From: <ha...@us...> - 2009-01-30 18:14:01
|
Revision: 10593 http://jmol.svn.sourceforge.net/jmol/?rev=10593&view=rev Author: hansonr Date: 2009-01-30 18:13:57 +0000 (Fri, 30 Jan 2009) Log Message: ----------- version=11.7.23_dev # new feature: load {ijk i'j'k' -1} loads crystal structure and packs unit cell Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-01-30 18:10:28 UTC (rev 10592) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-01-30 18:13:57 UTC (rev 10593) @@ -514,12 +514,12 @@ //set when unit cell is determined // x <= 555 and y >= 555 indicate a range of cells to load // AROUND the central cell 555 and that - // we should normalize (z = 1) or not (z = 0) + // we should normalize (z = 1) or pack unit cells (z = -1) or not (z = 0) this.latticeCells = latticeCells; isLatticeRange = (latticeCells[2] == 0 || latticeCells[2] == 1 || latticeCells[2] == -1) && (latticeCells[0] <= 555 && latticeCells[1] >= 555); doNormalize = (!isLatticeRange || latticeCells[2] == 1); - doFillUnitCell = (isLatticeRange && latticeCells[2] == -1); + doPackUnitCell = (isLatticeRange && latticeCells[2] == -1); setApplySymmetryToBonds(applySymmetryToBonds); } @@ -567,7 +567,7 @@ } boolean doNormalize = true; - boolean doFillUnitCell = false; + boolean doPackUnitCell = false; boolean isLatticeRange = false; void applySymmetry(int maxX, int maxY, int maxZ) throws Exception { @@ -655,7 +655,7 @@ } //always do the 555 cell first Matrix4f op = symmetry.getSpaceGroupOperation(0); - if (doFillUnitCell) + if (doPackUnitCell) ptOffset.set(0, 0, 0); for (int tx = minX; tx < maxX; tx++) for (int ty = minY; ty < maxY; ty++) @@ -668,7 +668,7 @@ Point3f c = new Point3f(atom); op.transform(c); symmetry.toCartesian(c); - if (doFillUnitCell) { + if (doPackUnitCell) { symmetry.toUnitCell(c, ptOffset); atom.set(c); symmetry.toFractional(atom); @@ -752,7 +752,7 @@ boolean isBaseCell = (baseCount == 0); boolean addBonds = (bondCount0 > bondIndex0 && applySymmetryToBonds); int[] atomMap = (addBonds ? new int[noSymmetryCount] : null); - if (doFillUnitCell) + if (doPackUnitCell) ptOffset.set(transX, transY, transZ); //symmetryRange < 0 : just check symop=1 set @@ -796,7 +796,7 @@ Atom special = null; Point3f cartesian = new Point3f(ptAtom); symmetry.toCartesian(cartesian); - if (doFillUnitCell) { + if (doPackUnitCell) { symmetry.toUnitCell(cartesian, ptOffset); ptAtom.set(cartesian); symmetry.toFractional(ptAtom); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-16 04:15:09
|
Revision: 10870 http://jmol.svn.sourceforge.net/jmol/?rev=10870&view=rev Author: hansonr Date: 2009-05-16 04:15:08 +0000 (Sat, 16 May 2009) Log Message: ----------- version=11.7.36_dev # new feature: Wien2k reader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-05-16 04:14:31 UTC (rev 10869) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-05-16 04:15:08 UTC (rev 10870) @@ -571,7 +571,6 @@ symmetry.setLattice(latt); } - void applySymmetry() throws Exception { //parameters are counts of unit cells as [a b c] applySymmetry(latticeCells[0], latticeCells[1], latticeCells[2]); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-06 19:41:30
|
Revision: 11689 http://jmol.svn.sourceforge.net/jmol/?rev=11689&view=rev Author: hansonr Date: 2009-11-06 19:41:23 +0000 (Fri, 06 Nov 2009) Log Message: ----------- version=11.9.8_dev # abstract public String loadInline(Vector arrayData, boolean isAppend); # @param arrayData a Vector of models, where each model is either a String # or a String[] or a Vector<String> Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-11-06 19:39:23 UTC (rev 11688) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2009-11-06 19:41:23 UTC (rev 11689) @@ -153,7 +153,8 @@ public AtomSetCollection(String fileTypeName, AtomSetCollectionReader atomSetCollectionReader) { this.fileTypeName = fileTypeName; - allowMultiple = (atomSetCollectionReader.desiredVibrationNumber < 0); + allowMultiple = (atomSetCollectionReader == null + || atomSetCollectionReader.desiredVibrationNumber < 0); // set the default PATH properties as defined in the SmarterJmolAdapter atomSetCollectionProperties.put("PATH_KEY", SmarterJmolAdapter.PATH_KEY); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-23 12:47:41
