SolvateRot1DistanceAttribute

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meshi.energy.solvateRot1
Class SolvateRot1DistanceAttribute

java.lang.Object
  meshi.energy.solvateRot1.SolvateRot1DistanceAttribute

All Implemented Interfaces:: MeshiAttribute

public class SolvateRot1DistanceAttribute
extends java.lang.Object
implements MeshiAttribute
extends java.lang.Object
implements MeshiAttribute

In the SolvateRot1Energy evaluation function these fields are to be recalculated for EVERY distance in the non-bonded list. They are used several times in the solvate evaluation process, and we would like to calculate them once. To this end we attach this special class as an attribute on each Distance instance. For each distance we calculate two sigmoid values: one for atom 1 in the distance (a1), and one for atom 2 in the distance (a2): sigmCa1 - The carbon index of atom 2 on atom 1. This value should be ~1.0 if atom 2 is spatially near atom 1. This index drops sigmoidally to zero the farther atom 2 is. sigmCa2 - The same as sigmCa1, except detailing the affect of atom 1 on atom 2. Also provided are the sigmoid values derivative relatives to the atom coordinates. They have the general form: dsigmCa{1/2}d{x/y/z}{1/2}

Field Summary
`double`	`dsigmCa1dx1`
`double`	`dsigmCa1dx2`
`double`	`dsigmCa1dy1`
`double`	`dsigmCa1dy2`
`double`	`dsigmCa1dz1`
`double`	`dsigmCa1dz2`
`double`	`dsigmCa2dx1`
`double`	`dsigmCa2dx2`
`double`	`dsigmCa2dy1`
`double`	`dsigmCa2dy2`
`double`	`dsigmCa2dz1`
`double`	`dsigmCa2dz2`
`double`	`sigmCa1`
`double`	`sigmCa2`

Fields inherited from interface meshi.util.MeshiAttribute
`BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE`

Fields inherited from interface meshi.util.MeshiAttribute

BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE

Constructor Summary
`SolvateRot1DistanceAttribute()`

Method Summary
`int`	`key()`
`void`	`resetAllSigmVals()`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

sigmCa1

public double sigmCa1

sigmCa2

public double sigmCa2

dsigmCa1dx1

public double dsigmCa1dx1

dsigmCa1dy1

public double dsigmCa1dy1

dsigmCa1dz1

public double dsigmCa1dz1

dsigmCa1dx2

public double dsigmCa1dx2

dsigmCa1dy2

public double dsigmCa1dy2

dsigmCa1dz2

public double dsigmCa1dz2

dsigmCa2dx1

public double dsigmCa2dx1

dsigmCa2dy1

public double dsigmCa2dy1

dsigmCa2dz1

public double dsigmCa2dz1

dsigmCa2dx2

public double dsigmCa2dx2

dsigmCa2dy2

public double dsigmCa2dy2

dsigmCa2dz2

public double dsigmCa2dz2

Constructor Detail