Revision: 20281
http://sourceforge.net/p/jmol/code/20281
Author: hansonr
Date: 2015-02-11 12:48:31 +0000 (Wed, 11 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.11"
bug fix: "USER MOD" not accepted at beginning of PDB file (MolProbity breaking
PDB format here)
bug fix: 02.10 may break loading ligand files
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-11
12:00:50 UTC (rev 20280)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-11
12:48:31 UTC (rev 20281)
@@ -1308,7 +1308,7 @@
atom.vib = V3.new3(siteMult, 0, Float.NaN);
}
asc.setCurrentModelInfo("isCIF", Boolean.TRUE);
- if (isMMCIF && !isLigand)
+ if (isMMCIF)
setModelPDB(true);
if (isMMCIF && skipping)
skipping = false;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2015-02-11
12:00:50 UTC (rev 20280)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2015-02-11
12:48:31 UTC (rev 20281)
@@ -606,7 +606,7 @@
"DBREF ", "SEQADV", "SEQRES", "MODRES",
"HELIX ", "SHEET ", "TURN ",
"CRYST1", "ORIGX1", "ORIGX2", "ORIGX3", "SCALE1", "SCALE2", "SCALE3",
- "ATOM ", "HETATM", "MODEL ", "LINK ",
+ "ATOM ", "HETATM", "MODEL ", "LINK ", "USER MOD ",
};
private final static String[] cgdLineStartRecords =
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-02-11 12:00:50 UTC
(rev 20280)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-02-11 12:48:31 UTC
(rev 20281)
@@ -81,7 +81,7 @@
private Viewer vwr;
public ModelSet ms;
- private ModelSet mergeModelSet;
+ private ModelSet modelSet0;
private boolean merging;
private boolean appendNew;
@@ -92,13 +92,13 @@
public int[] specialAtomIndexes;
public ModelLoader(Viewer vwr, String modelSetName,
- SB loadScript, Object asc, ModelSet mergeModelSet,
+ SB loadScript, Object asc, ModelSet modelSet0,
BS bsNew) {
this.vwr = vwr;
ms = new ModelSet(vwr, modelSetName);
JmolAdapter adapter = vwr.getModelAdapter();
- this.mergeModelSet = mergeModelSet;
- merging = (this.mergeModelSet != null && this.mergeModelSet.ac > 0);
+ this.modelSet0 = modelSet0;
+ merging = (modelSet0 != null && modelSet0.ac > 0);
if (merging) {
ms.canSkipLoad = false;
} else {
@@ -207,15 +207,15 @@
ms.someModelsHaveFractionalCoordinates = ms
.getMSInfoB("someModelsHaveFractionalCoordinates");
if (merging) {
- ms.haveBioModels |= mergeModelSet.haveBioModels;
- ms.bioModelset = mergeModelSet.bioModelset;
- ms.someModelsHaveSymmetry |= mergeModelSet
+ ms.haveBioModels |= modelSet0.haveBioModels;
+ ms.bioModelset = modelSet0.bioModelset;
+ ms.someModelsHaveSymmetry |= modelSet0
.getMSInfoB("someModelsHaveSymmetry");
- someModelsHaveUnitcells |= mergeModelSet
+ someModelsHaveUnitcells |= modelSet0
.getMSInfoB("someModelsHaveUnitcells");
- ms.someModelsHaveFractionalCoordinates |= mergeModelSet
+ ms.someModelsHaveFractionalCoordinates |= modelSet0
.getMSInfoB("someModelsHaveFractionalCoordinates");
- ms.someModelsHaveAromaticBonds |=
mergeModelSet.someModelsHaveAromaticBonds;
+ ms.someModelsHaveAromaticBonds |= modelSet0.someModelsHaveAromaticBonds;
ms.msInfo.put("someModelsHaveSymmetry",
Boolean.valueOf(ms.someModelsHaveSymmetry));
ms.msInfo.put("someModelsHaveUnitcells",
@@ -299,7 +299,7 @@
iModel = -1;
model = null;
if (merging)
- mergeTrajAndVib(mergeModelSet, ms);
+ mergeTrajAndVib(modelSet0, ms);
initializeAtomBondModelCounts(nAtoms);
if (bsNew != null && (doMinimize || is2D)) {
bsNew.setBits(baseAtomIndex, baseAtomIndex + nAtoms);
@@ -371,10 +371,10 @@
setAtomProperties();
if (adapter != null)
adapter.finish(asc);
- if (mergeModelSet != null) {
- mergeModelSet.releaseModelSet();
+ if (modelSet0 != null) {
+ modelSet0.releaseModelSet();
}
- mergeModelSet = null;
+ modelSet0 = null;
}
private void mergeTrajAndVib(ModelSet oldSet, ModelSet newSet) {
@@ -475,11 +475,11 @@
baseModelIndex = baseModelCount - 1;
ms.mc = baseModelCount;
}
- ms.ac = baseAtomIndex = mergeModelSet.ac;
- ms.bondCount = mergeModelSet.bondCount;
- mergeGroups = mergeModelSet.getGroups();
+ ms.ac = baseAtomIndex = modelSet0.ac;
+ ms.bondCount = modelSet0.bondCount;
+ mergeGroups = modelSet0.getGroups();
groupCount = baseGroupIndex = mergeGroups.length;
- ms.mergeModelArrays(mergeModelSet);
+ ms.mergeModelArrays(modelSet0);
ms.growAtomArrays(ms.ac + nAtoms);
} else {
ms.mc = adapterModelCount;
@@ -499,12 +499,12 @@
ms.modelNames = AU.arrayCopyS(ms.modelNames, ms.mc);
ms.frameTitles = AU.arrayCopyS(ms.frameTitles, ms.mc);
if (merging)
- for (int i = 0; i < mergeModelSet.mc; i++)
- (ms.am[i] = mergeModelSet.am[i]).ms = ms;
+ for (int i = 0; i < modelSet0.mc; i++)
+ (ms.am[i] = modelSet0.am[i]).ms = ms;
}
private void mergeGroups() {
- Map<String, Object> info = mergeModelSet.getAuxiliaryInfo(null);
+ Map<String, Object> info = modelSet0.getAuxiliaryInfo(null);
String[] mergeGroup3Lists = (String[]) info.get("group3Lists");
int[][] mergeGroup3Counts = (int[][]) info.get("group3Counts");
if (mergeGroup3Lists != null) {
@@ -518,7 +518,7 @@
}
//if merging PDB data into an already-present model, and the
//structure is defined, consider the current structures in that
- //model to be undefined. Not guarantee to work.
+ //model to be undefined. Not guaranteed to work.
if (!appendNew && ms.haveBioModels)
structuresDefinedInFile.clear(baseModelIndex);
}
@@ -551,11 +551,9 @@
modelName = (jmolData != null && jmolData.indexOf(";") > 2 ?
jmolData.substring(jmolData
.indexOf(":") + 2, jmolData.indexOf(";"))
: appendNew ? "" + (modelNumber % 1000000): "");
- boolean isPDBModel = setModelNameNumberProperties(ipt, iTrajectory,
+ setModelNameNumberProperties(ipt, iTrajectory,
modelName, modelNumber, modelProperties, modelAuxiliaryInfo,
jmolData);
- if (isPDBModel)
- jbr.setGroupLists(ipt);
if (ms.getInfo(ipt, "periodicOriginXyz") != null)
ms.someModelsHaveSymmetry = true;
}
@@ -591,29 +589,29 @@
finalizeModels(baseModelCount);
}
- private boolean setModelNameNumberProperties(
- int modelIndex,
- int trajectoryBaseIndex,
- String modelName,
- int modelNumber,
- Properties modelProperties,
- Map<String, Object>
modelAuxiliaryInfo,
- String jmolData) {
- boolean modelIsPDB = (modelAuxiliaryInfo != null
- && Boolean.TRUE == modelAuxiliaryInfo.get("isPDB"));
+ private void setModelNameNumberProperties(int modelIndex,
+ int trajectoryBaseIndex,
+ String modelName,
+ int modelNumber,
+ Properties modelProperties,
+ Map<String, Object>
modelAuxiliaryInfo,
+ String jmolData) {
if (appendNew) {
- ms.am[modelIndex] = (modelIsPDB ?