|
Revision: 12458 http://jmol.svn.sourceforge.net/jmol/?rev=12458&view=rev Author: hansonr Date: 2010-02-23 12:47:34 +0000 (Tue, 23 Feb 2010) Log Message: ----------- check for polymer or slab when symmetry lattice cell set is processed Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-02-23 12:45:58 UTC (rev 12457) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-02-23 12:47:34 UTC (rev 12458) @@ -702,14 +702,6 @@ maxZ = (maxY % 10) - 4; maxY = (maxY % 100) / 10 - 4; } - if (doPackUnitCell) { - minX--; - maxX++; - minY--; - maxY++; - minZ--; - maxZ++; - } switch ((int)getSymmetry().getUnitCellInfo(JmolConstants.INFO_DIMENSIONS)) { case 1: minY = minZ = 0; @@ -724,6 +716,14 @@ case 3: break; } + if (doPackUnitCell) { + minX--; + maxX++; + minY--; + maxY++; + minZ--; + maxZ++; + } this.maxX = maxX; this.maxY = maxY; this.maxZ = maxZ; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-28 15:44:05
|
Revision: 12515 http://jmol.svn.sourceforge.net/jmol/?rev=12515&view=rev Author: hansonr Date: 2010-02-28 15:43:58 +0000 (Sun, 28 Feb 2010) Log Message: ----------- version=11.9.32_dev # new feature: readers can now assign atomic data for atoms of the "property_" type # implemented for property_spin and property_magneticMoment in CrystalReader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-02-28 14:27:58 UTC (rev 12514) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-02-28 15:43:58 UTC (rev 12515) @@ -23,6 +23,7 @@ */ package org.jmol.adapter.smarter; +import java.util.Enumeration; import java.util.Hashtable; import java.util.Vector; import java.util.Properties; @@ -802,6 +803,8 @@ pt = symmetryAddAtoms(iAtomFirst, noSymmetryCount, tx, ty, tz, cell555Count, pt, iCell * operationCount); } + if (iCell * noSymmetryCount == atomCount - iAtomFirst) + appendAtomProperties(iCell); if (operationCount > 0) { String[] symmetryList = new String[operationCount]; for (int i = 0; i < operationCount; i++) @@ -1248,9 +1251,27 @@ Hashtable p = (Hashtable) getAtomSetAuxiliaryInfo(currentAtomSetIndex, "atomProperties"); if (p == null) setAtomSetAuxiliaryInfo("atomProperties", p = new Hashtable()); + if (!data.endsWith("\n")) + data += "\n"; p.put(key, data); } + private void appendAtomProperties(int nTimes) { + Hashtable p = (Hashtable) getAtomSetAuxiliaryInfo(currentAtomSetIndex, "atomProperties"); + if (p == null) + return; + Enumeration e = p.keys(); + while (e.hasMoreElements()) { + String key = (String) e.nextElement(); + String data = (String) p.get(key); + StringBuffer s = new StringBuffer(); + for (int i = nTimes; --i >= 0; ) + s.append(data); + p.put(key, s.toString()); + } + } + + /** * Sets auxiliary information for the AtomSet * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ni...@us...> - 2010-04-02 18:42:42
|
Revision: 12738 http://jmol.svn.sourceforge.net/jmol/?rev=12738&view=rev Author: nicove Date: 2010-04-02 18:42:36 +0000 (Fri, 02 Apr 2010) Log Message: ----------- Warning Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-02 18:41:33 UTC (rev 12737) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-02 18:42:36 UTC (rev 12738) @@ -1003,7 +1003,7 @@ } Matrix4f mat = new Matrix4f(); mat.set((float[]) biomts.get(i)); - Vector3f trans = new Vector3f(); + //Vector3f trans = new Vector3f(); for (int iAtom = iAtomFirst; iAtom < atomMax; iAtom++) { try { int atomSite = atoms[i].atomSite; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-05 03:10:05
|
