io.pdb
Class PDBAtomFormatter

java.lang.Object
  io.pdb.PDBAtomFormatter

public class PDBAtomFormatter

extends java.lang.Object

Author:

mika, vincent TODO add proper ATOM/HETATM support. currently everything is assumed to be ATOM, which is (in principle) only true for naturally occuring aminacids and nucleotides (with all due respect -- the pdb format is braindead).

Field Summary

(package private) static PrintfFormat	atomNumberFormat
(package private) static PrintfFormat	coordFormat
(package private) static PrintfFormat	nameFormat
(package private) static PrintfFormat	placeHolderFormat
(package private) static PrintfFormat	residueNumberFormat

Constructor Summary

PDBAtomFormatter()

Method Summary

static java.lang.String

format(double[][] positions, java.lang.String[] atomNames, java.lang.String[] residueNames, int[] residueNumbers) Takes arrays of atomic positions and names as well as the corresponding residue names and numbers and attempt to generate pdb atomic coordinates from it.

Methods inherited from class java.lang.Object

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

Field Detail

coordFormat

static final PrintfFormat coordFormat

atomNumberFormat

static final PrintfFormat atomNumberFormat

nameFormat

static final PrintfFormat nameFormat

residueNumberFormat

static final PrintfFormat residueNumberFormat

placeHolderFormat

static final PrintfFormat placeHolderFormat

Constructor Detail

PDBAtomFormatter

public PDBAtomFormatter()

Method Detail

format

public static java.lang.String format(double[][] positions,
                                      java.lang.String[] atomNames,
                                      java.lang.String[] residueNames,
                                      int[] residueNumbers)

Takes arrays of atomic positions and names as well as the corresponding residue names and numbers and attempt to generate pdb atomic coordinates from it. See ATOM field of pdb format spec.

Parameters:

positions -

atomNames -

residueNames -

residueNumbers -

Returns:

pdb formatted atomic information