public abstract class Utility extends MatrixPrinter implements java.io.Serializable
Constructor and Description |
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Utility() |
Modifier and Type | Method and Description |
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static org.openscience.cdk.interfaces.IAtomContainer |
canonicalise(org.openscience.cdk.interfaces.IAtomContainer org_mol) |
static java.util.Collection<org.openscience.cdk.interfaces.IAtom> |
circularFragment(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
int rootAtom,
int max)
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
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protected static org.openscience.cdk.interfaces.IAtomContainer |
getAtomContainer(org.openscience.cdk.interfaces.IAtom atom,
org.openscience.cdk.interfaces.IAtomContainerSet molset) |
protected static org.openscience.cdk.interfaces.IAtomContainer |
getAtomContainer(org.openscience.cdk.interfaces.IBond bond,
org.openscience.cdk.interfaces.IAtomContainerSet molset) |
protected static int |
getAtomIndexByID(org.openscience.cdk.interfaces.IAtomContainer molWithoutH,
org.openscience.cdk.interfaces.IAtom refAtom)
Return atom by ID match
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protected static java.util.List<org.openscience.cdk.interfaces.IAtom> |
getAtoms(org.openscience.cdk.interfaces.IAtomContainer mol) |
static java.lang.String |
getBondOrderSign(org.openscience.cdk.interfaces.IBond bond) |
protected static java.lang.String |
getCanonicalisedBondChangePattern(org.openscience.cdk.interfaces.IBond bond) |
protected static java.lang.String |
getCanonisedBondChangePattern(org.openscience.cdk.interfaces.IBond reactBond,
org.openscience.cdk.interfaces.IBond prodBond) |
static org.openscience.cdk.interfaces.IAtomContainer |
getCircularFragment(org.openscience.cdk.interfaces.IAtomContainer mol,
int startAtomIndex,
int radius) |
protected static java.util.List<ReactionCenterFragment> |
getCircularReactionPatternFingerprints(org.openscience.cdk.interfaces.IAtomContainer molOrignal,
org.openscience.cdk.interfaces.IAtom atom,
EnumSubstrateProduct type) |
static java.lang.String |
getCircularSMILES(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtom atom,
int level,
boolean remove_AAM)
Used CDK to generate smiles
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protected static java.lang.String |
getMoleculeID(org.openscience.cdk.interfaces.IAtom atom,
org.openscience.cdk.interfaces.IAtomContainerSet molset) |
protected static java.lang.String |
getMoleculeID(org.openscience.cdk.interfaces.IBond bond,
org.openscience.cdk.interfaces.IAtomContainerSet molset) |
static int |
getNeighbourBondOrderCountFromRing(org.openscience.cdk.interfaces.IBond ringBond,
org.openscience.cdk.interfaces.IRingSet singleRings) |
protected static java.lang.String |
getSignature(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtom atom,
int height)
Return Signature of height h
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static org.openscience.cdk.interfaces.IRingSet |
getSmallestRingSet(org.openscience.cdk.interfaces.IBond ringBond,
org.openscience.cdk.interfaces.IRingSet singleRings) |
static java.lang.String |
getSMILES(org.openscience.cdk.interfaces.IAtomContainer mol,
boolean remove_AAM)
Used CDK to generate smiles
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static java.lang.String |
getSMILES(org.openscience.cdk.interfaces.IReaction reaction,
boolean remove_AAM)
Used Chemaxon to generate smikrs
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protected static void |
initializeMolecule(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
protected static void |
setCircularFingerprints(java.lang.String rid,
org.openscience.cdk.interfaces.IAtomContainer molOrignal,
org.openscience.cdk.interfaces.IAtom atom,
java.util.Map<java.lang.Integer,IPatternFingerprinter> patternFP) |
protected static void |
setCircularSignatureFingerprints(java.lang.String rid,
org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtom atom,
java.util.Map<java.lang.Integer,IPatternFingerprinter> patternFP) |
protected static void |
setFragmentMatches(java.util.SortedMap<java.lang.String,java.lang.Integer> atomRCChangesMap,
java.util.List<org.openscience.cdk.interfaces.IAtomContainer> fragments) |
protected static void |
setReactionCenterMatches(IPatternFingerprinter atomRCChangesMap,
java.util.List<java.lang.String> signatures) |
printBEMatrix, printReactionMatrix, writeBEMatrix, writeReactionMatrix
public static java.lang.String getSMILES(org.openscience.cdk.interfaces.IReaction reaction, boolean remove_AAM)
reaction
- remove_AAM
- public static java.lang.String getCircularSMILES(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtom atom, int level, boolean remove_AAM) throws java.lang.Exception
mol
- atom
- level
- remove_AAM
- java.lang.Exception
public static java.lang.String getSMILES(org.openscience.cdk.interfaces.IAtomContainer mol, boolean remove_AAM)
mol
- remove_AAM
- protected static java.util.List<org.openscience.cdk.interfaces.IAtom> getAtoms(org.openscience.cdk.interfaces.IAtomContainer mol)
mol
- protected static java.lang.String getMoleculeID(org.openscience.cdk.interfaces.IBond bond, org.openscience.cdk.interfaces.IAtomContainerSet molset)
bond
- molset
- protected static java.lang.String getMoleculeID(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainerSet molset)
atom
- molset
- protected static org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(org.openscience.cdk.interfaces.IBond bond, org.openscience.cdk.interfaces.IAtomContainerSet molset)
bond
- molset
- protected static org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainerSet molset)
atom
- molset
- protected static int getAtomIndexByID(org.openscience.cdk.interfaces.IAtomContainer molWithoutH, org.openscience.cdk.interfaces.IAtom refAtom)
molWithoutH
- refAtom
- protected static java.lang.String getSignature(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtom atom, int height) throws java.lang.CloneNotSupportedException
mol
- atom
- height
- java.lang.CloneNotSupportedException
protected static void setFragmentMatches(java.util.SortedMap<java.lang.String,java.lang.Integer> atomRCChangesMap, java.util.List<org.openscience.cdk.interfaces.IAtomContainer> fragments) throws java.lang.CloneNotSupportedException
atomRCChangesMap
- fragments
- java.lang.CloneNotSupportedException
protected static void setReactionCenterMatches(IPatternFingerprinter atomRCChangesMap, java.util.List<java.lang.String> signatures)
atomRCChangesMap
- signatures
- protected static void setCircularSignatureFingerprints(java.lang.String rid, org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtom atom, java.util.Map<java.lang.Integer,IPatternFingerprinter> patternFP) throws org.openscience.cdk.exception.CDKException, java.lang.CloneNotSupportedException
rid
- mol
- atom
- patternFP
- org.openscience.cdk.exception.CDKException
java.lang.CloneNotSupportedException
protected static java.lang.String getCanonisedBondChangePattern(org.openscience.cdk.interfaces.IBond reactBond, org.openscience.cdk.interfaces.IBond prodBond)
reactBond
- prodBond
- protected static java.lang.String getCanonicalisedBondChangePattern(org.openscience.cdk.interfaces.IBond bond)
bond
- public static java.lang.String getBondOrderSign(org.openscience.cdk.interfaces.IBond bond)
bond
- public static int getNeighbourBondOrderCountFromRing(org.openscience.cdk.interfaces.IBond ringBond, org.openscience.cdk.interfaces.IRingSet singleRings)
ringBond
- singleRings
- public static org.openscience.cdk.interfaces.IRingSet getSmallestRingSet(org.openscience.cdk.interfaces.IBond ringBond, org.openscience.cdk.interfaces.IRingSet singleRings)
ringBond
- singleRings
- protected static void initializeMolecule(org.openscience.cdk.interfaces.IAtomContainer atomContainer) throws org.openscience.cdk.exception.CDKException
atomContainer
- Atom container where rings are to be markedorg.openscience.cdk.exception.CDKException
- if there is a problem in ring perception or
aromaticity detection, which is usually related to a timeout in the ring
finding code.public static org.openscience.cdk.interfaces.IAtomContainer getCircularFragment(org.openscience.cdk.interfaces.IAtomContainer mol, int startAtomIndex, int radius) throws java.lang.Exception
mol
- startAtomIndex
- radius
- java.lang.Exception
public static org.openscience.cdk.interfaces.IAtomContainer canonicalise(org.openscience.cdk.interfaces.IAtomContainer org_mol) throws java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
org_mol
- java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException
public static java.util.Collection<org.openscience.cdk.interfaces.IAtom> circularFragment(org.openscience.cdk.interfaces.IAtomContainer atomContainer, int rootAtom, int max) throws org.openscience.cdk.exception.CDKException
atomContainer
- The AtomContainer to be searchedrootAtom
- max
- org.openscience.cdk.exception.CDKException
protected static void setCircularFingerprints(java.lang.String rid, org.openscience.cdk.interfaces.IAtomContainer molOrignal, org.openscience.cdk.interfaces.IAtom atom, java.util.Map<java.lang.Integer,IPatternFingerprinter> patternFP) throws java.lang.Exception, java.lang.CloneNotSupportedException
rid
- molOrignal
- atom
- patternFP
- java.lang.Exception
java.lang.CloneNotSupportedException
protected static java.util.List<ReactionCenterFragment> getCircularReactionPatternFingerprints(org.openscience.cdk.interfaces.IAtomContainer molOrignal, org.openscience.cdk.interfaces.IAtom atom, EnumSubstrateProduct type) throws java.lang.Exception, java.lang.CloneNotSupportedException
molOrignal
- type
- atom
- java.lang.Exception
java.lang.CloneNotSupportedException