Field Detail

• atomTypes

  private static javajs.util.Lst<java.lang.String[]> atomTypes

• ffParams

  private java.util.Map<java.lang.Object,​java.lang.Object> ffParams

• uff2DParams

  private static java.util.Map<java.lang.Object,​java.lang.Object> uff2DParams

• uffParams

  private static java.util.Map<java.lang.Object,​java.lang.Object> uffParams

• bsAromatic

  private javajs.util.BS bsAromatic

• is2D

  private boolean is2D

• TOKEN_ELEMENT_ONLY

  private static final int TOKEN_ELEMENT_ONLY

  See Also:

  Constant Field Values

• TOKEN_ELEMENT_CHARGED

  private static final int TOKEN_ELEMENT_CHARGED

  See Also:

  Constant Field Values

• TOKEN_ELEMENT_CONNECTED

  private static final int TOKEN_ELEMENT_CONNECTED

  See Also:

  Constant Field Values

• TOKEN_AROMATIC

  private static final int TOKEN_AROMATIC

  See Also:

  Constant Field Values

• TOKEN_ELEMENT_SP

  private static final int TOKEN_ELEMENT_SP

  See Also:

  Constant Field Values

• TOKEN_ELEMENT_ALLYLIC

  private static final int TOKEN_ELEMENT_ALLYLIC

  See Also:

  Constant Field Values

• PT_ELEMENT

  private static final int PT_ELEMENT

  See Also:

  Constant Field Values

• PT_CHARGE

  private static final int PT_CHARGE

  See Also:

  Constant Field Values

• PT_CONNECT

  private static final int PT_CONNECT

  See Also:

  Constant Field Values

• tokenTypes

  private static final T[][] tokenTypes

Constructor Detail

• ForceFieldUFF

  public ForceFieldUFF​(Minimizer minimizer,
                       boolean isQuick)

Method Detail

• clear

  public void clear()

  Specified by:

  clear in class ForceField

• setModel

  public boolean setModel​(javajs.util.BS bsElements,
                          int elemnoMax)
                   throws JmolAsyncException

  Specified by:

  setModel in class ForceField

  Throws:

  JmolAsyncException

• setAtomTypes

  private void setAtomTypes​(javajs.util.BS bsElements,
                            int elemnoMax)

• getSearch

  private javajs.util.BS getSearch​(java.lang.String smarts,
                                   int elemnoMax,
                                   javajs.util.BS bsElements)

• getParameters

  private java.util.Map<java.lang.Object,​java.lang.Object> getParameters()

• getAtomTypes

  private javajs.util.Lst<java.lang.String[]> getAtomTypes()
                                                    throws JmolAsyncException

  Throws:

  JmolAsyncException