Class Pdb2Fasta

java.lang.Object
  meshi.util.MeshiProgram
      Pdb2Fasta

public class Pdb2Fasta
extends MeshiProgram

Nested Class Summary

private static class	Pdb2Fasta.MyAtom
private static class	Pdb2Fasta.MyChain
private static class	Pdb2Fasta.MyFilter
private static class	Pdb2Fasta.MyResidue

Field Summary

static java.lang.String[][]	dictionary
static java.lang.String	MONOMERS_TO_IGNORE
static java.lang.String	STANDARD_RESIDUES

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

Constructor Summary

Pdb2Fasta()

Method Summary

private static AtomList	getNewAtomList(AtomList originalAtomsList, MeshiLog log)
private static java.lang.String[]	join(java.lang.String s0, java.lang.String s1)
static void	main(java.lang.String[] args)
private static MeshiWriter	openFile(java.lang.String fileName)

Methods inherited from class meshi.util.MeshiProgram

about, debug, get2ndString, getb, getB, getd, getD, getFlag, getFlagedArgument, geti, getI, getOrderedArgument, getS, getS, initRandom, initRandom, initRandom, printGlobalTable, randomNumberGenerator, seed, tableGet, tableIncludes, tableSet, toString, verbose

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

MONOMERS_TO_IGNORE

public static final java.lang.String MONOMERS_TO_IGNORE

See Also:

Constant Field Values

STANDARD_RESIDUES

public static final java.lang.String STANDARD_RESIDUES

See Also:

Constant Field Values

dictionary

public static final java.lang.String[][] dictionary

Constructor Detail

Pdb2Fasta

public Pdb2Fasta()

Method Detail

join

private static java.lang.String[] join(java.lang.String s0,
                                       java.lang.String s1)

main

public static void main(java.lang.String[] args)

getNewAtomList

private static AtomList getNewAtomList(AtomList originalAtomsList,
                                       MeshiLog log)

openFile

private static MeshiWriter openFile(java.lang.String fileName)