meshi.energy.solvate
Class SolvateDistanceAttribute

java.lang.Object
  meshi.energy.solvate.SolvateDistanceAttribute

All Implemented Interfaces:

MeshiAttribute

Direct Known Subclasses:

SolvateDistanceAttributeBetweenPolars, SolvateDistanceAttributeNonPolarPolar, SolvateDistanceAttributePolarNonPolar, SolvateDistanceAttributeWithAhydrogen, SolvateDistanceAttributeWithNonPolar

public abstract class SolvateDistanceAttribute
extends java.lang.Object
implements MeshiAttribute

In the SolvateEnergy 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, and an hydrogen-bond strength value: sigmCa1 - The carbon index of atom 2 on atom 1. If atom 2 is not a carbon then this value should be zero. If atom 2 is a carbon then 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. sigmHBa1 - The hydrogen bond (HB) strength between atom 1 and 2. If atom 2 can not form HB with atom 1, because of its chemical type then this value should be zero. If atom 2 can form HB with atom 1 then this value should be ~1.0 if atom 1 and 2 are sufficiently close to create a HB, and if their orientation (defined also by their base atoms - see HydrogenBondDahiyat) permit hydrogen bonding. This value drops steeply to zero if the conditions to hydrogen bonding are violated. Also provided are the carbon sigmoid values derivative relatives to the atom coordinates. They have the general form: dsigmCa{1/2}d{x/y/z}{1/2}

Field Summary

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

SolvateDistanceAttribute()

Method Summary

int	key()
abstract SolvateDistanceType	type()

Methods inherited from class java.lang.Object

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

Constructor Detail

SolvateDistanceAttribute

public SolvateDistanceAttribute()

Method Detail

type

public abstract SolvateDistanceType type()

key

public int key()

Specified by:

key in interface MeshiAttribute