Revision: 12763 http://jmol.svn.sourceforge.net/jmol/?rev=12763&view=rev Author: hansonr Date: 2010-04-05 03:09:59 +0000 (Mon, 05 Apr 2010) Log Message: ----------- VERSION version=12.0.RC3 # bug fix: structures with 400000+ atoms may be loaded # bug fix: calculated hbonds not retaining energy or type when saved to state # bug fix: color hbonds ENERGY causes NPE when non-calculated HBonds are created # code: smarter SmarterJmolAdapter deletes atoms as it goes to conserve resources # - allows loading of much larger models # code: ModelLoader distinguishes between small molecules and large molecules # bug fix: simple model appended to model having unit cell does not show axes # # new feature: set smallMoleculeMaxAtoms [default 40000] # This parameter sets the maximum number of atoms for default rendering of the model. # Models with this number or fewer atoms will be rendered with the default spacefill # rendering and the default bond diameter; models with more than this number of atoms # will be displayed by default with <b>spacefill 0; wireframe 1</b> for chains that # contain bonds and <b>backbone</b> for those that do not in order to conserve resources. # # new feature: calculate hbonds {....} {....} for models with H atoms # - H atoms must be in first set; atoms to consider must be in second set. # - no restriction in second set as to atom type other than that H atom in that set will be ignored. # # -------------------------------------------------------------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-05 02:37:59 UTC (rev 12762) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-05 03:09:59 UTC (rev 12763) @@ -400,7 +400,7 @@ public void addAtom(Atom atom) { if (atomCount == atoms.length) { if (atomCount > 200000) - atoms = (Atom[])ArrayUtil.ensureLength(atoms, atomCount + 25000); + atoms = (Atom[])ArrayUtil.ensureLength(atoms, atomCount + 50000); else atoms = (Atom[])ArrayUtil.doubleLength(atoms); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-04-26 17:21:44
|
Revision: 12933 http://jmol.svn.sourceforge.net/jmol/?rev=12933&view=rev Author: hansonr Date: 2010-04-26 17:21:38 +0000 (Mon, 26 Apr 2010) Log Message: ----------- version=12.0.RC9_dev # new feature: isosurface periodicity {a b c} # -- can be applied AFTER the fact -- it is just a rendering method # -- best carried out with PACKED unit cells Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-26 17:16:37 UTC (rev 12932) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-04-26 17:21:38 UTC (rev 12933) @@ -682,24 +682,33 @@ atoms[i].ellipsoid = symmetry.getEllipsoid(atoms[i].anisoBorU); bondCount0 = bondCount; - symmetry.setFinalOperations(atoms, iAtomFirst, noSymmetryCount, doNormalize); + symmetry + .setFinalOperations(atoms, iAtomFirst, noSymmetryCount, doNormalize); int operationCount = symmetry.getSpaceGroupOperationCount(); minXYZ = new Point3i(); maxXYZ = new Point3i(maxX, maxY, maxZ); getSymmetry().setMinMaxLatticeParameters(minXYZ, maxXYZ); - if ((int)getSymmetry().getUnitCellInfo(JmolConstants.INFO_DIMENSIONS) < 3) - doPackUnitCell = false; + int dims = (int) getSymmetry().getUnitCellInfo( + JmolConstants.INFO_DIMENSIONS); if (doPackUnitCell) { minXYZ.x--; maxXYZ.x++; - minXYZ.y--; - maxXYZ.y++; - minXYZ.z--; - maxXYZ.z++; + if (dims > 1) { // not polymer + minXYZ.y--; + maxXYZ.y++; + if (dims > 2) { // not polymer or slab + minXYZ.z--; + maxXYZ.z++; + } + } } - int nCells = (maxXYZ.x - minXYZ.x) * (maxXYZ.y - minXYZ.y) * (maxXYZ.z - minXYZ.z); + int nCells = (maxXYZ.x - minXYZ.x) * (maxXYZ.y - minXYZ.y) + * (maxXYZ.z - minXYZ.z); int cartesianCount = (checkSpecial ? noSymmetryCount * operationCount - * nCells : symmetryRange > 0 ? noSymmetryCount * operationCount // checking against {1 1 1} + * nCells : symmetryRange > 0 ? noSymmetryCount * operationCount // checking + // against + // {1 1 + // 1} : symmetryRange < 0 ? 