- jbr.getBioModel(modelIndex, trajectoryBaseIndex,
- jmolData, modelProperties, modelAuxiliaryInfo)
- : new Model().set(ms, modelIndex, trajectoryBaseIndex,
- jmolData, modelProperties, modelAuxiliaryInfo));
+ boolean modelIsPDB = (modelAuxiliaryInfo != null && Boolean.TRUE ==
modelAuxiliaryInfo
+ .get("isPDB"));
+ ms.am[modelIndex] = (modelIsPDB ? jbr.getBioModel(modelIndex,
+ trajectoryBaseIndex, jmolData, modelProperties, modelAuxiliaryInfo)
+ : new Model().set(ms, modelIndex, trajectoryBaseIndex, jmolData,
+ modelProperties, modelAuxiliaryInfo));
ms.modelNumbers[modelIndex] = modelNumber;
ms.modelNames[modelIndex] = modelName;
+ if (modelIsPDB)
+ jbr.setGroupLists(modelIndex);
} else {
- // set appendNew false
- Object atomInfo =
modelAuxiliaryInfo.get("PDB_CONECT_firstAtom_count_max");
+ Object atomInfo = modelAuxiliaryInfo
+ .get("PDB_CONECT_firstAtom_count_max");
if (atomInfo != null)
- ms.setInfo(modelIndex, "PDB_CONECT_firstAtom_count_max", atomInfo);
+ ms.setInfo(modelIndex, "PDB_CONECT_firstAtom_count_max", atomInfo);
}
// this next sets the bitset length to avoid
// unnecessary calls to System.arrayCopy
@@ -633,10 +631,9 @@
models[modelIndex].insertionCount = (codes == null ? 0 : codes.length());
boolean isModelKit = (ms.modelSetName != null
&& ms.modelSetName.startsWith("Jmol Model Kit")
- || modelName.startsWith("Jmol Model Kit") || "Jme"
- .equals(ms.getInfo(modelIndex, "fileType")));
+ || modelName.startsWith("Jmol Model Kit") || "Jme".equals(ms.getInfo(
+ modelIndex, "fileType")));
models[modelIndex].isModelKit = isModelKit;
- return modelIsPDB;
}
/**
@@ -1032,10 +1029,10 @@
if (someModelsHaveUnitcells) {
ms.unitCells = new SymmetryInterface[ms.mc];
ms.haveUnitCells = true;
- boolean haveMergeCells = (mergeModelSet != null &&
mergeModelSet.unitCells != null);
+ boolean haveMergeCells = (modelSet0 != null && modelSet0.unitCells !=
null);
for (int i = 0, pt = 0; i < ms.mc; i++) {
if (haveMergeCells && i < baseModelCount) {
- ms.unitCells[i] = mergeModelSet.unitCells[i];
+ ms.unitCells[i] = modelSet0.unitCells[i];
} else {
ms.unitCells[i] = Interface.getSymmetry(vwr, "file");
float[] notionalCell = null;
@@ -1288,7 +1285,7 @@
bondsCache[j] = null;
}
- ms.setAtomNamesAndNumbers(0, baseAtomIndex, mergeModelSet);
+ ms.setAtomNamesAndNumbers(0, baseAtomIndex, modelSet0);
// find elements for the popup menus
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2015-02-11
12:00:50 UTC (rev 20280)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2015-02-11
12:48:31 UTC (rev 20281)
@@ -195,12 +195,11 @@
return nitrogenHydrogenPoint;
}
- public P3 getExplicitNH() {
+ public Atom getExplicitNH() {
Atom nitrogen = getNitrogenAtom();
Atom h = null;
Bond[] bonds = nitrogen.bonds;
- if (bonds == null)
- return null;
+ if (bonds != null)
for (int i = 0; i < bonds.length; i++)
if ((h = bonds[i].getOtherAtom(nitrogen)).getElementNumber() == 1)
return h;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-11 12:00:50 UTC
(rev 20280)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-11 12:48:31 UTC
(rev 20281)
@@ -804,6 +804,7 @@
int ac = ms.ac;
BS bsRes0 = new BS();
res0.setAtomBits(bsRes0);
+ Atom[] backbone = getBackbone(res0, null);
int r = g.getResno();
// just use a script -- it is much easier!
