uk.ac.ebi.beam

Class Functions

java.lang.Object

uk.ac.ebi.beam.Functions

public final class Functions
extends Object

Collection of utilities for transforming chemical graphs.

Author:

John May

Method Summary

Modifier and Type	Method and Description
static Graph	atomBasedDBStereo(Graph g) Convert any directional bond based stereo configuration to atom-based specification.
static Graph	bondBasedDBStereo(Graph g) Convert a graph with atom-based double-bond stereo configuration to bond-based specification (direction UP and DOWN bonds).
static Graph	canonicalize(Graph g, long[] labels) Apply the labeling labels[] to the graph g.
static Graph	collapse(Graph g) Collapse a graph with specified atom properties to one with organic subset atoms.
static Graph	expand(Graph g) Expand a graph with organic subsets to one with specified atom properties.
static Graph	normaliseDirectionalLabels(Graph g)
static Graph	randomise(Graph g) Randomise the atom order of the provided chemical graph.
static Graph	reverse(Graph g) Reverse the atom order of the provided chemical graph.

Methods inherited from class java.lang.Object

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

Method Detail

randomise

public static Graph randomise(Graph g)

Randomise the atom order of the provided chemical graph.

Parameters:

g - chemical graph

Returns:

a copy of the original graph with the order of the atoms randomised

reverse

public static Graph reverse(Graph g)

Reverse the atom order of the provided chemical graph.

Parameters:

g - chemical graph

Returns:

a copy of the original graph with the order of the atoms reversed

atomBasedDBStereo

public static Graph atomBasedDBStereo(Graph g)

Convert any directional bond based stereo configuration to atom-based specification.

Parameters:

g - chemical graph graph

Returns:

a copy of the original graph but with directional bonds removed and atom-based double-bond stereo configruation.

bondBasedDBStereo

public static Graph bondBasedDBStereo(Graph g)

Convert a graph with atom-based double-bond stereo configuration to bond-based specification (direction UP and DOWN bonds).

Parameters:

g - chemical graph graph

Returns:

a copy of the original graph but with bond-based stereo-chemistry

expand

public static Graph expand(Graph g)

Expand a graph with organic subsets to one with specified atom properties.

Parameters:

g - a chemical graph

Returns:

the chemical graph expanded

collapse

public static Graph collapse(Graph g)

Collapse a graph with specified atom properties to one with organic subset atoms.

Parameters:

g - a chemical graph

Returns:

the chemical graph expanded

normaliseDirectionalLabels

public static Graph normaliseDirectionalLabels(Graph g)
                                        throws uk.ac.ebi.beam.InvalidSmilesException

Throws:

uk.ac.ebi.beam.InvalidSmilesException

canonicalize

public static Graph canonicalize(Graph g,
                                 long[] labels)

Apply the labeling labels[] to the graph g. The labels are converted to a permutation which is then applied to the Graph and rearrange it's vertex order.

Parameters:

g - the graph to permute

labels - the vertex labels - for example from a cannibalisation algorithm

Returns:

a cpy of the original graph with it's vertices permuted by the labelling