1 // checking against symop=1555 set; just a box : 1 // not checking ); @@ -723,7 +732,7 @@ rmaxy = -Float.MAX_VALUE; rmaxz = -Float.MAX_VALUE; } - //always do the 555 cell first + // always do the 555 cell first Matrix4f op = symmetry.getSpaceGroupOperation(0); if (doPackUnitCell) ptOffset.set(0, 0, 0); @@ -778,7 +787,7 @@ pt = symmetryAddAtoms(iAtomFirst, noSymmetryCount, tx, ty, tz, cell555Count, pt, iCell * operationCount); } - if (iCell * noSymmetryCount == atomCount - iAtomFirst) + if (iCell * noSymmetryCount == atomCount - iAtomFirst) appendAtomProperties(iCell); setSymmetryOps(); setAtomSetAuxiliaryInfo("presymmetryAtomIndex", new Integer(iAtomFirst)); @@ -790,7 +799,7 @@ symmetry.setSpaceGroup(null); notionalUnitCell = new float[6]; coordinatesAreFractional = false; - //turn off global fractional conversion -- this will be model by model + // turn off global fractional conversion -- this will be model by model setAtomSetAuxiliaryInfo("hasSymmetry", Boolean.TRUE); setGlobalBoolean(GLOBAL_SYMMETRY); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-05-27 16:01:56
|
Revision: 13235 http://jmol.svn.sourceforge.net/jmol/?rev=13235&view=rev Author: hansonr Date: 2010-05-27 16:01:50 +0000 (Thu, 27 May 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-05-27 15:37:12 UTC (rev 13234) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-05-27 16:01:50 UTC (rev 13235) @@ -234,6 +234,7 @@ // auxiliary info // Clone each AtomSet int clonedAtoms = 0; + setAtomSetCollectionAuxiliaryInfo("loadState", collection.getAtomSetCollectionAuxiliaryInfo("loadState")); for (int atomSetNum = 0; atomSetNum < collection.atomSetCount; atomSetNum++) { newAtomSet(); atomSetAuxiliaryInfo[currentAtomSetIndex] = collection.atomSetAuxiliaryInfo[atomSetNum]; @@ -276,6 +277,7 @@ if (Boolean.TRUE.equals( collection.getAtomSetCollectionAuxiliaryInfo(globalBooleans[i]))) setGlobalBoolean(i); + } void setNoAutoBond() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-09-26 18:35:51
|
Revision: 14373 http://jmol.svn.sourceforge.net/jmol/?rev=14373&view=rev Author: hansonr Date: 2010-09-26 18:35:45 +0000 (Sun, 26 Sep 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-09-26 16:21:53 UTC (rev 14372) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2010-09-26 18:35:45 UTC (rev 14373) @@ -43,7 +43,6 @@ import org.jmol.api.VolumeDataInterface; import org.jmol.util.ArrayUtil; import org.jmol.util.BitSetUtil; -import org.jmol.util.Escape; import org.jmol.util.Logger; import org.jmol.util.Parser; import org.jmol.util.TextFormat; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-03 01:15:31
|
Revision: 15696 http://jmol.svn.sourceforge.net/jmol/?rev=15696&view=rev Author: hansonr Date: 2011-07-03 01:15:25 +0000 (Sun, 03 Jul 2011) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-07-03 00:04:43 UTC (rev 15695) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-07-03 01:15:25 UTC (rev 15696) @@ -535,14 +535,14 @@ } public void connectAll(int maxSerial) { - if (vConnect == null) { - return; - } int firstAtom = connectNextAtomIndex; for (int i = connectNextAtomSet; i < atomSetCount; i++) { - setGlobalBoolean(GLOBAL_CONECT); - setAtomSetAuxiliaryInfo("PDB_CONECT_firstAtom_count_max", new int[] {firstAtom, atomSetAtomCounts[i], maxSerial}, i); - setAtomSetAuxiliaryInfo("PDB_CONECT_bonds", vConnect, i); + setAtomSetAuxiliaryInfo("PDB_CONECT_firstAtom_count_max", new int[] { + firstAtom, atomSetAtomCounts[i], maxSerial }, i); + if (vConnect != null) { + setAtomSetAuxiliaryInfo("PDB_CONECT_bonds", vConnect, i); + setGlobalBoolean(GLOBAL_CONECT); + } firstAtom += atomSetAtomCounts[i]; } vConnect = null; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-10-29 05:24:07
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Revision: 16419 http://jmol.svn.sourceforge.net/jmol/?rev=16419&view=rev Author: hansonr Date: 2011-10-29 05:24:00 +0000 (Sat, 29 Oct 2011) Log Message: ----------- second shot at TLS parser for PDBReader. more fully tested. Adds REMARK 7 support (1zyg) Use getProperty auxiliaryInfo.models[1].tlsGroups to inspect. Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-10-28 15:17:56 UTC (rev 16418) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2011-10-29 05:24:00 UTC (rev 16419) @@ -1577,7 +1577,7 @@ * @param value The value for the property * @param atomSetIndex The index of the AtomSet to get the property */ - void setAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex) { + public void setAtomSetAuxiliaryInfo(String key, Object value, int atomSetIndex) { if (atomSetIndex < 0) return; if (atomSetAuxiliaryInfo[atomSetIndex] == null) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-06-27 08:21:43
|
Revision: 18370 http://sourceforge.net/p/jmol/code/18370 Author: hansonr Date: 2013-06-27 08:21:40 +0000 (Thu, 27 Jun 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-06-27 08:11:32 UTC (rev 18369) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-06-27 08:21:40 UTC (rev 18370) @@ -1475,10 +1475,8 @@ if (atomCount > 0) { int index = atomCount - 1; String atomName = atoms[index].atomName; - if (atomName != null) { + if (atomName != null) atomSymbolicMap.put(atomName, Integer.valueOf(index)); - System.out.println(this + " " + atomName); - } } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-11-06 14:15:29
|
Revision: 18914 http://sourceforge.net/p/jmol/code/18914 Author: hansonr Date: 2013-11-06 14:15:21 +0000 (Wed, 06 Nov 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-11-06 08:32:37 UTC (rev 18913) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2013-11-06 14:15:21 UTC (rev 18914) @@ -1485,6 +1485,7 @@ a.add(atoms[i]); a.scale(1f / bs.cardinality()); a.atomName = "Pt" + ichain; + a.chainID = e.getKey().intValue(); } iAtomFirst = atomMax; atomMax += nChain; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-05 21:07:01
|
Revision: 19604 http://sourceforge.net/p/jmol/code/19604 Author: hansonr Date: 2014-04-05 21:06:55 +0000 (Sat, 05 Apr 2014) Log Message: ----------- JmolVersion="14.1.14_2014.04.05" new feature: array.join() -- creates a flat array from an array of arrays: -- example: $x = [1,2,[3,4,5],[6,[7,8,9]]].join() $show x x = [ 1,2,3,4,5,6,7,8,9 ] new feature: DSSR output reading -- Defining the (Secondary) Structures of RNA -- see http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-%28secondary%29-structures-of-rna/ -- brain-child of Xiang-Jun Lu (3d...@gm...; Columbia University) -- use system command x3d-dssr.exe --input=xxxx.pdb > xxxx.out -- then in Jmol: load files "xxxx.pdb" + "xxxx.out" -- all DSSR information will be in auxiliaryInfo.models.dssr with the following keys: aMinorMotifs basePairs bulges coaxialStacks hairpinLoops helices internalLoops junctions kinkTurns kissingLoops multiplets riboseZippers singleStrandedSegments stems wobblePairs -- all entries are lists. -- most of these list entries have "nt" entries, and those are nucleotide residue identifiers, so Jmol's getProperty() "drill-down" capabilities allow for: x = getProperty("auxiliaryInfo.models.1.dssr.basepairs.nt") select @{x} new feature: minimal SQL logic in getProperty(): -- allows for simple SELECT, WHERE, LIKE, NOT LIKE, =, and != -- example: load files "c:/temp/dssr/1jj2/1jj2.pdb" + "c:/temp/dssr/1jj2/1jj2.out" print getProperty("auxiliaryInfo.models.1.dssr.basepairs","SELECT nt* WHERE bp=C-G") print getProperty("auxiliaryInfo.models.1.dssr.basepairs","SELECT nt* WHERE Saenger LIKE 19%") x = getProperty("auxiliaryInfo.models.dssr.kinkturns[SELECT nts WHERE type=Normal].nt") Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2014-04-05 20:39:40 UTC (rev 19603) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java 2014-04-05 21:06:55 UTC (rev 19604) @@ -1166,6 +1166,8 @@ + energyString); setAtomSetAuxiliaryInfo("EnergyString", energyString); setAtomSetAuxiliaryInfo("Energy", Float.valueOf(value)); + if (Float.isNaN(Float.valueOf(value).floatValue())) + System.out.println("testing here"); setAtomSetModelProperty("Energy", "" + value); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |