Package | Description |
---|---|
org.openscience.cdk.isomorphism | |
org.openscience.cdk.layout | |
org.openscience.cdk.smarts |
Modifier and Type | Class and Description |
---|---|
class |
DfPattern
The depth-first (DF) backtracking sub-structure matching algorithm so named
because it matches the molecule in a depth-first manner (bond by bond).
|
class |
Ullmann
A structure pattern which utilises the Ullmann algorithm (Ullmann J R. Journal of the Association for Computing Machinery. 1976. 23).
|
class |
VentoFoggia
A structure pattern which utilises the Vento-Foggia (VF) algorithm (Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26).
|
Modifier and Type | Method and Description |
---|---|
static Pattern |
Pattern.findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
VentoFoggia.findIdentical(IAtomContainer query)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
VentoFoggia.findIdentical(IAtomContainer query,
AtomMatcher atomMatcher,
BondMatcher bondMatcher)
Create a pattern which can be used to find molecules which are the same
as the
query structure. |
static Pattern |
Pattern.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
VentoFoggia.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
Ullmann.findSubstructure(IAtomContainer query)
Create a pattern which can be used to find molecules which contain the
query structure. |
static Pattern |
VentoFoggia.findSubstructure(IAtomContainer query,
AtomMatcher atomMatcher,
BondMatcher bondMatcher)
Create a pattern which can be used to find molecules which contain the
query structure. |
Modifier and Type | Method and Description |
---|---|
static TemplateHandler |
TemplateHandler.createFromSubstructure(Pattern ptrn,
IAtomContainer mol)
Create a template from a substructure pattern.
|
static TemplateHandler |
TemplateHandler.createFromSubstructure(Pattern ptrn,
Iterable<IAtomContainer> mols)
Create a template from a substructure pattern.
|
Modifier and Type | Class and Description |
---|---|
class |
SmartsPattern
A
Pattern for matching a single SMARTS query against multiple target
compounds. |
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