From: <ha...@us...> - 2012-04-19 03:18:06
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Revision: 17017 http://jmol.svn.sourceforge.net/jmol/?rev=17017&view=rev Author: hansonr Date: 2012-04-19 03:17:59 +0000 (Thu, 19 Apr 2012) Log Message: ----------- version=12.2.23_dev # bug fix: in 2bat, SIA was considered part of the carbohydrate chain because we were not checking bonding Modified Paths: -------------- branches/v12_2/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java branches/v12_2/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java branches/v12_2/Jmol/src/org/jmol/modelsetbio/BioPolymer.java branches/v12_2/Jmol/src/org/jmol/modelsetbio/CarbohydrateMonomer.java branches/v12_2/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java branches/v12_2/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/AlphaMonomer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -168,10 +168,6 @@ @Override boolean isConnectedAfter(Monomer possiblyPreviousMonomer) { - if (possiblyPreviousMonomer == null) - return true; - if (! (possiblyPreviousMonomer instanceof AlphaMonomer)) - return false; Atom atom1 = getLeadAtom(); Atom atom2 = possiblyPreviousMonomer.getLeadAtom(); return atom1.isBonded(atom2) || atom1.distance(atom2) <= 4.2f; Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/AminoMonomer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -140,10 +140,6 @@ @Override boolean isConnectedAfter(Monomer possiblyPreviousMonomer) { - if (possiblyPreviousMonomer == null) - return true; - if (! (possiblyPreviousMonomer instanceof AminoMonomer)) - return false; AminoMonomer other = (AminoMonomer)possiblyPreviousMonomer; return other.getCarbonylCarbonAtom().isBonded(getNitrogenAtom()); } Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/BioPolymer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -83,8 +83,8 @@ Monomer current; if (!(group instanceof Monomer) || (current = (Monomer) group).bioPolymer != null || previous != null - && previous.getClass() != current.getClass() - || checkConnections && !current.isConnectedAfter(previous)) + && (previous.getClass() != current.getClass() + || checkConnections && !current.isConnectedAfter(previous))) break; previous = current; count++; Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/CarbohydrateMonomer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/CarbohydrateMonomer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/CarbohydrateMonomer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -57,8 +57,6 @@ @Override boolean isConnectedAfter(Monomer possiblyPreviousMonomer) { - if (possiblyPreviousMonomer == null) - return true; for (int i = firstAtomIndex; i <= lastAtomIndex; i++) for (int j = possiblyPreviousMonomer.firstAtomIndex; j <= possiblyPreviousMonomer.lastAtomIndex; j++) { Atom a = chain.getAtom(i); Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/NucleicMonomer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -282,13 +282,9 @@ @Override boolean isConnectedAfter(Monomer possiblyPreviousMonomer) { - if (possiblyPreviousMonomer == null) - return true; Atom myPhosphorusAtom = getAtomFromOffsetIndex(NP); if (myPhosphorusAtom == null) return false; - if (! (possiblyPreviousMonomer instanceof NucleicMonomer)) - return false; NucleicMonomer other = (NucleicMonomer)possiblyPreviousMonomer; if (other.getAtomFromOffsetIndex(O3Pr).isBonded(myPhosphorusAtom)) return true; Modified: branches/v12_2/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java =================================================================== --- branches/v12_2/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2012-04-19 03:16:37 UTC (rev 17016) +++ branches/v12_2/Jmol/src/org/jmol/modelsetbio/PhosphorusMonomer.java 2012-04-19 03:17:59 UTC (rev 17017) @@ -101,10 +101,6 @@ @Override boolean isConnectedAfter(Monomer possiblyPreviousMonomer) { - if (possiblyPreviousMonomer == null) - return true; - if (! (possiblyPreviousMonomer instanceof PhosphorusMonomer)) - return false; // 1PN8 73:d and 74:d are 7.001 angstroms apart // but some P atoms are up to 7.4 angstroms apart float distance = This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |