jprot,amaus

Hi all 👋

🌱 I teach Computer Science at Tulane University.
🔭 I'm interested in proteins, math, and dnd.
- I have other interests too!
⚡ Fun fact: I spent a summer compiling my own linux from scratch.
- It took a whole summer because I had alot to learn in order to do it!

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jprot's Issues

Reading in PDB Files without element field causes crash

jProt is unable to read in PDB files that lack the element field in ATOM records. The following exception is thrown.

$ JProtMetrics --mol1-f TR288.pdb --mol2-f TR288TS010_1.pdb --ls --gdt -a
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
	at java.lang.String.charAt(String.java:646)
	at com.aaronpmaus.jProt.protein.Atom.<init>(Atom.java:92)
	at com.aaronpmaus.jProt.io.PDBFileIO.constructAtom(PDBFileIO.java:331)
	at com.aaronpmaus.jProt.io.PDBFileIO.constructAtoms(PDBFileIO.java:323)
	at com.aaronpmaus.jProt.io.PDBFileIO.constructProtein(PDBFileIO.java:283)
	at com.aaronpmaus.jProt.io.PDBFileIO.readInPDBFile(PDBFileIO.java:84)
	at com.aaronpmaus.jProt.executables.JProtMetrics.main(JProtMetrics.java:161)

Bond HashCodes Exceed MAXINT

It is possible for bond hash codes to exceed MAXINT.

Exception in thread "main" java.lang.NumberFormatException: For input string: "2147521476"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:583)
    at java.lang.Integer.parseInt(Integer.java:615)
    at com.aaronpmaus.jProt.protein.Bond.hashCode(Bond.java:104)
    at java.util.HashMap.hash(HashMap.java:338)
    at java.util.HashMap.put(HashMap.java:611)
    at java.util.HashSet.add(HashSet.java:219)
    at com.aaronpmaus.jProt.protein.Residue.addBond(Residue.java:348)
    at com.aaronpmaus.jProt.protein.Residue.addBond(Residue.java:343)
    at com.aaronpmaus.jProt.protein.Residue.initializeAminoAcid(Residue.java:164)
    at com.aaronpmaus.jProt.protein.Residue.<init>(Residue.java:101)
    at com.aaronpmaus.jProt.io.PDBFileIO.constructProtein(PDBFileIO.java:286)
    at com.aaronpmaus.jProt.io.PDBFileIO.readInPDBFile(PDBFileIO.java:84)
    at com.aaronpmaus.jProt.executables.JProtMetrics.main(JProtMetrics.java:161)

Handling Missing Backbone Atoms

Missing backbone CAs causes a crash when calculating the CADistanceMatrix.

Exception in thread "main" java.util.NoSuchElementException: No atom of name CA in residue 175: ASP
    at com.aaronpmaus.jProt.protein.Residue.getAtom(Residue.java:192)
    at com.aaronpmaus.jProt.tools.DistanceMatrixCalculator.calculateDistanceMatrix(DistanceMatrixCalculator.java:100)
    at com.aaronpmaus.jProt.metrics.Metrics.<init>(Metrics.java:132)
    at com.aaronpmaus.jProt.executables.JProtMetrics.main(JProtMetrics.java:164)
80001, 1fem_A.pdb, A, 1hbp_A.pdb, A,  ,  ,  , None,  , 4.87856, 98.864

1hbp_A.pdb only contains the N atom for Residue 175. This needs to be handled more gracefully.

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