Revision: 21157
http://sourceforge.net/p/jmol/code/21157
Author: hansonr
Date: 2016-06-23 11:33:52 +0000 (Thu, 23 Jun 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.7.0_2016.06.22"
new feature: settable chain string using {atomset}.chain = "xxx"
bug fix: compare(a,b,"isomer") does not detect ENANTIOMER (broken in 14.5.5)
bug fix: missing error trap for unsettable property setting
bug fix: load models {0 0 1} ... fails in script compiler
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2016-06-22 17:09:15 UTC (rev
21156)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2016-06-23 11:33:52 UTC (rev
21157)
@@ -380,16 +380,12 @@
// 100 times the bfactor(temperature) value
public int getBfactor100() {
short[] bfactor100s = group.chain.model.ms.bfactor100s;
- if (bfactor100s == null)
- return 0;
- return bfactor100s[i];
+ return (bfactor100s == null ? 0 : bfactor100s[i]);
}
- private float getHydrophobicity() {
+ public float getHydrophobicity() {
float[] values = group.chain.model.ms.hydrophobicities;
- if (values == null)
- return Elements.getHydrophobicity(group.groupID);
- return values[i];
+ return (values == null ? Elements.getHydrophobicity(group.groupID) :
values[i]);
}
public boolean setRadius(float radius) {
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-06-22
17:09:15 UTC (rev 21156)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2016-06-23
11:33:52 UTC (rev 21157)
@@ -74,6 +74,10 @@
abstract public class AtomCollection {
+ private final static float almost180 = (float) Math.PI * 0.95f;
+ private final static float sqrt3_2 = (float) (Math.sqrt(3) / 2);
+ private final static V3 vRef = V3.new3(3.14159f, 2.71828f, 1.41421f);
+
public Viewer vwr;
protected GData g3d;
/**
@@ -88,30 +92,6 @@
public Trajectory trajectory;
- ////////////////////////////////////////////////////////////////
- // these may or may not be allocated
- // depending upon the AtomSetCollection characteristics
- //
- // used by Atom:
- //
- String[] atomNames;
- String[] atomTypes;
- int[] atomSerials;
- int[] atomResnos;
- int[] atomSeqIDs;
- public Vibration[] vibrations;
- public float[] occupancies;
- short[] bfactor100s;
- float[] partialCharges;
- float[] bondingRadii;
- float[] hydrophobicities;
-
- public Object[][] atomTensorList; // specifically now for {*}.adpmin
{*}.adpmax
- public Map<String, Lst<Object>> atomTensors;
-
- protected int[] surfaceDistance100s;
-
-
////////////////////
private LabelToken labeler;
@@ -125,6 +105,8 @@
private int bfactor100Lo;
private int bfactor100Hi;
+ private boolean haveBSVisible, haveBSClickable;
+
private BS bsSurface;
private int nSurfaceAtoms;
private int surfaceDistanceMax;
@@ -141,50 +123,81 @@
public boolean haveStraightness;
- // be sure to add the name to the list below as well!
- final public static byte TAINT_ATOMNAME = 0;
- final public static byte TAINT_ATOMTYPE = 1;
- final public static byte TAINT_COORD = 2;
- final public static byte TAINT_ELEMENT = 3;
- final public static byte TAINT_FORMALCHARGE = 4;
- final public static byte TAINT_HYDROPHOBICITY = 5;
- final public static byte TAINT_BONDINGRADIUS = 6;
- final public static byte TAINT_OCCUPANCY = 7;
- final public static byte TAINT_PARTIALCHARGE = 8;
- final public static byte TAINT_TEMPERATURE = 9;
- final public static byte TAINT_VALENCE = 10;
- final public static byte TAINT_VANDERWAALS = 11;
- final public static byte TAINT_VIBRATION = 12;
- final public static byte TAINT_ATOMNO = 13;
- final public static byte TAINT_SEQID = 14;
- final public static byte TAINT_RESNO = 15;
- final public static byte TAINT_MAX = 16; // 1 more than last number, above
-
- public static String[] userSettableValues;
-
- private final static float almost180 = (float) Math.PI * 0.95f;
- private final static float sqrt3_2 = (float) (Math.sqrt(3) / 2);
- private final static V3 vRef = V3.new3(3.14159f, 2.71828f, 1.41421f);
-
- public BS[] tainted;
private BS bsHidden;
public BS bsVisible, bsClickable, bsModulated;
- private boolean haveBSVisible, haveBSClickable;
+ ////////////////////////////////////////////////////////////////
+ // these may or may not be allocated
+ // depending upon the AtomSetCollection characteristics
+ //
+ // used by Atom:
+ //
+ public Object[][] atomTensorList; // specifically now for {*}.adpmin
{*}.adpmax
+ public Map<String, Lst<Object>> atomTensors;
+
+ protected int[] surfaceDistance100s;
+
+ ///// SETTABLE atomic properties ///////////////
+ //
+ // The following references must be made if a new property is added to this
list:
+ //
+ // 1) Add a new static value to the following TAINT_XXXX list.
+ // 2) Add its T.map name to the list in setupAC().
+ // 3) Follow all references to both atomType (for a string), formalCharge
(for an int), or partialCharge (for a float)
+ // These will include a reference in setAPa() and setAtomData() here and
+ // to getAtomicPropertyStateBuffer() in viewer.StateCreator
+ // 4) add the settable attribute to the static int XXXX definition in
script.T
+ // 5) check that {*}.xxxx = ....; write state test.spt, and script test.spt
all work properly
+
+ public BS[] tainted;
+ public static String[] userSettableValues;
+
protected void setupAC() {
bsHidden = new BS();
bsVisible = new BS();
bsClickable = new BS();
// this allows the Google Closure compiler to skip all the TAINTED defs in
Clazz.defineStatics
if (userSettableValues == null)
- userSettableValues = "atomName atomType coord element formalCharge
hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals
vibrationVector atomNo seqID resNo".split(" ");
+ userSettableValues = ("atomName atomType coord element formalCharge
hydrophobicity " +
+ "ionic occupancy partialCharge temperature valence vanderWaals
vibrationVector " +
+ "atomNo seqID resNo chain").split(" ");
}
+
+ final public static int TAINT_ATOMNAME = 0;
+ final public static int TAINT_ATOMTYPE = 1;
+ final public static int TAINT_COORD = 2;
+ final public static int TAINT_ELEMENT = 3;
+ final public static int TAINT_FORMALCHARGE = 4;
+ final public static int TAINT_HYDROPHOBICITY = 5;
+ final public static int TAINT_BONDINGRADIUS = 6;
+ final public static int TAINT_OCCUPANCY = 7;
+ final public static int TAINT_PARTIALCHARGE = 8;
+ final public static int TAINT_TEMPERATURE = 9;
+ final public static int TAINT_VALENCE = 10;
+ final public static int TAINT_VANDERWAALS = 11;
+ final public static int TAINT_VIBRATION = 12;
+ final public static int TAINT_ATOMNO = 13;
+ final public static int TAINT_SEQID = 14;
+ final public static int TAINT_RESNO = 15;
+ final public static int TAINT_CHAIN = 16;
+ final public static int TAINT_MAX = 17; // 1 more than last number, above
- protected void releaseModelSet() {
- releaseModelSetAC();
- }
+ String[] atomNames;
+ String[] atomTypes;
+ // String[] chainIDs; not necessary, as there is a place for this already in
atom.group.chain
+ int[] atomSerials;
+ int[] atomResnos;
+ int[] atomSeqIDs;
+ public Vibration[] vibrations;
+ public float[] occupancies;
+ short[] bfactor100s;
+ float[] partialCharges;
+ float[] bondingRadii;
+ float[] hydrophobicities;
+
+
protected void releaseModelSetAC() {
at = null;
vwr = null;
@@ -571,21 +584,20 @@
Atom atom = at[i];
switch (tok) {
case T.atomname:
- taintAtom(i, TAINT_ATOMNAME);
- setAtomName(i, sValue);
+ setAtomName(i, sValue, true);
break;
+ case T.atomtype:
+ setAtomType(i, sValue);
+ break;
+ case T.chain:
+ setChainID(i, sValue);
+ break;
case T.atomno:
- taintAtom(i, TAINT_ATOMNO);
- setAtomNumber(i, iValue);
+ setAtomNumber(i, iValue, true);
break;
case T.seqid:
- taintAtom(i, TAINT_SEQID);
setAtomSeqID(i, iValue);
break;
- case T.atomtype:
- taintAtom(i, TAINT_ATOMTYPE);
- setAtomType(i, sValue);
- break;
case T.atomx:
case T.x:
setAtomCoord(i, fValue, atom.y, atom.z);
@@ -617,35 +629,37 @@
break;
case T.elemno:
case T.element:
- setElement(atom, iValue);
+ setElement(atom, iValue, true);
break;
case T.formalcharge:
atom.setFormalCharge(iValue);
taintAtom(i, TAINT_FORMALCHARGE);
break;
case T.hydrophobicity:
- if (setHydrophobicity(i, fValue))
- taintAtom(i, TAINT_HYDROPHOBICITY);
+ setHydrophobicity(i, fValue);
break;
- case T.label:
- case T.format:
- vwr.shm.setAtomLabel(sValue, i);
- break;
case T.occupancy:
// a legacy thing
if (fValue < 2 && fValue > 0.01f)
fValue = 100 * fValue;
- if (setOccupancy(i, fValue))
- taintAtom(i, TAINT_OCCUPANCY);
+ setOccupancy(i, fValue, true);
break;
case T.partialcharge:
- if (setPartialCharge(i, fValue))
- taintAtom(i, TAINT_PARTIALCHARGE);
+ setPartialCharge(i, fValue, true);
break;
case T.bondingradius:
- if (setBondingRadius(i, fValue))
- taintAtom(i, TAINT_BONDINGRADIUS);
+ setBondingRadius(i, fValue);
break;
+ case T.temperature:
+ setBFactor(i, fValue, true);
+ break;
+ case T.resno:
+ setAtomResno(i, iValue);
+ break;
+ case T.label:
+ case T.format:
+ vwr.shm.setAtomLabel(sValue, i);
+ break;
case T.radius:
case T.spacefill:
if (fValue < 0)
@@ -657,14 +671,6 @@
case T.selected:
vwr.slm.setSelectedAtom(atom.i, (fValue != 0));
break;
- case T.temperature:
- if (setBFactor(i, fValue))
- taintAtom(i, TAINT_TEMPERATURE);
- break;
- case T.resno:
- setAtomResno(i, iValue);
- taintAtom(i, TAINT_RESNO);
- break;
case T.valence:
atom.setValence(iValue);
taintAtom(i, TAINT_VALENCE);
@@ -690,14 +696,6 @@
}
}
- protected void setElement(Atom atom, int atomicNumber) {
- taintAtom(atom.i, TAINT_ELEMENT);
- atom.setAtomicAndIsotopeNumber(atomicNumber);
- atom.paletteID = PAL.CPK.id;
- atom.colixAtom = vwr.cm.getColixAtomPalette(atom,
- PAL.CPK.id);
- }
-
/**
* also handles modulation info
*
@@ -791,104 +789,143 @@
setAtomVibrationVector(atomIndex, v);
}
- public void setAtomName(int atomIndex, String name) {
- byte id = (((ModelSet)this).am[at[atomIndex].mi].isBioModel ?
vwr.getJBR().lookupSpecialAtomID(name) : 0);
+ public void setAtomName(int atomIndex, String name, boolean doTaint) {
+ if (doTaint && name.equals(at[atomIndex].getAtomName()))
+ return;
+ // can't set the name of a bioatom
+ byte id = (((ModelSet) this).am[at[atomIndex].mi].isBioModel ? vwr.getJBR()
+ .lookupSpecialAtomID(name) : 0);
at[atomIndex].atomID = id;
- if (id > 0)
- return;
- if (atomNames == null)
- atomNames = new String[at.length];
- atomNames[atomIndex] = name;
+ if (id <= 0) {
+ if (atomNames == null)
+ atomNames = new String[at.length];
+ atomNames[atomIndex] = name;
+ }
+ if (doTaint)
+ taintAtom(atomIndex, TAINT_ATOMNAME);
}
- protected void setAtomType(int atomIndex, String type) {
- if (atomTypes == null)
- atomTypes = new String[at.length];
- atomTypes[atomIndex] = type;
+ private void setAtomType(int atomIndex, String type) {
+ if (type.equals(at[atomIndex].getAtomType()))
+ return;
+ if (atomTypes == null)
+ atomTypes = new String[at.length];
+ atomTypes[atomIndex] = type;
+ return;
}
- public boolean setAtomNumber(int atomIndex, int atomno) {
- if (atomSerials == null) {
+ private void setChainID(int atomIndex, String id) {
+ if (id.equals(at[atomIndex].getChainIDStr()))
+ return;
+ int intid = at[atomIndex].getChainID();
+ BS bs = getChainBits(intid);
+ Chain c = at[atomIndex].group.chain;
+ c.chainID = vwr.getChainID(id, true);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ taintAtom(i, TAINT_CHAIN);
+ }
+
+ public void setAtomNumber(int atomIndex, int atomno, boolean doTaint) {
+ if (doTaint && atomno == at[atomIndex].getAtomNumber())
+ return;
+ if (atomSerials == null)
atomSerials = new int[at.length];
- }
atomSerials[atomIndex] = atomno;
- return true;
+ if (doTaint)
+ taintAtom(atomIndex, TAINT_ATOMNO);
}
- public boolean setAtomResno(int atomIndex, int resno) {
- if (atomResnos == null) {
+ protected void setElement(Atom atom, int atomicNumber, boolean doTaint) {
+ if (doTaint && atom.getElementNumber() == atomicNumber)
+ return;
+ atom.setAtomicAndIsotopeNumber(atomicNumber);
+ atom.paletteID = PAL.CPK.id;
+ atom.colixAtom = vwr.cm.getColixAtomPalette(atom,
+ PAL.CPK.id);
+ if (doTaint)
+ taintAtom(atom.i, TAINT_ELEMENT);
+ }
+
+ private void setAtomResno(int atomIndex, int resno) {
+ if (resno == at[atomIndex].getResno())
+ return;
+ at[atomIndex].group.setResno(resno);
+ if (atomResnos == null)
atomResnos = new int[at.length];
- }
atomResnos[atomIndex] = resno;
- at[atomIndex].group.setResno(resno);
- return true;
+ taintAtom(atomIndex, TAINT_RESNO);
}
- public boolean setAtomSeqID(int atomIndex, int seqID) {
- if (atomSeqIDs == null) {
+ private void setAtomSeqID(int atomIndex, int seqID) {
+ if (seqID == at[atomIndex].getSeqID())
+ return;
+ if (atomSeqIDs == null)
atomSeqIDs = new int[at.length];
- }
atomSeqIDs[atomIndex] = seqID;
- return true;
+ taintAtom(atomIndex, TAINT_SEQID);
}
- protected boolean setOccupancy(int atomIndex, float occupancy) {
+ protected void setOccupancy(int atomIndex, float occupancy, boolean doTaint)
{
+ if (doTaint && occupancy == at[atomIndex].getOccupancy100())
+ return;
if (occupancies == null) {
if (occupancy == 100)
- return false; // 100 is the default;
+ return; // 100 is the default;
occupancies = new float[at.length];
for (int i = at.length; --i >= 0;)
occupancies[i] = 100;
}
occupancies[atomIndex] = occupancy;
- return true;
+ if (doTaint)
+ taintAtom(atomIndex, TAINT_OCCUPANCY);
}
- protected boolean setPartialCharge(int atomIndex, float partialCharge) {
- if (Float.isNaN(partialCharge))
- return false;
+ protected void setPartialCharge(int atomIndex, float partialCharge, boolean
doTaint) {
+ if (Float.isNaN(partialCharge) || doTaint && partialCharge ==
at[atomIndex].getPartialCharge())
+ return;
if (partialCharges == null) {
if (partialCharge == 0)
- return false; // no need to store a 0.
+ return; // no need to store a 0.
partialCharges = new float[at.length];
}
partialCharges[atomIndex] = partialCharge;
- return true;
+ if (doTaint)
+ taintAtom(atomIndex, TAINT_PARTIALCHARGE);
}
- protected boolean setBondingRadius(int atomIndex, float radius) {
- if (Float.isNaN(radius))
- return false;
- if (bondingRadii == null) {
+ private void setBondingRadius(int atomIndex, float radius) {
+ if (Float.isNaN(radius) || radius == at[atomIndex].getBondingRadius())
+ return;
+ if (bondingRadii == null)
bondingRadii = new float[at.length];
- }
bondingRadii[atomIndex] = radius;
- return true;
+ taintAtom(atomIndex, TAINT_BONDINGRADIUS);
}
- protected boolean setBFactor(int atomIndex, float bfactor) {
- if (Float.isNaN(bfactor))
- return false;
+ protected void setBFactor(int atomIndex, float bfactor, boolean doTaint) {
+ if (Float.isNaN(bfactor) || doTaint && bfactor ==
at[atomIndex].getBfactor100())
+ return;
if (bfactor100s == null) {
- if (bfactor == 0 && bfactor100s == null) // there's no need to store a 0.
- return false;
+ if (bfactor == 0) // there's no need to store a 0.
+ return;
bfactor100s = new short[at.length];
}
bfactor100s[atomIndex] = (short) ((bfactor < -327.68f ? -327.68f
: bfactor > 327.67 ? 327.67 : bfactor) * 100 + (bfactor < 0 ? -0.5 :
0.5));
- return true;
+ if (doTaint)
+ taintAtom(atomIndex, TAINT_TEMPERATURE);
}
- protected boolean setHydrophobicity(int atomIndex, float value) {
- if (Float.isNaN(value))
- return false;
+ private void setHydrophobicity(int atomIndex, float value) {
+ if (Float.isNaN(value) || value == at[atomIndex].getHydrophobicity())
+ return;
if (hydrophobicities == null) {
hydrophobicities = new float[at.length];
for (int i = 0; i < at.length; i++)
hydrophobicities[i] = Elements.getHydrophobicity(at[i].group.groupID);
}
hydrophobicities[atomIndex] = value;
- return true;
+ taintAtom(atomIndex, TAINT_HYDROPHOBICITY);
}
// loading data
@@ -928,8 +965,11 @@
fData[atomIndex] = x;
bs.set(atomIndex);
continue;
+ case TAINT_ATOMNAME:
+ setAtomName(atomIndex, tokens[pt], true);
+ break;
case TAINT_ATOMNO:
- setAtomNumber(atomIndex, (int) x);
+ setAtomNumber(atomIndex, (int) x, true);
break;
case TAINT_RESNO:
setAtomResno(atomIndex, (int) x);
@@ -937,12 +977,12 @@
case TAINT_SEQID:
setAtomSeqID(atomIndex, (int) x);
break;
- case TAINT_ATOMNAME:
- setAtomName(atomIndex, tokens[pt]);
- break;
case TAINT_ATOMTYPE:
setAtomType(atomIndex, tokens[pt]);
break;
+ case TAINT_CHAIN:
+ setChainID(atomIndex, tokens[pt]);
+ break;
case TAINT_ELEMENT:
atom.setAtomicAndIsotopeNumber((int)x);
atom.paletteID = PAL.CPK.id;
@@ -958,10 +998,10 @@
setBondingRadius(atomIndex, x);
break;
case TAINT_PARTIALCHARGE:
- setPartialCharge(atomIndex, x);
+ setPartialCharge(atomIndex, x, true);
break;
case TAINT_TEMPERATURE:
- setBFactor(atomIndex, x);
+ setBFactor(atomIndex, x, true);
break;
case TAINT_VALENCE:
atom.setValence((int)x);
@@ -970,7 +1010,7 @@
atom.setRadius(x);
break;
}
- taintAtom(atomIndex, (byte) type);
+ taintAtom(atomIndex, type);
}
if (type == TAINT_MAX && n > 0)
vwr.setData(name, new Object[] {name, fData, bs,
Integer.valueOf(JmolDataManager.DATA_TYPE_AF)}, 0, 0, 0, 0, 0);
@@ -1033,11 +1073,11 @@
return (isExplicit ? TAINT_MAX : -1);
}
- public BS getTaintedAtoms(byte type) {
+ public BS getTaintedAtoms(int type) {
return tainted == null ? null : tainted[type];
}
- public void taintAtoms(BS bsAtoms, byte type) {
+ public void taintAtoms(BS bsAtoms, int type) {
canSkipLoad = false;
if (!preserveState)
return;
@@ -1045,7 +1085,7 @@
taintAtom(i, type);
}
- protected void taintAtom(int atomIndex, byte type) {
+ protected void taintAtom(int atomIndex, int type) {
if (!preserveState)
return;
if (tainted == null)
@@ -1057,7 +1097,7 @@
validateBspfForModel(((ModelSet)
this).am[at[atomIndex].mi].trajectoryBaseIndex, false);
}
- private void untaint(int atomIndex, byte type) {
+ private void untaint(int atomIndex, int type) {
if (!preserveState)
return;
if (tainted == null || tainted[type] == null)
@@ -1065,7 +1105,7 @@
tainted[type].clear(atomIndex);
}
- public void setTaintedAtoms(BS bs, byte type) {
+ public void setTaintedAtoms(BS bs, int type) {
if (!preserveState)
return;
if (bs == null) {
@@ -1081,7 +1121,7 @@
BSUtil.copy2(bs, tainted[type]);
}
- public void unTaintAtoms(BS bs, byte type) {
+ public void unTaintAtoms(BS bs, int type) {
if (tainted == null || tainted[type] == null)
return;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1))
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2016-06-22
17:09:15 UTC (rev 21156)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2016-06-23
11:33:52 UTC (rev 21157)
@@ -73,10 +73,6 @@
freeBonds[i] = new Bond[MAX_NUM_TO_CACHE][];
setupAC();
}
- @Override
- protected void releaseModelSet() {
- releaseModelSetBC();
- }
protected void releaseModelSetBC() {
bo = null;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2016-06-22 17:09:15 UTC
(rev 21156)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2016-06-23 11:33:52 UTC
(rev 21157)
@@ -219,7 +219,6 @@
setupBC();
}
- @Override
protected void releaseModelSet() {
am = null;
closest[0] = null;
@@ -2952,10 +2951,10 @@
boolean isDelete = false;
if (atomicNumber > 0) {
- setElement(atom, atomicNumber);
+ setElement(atom, atomicNumber, false);
vwr.shm.setShapeSizeBs(JC.SHAPE_BALLS, 0, vwr.rd,
BSUtil.newAndSetBit(atomIndex));
- setAtomName(atomIndex, type + atom.getAtomNumber());
+ setAtomName(atomIndex, type + atom.getAtomNumber(), false);
if (!am[atom.mi].isModelKit)
taintAtom(atomIndex, TAINT_ATOMNAME);
} else if (type.equals("Pl")) {
@@ -3131,9 +3130,9 @@
growAtomArrays(ac + 100); // only due to added hydrogens
at[ac] = atom;
- setBFactor(ac, bfactor);
- setOccupancy(ac, occupancy);
- setPartialCharge(ac, partialCharge);
+ setBFactor(ac, bfactor, false);
+ setOccupancy(ac, occupancy, false);
+ setPartialCharge(ac, partialCharge, false);
if (tensors != null)
setAtomTensors(ac, tensors);
atom.group = group;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java 2016-06-22
17:09:15 UTC (rev 21156)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java 2016-06-23
11:33:52 UTC (rev 21157)
@@ -678,9 +678,9 @@
if (lastSetH == Integer.MIN_VALUE || atoms[iAtom].mi !=
atoms[lastSetH].mi)
maxSerial = ((int[]) ms.getInfo(atoms[lastSetH = iAtom].mi,
"PDB_CONECT_firstAtom_count_max"))[2];
bsAddedHydrogens.clear(iAtom);
- ms.setAtomName(iAtom, name);
+ ms.setAtomName(iAtom, name, false);
atoms[iAtom].setT(pt);
- ms.setAtomNumber(iAtom, ++maxSerial);
+ ms.setAtomNumber(iAtom, ++maxSerial, false);
atoms[iAtom].atomSymmetry = atoms[iTo].atomSymmetry;
ml.undeleteAtom(iAtom);
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2016-06-22 17:09:15 UTC (rev
21156)
+++ trunk/Jmol/src/org/jmol/script/T.java 2016-06-23 11:33:52 UTC (rev
21157)
@@ -543,7 +543,7 @@
public final static int atomtype = strproperty | 1 | settable;
public final static int atomname = strproperty | 2 | settable;
public final static int altloc = strproperty | 3;
- public final static int chain = strproperty | 4;
