From: <ha...@us...> - 2010-02-28 17:08:39
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Revision: 12521 http://jmol.svn.sourceforge.net/jmol/?rev=12521&view=rev Author: hansonr Date: 2010-02-28 17:08:32 +0000 (Sun, 28 Feb 2010) Log Message: ----------- Gromacs fix Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java Modified: branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 16:49:25 UTC (rev 12520) +++ branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 17:08:32 UTC (rev 12521) @@ -62,21 +62,11 @@ float cellOffset; private void readHeader() throws Exception { -//216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 readLineTrimmed(); checkLineForScript(); atomSetCollection.newAtomSet(); atomSetCollection.setAtomSetName(line); atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE); - int pt = line.indexOf("BOX(M)="); - if (pt < 0) - return; - float a = 10 * parseFloat(line.substring(pt + 7)); - if (Float.isNaN(a)) - return; - cellOffset = a / 2; - setUnitCell(a, a, a, 90, 90, 90); - setSpaceGroupName("P1"); } /* This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-28 17:14:49
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Revision: 12523 http://jmol.svn.sourceforge.net/jmol/?rev=12523&view=rev Author: hansonr Date: 2010-02-28 17:14:39 +0000 (Sun, 28 Feb 2010) Log Message: ----------- Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java Modified: branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 17:09:30 UTC (rev 12522) +++ branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 17:14:39 UTC (rev 12523) @@ -59,8 +59,6 @@ return 0; } - float cellOffset; - private void readHeader() throws Exception { readLineTrimmed(); checkLineForScript(); @@ -94,9 +92,9 @@ atom.group3 = parseToken(line, 5, 9).trim(); //allowing for 4 characters atom.atomName = line.substring(11, 15).trim(); atom.atomSerial = parseInt(line, 15, 20); - atom.x = parseFloat(line, 20, 28) * 10 - cellOffset; - atom.y = parseFloat(line, 28, 36) * 10 - cellOffset; - atom.z = parseFloat(line, 36, 44) * 10 - cellOffset; + atom.x = parseFloat(line, 20, 28) * 10; + atom.y = parseFloat(line, 28, 36) * 10; + atom.z = parseFloat(line, 36, 44) * 10; if (Float.isNaN(atom.x) || Float.isNaN(atom.y) || Float.isNaN(atom.z)) { Logger.warn("line cannot be read for GROMACS atom data: " + line); atom.set(0, 0, 0); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2010-02-28 17:15:20
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Revision: 12524 http://jmol.svn.sourceforge.net/jmol/?rev=12524&view=rev Author: hansonr Date: 2010-02-28 17:15:14 +0000 (Sun, 28 Feb 2010) Log Message: ----------- Modified Paths: -------------- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java Modified: branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java =================================================================== --- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 17:14:39 UTC (rev 12523) +++ branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GromacsReader.java 2010-02-28 17:15:14 UTC (rev 12524) @@ -113,9 +113,9 @@ float vz = parseFloat(line, 60, 68) * 10; if (Float.isNaN(vx) || Float.isNaN(vy) || Float.isNaN(vz)) continue; - atom.vectorX = vx; - atom.vectorY = vy; - atom.vectorZ = vz; + atom.vectorX = vx; + atom.vectorY = vy; + atom.vectorZ = vz; } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |