Package com.actelion.research.chem
Class ScaffoldHelper
- java.lang.Object
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- com.actelion.research.chem.ScaffoldHelper
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public class ScaffoldHelper extends java.lang.Object
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Constructor Summary
Constructors Constructor Description ScaffoldHelper()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
createMostCentralRingSystem(StereoMolecule mol)
Modifies mol in-place to represent the most central ring system of the original mol.static void
createMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)
Modifies mol in-place to represent the Murcko scaffold from the original mol.static boolean[]
findMostCentralRingSystem(StereoMolecule mol)
This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.static boolean[]
findMurckoScaffold(StereoMolecule mol)
This method flags all atoms that are a member of the Murcko fragment of mol.static StereoMolecule
getMostCentralRingSystem(StereoMolecule mol)
Creates most central ring system as new StereoMolecule from mol without touching mol.static StereoMolecule
getMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)
Creates Murcko scaffold as new StereoMolecule from mol without touching mol.
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Method Detail
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createMurckoScaffold
public static void createMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)
Modifies mol in-place to represent the Murcko scaffold from the original mol. If skeletonOnly is true, then all bond types are reduced to non-stereo-single bonds and all atoms are converted to carbon atoms.- Parameters:
mol
- may be an empty molecule if there are no ring systemsskeletonOnly
- reduce to simple skeleton
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getMurckoScaffold
public static StereoMolecule getMurckoScaffold(StereoMolecule mol, boolean skeletonOnly)
Creates Murcko scaffold as new StereoMolecule from mol without touching mol. If skeletonOnly is true, then all bond types are reduced to non-stereo-single bonds and all atoms are converted to carbon atoms.- Parameters:
mol
-skeletonOnly
- reduce to simple skeleton- Returns:
- Murcko scaffold or null, if mol does not contain any rings
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findMurckoScaffold
public static boolean[] findMurckoScaffold(StereoMolecule mol)
This method flags all atoms that are a member of the Murcko fragment of mol. The Murcko fragment is detected in three steps: - flag all ring atoms - recursively flag all atoms that are on a direct path connecting any two flagged atoms - recursively flag all atoms that are connected to any flagged atom via double bond Hydrogen atoms are neglected.- Parameters:
mol
-- Returns:
- null if mol doesn't contain any rings
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createMostCentralRingSystem
public static void createMostCentralRingSystem(StereoMolecule mol)
Modifies mol in-place to represent the most central ring system of the original mol.- Parameters:
mol
- may be an empty molecule if there are no ring systems
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getMostCentralRingSystem
public static StereoMolecule getMostCentralRingSystem(StereoMolecule mol)
Creates most central ring system as new StereoMolecule from mol without touching mol.- Parameters:
mol
-- Returns:
- most central ring system or null if there is none
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findMostCentralRingSystem
public static boolean[] findMostCentralRingSystem(StereoMolecule mol)
This method flags all atoms that are a member of that ring system in mol, which is most central within this molecule graph.- Parameters:
mol
-- Returns:
- null if mol does not contain any rings
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