Package com.actelion.research.chem.conf
Class TorsionDescriptorHelper
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- com.actelion.research.chem.conf.TorsionDescriptorHelper
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public class TorsionDescriptorHelper extends java.lang.Object
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Constructor Summary
Constructors Constructor Description TorsionDescriptorHelper(StereoMolecule mol)
TorsionDescriptorHelper(StereoMolecule mol, int[] rotatableBond)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static int[]
findRotatableBonds(StereoMolecule mol)
Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor().TorsionDescriptor
getTorsionDescriptor()
Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds.TorsionDescriptor
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.
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Constructor Detail
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TorsionDescriptorHelper
public TorsionDescriptorHelper(StereoMolecule mol)
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TorsionDescriptorHelper
public TorsionDescriptorHelper(StereoMolecule mol, int[] rotatableBond)
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Method Detail
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getTorsionDescriptor
public TorsionDescriptor getTorsionDescriptor()
Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor using the default method to detect rotatable bonds. The torsion descriptor is not canonical, unless the passed molecule is canonical. Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
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getTorsionDescriptor
public TorsionDescriptor 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. This TorsionDescriptorHelper uses the default method to detect rotatable bonds. The torsion descriptor is not canonical, unless the passed molecule is canonical. Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
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findRotatableBonds
public static int[] findRotatableBonds(StereoMolecule mol)
Calculates an array of all rotatable bonds that can be used multiple times as parameter to calculateDescriptor(). If the molecule contains marked atoms, these are not considered part of the molecule, when detecting rotatable bonds. Any non-aromatic, non-3-ring single bond with at least one non-H, non-marked neighbor to either side is considered a rotatable bond, if none of the bond atoms is marked. An exception are linear chains of sp-hybridized atoms, of which not more than one bond is considered rotatable.
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