Package com.actelion.research.chem.forcefield.mmff

Class Tables

java.lang.Object

com.actelion.research.chem.forcefield.mmff.Tables

public final class Tables
extends java.lang.Object

A collection of tables with the official parameters of the MMFF94/MMFF94s force field variants.

Field Summary

Fields

Modifier and Type	Field	Description
Angle	angle
Atom	atom
Bndk	bndk
Bond	bond
Charge	chge
CovRad	covrad
Def	def
Dfsb	dfsb
HerschbachLaurie	hblaurie
OutOfPlane	oop
Stbn	stbn
Torsion	torsion
VanDerWaals	vdws

Constructor Summary

Constructors

Constructor	Description
Tables(java.lang.String csv_angle, java.lang.String csv_atom, java.lang.String csv_bci, java.lang.String csv_bndk, java.lang.String csv_bond, java.lang.String csv_covrad, java.lang.String csv_dfsb, java.lang.String csv_def, java.lang.String csv_hblaurie, java.lang.String csv_oop, java.lang.String csv_pbci, java.lang.String csv_stbn, java.lang.String csv_torsion, java.lang.String csv_vdws)	Construct a new Tables object.

Method Summary

Modifier and Type	Method	Description
static Tables	newMMFF94(java.lang.String tableSet)	Returns a new MMFF94 table.

Methods inherited from class java.lang.Object

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

Field Detail

angle

public final Angle angle

atom

public final Atom atom

bndk

public final Bndk bndk

bond

public final Bond bond

covrad

public final CovRad covrad

dfsb

public final Dfsb dfsb

def

public final Def def

hblaurie

public final HerschbachLaurie hblaurie

oop

public final OutOfPlane oop

chge

public final Charge chge

stbn

public final Stbn stbn

torsion

public final Torsion torsion

vdws

public final VanDerWaals vdws

Constructor Detail

Tables

public Tables(java.lang.String csv_angle,
              java.lang.String csv_atom,
              java.lang.String csv_bci,
              java.lang.String csv_bndk,
              java.lang.String csv_bond,
              java.lang.String csv_covrad,
              java.lang.String csv_dfsb,
              java.lang.String csv_def,
              java.lang.String csv_hblaurie,
              java.lang.String csv_oop,
              java.lang.String csv_pbci,
              java.lang.String csv_stbn,
              java.lang.String csv_torsion,
              java.lang.String csv_vdws)

Construct a new Tables object. Takes several string paths to CSV files to be used for the different parameter tables.

Parameters:

csv_angle - Path to the angles parameter table. The angle table holds ideal angle and force constant values.

csv_atom - Path to the atoms parameter table. This table specifies the chemical, topological and geometrical properties associated with each of the MMFF atom types.

csv_bci - Path to the bond charge increments table. This table is used for the MMFF partial charge computation.

csv_bndk - Path to the bond length and default force constants table. Used as fallback values if bond parameters are not found in csv_bond.

csv_bond - Path to the bond parameters table. Holds the ideal length and force constants for bonds between MMFF atom typed atoms.

csv_covrad - Path to the CovRad CSV table.

csv_dfsb - Path to the Dfsb CSV table. Holds the default stretch bend parameters.

csv_def - Path to the default types table. Holds fallback MMFF types for atoms. Used to help find matches for energy terms in their parameter tables.

csv_hblaurie - Path to the HerschbachLaurie table. Parameters table for Badger's rule.

csv_oop - Path to the out of plane parameters table. Holds the force constant parameter.

csv_pbci - Path to the partial bond charge increments and formal charge adjustments table.

csv_stbn - Path to the stretch bend parameters table. Holds the force constants for both i-j-k and k-j-i atom configurations.

csv_torsion - Path to the torsional parameters table. Holds the three force constants for given MMFF atom types.

csv_vdws - Path to the van der Waals parameters table.

Method Detail

newMMFF94

public static Tables newMMFF94(java.lang.String tableSet)

Returns a new MMFF94 table. The paths provided here are correct when running the project using ant/eclipse or from the same directory as build.xml and the README.