From: <ha...@us...> - 2008-10-11 20:15:41
|
Revision: 10064 http://jmol.svn.sourceforge.net/jmol/?rev=10064&view=rev Author: hansonr Date: 2008-10-11 20:15:37 +0000 (Sat, 11 Oct 2008) Log Message: ----------- version=11.7.3_dev load SELECT/TRAJECTORY # new feature: load SELECT ({bitset}) # new feature: load TRAJECTORY ({bitset}) # new feature: load APPEND SELECT Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-10-11 20:15:09 UTC (rev 10063) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-10-11 20:15:37 UTC (rev 10064) @@ -296,14 +296,14 @@ .intValue(); } else if (htParams.containsKey("firstLastStep")) { isTrajectory = (desiredModelNumber == -1); - firstLastStep = (int[]) htParams.get("firstLastStep"); + firstLastStep = (int[]) htParams.get("firstLastStep"); if (firstLastStep[2] == 0) firstLastStep[1] = -1; } else if (htParams.containsKey("bsModels")) { isTrajectory = (desiredModelNumber == -1); bsModels = (BitSet) htParams.get("bsModels"); desiredModelNumber = Integer.MIN_VALUE; - } + } if (bsModels == null && firstLastStep != null) { if (firstLastStep[0] < 0) firstLastStep[0] = 0; @@ -311,16 +311,12 @@ firstLastStep[1] = -1; if (firstLastStep[2] < 1) firstLastStep[2] = 1; - if (firstLastStep[1] == firstLastStep[0]) { - desiredModelNumber = firstLastStep[0] + 1; - } else { - desiredModelNumber = Integer.MIN_VALUE; - bsModels = new BitSet(); - bsModels.set(firstLastStep[0] + 1); - if (firstLastStep[1] > firstLastStep[0]) { - for (int i = firstLastStep[0]; i <= firstLastStep[1]; i += firstLastStep[2]) - bsModels.set(i); - } + desiredModelNumber = Integer.MIN_VALUE; + bsModels = new BitSet(); + bsModels.set(firstLastStep[0] + 1); + if (firstLastStep[1] > firstLastStep[0]) { + for (int i = firstLastStep[0]; i <= firstLastStep[1]; i += firstLastStep[2]) + bsModels.set(i); } } if (bsModels != null) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-10-11 21:39:41
|
Revision: 10067 http://jmol.svn.sourceforge.net/jmol/?rev=10067&view=rev Author: hansonr Date: 2008-10-11 21:39:36 +0000 (Sat, 11 Oct 2008) Log Message: ----------- version=11.7.3_dev # new feature: load "xxxx.prmtop" COORD ({bitset}) "mdcrd::md1.crd" Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-10-11 21:07:31 UTC (rev 10066) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2008-10-11 21:39:36 UTC (rev 10067) @@ -321,7 +321,7 @@ bsModels.set(i); } } - if (bsModels != null) + if (bsModels != null && (firstLastStep == null || firstLastStep[1] != -1)) lastModelNumber = BitSetUtil.length(bsModels); if (params == null) return; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-03-20 05:47:53
|
Revision: 10729 http://jmol.svn.sourceforge.net/jmol/?rev=10729&view=rev Author: hansonr Date: 2009-03-20 05:47:48 +0000 (Fri, 20 Mar 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-03-20 05:36:57 UTC (rev 10728) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-03-20 05:47:48 UTC (rev 10729) @@ -786,6 +786,7 @@ v.normalize(); System.out.println (" st 3 " + v); matrixRotate.setColumn(2, v); + atomSetCollection.setAtomSetAuxiliaryInfo("defaultRotation",new Matrix3f(matrixRotate)); atomSetCollection.setTransform(matrixRotate); // String view = "resetQuaternion = quaternion({"+tokens[4] + " " + tokens[5] + " " + tokens[6]+"},{" This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-16 17:09:55
|
Revision: 10878 http://jmol.svn.sourceforge.net/jmol/?rev=10878&view=rev Author: hansonr Date: 2009-05-16 17:09:17 +0000 (Sat, 16 May 2009) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-05-16 17:03:11 UTC (rev 10877) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-05-16 17:09:17 UTC (rev 10878) @@ -375,7 +375,7 @@ // three options include: // = -1: normal -- use operators if present or name if not // = -2: user is supplying operators or name - // >=0: spacegroup fully determined; 9999 will be based on user-supplied operators + // >=0: spacegroup fully determined // = -999: ignore -- just the operators desiredSpaceGroupIndex = ((Integer) htParams.get("spaceGroupIndex")) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-05-22 20:36:27
|
Revision: 10901 http://jmol.svn.sourceforge.net/jmol/?rev=10901&view=rev Author: hansonr Date: 2009-05-22 20:36:09 +0000 (Fri, 22 May 2009) Log Message: ----------- 11.7.38 VERSION # spartan smol reader broken in 11.7.37 oops -- sorry about that! Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-05-22 20:26:38 UTC (rev 10900) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-05-22 20:36:09 UTC (rev 10901) @@ -550,7 +550,7 @@ } private Matrix3f matrixRotate; - protected void setTransform(float x1, float y1, float z1, float x2, float y2, + public void setTransform(float x1, float y1, float z1, float x2, float y2, float z2, float x3, float y3, float z3) { if (matrixRotate != null) return; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-06-26 07:56:19
|
Revision: 11124 http://jmol.svn.sourceforge.net/jmol/?rev=11124&view=rev Author: hansonr Date: 2009-06-26 07:56:18 +0000 (Fri, 26 Jun 2009) Log Message: ----------- version=11.7.45_dev # code: refactored readers, allowing for more obvious initialization/finalization methods Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-06-26 07:55:03 UTC (rev 11123) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-06-26 07:56:18 UTC (rev 11124) @@ -194,6 +194,11 @@ return finalize(htParams, filename); } + public abstract void readAtomSetCollection(BufferedReader reader); + + public void readAtomSetCollectionFromDOM(Object DOMNode) { + } + private Object finalize(Hashtable htParams, String filename) { if (!htParams.containsKey("templateAtomCount")) htParams.put("templateAtomCount", new Integer(atomSetCollection @@ -222,11 +227,6 @@ return atomSetCollection; } - public abstract void readAtomSetCollection(BufferedReader reader); - - public void readAtomSetCollectionFromDOM(Object DOMNode) { - } - protected void setError(Exception e) { e.printStackTrace(); if (line == null) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2009-11-07 15:26:02
|
Revision: 11698 http://jmol.svn.sourceforge.net/jmol/?rev=11698&view=rev Author: hansonr Date: 2009-11-07 15:25:55 +0000 (Sat, 07 Nov 2009) Log Message: ----------- version=11.9.8_dev # bug fix: GAMESS reader not reading all vibrational frequencies # code: refactoring of readers to standardize vibration loading # # new feature: load "xxxx.xxx" [-vibration number] # loads only the specific vibration model. # Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-11-07 15:25:11 UTC (rev 11697) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2009-11-07 15:25:55 UTC (rev 11698) @@ -710,15 +710,10 @@ boolean[] ignore, boolean isWide, int col0, int colWidth) throws Exception { - String[][] data = new String[isWide ? atomCount : atomCount * 3][]; - fillDataBlock(data, col0, colWidth); - fillFrequencies(data, iAtom0, atomCount, ignore, isWide); - } - - protected void fillFrequencies(String[][] data, int iAtom0, int atomCount, - boolean[] ignore, boolean isWide) { + int nLines = (isWide ? atomCount : atomCount * 3); int nFreq = ignore.length; - int nLines = data.length; + String[][] data = new String[nLines][]; + fillDataBlock(data, col0, colWidth); for (int i = 0, atomPt = 0; i < nLines; i++, atomPt++) { String[] values = data[i]; String[] valuesY = (isWide ? null : data[++i]); @@ -731,6 +726,8 @@ if (ignore[j]) continue; int iAtom = iAtom0 + atomCount * j + atomPt; + if (Logger.debugging) + Logger.debug("vib " + iAtom + "/" + j + ": " + vx + " " + vy + " " + vz); atomSetCollection.addVibrationVector(iAtom, vx, vy, vz); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-03-08 13:41:24
|
Revision: 12577 http://jmol.svn.sourceforge.net/jmol/?rev=12577&view=rev Author: hansonr Date: 2010-03-08 13:41:15 +0000 (Mon, 08 Mar 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-03-08 13:38:59 UTC (rev 12576) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-03-08 13:41:15 UTC (rev 12577) @@ -233,6 +233,12 @@ return true; } + /** + * sets continuing and doProcessLines + * + * @return TRUE if continuing, FALSE if not + * + */ public boolean checkLastModel() { if (isLastModel(modelNumber) && doProcessLines) { continuing = false; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-03-25 12:15:16
|
Revision: 12697 http://jmol.svn.sourceforge.net/jmol/?rev=12697&view=rev Author: hansonr Date: 2010-03-25 12:15:09 +0000 (Thu, 25 Mar 2010) Log Message: ----------- version=11.9.36_dev # new feature: GenNBO file reader for xx.31-.41 files and .nbo output if in that directory # bug fix: Spartan and WebMO orbitals are already normalized! Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-03-25 12:10:07 UTC (rev 12696) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-03-25 12:15:09 UTC (rev 12697) @@ -798,10 +798,12 @@ String[] tokens = new String[0]; int pt = 0; for (int i = 0; i < temp.length; i++) { - while (pt >= tokens.length) { + while (tokens != null && pt >= tokens.length) { tokens = getTokens(readLine()); pt = 0; } + if (tokens == null) + break; temp[i] = parseFloat(tokens[pt++]); } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-10-18 18:37:56
|
Revision: 14502 http://jmol.svn.sourceforge.net/jmol/?rev=14502&view=rev Author: hansonr Date: 2010-10-18 18:37:49 +0000 (Mon, 18 Oct 2010) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-10-18 18:36:11 UTC (rev 14501) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-10-18 18:37:49 UTC (rev 14502) @@ -640,12 +640,14 @@ doSetOrientation = !checkFilter("NOORIENT"); addVibrations = !checkFilter(FILTER_NOVIB); readMolecularOrbitals = !checkFilter(FILTER_NOMO); + if (filter == null) + return; filterAtomType = checkFilter("*.") || checkFilter("!."); filterGroup3 = checkFilter("["); filterChain = checkFilter(":"); filterAltLoc = checkFilter("%"); haveAtomFilter = filterAtomType || filterGroup3 || filterChain || filterAltLoc; - if (filter != null && bsFilter == null) { + if (bsFilter == null) { // bsFilter is usually null, but from MDTOP it gets set to indicate // which atoms were selected by the filter. This then // gets used by COORD files to load just those coordinates This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-10-18 19:14:52
|
Revision: 14507 http://jmol.svn.sourceforge.net/jmol/?rev=14507&view=rev Author: hansonr Date: 2010-10-18 19:14:46 +0000 (Mon, 18 Oct 2010) Log Message: ----------- version=12.1.16_dev # code: load FILTER clean-up, standardization Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-10-18 19:05:05 UTC (rev 14506) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-10-18 19:14:46 UTC (rev 14507) @@ -620,10 +620,7 @@ protected boolean addVibrations; public boolean readMolecularOrbitals; - // MANY: - protected final static String FILTER_NOVIB = "NOVIB"; - protected final static String FILTER_NOMO = "NOMO"; - + // MANY: "NOVIB" "NOMO" // CSF, SPARTAN: "NOORIENT" // CRYSTAL: "CONV" (conventional), "INPUT" // GAMESS-US: "CHARGE=LOW" @@ -638,8 +635,8 @@ filter0 = filter0.toUpperCase(); filter = filter0; doSetOrientation = !checkFilter("NOORIENT"); - addVibrations = !checkFilter(FILTER_NOVIB); - readMolecularOrbitals = !checkFilter(FILTER_NOMO); + addVibrations = !checkFilter("NOVIB"); + readMolecularOrbitals = !checkFilter("NOMO"); if (filter == null) return; filterAtomType = checkFilter("*.") || checkFilter("!."); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-01-31 19:38:55
|
Revision: 15083 http://jmol.svn.sourceforge.net/jmol/?rev=15083&view=rev Author: hansonr Date: 2011-01-31 19:38:49 +0000 (Mon, 31 Jan 2011) Log Message: ----------- fix for crystal reader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-01-31 14:15:28 UTC (rev 15082) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-01-31 19:38:49 UTC (rev 15083) @@ -1053,6 +1053,13 @@ return line; } + protected String discardLinesUntilContains(String s1, String s2) + throws Exception { + while (readLine() != null && line.indexOf(s1) < 0 && line.indexOf(s2) < 0) { + } + return line; + } + protected void discardLinesUntilBlank() throws Exception { while (readLine() != null && line.trim().length() != 0) { } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-04-11 02:03:16
|
Revision: 15379 http://jmol.svn.sourceforge.net/jmol/?rev=15379&view=rev Author: hansonr Date: 2011-04-11 02:03:09 +0000 (Mon, 11 Apr 2011) Log Message: ----------- version=12.0.41_dev # bug fix: PDB load filter mix of (CONF or BIOMOLECULE) and chain filter such as *:A will include additional chains ("C", "O", "N", "S", etc.) Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-04-10 01:50:01 UTC (rev 15378) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-04-11 02:03:09 UTC (rev 15379) @@ -773,7 +773,7 @@ private boolean filterReject(String f, String code, String atomCode) { return (f.indexOf(code) >= 0 && (f.indexOf("!" + code) >= 0 ? f - .indexOf(atomCode) >= 0 : f.indexOf(atomCode) < 0)); + .indexOf(code + atomCode) >= 0 : f.indexOf(code + atomCode) < 0)); } protected void set2D() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-07-02 16:27:35
|
Revision: 15683 http://jmol.svn.sourceforge.net/jmol/?rev=15683&view=rev Author: hansonr Date: 2011-07-02 16:27:29 +0000 (Sat, 02 Jul 2011) Log Message: ----------- version=12.1.51_dev # code: Viewer passes stateScriptVersionInt on to file readers # obscure bug fix: This fix: http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java?r1=13502&r2=13525 # broke Jmol reading of the Epcot hemoglobin file. Only relevant to sequential or trajectory PDB files that do not have MODEL statements. # So then any version starting with 12.0.RC_24 (7/8/2010) through now (7/2/2011) will read the files # correctly -- not missing the first atom -- but that messes up earlier scripts. Unfortunately the Epcot business # (Touch-A-Molecule) was written using 12.9.23 (1/24/2010), so that is affected. # This fix only affects states written prior to 12.0.RC_1 and just makes it so that they display correctly (though missing that one atom) # when they involve PDB trajectories of file without MODEL records separating models. Pretty sure this is just that one file. # Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-07-02 16:26:42 UTC (rev 15682) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-07-02 16:27:29 UTC (rev 15683) @@ -201,7 +201,7 @@ String fileName; - protected int stateScriptVersionInt; // for compatiblity PDB reader Jmol 12.0.RC24 fix + protected int stateScriptVersionInt = Integer.MAX_VALUE; // for compatiblity PDB reader Jmol 12.0.RC24 fix // http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java?r1=13502&r2=13525 void setup(String fileName, Map<String, Object> htParams, Object reader) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2011-09-09 11:43:41
|
Revision: 16049 http://jmol.svn.sourceforge.net/jmol/?rev=16049&view=rev Author: hansonr Date: 2011-09-09 11:43:34 +0000 (Fri, 09 Sep 2011) Log Message: ----------- Castep reader phonon Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-09-09 11:42:44 UTC (rev 16048) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2011-09-09 11:43:34 UTC (rev 16049) @@ -175,6 +175,7 @@ protected OutputStream os; protected boolean iHaveFractionalCoordinates; protected boolean doPackUnitCell; + protected String supercell; // private state variables @@ -190,7 +191,6 @@ private Point3f fileOffset; private Point3f fileOffsetFractional; private Point3f unitCellOffset; - private String supercell; private boolean unitCellOffsetFractional; /* This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-06-03 23:36:21
|
Revision: 17248 http://jmol.svn.sourceforge.net/jmol/?rev=17248&view=rev Author: hansonr Date: 2012-06-03 23:36:15 +0000 (Sun, 03 Jun 2012) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-06-03 23:35:28 UTC (rev 17247) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-06-03 23:36:15 UTC (rev 17248) @@ -190,7 +190,7 @@ private int[] firstLastStep; private int lastModelNumber = Integer.MAX_VALUE; private int desiredSpaceGroupIndex = -1; - protected Point3f fileScaling; + private Point3f fileScaling; private Point3f fileOffset; private Point3f fileOffsetFractional; private Point3f unitCellOffset; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2012-08-26 23:59:33
|
Revision: 17482 http://jmol.svn.sourceforge.net/jmol/?rev=17482&view=rev Author: hansonr Date: 2012-08-26 23:59:25 +0000 (Sun, 26 Aug 2012) Log Message: ----------- oops! jspecview reference Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-08-26 16:11:54 UTC (rev 17481) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2012-08-26 23:59:25 UTC (rev 17482) @@ -46,7 +46,7 @@ import javax.vecmath.Point3f; import javax.vecmath.Vector3f; -import jspecview.util.TextFormat; +import org.jmol.util.TextFormat; /* * Notes 9/2006 Bob Hanson This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-02-05 17:58:29
|
Revision: 17905 http://jmol.svn.sourceforge.net/jmol/?rev=17905&view=rev Author: hansonr Date: 2013-02-05 17:58:22 +0000 (Tue, 05 Feb 2013) Log Message: ----------- ___JmolVersion="13.1.13_dev" bug fix: load CENTROID does not always work -- wrong implicit normalization flag (was -1 instead of 1) Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-02-05 16:18:54 UTC (rev 17904) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-02-05 17:58:22 UTC (rev 17905) @@ -481,6 +481,8 @@ latticeCells[1] = (int) pt.y; latticeCells[2] = (int) pt.z; doCentroidUnitCell = (htParams.containsKey("centroid")); + if (doCentroidUnitCell && (latticeCells[2] == -1 || latticeCells[2] == 0)) + latticeCells[2] = 1; centroidPacked = doCentroidUnitCell && htParams.containsKey("packed"); doPackUnitCell = !doCentroidUnitCell && (htParams.containsKey("packed") || latticeCells[2] < 0); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2013-12-04 16:47:51
|
Revision: 19054 http://sourceforge.net/p/jmol/code/19054 Author: hansonr Date: 2013-12-04 16:47:47 +0000 (Wed, 04 Dec 2013) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-12-04 16:29:24 UTC (rev 19053) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2013-12-04 16:47:47 UTC (rev 19054) @@ -380,6 +380,8 @@ if (htParams.get("pdbNoHydrogens") != null) atomSetCollection.setAtomSetCollectionAuxiliaryInfo("pdbNoHydrogens", htParams.get("pdbNoHydrogens")); + if (checkFilterKey("ADDHYDROGENS")) + atomSetCollection.setAtomSetCollectionAuxiliaryInfo("pdbAddHydrogens",Boolean.TRUE); } protected void setPdb() { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-04-10 12:53:36
|
Revision: 19634 http://sourceforge.net/p/jmol/code/19634 Author: hansonr Date: 2014-04-10 12:53:33 +0000 (Thu, 10 Apr 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-04-10 11:30:28 UTC (rev 19633) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-04-10 12:53:33 UTC (rev 19634) @@ -1652,7 +1652,7 @@ } protected void processDSSR(GenericLineReader reader) throws Exception { - appendLoadNote(((JmolDSSRParser) Interface.getOption("dssr.DSSRParser")).process( + appendLoadNote(((JmolDSSRParser) Interface.getOption("dssx.DSSRParser")).process( asc.getAtomSetAuxiliaryInfo(Integer.MAX_VALUE), reader)); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-05 03:02:51
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Revision: 19773 http://sourceforge.net/p/jmol/code/19773 Author: hansonr Date: 2014-06-05 03:02:36 +0000 (Thu, 05 Jun 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-06-04 23:33:17 UTC (rev 19772) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-06-05 03:02:36 UTC (rev 19773) @@ -871,6 +871,8 @@ doReadMolecularOrbitals = !checkFilterKey("NOMO"); useAltNames = checkFilterKey("ALTNAME"); reverseModels = checkFilterKey("REVERSEMODELS"); + if (filter == null) + return; if (checkFilterKey("HETATM")) { filterHetero = true; filter = PT.rep(filter, "HETATM", "HETATM-Y"); @@ -879,8 +881,10 @@ filterHetero = true; filter = PT.rep(filter, "ATOM", "HETATM-N"); } - if (checkFilterKey("NAME=")) { - nameRequired = filter.substring(filter.indexOf("NAME=") + 5); + if (filter.indexOf("CELL=") >= 0) + altCell = filter.substring(filter.indexOf("CELL=") + 5); // must be last filter option + nameRequired = PT.getQuotedAttribute(filter, "NAME"); + if (nameRequired != null) { if (nameRequired.startsWith("'")) nameRequired = PT.split(nameRequired, "'")[1]; else if (nameRequired.startsWith("\"")) @@ -888,11 +892,6 @@ filter0 = filter = PT.rep(filter, nameRequired, ""); filter0 = filter = PT.rep(filter, "NAME=", ""); } - if (checkFilterKey("CELL=")) { - altCell = filter0.substring(filter.indexOf("CELL=") + 5).toLowerCase(); - } - if (filter == null) - return; filterAtomName = checkFilterKey("*.") || checkFilterKey("!."); filterElement = checkFilterKey("_"); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2014-06-05 03:49:57
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Revision: 19774 http://sourceforge.net/p/jmol/code/19774 Author: hansonr Date: 2014-06-05 03:49:49 +0000 (Thu, 05 Jun 2014) Log Message: ----------- Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-06-05 03:02:36 UTC (rev 19773) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2014-06-05 03:49:49 UTC (rev 19774) @@ -881,8 +881,11 @@ filterHetero = true; filter = PT.rep(filter, "ATOM", "HETATM-N"); } - if (filter.indexOf("CELL=") >= 0) - altCell = filter.substring(filter.indexOf("CELL=") + 5); // must be last filter option + + // can't use getFilter() here because form includes a semicolon: + // cell=a+b,a-b,c;0,1/2,1/2 + if (checkFilterKey("CELL=")) + altCell = filter.substring(filter.indexOf("CELL=") + 5).toLowerCase(); // must be last filter option nameRequired = PT.getQuotedAttribute(filter, "NAME"); if (nameRequired != null) { if (nameRequired.startsWith("'")) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <pie...@us...> - 2015-06-16 22:16:40
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Revision: 20582 http://sourceforge.net/p/jmol/code/20582 Author: pierocanepa Date: 2015-06-16 22:16:37 +0000 (Tue, 16 Jun 2015) Log Message: ----------- I added a safety measure [s = PT.rep(s, "-", " -"] when filling an Array of Floats in case the line contains something like below. We need to add an extra spaces between -4.055348000 and -15.134771000 -4.055348000-15.134771000 -0.000000000 Bob I'm sending you a file to reproduce the error. Search for line containing "direct lattice vectors" Cheers ! Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2015-06-16 12:41:19 UTC (rev 20581) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2015-06-16 22:16:37 UTC (rev 20582) @@ -1312,6 +1312,7 @@ if (s == null) s = rd(); if (width == 0) { + s = PT.rep(s, "-", " -"); tokens = PT.getTokens(s); } else { tokens = new String[s.length() / width]; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2015-06-18 13:58:40
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Revision: 20588 http://sourceforge.net/p/jmol/code/20588 Author: hansonr Date: 2015-06-18 13:58:37 +0000 (Thu, 18 Jun 2015) Log Message: ----------- moving fix to VaspOutcarReader Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2015-06-18 13:37:25 UTC (rev 20587) +++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2015-06-18 13:58:37 UTC (rev 20588) @@ -1312,7 +1312,6 @@ if (s == null) s = rd(); if (width == 0) { - s = PT.rep(s, "-", " -"); tokens = PT.getTokens(s); } else { tokens = new String[s.length() / width]; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |