From: <ha...@us...> - 2007-11-20 04:10:25
|
Revision: 8640 http://jmol.svn.sourceforge.net/jmol/?rev=8640&view=rev Author: hansonr Date: 2007-11-19 20:10:23 -0800 (Mon, 19 Nov 2007) Log Message: ----------- version=11.3.46_dev # bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java Modified: trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2007-11-20 04:09:59 UTC (rev 8639) +++ trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2007-11-20 04:10:23 UTC (rev 8640) @@ -247,7 +247,9 @@ if (! (possiblyPreviousMonomer instanceof NucleicMonomer)) return false; NucleicMonomer other = (NucleicMonomer)possiblyPreviousMonomer; - return other.getAtomFromOffsetIndex(O3Pr).isBonded(myPhosphorusAtom); + if (other.getAtomFromOffsetIndex(O3Pr).isBonded(myPhosphorusAtom)) + return true; + return super.isConnectedAfter(possiblyPreviousMonomer); } //////////////////////////////////////////////////////////////// Modified: trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2007-11-20 04:09:59 UTC (rev 8639) +++ trunk/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2007-11-20 04:10:23 UTC (rev 8640) @@ -31,7 +31,7 @@ private final static byte[] phosphorusOffsets = { 0 }; - private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE = 7.5f; + private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE = 8.0f; protected boolean isPurine; protected boolean isPyrimidine; @@ -45,6 +45,7 @@ specialAtomIndexes[JmolConstants.ATOMID_NUCLEIC_PHOSPHORUS] != firstIndex) return null; + System.out.println("phosphorus monomer "+ firstIndex + " "+ lastIndex); return new PhosphorusMonomer(chain, group3, seqcode, firstIndex, lastIndex, phosphorusOffsets); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2007-12-19 14:36:24
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Revision: 8818 http://jmol.svn.sourceforge.net/jmol/?rev=8818&view=rev Author: hansonr Date: 2007-12-19 06:36:11 -0800 (Wed, 19 Dec 2007) Log Message: ----------- code refactoring Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2007-12-19 14:34:04 UTC (rev 8817) +++ trunk/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2007-12-19 14:36:11 UTC (rev 8818) @@ -174,7 +174,7 @@ closest[0] = alpha; } - public Quaternion getQuaternion() { + Quaternion getQuaternion() { /* * also NucleicMonomer * Modified: trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2007-12-19 14:34:04 UTC (rev 8817) +++ trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2007-12-19 14:36:11 UTC (rev 8818) @@ -322,7 +322,7 @@ return true; } - public Quaternion getQuaternion() { + Quaternion getQuaternion() { return null; } } Modified: trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2007-12-19 14:34:04 UTC (rev 8817) +++ trunk/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2007-12-19 14:36:11 UTC (rev 8818) @@ -285,7 +285,7 @@ } } - public Quaternion getQuaternion() { + Quaternion getQuaternion() { /* * also AminoMonomer * This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <ha...@us...> - 2008-02-07 18:22:42
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Revision: 8981 http://jmol.svn.sourceforge.net/jmol/?rev=8981&view=rev Author: hansonr Date: 2008-02-07 10:22:39 -0800 (Thu, 07 Feb 2008) Log Message: ----------- 11.5.6 efficiencies and debug comments Modified Paths: -------------- trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java Modified: trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2008-02-07 18:18:47 UTC (rev 8980) +++ trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2008-02-07 18:22:39 UTC (rev 8981) @@ -32,6 +32,7 @@ AlphaPolymer(Monomer[] monomers) { super(monomers); + //System.out.println("new AlphaPolymer " + monomers[0].getChainID() + " " + monomers[0].getSeqcodeString() + " " + monomers[monomers.length - 1].getSeqcodeString()); } public void addSecondaryStructure(byte type, @@ -41,6 +42,7 @@ if ((indexStart = getIndex(startChainID, startSeqcode)) == -1 || (indexEnd = getIndex(endChainID, endSeqcode)) == -1) return; + //System.out.println("AlphaPolymer addSecStr " + type + " " + indexStart + " " + indexEnd); addSecondaryStructure(type, indexStart, indexEnd); } Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java =================================================================== --- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-02-07 18:18:47 UTC (rev 8980) +++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2008-02-07 18:22:39 UTC (rev 8981) @@ -224,16 +224,20 @@ int getIndex(char chainID, int seqcode) { int i; - for (i = monomerCount; --i >= 0; ) - if (monomers[i].getSeqcode() == seqcode && - monomers[i].getChainID() == chainID) - break; + for (i = monomerCount; --i >= 0;) + if (monomers[i].getChainID() == chainID) { + //System.out.println("BioPolymer getIndex seqcode monomers[i].seqcode " + chainID + " " + // + Group.getSeqcodeString(seqcode) + " " + //+ Group.getSeqcodeString(monomers[i].getSeqcode())); + if (monomers[i].getSeqcode() == seqcode) + break; + } return i; } final Point3f getLeadPoint(int monomerIndex) { return monomers[monomerIndex].getLeadAtomPoint(); - } + } final Point3f getInitiatorPoint() { return monomers[0].getInitiatorAtom(); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |