Package com.actelion.research.chem.descriptor.pharmacophoretree

Class PharmacophoreTreeGenerator

java.lang.Object

com.actelion.research.chem.descriptor.pharmacophoretree.PharmacophoreTreeGenerator

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

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAX_RING_SIZE
static java.util.Set<java.lang.String>	RGROUPS

Method Summary

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 react
static double[]	getAtomVolumes(StereoMolecule mol)
static java.util.List<java.lang.Integer>	getSmallestRingsOfAtom(RingCollection rc, int atom)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_RING_SIZE

public static final int MAX_RING_SIZE

See Also:

Constant Field Values

RGROUPS

public static final java.util.Set<java.lang.String> RGROUPS

Method Detail

generate

public static PharmacophoreTree generate(StereoMolecule mol)

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:

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)

getSmallestRingsOfAtom

public static java.util.List<java.lang.Integer> getSmallestRingsOfAtom(RingCollection rc,
                                                                       int atom)

getAtomVolumes

public static double[] getAtomVolumes(StereoMolecule mol)