From: <ha...@us...> - 2013-04-22 12:29:37
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Revision: 18146 http://sourceforge.net/p/jmol/code/18146 Author: hansonr Date: 2013-04-22 12:29:31 +0000 (Mon, 22 Apr 2013) Log Message: ----------- ___JmolVersion="13.1.15_dev_2013.04.22" TODO: PyMOL movies, electron density, CGO bug fix: PyMOL radii are not appropriate for isosurfaces -- let Jmol calculate them itself Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2013-04-22 10:04:15 UTC (rev 18145) +++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2013-04-22 12:29:31 UTC (rev 18146) @@ -752,6 +752,7 @@ PyMOL.nonbonded_size, nonBondedSize); rad = -atom.radius * myNonBondedSize; } + atom.radius = Float.NaN; // sorry, can't use these for surfaces if (rad != 0) addSpacefill(iAtom, rad); if (reps[PyMOL.REP_CARTOON].get(iAtom)) { Modified: trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java =================================================================== --- trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-04-22 10:04:15 UTC (rev 18145) +++ trunk/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java 2013-04-22 12:29:31 UTC (rev 18146) @@ -162,7 +162,6 @@ boolean getRadii, boolean getMolecules, boolean getAllModels, boolean addNearbyAtoms, boolean getAtomMinMax, float marginAtoms) { - if (addNearbyAtoms) getRadii = true; // set atomRadiusData to 100% if it has not been set already Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java =================================================================== --- trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2013-04-22 10:04:15 UTC (rev 18145) +++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoSolventReader.java 2013-04-22 12:29:31 UTC (rev 18146) @@ -963,7 +963,7 @@ P3 ptC = atomXyz[ic]; float rCS = atomRadius[ic] + solventRadius; float dCT = Measure.distanceToPlane(plane, ptC); - if (Math.abs(dCT) >= rCS)// * 0.9f) + if (Math.abs(dCT) >= rCS * 0.9f) // need a fudge factor here to avoid extremely // flat situations (1bna isosurface solvent 1.4) return false; // out of range Modified: trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java =================================================================== --- trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2013-04-22 10:04:15 UTC (rev 18145) +++ trunk/Jmol/src/org/jmol/renderbio/BioShapeRenderer.java 2013-04-22 12:29:31 UTC (rev 18146) @@ -175,6 +175,7 @@ } private boolean initializePolymer(BioShape bioShape) { + BS bsDeleted = viewer.getDeletedAtoms(); if (viewer.isJmolDataFrameForModel(bioShape.modelIndex)) { controlPoints = bioShape.bioPolymer.getControlPoints(true, 0, false); } else { @@ -193,7 +194,7 @@ bioShape.falsifyMesh(); for (int i = monomerCount; --i >= 0;) { if ((monomers[i].shapeVisibilityFlags & myVisibilityFlag) == 0 - || modelSet.isAtomHidden(leadAtomIndices[i])) + || modelSet.isAtomHidden(leadAtomIndices[i]) || bsDeleted != null && bsDeleted.get(leadAtomIndices[i])) continue; Atom lead = modelSet.atoms[leadAtomIndices[i]]; if (!g3d.isInDisplayRange(lead.screenX, lead.screenY)) Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-22 10:04:15 UTC (rev 18145) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-04-22 12:29:31 UTC (rev 18146) @@ -9,10 +9,12 @@ # The quotes above look odd for a parameter file, but they are # important for the JavaScript version of Jmol. -___JmolVersion="13.1.15_dev_2013.04.21c" +___JmolVersion="13.1.15_dev_2013.04.22" TODO: PyMOL movies, electron density, CGO +bug fix: PyMOL radii are not appropriate for isosurfaces -- let Jmol calculate them itself +bug fix: deleting atoms does not remove bioshape rendering bug fix: isosurface in multi-model context saved in state with wrong model number bug fix: PyMOL label fix, including fonts bug fix: PyMOL rockets, nucleic acid rendering This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |