Uses of Class
com.actelion.research.chem.conf.Conformer

Packages that use Conformer

Package	Description
com.actelion.research.chem.alignment3d
com.actelion.research.chem.conf
com.actelion.research.chem.conf.torsionstrain
com.actelion.research.chem.docking
com.actelion.research.chem.docking.scoring
com.actelion.research.chem.docking.scoring.chemscore
com.actelion.research.chem.docking.scoring.idoscore
com.actelion.research.chem.docking.scoring.plp
com.actelion.research.chem.phesa
com.actelion.research.chem.phesa.pharmacophore
com.actelion.research.chem.potentialenergy
org.openmolecules.chem.conf.gen
org.openmolecules.chem.conf.so

Uses of Conformer in com.actelion.research.chem.alignment3d

Constructors in com.actelion.research.chem.alignment3d with parameters of type Conformer

Constructor	Description
KabschAlignment(Conformer conf1, Conformer conf2)	first conformer is the reference, second conformer is rotated and translated to minimize the RMSD

Uses of Conformer in com.actelion.research.chem.conf

Methods in com.actelion.research.chem.conf that return Conformer

Modifier and Type	Method	Description
Conformer	Conformer.center()	Translate this conformer's coordinates such that its center of gravity is moved to P(0,0,0) assuming all atoms have the same mass.
Conformer	Conformer.translate(double dx, double dy, double dz)	Translate this conformer's coordinates by adding the dx,dy,dz shifts to all atom coordinates.

Methods in com.actelion.research.chem.conf with parameters of type Conformer

Modifier and Type	Method	Description
static double	TorsionDB.calculateTorsionExtended(Conformer conformer, int[] atom)	Calculates a signed torsion like calculateTorsion().
int	Conformer.compareTo(Conformer c)
void	Conformer.copyFrom(Conformer conformer)	Copies the conformer's atom coordinates to this Conformer.
boolean	Conformer.equals(Conformer c)
TorsionDescriptor	TorsionDescriptorHelper.getTorsionDescriptor(Conformer conformer)	Creates a TorsionDescriptor from the coordinates of the passed conformer assuming that its underlying molecule is the same that waas passed to this TorsionDescriptorHelper's constructor.
void	BondRotationHelper.rotateAroundBond(int bond, double alpha, Conformer conf, boolean biggerSide)	rotate torsion angle of a conformer

Constructors in com.actelion.research.chem.conf with parameters of type Conformer

Constructor	Description
Conformer(Conformer c)	Creates a new conformer as an exact copy of the given one.
Conformer(Conformer c, StereoMolecule mol)	Use at own risk!! Initializes the conformer as a copy of c but replaces the StereoMolecule by the supplied molecule.
SymmetryCorrectedRMSDCalculator(Conformer conf1, Conformer conf2)

Uses of Conformer in com.actelion.research.chem.conf.torsionstrain

Methods in com.actelion.research.chem.conf.torsionstrain with parameters of type Conformer

Modifier and Type	Method	Description
static StatisticalTorsionTerm	StatisticalTorsionTerm.create(Conformer conf, int[] atoms, java.lang.String torsionID)
static void	StatisticalTorsionTerm.getCartesianTorsionGradient(int[] atoms, Conformer conf, double[] gradient, double dEdPhi, Coordinates[] coords, int[][] rearAtoms)

Uses of Conformer in com.actelion.research.chem.docking

Methods in com.actelion.research.chem.docking that return Conformer

Modifier and Type	Method	Description
Conformer	LigandPose.getLigConf()

Methods in com.actelion.research.chem.docking with parameters of type Conformer

Modifier and Type	Method	Description
static Matrix	DockingUtils.calculateMassCovarianceMatrix(Conformer conf)
static Matrix	DockingUtils.createInitialOrientation(Conformer conf)
static Coordinates	DockingUtils.getCOM(Conformer conf)

Constructors in com.actelion.research.chem.docking with parameters of type Conformer

Constructor	Description
LigandPose(Conformer ligConf, AbstractScoringEngine engine, double e0)

Uses of Conformer in com.actelion.research.chem.docking.scoring

Fields in com.actelion.research.chem.docking.scoring declared as Conformer

Modifier and Type	Field	Description
protected Conformer	AbstractScoringEngine.receptorConf

Methods in com.actelion.research.chem.docking.scoring that return Conformer

Modifier and Type	Method	Description
Conformer	AbstractScoringEngine.getReceptorConf()

Uses of Conformer in com.actelion.research.chem.docking.scoring.chemscore

Methods in com.actelion.research.chem.docking.scoring.chemscore with parameters of type Conformer

Modifier and Type	Method	Description
static HBTerm	HBTerm.create(Conformer receptor, Conformer ligand, int acceptor, int donor, int hydrogen, boolean isLigAtomAcceptor, boolean isLigAtomDonor, int[] acceptorNeighbours, double scale)
static MetalTerm	MetalTerm.create(Conformer ligand, int acceptor, int[] acceptorNeighbours, Coordinates fitPoint, double scale)
static SimpleMetalTerm	SimpleMetalTerm.create(Conformer receptor, Conformer ligand, int acceptor, int metal, int[] acceptorNeighbours, double scale)

Uses of Conformer in com.actelion.research.chem.docking.scoring.idoscore

Methods in com.actelion.research.chem.docking.scoring.idoscore with parameters of type Conformer

Modifier and Type	Method	Description
static InteractionTerm	InteractionTerm.create(Conformer receptor, Conformer ligand, int p, int l, int[] receptorAtomTypes, int[] ligandAtomTypes)

Uses of Conformer in com.actelion.research.chem.docking.scoring.plp

Methods in com.actelion.research.chem.docking.scoring.plp with parameters of type Conformer

Modifier and Type	Method	Description
static PLPTerm	PLPTerm.create(Conformer receptor, Conformer ligand, int recAtom, int ligAtom, java.util.Map<java.lang.String,java.lang.Double> term)
static REPTerm	REPTerm.create(Conformer receptor, Conformer ligand, int recAtom, int ligAtom)

Uses of Conformer in com.actelion.research.chem.phesa

Methods in com.actelion.research.chem.phesa with parameters of type Conformer

Modifier and Type	Method	Description
static Matrix	PheSAAlignment.createCanonicalOrientation(Conformer conf, MolecularVolume molGauss)
static Matrix	PheSAAlignment.preProcess(Conformer conf, MolecularVolume molVol)	Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system
static void	PheSAAlignment.rotateMol(Conformer conf, double[] transform)
static void	PheSAAlignment.rotateMol(Conformer conf, Matrix rotMat)
static void	PheSAAlignment.rotateMol(Conformer conf, Quaternion rotor, double[] transl)
void	MolecularVolume.update(Conformer conf)
void	Gaussian3D.updateCoordinates(Conformer conf)
void	VolumeGaussian.updateCoordinates(Conformer conf)

Constructors in com.actelion.research.chem.phesa with parameters of type Conformer

Constructor	Description
MolecularVolume(MolecularVolume original, Conformer conf)

Uses of Conformer in com.actelion.research.chem.phesa.pharmacophore

Methods in com.actelion.research.chem.phesa.pharmacophore with parameters of type Conformer

Modifier and Type	Method	Description
void	AcceptorPoint.updateCoordinates(Conformer conf)
void	AromRingPoint.updateCoordinates(Conformer conf)
void	ChargePoint.updateCoordinates(Conformer conf)
void	DonorPoint.updateCoordinates(Conformer conf)
void	ExitVectorPoint.updateCoordinates(Conformer conf)
void	IPharmacophorePoint.updateCoordinates(Conformer conf)
void	PPGaussian.updateCoordinates(Conformer conf)

Uses of Conformer in com.actelion.research.chem.potentialenergy

Constructors in com.actelion.research.chem.potentialenergy with parameters of type Conformer

Constructor	Description
AngleConstraint(Conformer conf, int[] angleAtoms, double targetAngle)
BondConstraint(Conformer conf, int[] bondAtoms, double targetDistance)
EmpiricalLigandStrain(Conformer conf, int[] atomTypes, BondRotationHelper torsionHelper)
PositionConstraint(Conformer conf, int atom, double k, double d)
TorsionConstraint(Conformer conf, int[] torsionAtoms, double targetValue, double width)	Term that forces a torsion angle with a harmonic potential to a range of acceptable values (range given by the width)

Uses of Conformer in org.openmolecules.chem.conf.gen

Methods in org.openmolecules.chem.conf.gen that return Conformer

Modifier and Type	Method	Description
Conformer	ConformerGenerator.generateConformerFromTorsionSet(TorsionSet torsionset)	Computes a conformer from a TorsionSet object.
Conformer	ConformerGenerator.getNextConformer()
Conformer	ConformerGenerator.getNextConformer(TorsionSet[] torsion_set_out)	Creates the next random, likely or systematic new(!) conformer of the molecule that was passed when calling initializeConformers().
Conformer	ConformerGenerator.getOneConformer(StereoMolecule mol)	Fills all free valences of mol with explicit hydrogens and tries to create a reasonable conformer by starting with the most likely torsion set.

Methods in org.openmolecules.chem.conf.gen with parameters of type Conformer

Modifier and Type	Method	Description
void	RotatableBond.connectFragments(Conformer conformer, boolean[] isAttached, int[] fragmentPermutation)	Checks both rigid fragments that are connected by this bond, whether they have been attached to the conformer yet, i.e.
void	RotatableBond.rotateTo(Conformer conformer, short torsion)	Rotate the smaller side of the molecule around this bond to reach the defined torsion angle.
void	RotatableBond.rotateToIndex(Conformer conformer, int torsionIndex)	Rotate the smaller side of the molecule around this bond to reach the torsion angle defined by torsionIndex.

Constructors in org.openmolecules.chem.conf.gen with parameters of type Conformer

Constructor	Description
RigidFragment(int coreAtomCount, int[] coreToFragmentAtom, int[] fragmentToOriginalAtom, int[] extendedToFragmentAtom, int[] originalToExtendedAtom, Conformer[] conformerList, double[] conformerLikelyhood)

Uses of Conformer in org.openmolecules.chem.conf.so

Subclasses of Conformer in org.openmolecules.chem.conf.so

Modifier and Type	Class	Description
class	SelfOrganizedConformer

Methods in org.openmolecules.chem.conf.so with parameters of type Conformer

Modifier and Type	Method	Description
double	AxialStereoRule.addStrain(Conformer conformer, double[] atomStrain)
abstract double	ConformationRule.addStrain(Conformer conformer, double[] atomStrain)
double	DistanceRule.addStrain(Conformer conformer, double[] atomStrain)
double	PlaneRule.addStrain(Conformer conformer, double[] atomStrain)
double	StraightLineRule.addStrain(Conformer conformer, double[] atomStrain)
double	TetrahedralStereoRule.addStrain(Conformer conformer, double[] atomStrain)
double	TorsionRule.addStrain(Conformer conformer, double[] atomStrain)
boolean	AxialStereoRule.apply(Conformer conformer, double cycleFactor)
abstract boolean	ConformationRule.apply(Conformer conformer, double cycleFactor)
boolean	DistanceRule.apply(Conformer conformer, double cycleFactor)
boolean	PlaneRule.apply(Conformer conformer, double cycleFactor)
boolean	StraightLineRule.apply(Conformer conformer, double cycleFactor)
boolean	TetrahedralStereoRule.apply(Conformer conformer, double cycleFactor)
boolean	TorsionRule.apply(Conformer conformer, double cycleFactor)
protected void	ConformationRule.moveAtomWithUnboundedNeighbors(Conformer conformer, int atom, double dx, double dy, double dz)
protected void	ConformationRule.moveGroup(Conformer conformer, int atom, int[] notList, double dx, double dy, double dz)	Move one atom and all non-ring-bond substituents, provided attachment atom is not part of the notList.
protected void	ConformationRule.moveSubstituent(Conformer conformer, int rootAtom, int firstAtom, double dx, double dy, double dz)	Moves all atoms of the substituent connected to rootAtom starting with firstAtom.
protected void	ConformationRule.rotateAtom(Conformer conformer, int atom, int refAtom, Coordinates unit, double theta)