Class PharmacophoreTreeGenerator
- java.lang.Object
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- com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator
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public class PharmacophoreTreeGenerator extends java.lang.Object
Generates a PharmacophoreTree from a StereoMolecule. Calculates chemical features and steric properties of the nodes spanning the tree. Cycles are resolved by merging nodes and introducing zero-nodes.- Author:
- joel
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Field Summary
Fields Modifier and Type Field Description static int
MAX_RING_SIZE
static java.util.Set<java.lang.String>
RGROUPS
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
addNode(PharmacophoreNode node, java.util.List<PharmacophoreNode> nodes, java.util.Map<java.lang.Integer,java.util.List<java.lang.Integer>> atomToNodes)
static PharmacophoreTree
generate(StereoMolecule mol)
static PharmacophoreTree
generate(StereoMolecule mol, java.util.Map<java.lang.Integer,java.util.List<java.lang.Integer>> atomToNodes, java.util.List<java.util.Set<java.lang.Integer>> rings)
the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they reactstatic double[]
getAtomVolumes(StereoMolecule mol)
static java.util.List<java.lang.Integer>
getSmallestRingsOfAtom(RingCollection rc, int atom)
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Field Detail
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MAX_RING_SIZE
public static final int MAX_RING_SIZE
- See Also:
- Constant Field Values
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RGROUPS
public static final java.util.Set<java.lang.String> RGROUPS
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Method Detail
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generate
public static PharmacophoreTree generate(StereoMolecule mol)
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generate
public static PharmacophoreTree generate(StereoMolecule mol, java.util.Map<java.lang.Integer,java.util.List<java.lang.Integer>> atomToNodes, java.util.List<java.util.Set<java.lang.Integer>> rings)
the parameter rings can be used for fragments/building blocks to submit atoms that will belong to a ring after they react- Parameters:
mol
-atomToNodes
-rings
-- Returns:
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addNode
public static void addNode(PharmacophoreNode node, java.util.List<PharmacophoreNode> nodes, java.util.Map<java.lang.Integer,java.util.List<java.lang.Integer>> atomToNodes)
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getSmallestRingsOfAtom
public static java.util.List<java.lang.Integer> getSmallestRingsOfAtom(RingCollection rc, int atom)
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getAtomVolumes
public static double[] getAtomVolumes(StereoMolecule mol)
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