@PublicAPI public class Decomposition extends java.lang.Object
RGroupDecomposition
results.RGroupDecomposition.findFirstDecomposition()
,
RGroupDecomposition.findNextDecomposition()
,
RGroupDecomposition.findDecomposition()
Modifier | Constructor and Description |
---|---|
protected |
Decomposition(Molecule query,
Molecule target,
int[][] groupHit,
Molecule[] ligands,
Molecule scaffold)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
color()
Colors ligands, scaffold, query and target by setting color data in atoms by calling
MolAtom.setSetSeq(int) . |
static void |
color(Molecule mol)
Colors a molecule by setting color data in atoms by calling
MolAtom.setSetSeq(int) . |
static void |
color(Molecule mol,
java.lang.String colorTag)
Colors a molecule by setting color data
in the specified molecule property (SDF tag).
|
void |
color(java.lang.String colorTag)
Colors ligands, scaffold, query and target by setting color data
in the specified molecule property (SDF tag).
|
boolean |
equals(java.lang.Object o)
Returns
true if this decomposition is equivalent to the specified decomposition. |
int[][] |
getGroupHit()
Returns the group hit corresponding to the R-group decomposition.
|
int[] |
getLigandIds()
Returns the target ligand IDs.
|
Molecule[] |
getLigands()
Returns the R-ligand array.
|
Molecule |
getQuery()
Returns the R-grouped query used in the R-group decomposition.
|
Molecule |
getScaffold()
Returns the scaffold in target.
|
Molecule |
getTarget()
Returns the target.
|
int |
hashCode() |
public boolean equals(java.lang.Object o)
true
if this decomposition is equivalent to the specified decomposition.
Equivalent decompositions correspond to the same query and target and provide equivalent
scaffold and R-ligands.equals
in class java.lang.Object
o
- the other decompositiontrue
if this decomposition is equivalent to the other decompositionpublic int hashCode()
hashCode
in class java.lang.Object
public Molecule getQuery()
public Molecule getTarget()
public int[][] getGroupHit()
Search.findNext()
for a detailed description.public Molecule[] getLigands()
null
to other
query atoms.public Molecule getScaffold()
public int[] getLigandIds()
-2
for atoms outside the group hit
-1
for scaffold atoms
public void color()
MolAtom.setSetSeq(int)
. This coloring method can be used with MRV output.
The atom set values are the following:
1
for scaffold atoms
R-atom ID + 1
for query R-atoms and target R-ligands
(in case of R-bridging the R-atom with least query atom index is used)
0
for target atoms falling outside the decomposition (unmapped fragments)
color(java.lang.String)
public static void color(Molecule mol)
MolAtom.setSetSeq(int)
. This coloring method can be used with MRV output.
The atom set values are the following:
1
for scaffold atoms
R-atom ID + 1
for query R-atoms and target R-ligands
(in case of R-bridging the R-atom with least query atom index is used)
mol
- the input/output moleculepublic void color(java.lang.String colorTag)
0
for scaffold atoms
-
for others
MView
with the following parametrization:
mview -t DMAP -p Colors.ini mols.sdfwhere
DMAP
is the color SDF tag, Colors.ini
is the coloring
configuration file containing symbol - color pairs, e.g.:
0=red -=black 1=green 2=blue 3=orange 4=fuchsia empty=black other=gray
colorTag
- the property name (SDF tag) storing the color datacolor()
public static void color(Molecule mol, java.lang.String colorTag)
0
for scaffold atoms
MView
with the following parametrization:
mview -t DMAP -p Colors.ini mols.sdfwhere
DMAP
is the color SDF tag, Colors.ini
is the coloring
configuration file containing symbol - color pairs, e.g.:
0=red -=black 1=green 2=blue 3=orange 4=fuchsia empty=black other=gray
mol
- the input/output molecule to be coloredcolorTag
- the property name (SDF tag) storing the color data