Uses of Class
com.actelion.research.chem.conf.Conformer
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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.alignment3d.transformation
Methods in com.actelion.research.chem.alignment3d.transformation with parameters of type Conformer Modifier and Type Method Description default void
Transformation. apply(Conformer conf)
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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.void
BondRotationHelper. rotateAroundBond(int bondIndex, double alpha, Conformer conf, boolean biggerSide)
rotate torsion angle of a conformerConstructors 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)
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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)
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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)
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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()
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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)
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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)
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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)
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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 Matrix
MolecularVolume. createCanonicalOrientation(Conformer conf)
Matrix
ShapeVolume. createCanonicalOrientation(Conformer conf)
Rotation
ShapeVolume. preProcess(Conformer conf)
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[][] m)
static void
PheSAAlignment. rotateMol(Conformer conf, Quaternion rotor, double[] transl)
static void
PheSAAlignment. rotateMolAroundAxis180(Conformer conf, PheSAAlignment.axis a)
void
MolecularVolume. update(Conformer conf)
void
ShapeVolume. update(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.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 com.actelion.research.chem.prediction
Methods in com.actelion.research.chem.prediction with parameters of type Conformer Modifier and Type Method Description static double
GlobularityCalculator. assessGlobularityFromSVD(Conformer conf)
Calculates the globularity of a conformer (flat=0, round=1) from 3D coordinates -
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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