Uses of Class
com.actelion.research.chem.conf.Conformer
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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.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. -
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 systemstatic 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)
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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
IPharmacophorePoint. updateCoordinates(Conformer conf)
void
PPGaussian. updateCoordinates(Conformer conf)
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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)
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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)
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