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donaldlab / osprey-gui

A cross-platform GUI for OSPREY 3
GNU General Public License v2.0
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Residues with same identifier causes crash #5

Open gusennan opened 4 years ago

gusennan commented 4 years ago

As of b8cc6c54fa21d2ff5df6b7d24cc0d4c4a062bece, opening 5XNL from rcsb.org crashes with:

java.lang.IllegalArgumentException: residue number A11 is already present in this collection
    at edu.duke.cs.osprey.structure.Residues.set(Residues.java:90)
    at edu.duke.cs.osprey.structure.Residues.add(Residues.java:76)
    at edu.duke.cs.osprey.structure.Molecule.appendResidue(Molecule.java:158)
    at edu.duke.cs.osprey.structure.PDBIO$ResInfo.flush(PDBIO.java:102)
    at edu.duke.cs.osprey.structure.PDBIO.readMols(PDBIO.java:212)
    at edu.duke.cs.osprey.structure.PDBIO.readMols(PDBIO.java:153)
    at edu.duke.cs.osprey.structure.PDBIO.readAll(PDBIO.java:147)
    at edu.duke.cs.osprey.structure.PDBIO.read(PDBIO.java:143)
    at edu.duke.cs.ospreygui.io.PDBKt.fromPDB(PDB.kt:47)
    at edu.duke.cs.ospreygui.features.win.ImportPDB$open$1.invoke(ImportPDB.kt:36)
    at edu.duke.cs.ospreygui.features.win.ImportPDB$open$1.invoke(ImportPDB.kt:17)
    at edu.duke.cs.molscope.gui.WindowCore$winCommands$1.showExceptions(Window.kt:256)
    at edu.duke.cs.ospreygui.features.win.ImportPDB.open(ImportPDB.kt:33)
    at edu.duke.cs.ospreygui.features.win.ImportPDB.menu(ImportPDB.kt:28)
    at edu.duke.cs.molscope.gui.WindowCore$render$1.invoke(Window.kt:304)
    at edu.duke.cs.molscope.gui.WindowCore$render$1.invoke(Window.kt:125)
    at edu.duke.cs.molscope.render.WindowRenderer$render$1.invoke(WindowRenderer.kt:123)
    at edu.duke.cs.molscope.render.WindowRenderer$render$1.invoke(WindowRenderer.kt:11)
    at cuchaz.kludge.imgui.Imgui.frame(imgui.kt:450)
    at edu.duke.cs.molscope.render.WindowRenderer.render(WindowRenderer.kt:122)
    at edu.duke.cs.molscope.gui.WindowCore.render$molscope(Window.kt:296)
    at edu.duke.cs.molscope.gui.Window.render(Window.kt:58)
    at edu.duke.cs.ospreygui.MainKt.main(main.kt:69)
    at edu.duke.cs.ospreygui.MainKt.main(main.kt)