From: Miguel <mig...@us...> - 2005-09-15 03:56:46
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Update of /cvsroot/jmol/Jmol/src/org/jmol/viewer In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19581/src/org/jmol/viewer Modified Files: NucleicMonomer.java Log Message: nucleic monitor supports lead atom identification on secondary shapes Index: NucleicMonomer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/NucleicMonomer.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- NucleicMonomer.java 15 Sep 2005 03:22:58 -0000 1.3 +++ NucleicMonomer.java 15 Sep 2005 03:56:39 -0000 1.4 @@ -63,8 +63,7 @@ ~JmolConstants.ATOMID_H3T_TERMINUS, // 23 H3T terminus JmolConstants.ATOMID_O3_PRIME, // 24 O3' terminus ~JmolConstants.ATOMID_NUCLEIC_PHOSPHORUS, // 25 P phosphorus - JmolConstants.ATOMID_C5_PRIME, // 26 C5' - JmolConstants.ATOMID_C3_PRIME, // 27 C3' + JmolConstants.ATOMID_C3_PRIME, // 26 C3' }; static Monomer @@ -188,12 +187,12 @@ return getAtomFromOffsetIndex(25); } - Atom getC5PrimeAtom() { - return getAtomFromOffsetIndex(26); + Atom getO5PrimeAtom() { + return getAtomFromOffsetIndex(22); } Atom getC3PrimeAtom() { - return getAtomFromOffsetIndex(27); + return getAtomFromOffsetIndex(26); } void getBaseRing6Points(Point3f[] ring6Points) { @@ -230,18 +229,18 @@ short madBegin, short madEnd) { Viewer viewer = chain.frame.viewer; Atom competitor = closest.atom; - Atom phosphorus = getPhosphorusAtom(); - Atom c5prime = getC5PrimeAtom(); + Atom lead = getLeadAtom(); + Atom o5prime = getO5PrimeAtom(); Atom c3prime = getC3PrimeAtom(); short mar = (short)(madBegin / 2); - if (mar < 1600) - mar = 1600; - int radius = viewer.scaleToScreen(phosphorus.getScreenZ(), mar); + if (mar < 1900) + mar = 1900; + int radius = viewer.scaleToScreen(lead.getScreenZ(), mar); if (radius < 4) radius = 4; - if (phosphorus.isCursorOnTop(x, y, radius, competitor) || - c5prime.isCursorOnTop(x, y, radius + (radius >> 2), competitor) || + if (lead.isCursorOnTop(x, y, radius, competitor) || + o5prime.isCursorOnTop(x, y, radius, competitor) || c3prime.isCursorOnTop(x, y, radius, competitor)) - closest.atom = phosphorus; + closest.atom = lead; } } |