chemaxon.marvin.space
Class AtomProperty.MoleculeAtomProperty

java.lang.Object
  chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty

All Implemented Interfaces:

MoleculeIterators.AtomPropertyInterface

Enclosing class:

AtomProperty

public class AtomProperty.MoleculeAtomProperty

extends java.lang.Object

implements MoleculeIterators.AtomPropertyInterface

Field Summary

protected Molecule

mol

Constructor Summary

AtomProperty.MoleculeAtomProperty()

Method Summary

float	getBFactor(int atomIndex) Gets the temperature factor of the given atom.
float	getCharge(int atomIndex) Gets the formal charge of the atom.
java.lang.String	getLabel(int atomIndex) Gets the label associated with the atom.
float	getPartialAtomCharge(int atomIndex) Gets the partial atomic charge on the current atom.
int	getResidueTypeId(int atomIndex) Gets the residue type of the specified atom.
int	getSecondaryStructureType(int atomIndex) Gets the type of the secondary structure element which the current atom belongs to.
int	getType(int atomIndex) Gets the element type of the specified atom.
float	getX(int atomIndex) Gets the first coordinate of the atom.
float	getY(int atomIndex) Gets the second coordinate of the atom.
float	getZ(int atomIndex) Gets the third coordinate of the atom.
void	setMolecule(java.lang.Object mol) Associates a molecule with the Property handler.

Methods inherited from class java.lang.Object

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

Field Detail

mol

protected Molecule mol

Constructor Detail

AtomProperty.MoleculeAtomProperty

public AtomProperty.MoleculeAtomProperty()

Method Detail

setMolecule

public void setMolecule(java.lang.Object mol)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Associates a molecule with the Property handler. The Class type is Object since this is the only common ancestor of MacroMolecule and Molecule.

Specified by:

setMolecule in interface MoleculeIterators.AtomPropertyInterface

Parameters:

mol -

getType

public int getType(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the element type of the specified atom.

Specified by:

getType in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

type of the atom (atomic number)

getLabel

public java.lang.String getLabel(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the label associated with the atom. If no label is defined the element symbol is returned.

Specified by:

getLabel in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

label or element symbol

getCharge

public float getCharge(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the formal charge of the atom.

Specified by:

getCharge in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

formal charge

getBFactor

public float getBFactor(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the temperature factor of the given atom.

Specified by:

getBFactor in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

temperature factor

getPartialAtomCharge

public float getPartialAtomCharge(int atomIndex)
                           throws java.lang.Exception

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the partial atomic charge on the current atom.

Specified by:

getPartialAtomCharge in interface MoleculeIterators.AtomPropertyInterface

Returns:

partial charge

Throws:

java.lang.Exception - PluginException can be thrown, but PluginException cannot be referred to in this class because the AWT applet package does not include Plugins.

getResidueTypeId

public int getResidueTypeId(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the residue type of the specified atom. It the corresponding molecule is not a macromolecule (protein or nucleic acid chain) the atom is not part of a residue, thus it has no residue type. The returned value is chemaxon.marvin.modules.PDBResidues.UNKNOWN_RESIDUE_TYPE_ID.

Specified by:

getResidueTypeId in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex -

Returns:

internal residue type index

See Also:

PDBResidues

getSecondaryStructureType

public int getSecondaryStructureType(int atomIndex)

Gets the type of the secondary structure element which the current atom belongs to. This method makes sense for MacroMolecule.Protein atoms only. It is declared here in order to support higher level polymorphism.

Specified by:

getSecondaryStructureType in interface MoleculeIterators.AtomPropertyInterface

Returns:

internal indetifier of SS type, see corresponding constants

getX

public float getX(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the first coordinate of the atom.

Specified by:

getX in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

x coordinate

getY

public float getY(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the second coordinate of the atom.

Specified by:

getY in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

y coordinate

getZ

public float getZ(int atomIndex)

Description copied from interface: MoleculeIterators.AtomPropertyInterface

Gets the third coordinate of the atom.

Specified by:

getZ in interface MoleculeIterators.AtomPropertyInterface

Parameters:

atomIndex - internal index of the atom

Returns:

z coordinate