Package edu.duke.cs.osprey.energy

Class ResInterGen

java.lang.Object

edu.duke.cs.osprey.energy.ResInterGen

public class ResInterGen
extends Object

Helper class to create ResidueInteractions First call ResInterGen.of(yourConfSpace), then .addXXX() for each interactions you wish to add.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	ResInterGen.InterOffsetter
static interface	ResInterGen.IntraOffsetter
static interface	ResInterGen.ShellOffsetter

Method Summary

Modifier and Type	Method	Description
ResInterGen	addAll(RCTuple frag)	adds all possible residue interactions
ResInterGen	addInter(int pos1, int pos2)	energy += E(pos1, pos2)
ResInterGen	addInter(int pos1, int pos2, double weight, double offset)	energy += [E(pos1, pos2) + offset]*weight
ResInterGen	addInters(RCTuple frag)	energy += E(pos1, pos2) for all pos2 < pos1 in frag
ResInterGen	addInters(RCTuple frag, double weight, ResInterGen.InterOffsetter offsetter)	energy += [E(pos1, pos2) + offset(pos1, pos2)]*weight for all pos2 < pos1 in frag
ResInterGen	addIntra(int pos)	energy += E(pos)
ResInterGen	addIntra(int pos, double weight, double offset)	energy += [E(pos) + offset]*weight
ResInterGen	addIntras(RCTuple frag)	energy += E(pos) for all pos in frag
ResInterGen	addIntras(RCTuple frag, double weight, ResInterGen.IntraOffsetter offsetter)	energy += [E(pos) + offset(pos)]*weight for all pos in frag
ResInterGen	addShell(int pos)	energy += E(pos, s) for all s in shell
ResInterGen	addShell(int pos, double weight, double offset)	energy += [E(pos, s) + offset]*weight for all s in shell
ResInterGen	addShell(RCTuple frag)	energy += E(pos, s) for all pos in frag, s in shell
ResInterGen	addShell(RCTuple frag, double weight, ResInterGen.ShellOffsetter offsetter)	energy += [E(pos, s) + offset(pos, s)]*weight for all pos in frag, s in shell
ResInterGen	addShellInters()	energy += E(s, s) for all pairs of s in shell
ResInterGen	addShellIntras()	energy += E(s) for all s in shell
String	getResNum(int pos)
ResidueInteractions	make()
static ResInterGen	of(SimpleConfSpace confSpace)

Methods inherited from class java.lang.Object

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

Method Details

of

public static ResInterGen of(SimpleConfSpace confSpace)

make

public ResidueInteractions make()

getResNum

public String getResNum(int pos)

addIntra

public ResInterGen addIntra(int pos)

energy += E(pos)

addIntra

public ResInterGen addIntra(int pos,
 double weight,
 double offset)

energy += [E(pos) + offset]*weight

addIntras

public ResInterGen addIntras(RCTuple frag)

energy += E(pos) for all pos in frag

addIntras

public ResInterGen addIntras(RCTuple frag,
 double weight,
 ResInterGen.IntraOffsetter offsetter)

energy += [E(pos) + offset(pos)]*weight for all pos in frag

addInter

public ResInterGen addInter(int pos1,
 int pos2)

energy += E(pos1, pos2)

addInter

public ResInterGen addInter(int pos1,
 int pos2,
 double weight,
 double offset)

energy += [E(pos1, pos2) + offset]*weight

addInters

public ResInterGen addInters(RCTuple frag)

energy += E(pos1, pos2) for all pos2 < pos1 in frag

addInters

public ResInterGen addInters(RCTuple frag,
 double weight,
 ResInterGen.InterOffsetter offsetter)

energy += [E(pos1, pos2) + offset(pos1, pos2)]*weight for all pos2 < pos1 in frag

addShell

public ResInterGen addShell(int pos)

energy += E(pos, s) for all s in shell

addShell

public ResInterGen addShell(int pos,
 double weight,
 double offset)

energy += [E(pos, s) + offset]*weight for all s in shell

addShell

public ResInterGen addShell(RCTuple frag)

energy += E(pos, s) for all pos in frag, s in shell

addShell

public ResInterGen addShell(RCTuple frag,
 double weight,
 ResInterGen.ShellOffsetter offsetter)

energy += [E(pos, s) + offset(pos, s)]*weight for all pos in frag, s in shell

addShellIntras

public ResInterGen addShellIntras()

energy += E(s) for all s in shell

addShellInters

public ResInterGen addShellInters()

energy += E(s, s) for all pairs of s in shell

addAll

public ResInterGen addAll(RCTuple frag)

adds all possible residue interactions