Package chemaxon.sss.search
Class Decomposition
- java.lang.Object
-
- chemaxon.sss.search.Decomposition
-
@PublicAPI public class Decomposition extends Object
Class storingRGroupDecomposition
results.
-
-
Constructor Summary
Constructors Modifier Constructor Description protected
Decomposition(Molecule query, Molecule target, int[][] groupHit, Molecule[] ligands, Molecule scaffold)
Constructor.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
color()
Colors ligands, scaffold, query and target by setting color data in atoms by callingMolAtom.setSetSeq(int)
.static void
color(Molecule mol)
Colors a molecule by setting color data in atoms by callingMolAtom.setSetSeq(int)
.static void
color(Molecule mol, String colorTag)
Colors a molecule by setting color data in the specified molecule property (SDF tag).void
color(String colorTag)
Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag).boolean
equals(Object o)
Returnstrue
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()
-
-
-
Method Detail
-
equals
public boolean equals(Object o)
Returnstrue
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.
-
getQuery
public Molecule getQuery()
Returns the R-grouped query used in the R-group decomposition.- Returns:
- the R-grouped query.
-
getTarget
public Molecule getTarget()
Returns the target.- Returns:
- the target
-
getGroupHit
public int[][] getGroupHit()
Returns the group hit corresponding to the R-group decomposition. The group hit assigns the matching target index array for each query atom index. Negative entries refer to implicit H matches or specific constants, seeSearch.findNext()
for a detailed description.- Returns:
- the group hit corresponding to the R-group decomposition
-
getLigands
public Molecule[] getLigands()
Returns the R-ligand array. This array maps query atom indexes to the corresponding R-ligand molecules for undefined R-atoms and assignsnull
to other query atoms.- Returns:
- the R-ligand array
-
getScaffold
public Molecule getScaffold()
Returns the scaffold in target.- Returns:
- the scaffold
-
getLigandIds
public int[] getLigandIds()
Returns the target ligand IDs. This is a map of target atoms:-
-2
for atoms outside the group hit -
-1
for scaffold atoms - least corresponding query R-atom index for R-ligands
- Returns:
- the target ligand IDs
-
-
color
public void color()
Colors ligands, scaffold, query and target by setting color data in atoms by callingMolAtom.setSetSeq(int)
. This coloring method can be used with MRV output. The atom set values are the following:1
for scaffold atomsR-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)
- See Also:
color(java.lang.String)
-
color
public static void color(Molecule mol)
Colors a molecule by setting color data in atoms by callingMolAtom.setSetSeq(int)
. This coloring method can be used with MRV output. The atom set values are the following:1
for scaffold atomsR-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)
- Parameters:
mol
- the input/output molecule
-
color
public void color(String colorTag)
Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag). This coloring method can be used with both SDF and MRV output. The color data is a ';'-separated string of atom symbols in atom index order. The symbols are the following:0
for scaffold atoms- the corresponding query R-atom ID (in case of R-bridging the R-atom with least query atom index is used)
-
for others
MView
with the following parametrization:mview -t DMAP -p Colors.ini mols.sdf
whereDMAP
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
- Parameters:
colorTag
- the property name (SDF tag) storing the color data- See Also:
color()
-
color
public static void color(Molecule mol, String colorTag)
Colors a molecule by setting color data in the specified molecule property (SDF tag). This coloring method can be used with both SDF and MRV output. The color data is a ';'-separated string of atom symbols in atom index order. The symbols are the following:0
for scaffold atoms- the corresponding query R-atom ID (in case of R-bridging the R-atom with least query atom index is used)
MView
with the following parametrization:mview -t DMAP -p Colors.ini mols.sdf
whereDMAP
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
- Parameters:
mol
- the input/output molecule to be coloredcolorTag
- the property name (SDF tag) storing the color data
-
-