org.jmol.viewer
Class FrameExportJmolAdapter

java.lang.Object
  org.jmol.api.JmolAdapter
      org.jmol.viewer.FrameExportJmolAdapter

public final class FrameExportJmolAdapter
extends JmolAdapter

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.api.JmolAdapter

JmolAdapter.Logger, JmolAdapter.StructureIterator

Field Summary

Fields inherited from class org.jmol.api.JmolAdapter

logger, ORDER_AROMATIC, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_STEREO_FAR, ORDER_STEREO_NEAR

Method Summary

JmolAdapter.AtomIterator	getAtomIterator(java.lang.Object clientFile) Get an AtomIterator for retrieval of all atoms in the file.
java.lang.String	getAtomSetCollectionName(java.lang.Object clientFile) Get the name of the atom set collection, if known.
JmolAdapter.BondIterator	getBondIterator(java.lang.Object clientFile) Get a BondIterator for retrieval of all bonds in the file.
int	getEstimatedAtomCount(java.lang.Object clientFile) Get the estimated number of atoms contained in the file.
float[]	getNotionalUnitcell(java.lang.Object clientFile) Get the notional unit cell.

Methods inherited from class org.jmol.api.JmolAdapter

canonizeAlphaDigit, canonizeAlternateLocationID, canonizeChainID, canonizeInsertionCode, coordinatesAreFractional, finish, getAtomSetCollectionProperties, getAtomSetCount, getAtomSetName, getAtomSetNumber, getAtomSetProperties, getClientAtomStringProperty, getFileTypeName, getPdbScaleMatrix, getPdbScaleTranslate, getStructureIterator, openBufferedReader, openBufferedReader, openBufferedReaders, openBufferedReaders, openDOMReader, openDOMReader

Methods inherited from class java.lang.Object

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

Method Detail

getAtomSetCollectionName

public java.lang.String getAtomSetCollectionName(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get the name of the atom set collection, if known.

Some file formats contain a formal name of the molecule in the file. If this method returns null then the JmolViewer will automatically supply the file/URL name as a default.

Overrides:

getAtomSetCollectionName in class JmolAdapter

Returns:

The atom set collection name or null

getEstimatedAtomCount

public int getEstimatedAtomCount(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get the estimated number of atoms contained in the file.

Just return -1 if you don't know (or don't want to figure it out)

Specified by:

getEstimatedAtomCount in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The estimated number of atoms in the file

getNotionalUnitcell

public float[] getNotionalUnitcell(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get the notional unit cell.

This method returns the parameters that define a crystal unitcell the parameters are returned in a float[] in the following order a, b, c, alpha, beta, gamma
a, b, c : angstroms
alpha, beta, gamma : degrees
if there is no unit cell data then return null

Overrides:

getNotionalUnitcell in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The array of the values or null

getAtomIterator

public JmolAdapter.AtomIterator getAtomIterator(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get an AtomIterator for retrieval of all atoms in the file.

This method may not return null.

Specified by:

getAtomIterator in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

An AtomIterator

See Also:

JmolAdapter.AtomIterator

getBondIterator

public JmolAdapter.BondIterator getBondIterator(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get a BondIterator for retrieval of all bonds in the file.

If this method returns null and no bonds are defined then the JmolViewer will automatically apply its rebonding code to build bonds between atoms.

Overrides:

getBondIterator in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

A BondIterator or null

See Also:

JmolAdapter.BondIterator