+ public final static int chain = strproperty | 4 | settable;
public final static int element = strproperty | 5 | settable;
public final static int group = strproperty | 6;
public final static int group1 = strproperty | 7;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-06-22 17:09:15 UTC
(rev 21156)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-06-23 11:33:52 UTC
(rev 21157)
@@ -49,6 +49,8 @@
Jmol.___JmolVersion="14.7.0_2016.06.22"
+new feature: settable chain string using {atomset}.chain = "xxx"
+
bug fix: compare(a,b,"isomer") does not detect ENANTIOMER (broken in 14.5.5)
bug fix: missing error trap for unsettable property setting
bug fix: load models {0 0 1} ... fails in script compiler
Modified: trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java 2016-06-22
17:09:15 UTC (rev 21156)
+++ trunk/Jmol/src/org/jmol/viewer/JmolStateCreator.java 2016-06-23
11:33:52 UTC (rev 21157)
@@ -27,9 +27,9 @@
abstract String getFunctionCalls(String selectedFunction);
- abstract String getAtomicPropertyState(byte taintCoord, BS bsSelected);
+ abstract String getAtomicPropertyState(int taintCoord, BS bsSelected);
- abstract void getAtomicPropertyStateBuffer(SB commands, byte type,
+ abstract void getAtomicPropertyStateBuffer(SB commands, int type,
BS bs, String name, float[] data);
abstract void undoMoveAction(int action, int n);
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-06-22 17:09:15 UTC
(rev 21156)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2016-06-23 11:33:52 UTC
(rev 21157)
@@ -179,7 +179,7 @@
private String getDataState(SB sfunc) {
SB commands = new SB();
boolean haveData = false;
- String atomProps = getAtomicPropertyState((byte) -1, null);
+ String atomProps = getAtomicPropertyState(-1, null);
if (atomProps.length() > 0) {
haveData = true;
commands.append(atomProps);
@@ -1514,18 +1514,18 @@
}
}
- private static boolean isTainted(BS[] tainted, int atomIndex, byte type) {
+ private static boolean isTainted(BS[] tainted, int atomIndex, int type) {
return (tainted != null && tainted[type] != null && tainted[type]
.get(atomIndex));
}
@Override
- String getAtomicPropertyState(byte taintWhat, BS bsSelected) {
+ String getAtomicPropertyState(int taintWhat, BS bsSelected) {
if (!vwr.g.preserveState)
return "";
BS bs;
SB commands = new SB();
- for (byte type = 0; type < AtomCollection.TAINT_MAX; type++)
+ for (int type = 0; type < AtomCollection.TAINT_MAX; type++)
if (taintWhat < 0 || type == taintWhat)
if ((bs = (bsSelected != null ? bsSelected : vwr
.ms.getTaintedAtoms(type))) != null)
@@ -1534,7 +1534,7 @@
}
@Override
- void getAtomicPropertyStateBuffer(SB commands, byte type, BS bs,
+ void getAtomicPropertyStateBuffer(SB commands, int type, BS bs,
String label, float[] fData) {
if (!vwr.g.preserveState)
return;
@@ -1563,6 +1563,9 @@
case AtomCollection.TAINT_ATOMNO:
s.appendI(atoms[i].getAtomNumber());
break;
+ case AtomCollection.TAINT_CHAIN:
+ s.append(atoms[i].getChainIDStr());
+ break;
case AtomCollection.TAINT_RESNO:
s.appendI(atoms[i].group.getResno());
break;
@@ -1729,8 +1732,8 @@
sb.append("#" + type + " " + taintedAtom + " " + (new Date()) + "\n");
if (taintedAtom >= 0) {
bs = vwr.getModelUndeletedAtomsBitSet(modelIndex);
- vwr.ms.taintAtoms(bs, (byte) type);
- sb.append(getAtomicPropertyState((byte) -1, null));
+ vwr.ms.taintAtoms(bs, type);
+ sb.append(getAtomicPropertyState(-1, null));
} else {
bs = vwr.getModelUndeletedAtomsBitSet(modelIndex);
sb.append("zap ");
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