Package ffx.potential.parameters

Class VDWType

java.lang.Object
ffx.potential.parameters.BaseType
ffx.potential.parameters.VDWType
All Implemented Interfaces:
Comparator<String>
@FFXProperty(name="vdw",clazz=java.lang.String.class,propertyGroup=PotentialFunctionParameter,description="[1 integer and 3 reals]\nProvides values for a single van der Waals parameter. The integer modifier, if positive,\ngives the atom class number for which vdw parameters are to be defined. Note that vdw parameters are given for atom classes, not atom types.\nThe three real number modifiers give the values of the atom size in Angstroms, homoatomic well depth in kcal/mole,\nand an optional reduction factor for univalent atoms.\n") @FFXProperty(name="vdw14",clazz=java.lang.String.class,propertyGroup=PotentialFunctionParameter,description="[1 integer and 2 reals]\nProvides values for a single van der Waals parameter for use in 1-4 nonbonded interactions.\nThe integer modifier, if positive, gives the atom class number for which vdw parameters are to be defined.\nNote that vdw parameters are given for atom classes, not atom types.\nThe two real number modifiers give the values of the atom size in Angstroms and the homoatomic well depth in kcal/mole.\nReduction factors, if used, are carried over from the vdw keyword for the same atom class.\n") public final class VDWType extends BaseType implements Comparator<String>
The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.
Since:
1.0
Author:
Michael J. Schnieders

  • Field Details

    • DEFAULT_GAMMA

      public static final double DEFAULT_GAMMA
      The default gamma parameter in Halgren’s buffered 14-7 vdw potential energy functional form.
      See Also:

    • DEFAULT_DELTA

      public static final double DEFAULT_DELTA
      The default delta parameter in Halgren’s buffered 14-7 vdw potential energy functional form.
      See Also:

    • DEFAULT_EPSILON_RULE

      public static final VDWType.EPSILON_RULE DEFAULT_EPSILON_RULE
      The default epsilon combining rule.

    • DEFAULT_RADIUS_RULE

      public static final VDWType.RADIUS_RULE DEFAULT_RADIUS_RULE
      The default radius combining rule.

    • DEFAULT_RADIUS_SIZE

      public static final VDWType.RADIUS_SIZE DEFAULT_RADIUS_SIZE
      The default radius size.

    • DEFAULT_RADIUS_TYPE

      public static final VDWType.RADIUS_TYPE DEFAULT_RADIUS_TYPE
      The default radius type.

    • DEFAULT_VDW_TYPE

      public static final VDWType.VDW_TYPE DEFAULT_VDW_TYPE
      The default van der Waals functional form type.

    • DEFAULT_VDW_12_SCALE

      public static final double DEFAULT_VDW_12_SCALE
      The default van der Waals scale factor for 1-2 (bonded) interactions.
      See Also:

    • DEFAULT_VDW_13_SCALE

      public static final double DEFAULT_VDW_13_SCALE
      The default van der Waals scale factor for 1-3 (angle) interactions.
      See Also:

    • DEFAULT_VDW_14_SCALE

      public static final double DEFAULT_VDW_14_SCALE
      The default van der Waals scale factor for 1-4 (torisonal) interactions.
      See Also:

    • radius

      public final double radius
      The radius of the minimum well depth energy (angstroms).

    • wellDepth

      public final double wellDepth
      The minimum energy of the vdw function (kcal/mol).

    • reductionFactor

      public final double reductionFactor
      Reduction factor for evaluating van der Waals pairs. Valid range: 0.0 .GT. reduction .LE. 1.0 Usually only hydrogen atoms have a reduction factor. Setting the reduction to .LT. 0.0 indicates it is not being used.

    • atomClass

      public int atomClass
      The atom class that uses this van der Waals parameter.

  • Constructor Details

    • VDWType

      public VDWType(int atomClass, double radius, double wellDepth, double reductionFactor)
      van der Waals constructor. If the reduction factor is .LE. 0.0, no reduction is used for this atom type.
      Parameters:
      atomClass - The atom class that uses this van der Waals parameter.
      radius - The radius of the minimum well depth energy (angstroms).
      wellDepth - The minimum energy of the vdw function (kcal/mol).
      reductionFactor - Reduction factor for evaluating van der Waals pairs.

    • VDWType

      public VDWType(int atomClass, double radius, double wellDepth, double reductionFactor, VDWType.VDWMode vdwMode)
      van der Waals constructor. If the reduction factor is .LE. 0.0, no reduction is used for this atom type.
      Parameters:
      atomClass - The atom class that uses this van der Waals parameter.
      radius - The radius of the minimum well depth energy (angstroms).
      wellDepth - The minimum energy of the vdw function (kcal/mol).
      reductionFactor - Reduction factor for evaluating van der Waals pairs.
      vdwMode - The VDWMode to use.

  • Method Details

    • average

      public static VDWType average(VDWType vdwType1, VDWType vdwType2, int atomClass)
      Average two VDWType objects.
      Parameters:
      vdwType1 - The first VDWType.
      vdwType2 - The second VDWType.
      atomClass - The new atom class.
      Returns:
      The new averaged VDWType.

    • parse

      public static VDWType parse(String input, String[] tokens)
      Construct a VDWType from multiple input lines.
      Parameters:
      input - The overall input String.
      tokens - The input String tokenized.
      Returns:
      a VDWType instance.

    • parseVDW14

      public static VDWType parseVDW14(String input, String[] tokens)
      Construct a 1-4 VDWType from multiple input lines.
      Parameters:
      input - The overall input String.
      tokens - The input String tokenized.
      Returns:
      a VDWType instance.

    • compare

      public int compare(String s1, String s2)
      Specified by:
      compare in interface Comparator<String>

    • equals

      public boolean equals(Object o)
      Specified by:
      equals in interface Comparator<String>
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()

      Basic toString method.

      Nicely formatted van der Waals type.

      Overrides:
      toString in class BaseType

    • getXMLForce

      public static Element getXMLForce(Document doc, ForceField forceField)
      Create an AmoebaVdwForce force node.
      Parameters:
      doc - the Document instance.
      forceField - the ForceField to collect constants from.
      Returns:
      The AmoebaVdwForce force node.

    • toXML

      public Element toXML(Document doc)
      Write VDWType to OpenMM XML format.