Skip to content

Residues with same identifier causes crash #5

@gusennan

Description

@gusennan

As of b8cc6c5, 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)

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions