Package edu.duke.cs.osprey.plug

Class RCPairVDWChecker

java.lang.Object

edu.duke.cs.osprey.plug.RCPairVDWChecker

public class RCPairVDWChecker
extends Object

This class looks for possible contacts between atoms in a pair of RCs or between an RC and the shell if there's just one RC It makes a polytope representing the geometrically favorable region, or determines there is none For now, assuming a polytope suffices and that pushing any of the good contacts that are possible anywhere in the voxel out of the favorable distance range will create a hole or clash Then higher-order checks on the voxels (up to full confs) can limit themselves to the intersection of pairwise polytopes, and can check the contacts in each pair to make sure each atom that should have a contact does have one

Constructor Summary

Constructors

Constructor	Description
RCPairVDWChecker(ConfSpace cSpace, RCTuple tup, ArrayList<Residue> shellResidues)
RCPairVDWChecker(Residue res1, RC rc1, Residue res2, RC rc2, ArrayList<Residue> shellResidues)

Method Summary

Modifier and Type	Method	Description
RCTuplePolytope	buildPolytope()
ArrayList<org.apache.commons.math3.optim.linear.LinearConstraint>	calcPolytopeConstr()
ArrayList<org.apache.commons.math3.optim.linear.LinearConstraint>	calcPolytopeConstr(ArrayList<String> atomPairNames)
boolean	checkVDW()

Methods inherited from class java.lang.Object

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

Constructor Details

RCPairVDWChecker

public RCPairVDWChecker(Residue res1,
 RC rc1,
 Residue res2,
 RC rc2,
 ArrayList<Residue> shellResidues)

RCPairVDWChecker

public RCPairVDWChecker(ConfSpace cSpace,
 RCTuple tup,
 ArrayList<Residue> shellResidues)

Method Details

checkVDW

public boolean checkVDW()

calcPolytopeConstr

public ArrayList<org.apache.commons.math3.optim.linear.LinearConstraint> calcPolytopeConstr()

calcPolytopeConstr

public ArrayList<org.apache.commons.math3.optim.linear.LinearConstraint> calcPolytopeConstr(ArrayList<String> atomPairNames)

buildPolytope

public RCTuplePolytope buildPolytope()