meshi.molecularElements.atoms
Class AtomList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<Atom>
              meshi.molecularElements.atoms.AtomList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<Atom>, java.util.Collection<Atom>, java.util.List<Atom>, java.util.RandomAccess

Direct Known Subclasses:

ImageAtomList

public class AtomList
extends java.util.ArrayList<Atom>

A list of Atoms

See Also:

Serialized Form

Nested Class Summary

static class	AtomList.AcceptChainFilter
static class	AtomList.BackboneFilter
static class	AtomList.IsAtom
static class	AtomList.IsDefrostedFilter
static class	AtomList.IsFrozenFilter
static class	AtomList.NonHydrogen
static class	AtomList.RejectChainFilter

Field Summary

private java.lang.String	comment
private MolecularSystem	molecularSystem
private MeshiLineReader	sourceFile

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

AtomList()

AtomList(Atom atom)

AtomList(int initialCapaciy)

AtomList(MeshiLineReader file, Filter lineFilter)
An atom list based on a PDB file In a multiple model file (such as NMR's) only model 1 is read.

AtomList(PdbReader file)
An atom list based on a PDB file

AtomList(ResidueList residues)
An atom list based on a residue list

AtomList(java.lang.String fileName)

AtomList(java.lang.String fileName, Filter lineFilter)

AtomList(java.lang.String dir, java.lang.String fileName)

Method Summary

boolean	add(Atom atom)
void	assertSingleResidue() Asserts that this AtomList is comprised of atoms belonging to a single residue.
Atom	atomAt(int i) Returns the atom in position i of the list.
AtomList	backbone()
AtomList	CAFilter()
AtomList	CAnoImageFilter()
boolean	checkSingleResidue() Checks if this AtomList is comprised of atoms belonging to a single residue.
java.lang.String	comment()
void	defrost()
AtomList	defrostedAtoms()
AtomList	filter(Filter filter) Extracts the list elements that pass the filter.
void	freeze()
void	freeze(Filter filter)
AtomList	frozenAtoms()
boolean	frozenAtomsExist()
AtomList	fullOccupancyFilter()
AtomList	getChainAtoms(java.lang.String chainLetter)
double	getRms(AtomList otherList)
AtomList	getSourceAtoms()
boolean	includesNowhereAtoms()
MolecularSystem	molecularSystem()
void	moveCMtoOrigin()
AtomList	noOXTFilter()
void	print()
void	print(MeshiWriter writer)
double	radius() of gyration of the list atoms.
double	radius2()
Rms	rms(AtomList otherList) RMS deviation between this list of atom and some other list.
boolean	sameAtoms(AtomList other) Returns true if the parameter has the same length and the same composition in terms of atom names.
void	setComment(java.lang.String s)
void	setMolecularSystem(MolecularSystem MolecularSystem)
void	setResidue(Residue residue) Sets the parameter to be the residue of this atom.
AtomList	somewhere()
boolean	sortable()
MeshiLineReader	sourceFile()
AtomList[]	splitToChains()
Atom[]	toArrayOfAtoms()
java.lang.String	toString()
int	whereIs(Atom atom)

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

sourceFile

private MeshiLineReader sourceFile

molecularSystem

private MolecularSystem molecularSystem

comment

private java.lang.String comment

Constructor Detail

AtomList

public AtomList()

AtomList

public AtomList(Atom atom)

AtomList

public AtomList(int initialCapaciy)

AtomList

public AtomList(MeshiLineReader file,
                Filter lineFilter)

An atom list based on a PDB file In a multiple model file (such as NMR's) only model 1 is read. Currently whenever there are two alternative atom positions present, only position A is taken.

AtomList

public AtomList(PdbReader file)

An atom list based on a PDB file

AtomList

public AtomList(java.lang.String dir,
                java.lang.String fileName)

AtomList

public AtomList(java.lang.String fileName,
                Filter lineFilter)

AtomList

public AtomList(java.lang.String fileName)

AtomList

public AtomList(ResidueList residues)

An atom list based on a residue list

Method Detail

molecularSystem

public MolecularSystem molecularSystem()

setMolecularSystem

public void setMolecularSystem(MolecularSystem MolecularSystem)

filter

public AtomList filter(Filter filter)

Extracts the list elements that pass the filter.

add

public boolean add(Atom atom)

Specified by:

add in interface java.util.Collection<Atom>

Specified by:

add in interface java.util.List<Atom>

Overrides:

add in class java.util.ArrayList<Atom>

rms

public Rms rms(AtomList otherList)

RMS deviation between this list of atom and some other list.

getRms

public double getRms(AtomList otherList)

atomAt

public Atom atomAt(int i)

Returns the atom in position i of the list.

whereIs

public int whereIs(Atom atom)

radius

public double radius()

of gyration of the list atoms. SQRT{ SIGMA_OVER_ALL_ATOMS([(x-X)^2+(y-Y)^2+(z-Z)^2]/N)}
Where (x,y,z) are the atom coordinates and (X,Y,Z) are the coordinates of the center of mass.

radius2

public double radius2()

setResidue

public void setResidue(Residue residue)

Sets the parameter to be the residue of this atom.

toArrayOfAtoms

public Atom[] toArrayOfAtoms()

sourceFile

public MeshiLineReader sourceFile()

frozenAtomsExist

public boolean frozenAtomsExist()

freeze

public void freeze()

freeze

public void freeze(Filter filter)

defrost

public void defrost()

fullOccupancyFilter

public AtomList fullOccupancyFilter()

noOXTFilter

public AtomList noOXTFilter()

backbone

public AtomList backbone()

sortable

public boolean sortable()

toString

public java.lang.String toString()

Overrides:

toString in class java.util.AbstractCollection<Atom>

CAFilter

public AtomList CAFilter()

CAnoImageFilter

public AtomList CAnoImageFilter()

frozenAtoms

public AtomList frozenAtoms()

defrostedAtoms

public AtomList defrostedAtoms()

sameAtoms

public boolean sameAtoms(AtomList other)

Returns true if the parameter has the same length and the same composition in terms of atom names. Current implementation, rather inefficient.

assertSingleResidue

public void assertSingleResidue()

Asserts that this AtomList is comprised of atoms belonging to a single residue.

Throws:

MeshiException - if the assertion fails.

checkSingleResidue

public boolean checkSingleResidue()

Checks if this AtomList is comprised of atoms belonging to a single residue.

splitToChains

public AtomList[] splitToChains()

getChainAtoms

public AtomList getChainAtoms(java.lang.String chainLetter)

getSourceAtoms

public AtomList getSourceAtoms()

somewhere

public AtomList somewhere()

moveCMtoOrigin

public void moveCMtoOrigin()

includesNowhereAtoms

public boolean includesNowhereAtoms()

setComment

public void setComment(java.lang.String s)

print

public void print()

print

public void print(MeshiWriter writer)

comment

public java.lang.String comment()