(-1);
- BitSet bs2 = viewer.getModelAtomBitSet(ptDataFrame);
- bs2.and(bs);
+ // data frame can't be 0.
+ viewer.setCurrentModelIndex(ptDataFrame, true);
+// BitSet bs2 = viewer.getModelAtomBitSet(ptDataFrame);
+ // bs2.and(bs);
//need to be able to set data directly as well.
- viewer.display(BitSetUtil.setAll(viewer.getAtomCount()), bs2, tQuiet);
+ // viewer.display(BitSetUtil.setAll(viewer.getAtomCount()), bs2, tQuiet);
return;
}
+ String script;
switch (datatype) {
case JmolConstants.JMOL_DATA_RAMACHANDRAN:
- loadPdbDataWithScript(modelIndex,
- type,
- "frame 0.0; frame last; reset; center {0 0 0};zoomTo 0 (visible) 0;"
- + "select visible; color structure; select *;"
- + "draw ramaAxisX%N% {-10 0 0} {10 0 0};draw ramaAxisY%N% {0 -10 0} {0 10 0};");
+ default:
+ script = "frame 0.0; frame last; reset; center {0 0 0};"
+ + "select visible; color structure; select *;"
+ + "draw ramaAxisX%N% {20 0 0} {-20 0 0} \"phi\";"
+ + "draw ramaAxisY%N% {0 20 0} {0 -20 0} \"psi\";";
break;
- case JmolConstants.JMOL_DATA_QUATERNION:
- loadPdbDataWithScript(modelIndex,
- type,
- "frame 0.0; frame last; reset; center {0 0 0};zoomTo 0 (visible) 0;"
- + "select visible; trace 0.1; color trace structure; select *;"
- + "isosurface quatSphere%N% resolution 1.0 sphere 10.0 mesh nofill translucent 0.8;");
+ case JmolConstants.JMOL_DATA_QUATERNION:
+ script = "frame 0.0; frame last; reset; center {0 0 0};"
+ + "select visible; trace 0.1; color trace structure; select *;"
+ + "isosurface quatSphere%N% resolution 1.0 sphere 10.0 mesh nofill translucent 0.8;";
break;
}
- }
-
- private void loadPdbDataWithScript(int modelIndex, String type, String script)
- throws ScriptException {
String[] savedFileInfo = viewer.getFileInfo();
- boolean isOK = viewer.loadInline(viewer.getPdbData(type), '\n', true);
+ boolean isOK = viewer.loadInline(viewer.getPdbData(modelIndex, type), '\n', true);
viewer.setFileInfo(savedFileInfo);
if (!isOK)
return;
int modelCount = viewer.getModelCount();
runScript(TextFormat.simpleReplace(script, "%N%", "" + modelCount));
- viewer.setPtJmolDataFrame(type, modelIndex);
+ viewer.setJmolDataFrame(type, modelIndex, modelCount - 1);
+ viewer.addStateScript("frame " + viewer.getModelNumberDotted(modelIndex)
+ + "; " + type + ";", false);
showString("frame " + viewer.getModelName(-modelCount) + " created: "
+ type);
}
@@ -5443,15 +5439,16 @@
if (statementLength == 1) {
bsConfigurations = viewer.setConformation();
viewer
- .addStateScript("select " + Escape.escape(viewer.getSelectionSet()));
- viewer.addStateScript("configuration;");
+ .addStateScript("select "
+ + Escape.escape(viewer.getSelectionSet())
+ + "; configuration;", true);
} else {
checkLength2();
if (isSyntaxCheck)
return;
int n = intParameter(1);
bsConfigurations = viewer.setConformation(n - 1);
- viewer.addStateScript("configuration " + n + ";");
+ viewer.addStateScript("configuration " + n + ";", true);
}
if (isSyntaxCheck)
return;
@@ -5718,7 +5715,7 @@
case Token.surface:
viewer.calculateSurface(null, null, -1);
if (!isSyntaxCheck)
- viewer.addStateScript(thisCommand);
+ viewer.addStateScript(thisCommand, true);
return;
case Token.identifier:
if (parameterAsString(1).equalsIgnoreCase("AROMATIC")) {
@@ -5900,6 +5897,13 @@
boolean useModelNumber = true;
// for now -- as before -- remove to implement
// frame/model difference
+ if (statementLength == 1 && !isTrajectory && offset == 1) {
+ int modelIndex = viewer.getCurrentModelIndex();
+ if (!isSyntaxCheck && modelIndex >= 0
+ && (modelIndex = viewer.getJmolDataSourceFrame(modelIndex)) >= 0)
+ viewer.setCurrentModelIndex(modelIndex, true);
+ return;
+ }
if (getToken(offset).tok == Token.minus) {
++offset;
checkStatementLength(offset + 1);
@@ -5915,6 +5919,7 @@
boolean isHyphen = false;
int[] frameList = new int[] { -1, -1 };
int nFrames = 0;
+
for (int i = offset; i < statementLength; i++) {
switch (getToken(i).tok) {
case Token.all:
@@ -6814,7 +6819,7 @@
String str = label;
if (isAtoms) {
if (str == null) {
- str = modelSet.getAtomAt(j).getIdentity();
+ str = modelSet.getAtomAt(j).getInfo();
} else {
str = modelSet.getAtomAt(j).formatLabel(str, '\0', indices);
for (int k = 0; k < nProp; k++)
@@ -7975,7 +7980,10 @@
} else if (data == "PDB" || data == "XYZ" || data == "MOL") {
data = viewer.getData("selected", data);
} else if (data == "QUAT" || data == "RAMA") {
- data = viewer.getPdbData(type2);
+ int modelIndex = viewer.getCurrentModelIndex();
+ if (modelIndex < 0)
+ multipleModelsNotOK("write " + type2);
+ data = viewer.getPdbData(modelIndex, type2);
} else if (data == "FUNCS") {
data = getFunctionCalls("");
} else if (data == "FILE") {
@@ -8092,13 +8100,15 @@
str = "scaleAngstromsPerInch";
break;
case Token.quaternion:
+ case Token.ramachandran:
if (isSyntaxCheck)
return;
- msg = viewer.getPdbData("quaternion w");
+ int modelIndex = viewer.getCurrentModelIndex();
+ if (modelIndex < 0)
+ multipleModelsNotOK("show " + theToken.value);
+ msg = viewer.getPdbData(modelIndex,
+ theTok == Token.quaternion ? "quaternion w" : "ramachandran");
break;
- case Token.ramachandran:
- msg = viewer.getPdbData("ramachandran");
- break;
case Token.identifier:
if (str.equalsIgnoreCase("historyLevel")) {
value = "" + commandHistoryLevelMax;
@@ -8389,7 +8399,7 @@
viewer.loadShape(JmolConstants.SHAPE_MO);
int modelIndex = viewer.getDisplayModelIndex();
if (modelIndex < 0)
- multipleModelsNotOK();
+ multipleModelsNotOK("MO isosurfaces");
Hashtable moData = (Hashtable) viewer.getModelAuxiliaryInfo(modelIndex,
"moData");
if (moData == null)
@@ -9038,7 +9048,7 @@
int modelIndex = viewer.getDisplayModelIndex();
int offset = Integer.MAX_VALUE;
if (!isSyntaxCheck && modelIndex < 0)
- multipleModelsNotOK();
+ multipleModelsNotOK("MO isosurfaces");
viewer.loadShape(JmolConstants.SHAPE_MO);
if (tokAt(1) == Token.list && listIsosurface(JmolConstants.SHAPE_MO))
return true;
@@ -9193,7 +9203,7 @@
if (modelIndex == 0)
modelIndex = viewer.getDisplayModelIndex();
if (modelIndex < 0)
- multipleModelsNotOK();
+ multipleModelsNotOK("MO isosurfaces");
Hashtable moData = (Hashtable) viewer.getModelAuxiliaryInfo(modelIndex,
"jmolSurfaceInfo");
if (moData != null && ((String) moData.get("surfaceDataType")).equals("mo")) {
@@ -9908,8 +9918,8 @@
// new ScriptException(message);
// }
- private void multipleModelsNotOK() throws ScriptException {
- evalError(GT._("MO isosurfaces require that only one model be displayed"));
+ private void multipleModelsNotOK(String what) throws ScriptException {
+ evalError(GT._("{0} require that only one model be displayed", what));
}
private void unrecognizedCommand() throws ScriptException {
@@ -11085,15 +11095,12 @@
private boolean evaluateLabel(Token[] args) throws ScriptException {
Token x1 = getX();
- if (args.length != 1)
+ String format = (args.length == 0 ? "%U" : Token.sValue(args[0]));
+ if (args.length > 1 || x1.tok != Token.bitset)
return false;
if (isSyntaxCheck)
return addX("");
- Token x2 = args[0];
- if (x1.tok != Token.bitset || x2.tok != Token.string)
- return false;
- return addX(getBitsetIdent(Token.bsSelect(x1), Token.sValue(x2),
- x1.value, true));
+ return addX(getBitsetIdent(Token.bsSelect(x1), format, x1.value, true));
}
private boolean evaluateWithin(Token[] args) throws ScriptException {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-11-03 03:56:59 UTC (rev 8558)
@@ -1,5 +1,10 @@
-version=11.3.40_dev
+version=11.3.40
+# new feature: Ramachandran/Model commands switch between plot and model
+# -- one Ramachandran plot per model
+# -- axes labels and special hover label for Ramachandran plots
+# -- Ramachandran saved in state
+
# bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms.
# bug fix: @{} for within(1.0,point,@{....})
Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -69,7 +69,7 @@
// leaving or entering data frame? Then restore new frame's index
if (fromDataFrame || toDataFrame) {
viewer.restoreOrientation(toDataFrame ? viewer.getJmolDataFrameType(modelIndex)
- : "modelSet", 0);
+ : "modelSet", -1);
}
}
if (modelSet == null || modelIndex < 0
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -1636,7 +1636,8 @@
if (!Float.isNaN(navDepth))
setNavigationDepthPercent(0, navDepth);
}
- viewer.requestRepaintAndWait();
+ if (floatSecondsTotal >= 0)
+ viewer.requestRepaintAndWait();
viewer.setInMotion(false);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2007-11-02 19:22:22 UTC (rev 8557)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2007-11-03 03:56:59 UTC (rev 8558)
@@ -560,7 +560,7 @@
void moveTo(float floatSecondsTotal, Matrix3f rotationMatrix, Point3f center,
float zoom, float xTrans, float yTrans, float rotationRadius,
Point3f navCenter, float xNav, float yNav, float navDepth) {
- //from StateManager
+ //from StateManager -- -1 for time --> no repaint
transformManager.moveTo(floatSecondsTotal, rotationMatrix, center, zoom,
xTrans, yTrans, rotationRadius, navCenter, xNav, yNav, navDepth);
}
@@ -1704,8 +1704,8 @@
modelSet.fillAtomData(atomData, mode);
}
- void addStateScript(String script) {
- modelSet.addStateScript(script);
+ void addStateScript(String script, boolean addFrameNumber) {
+ modelSet.addStateScript(script, addFrameNumber);
}
public boolean getEchoStateActive() {
@@ -1833,7 +1833,7 @@
public void calculateStructures() {
//Eval
modelSet.calculateStructures(repaintManager.currentModelIndex);
- addStateScript("calculate structure");
+ addStateScript("calculate structure", true);
}
void clearBfactorRange() {
@@ -2380,7 +2380,7 @@
int autoHbond(BitSet bsBonds) {
//Eval
BitSet bs = getSelectionSet();
- addStateScript("calculate hbonds");
+ addStateScript("calculate hbonds", false);
return autoHbond(bs, bs, bsBonds);
}
@@ -5726,26 +5726,30 @@
return (String) Eval.evaluateExpression(this, exp);
}
- String getPdbData(String type) {
- return modelSet.getPdbData(type, selectionManager.bsSelection);
+ String getPdbData(int modelIndex, String type) {
+ return modelSet.getPdbData(modelIndex, type);
}
- boolean isJmolDataFrame(int modelIndex) {
+ public boolean isJmolDataFrame(int modelIndex) {
return modelSet.isJmolDataFrame(modelIndex);
}
- int getPtJmolDataFrame(String type) {
- return modelSet.getPtJmolDataFrame(type);
+ int getJmolDataFrameIndex(int modelIndex, String type) {
+ return modelSet.getJmolDataFrameIndex(modelIndex, type);
}
- void setPtJmolDataFrame(String type, int modelIndex) {
- modelSet.setPtJmolDataFrame(type, modelIndex);
+ void setJmolDataFrame(String type, int modelIndex, int dataIndex) {
+ modelSet.setJmolDataFrame(type, modelIndex, dataIndex);
}
String getJmolDataFrameType(int modelIndex) {
return modelSet.getJmolDataFrameType(modelIndex);
}
+ public int getJmolDataSourceFrame(int modelIndex) {
+ return modelSet.getJmolDataSourceFrame(modelIndex);
+ }
+
public void setAtomCoord(int atomIndex, float x, float y, float z) {
//Frame equivalent used in DATA "coord set"
modelSet.setAtomCoord(atomIndex, x, y, z);
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