@@ -830,12 +831,21 @@
+ " var c = {!res0 & connected(res0)}\n"
+ " var N2 = {*.N & c}\n"
+ " var C0 = {*.C & c}\n"
+ + " var angleH = ({*.H and res0} ? angle({*.C and res0},{*.CA
and res0},{*.N and res0},{*.H and res0}) : 1000)\n"
+ " delete res0\n"
+ " if (N2) {\n"
- + " delete *.OXT and res1\n"
+ + " delete (*.OXT,*.HXT) and res1\n"
+ " connect {N2} {keyatoms & *.C}\n"
+ " }\n"
- + " if (C0) {\n"
+ + " if (C0) {\n" // not terminal
+ + " if ({res1 and _H & connected(*.N)} == 1) {\n" // proline
or proline-like
+ + " delete *.H and res1\n"
+ + " } else {\n"
+ + " var x = angle({*.C and res1},{*.CA and res1},{*.N and
res1},{*.H and res1})\n"
+ + " rotate branch {*.CA and res1} {*.N and res1}
@{angleH-x}\n"
+ + " delete *.H2 and res1\n"
+ + " delete *.H3 and res1\n"
+ + " }\n"
+ " connect {C0} {keyatoms & *.N}\n"
+ " }\n"
+ " }\n"
@@ -859,9 +869,13 @@
return false;
}
AminoMonomer res1 = (AminoMonomer) g;
-
+
+ // fix h position as same as previous group
+ getBackbone(res1, backbone);
// must get new group into old chain
+ // note that the terminal N if replacing the N-terminus will only have
two H atoms
+
Group[] groups = res0.chain.groups;
for (int i = groups.length; --i >= 0;)
if (groups[i] == res0) {
@@ -889,6 +903,34 @@
/////////////////////////////////////////////////////////////////////////
+ /**
+ * @param res1
+ * @param backbone
+ * @return [C O CA N H]
+ */
+ private Atom[] getBackbone(AminoMonomer res1, Atom[] backbone) {
+ Atom[] b = new Atom[] {res1.getCarbonylCarbonAtom(),
res1.getCarbonylOxygenAtom(),
+ res1.getLeadAtom(), res1.getNitrogenAtom(), res1.getExplicitNH() };
+ if (backbone == null) {
+ // don't place H if there is more than one covalent H on res0.N
+ if (b[3].getCovalentHydrogenCount() > 1)
+ b[4] = null;
+ } else {
+ for (int i = 0; i < 5; i++) {
+ Atom a0 = backbone[i];
+ Atom a1 = b[i];
+ if (a0 != null && a1 != null)
+ a1.setT(a0);
+ }
+ }
+ return b;
+
+
+
+ // TODO
+
+ }
+
BioModel(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex,
String jmolData, Properties properties, Map<String, Object>
auxiliaryInfo) {
vwr = modelSet.vwr;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-11 12:00:50 UTC
(rev 20280)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-11 12:48:31 UTC
(rev 20281)
@@ -15,8 +15,13 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.02.10"
+Jmol.___JmolVersion="14.3.12_2015.02.11"
+bug fix: "USER MOD" not accepted at beginning of PDB file (MolProbity
breaking PDB format here)
+bug fix: 02.10 may break loading ligand files
+
+JmolVersion="14.3.12_2015.02.10"
+
bug fix: color $contact1 "roygb" range -0.5 1.0; broken (in state after using
CONTACT)
bug fix: mmCIF reader does not flag first model of a multimodel set as type PDB
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