public class CdkChemicalImpl extends Object implements gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>
| Constructor and Description |
|---|
CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
gov.nih.ncats.molwitch.ChemicalSource source) |
CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
java.util.function.Supplier<? extends gov.nih.ncats.molwitch.ChemicalSource> source) |
| Modifier and Type | Method and Description |
|---|---|
gov.nih.ncats.molwitch.Atom |
addAtom(gov.nih.ncats.molwitch.Atom a) |
gov.nih.ncats.molwitch.Atom |
addAtom(gov.nih.ncats.molwitch.isotopes.Isotope isotope) |
gov.nih.ncats.molwitch.Atom |
addAtom(String symbol) |
gov.nih.ncats.molwitch.Atom |
addAtomByAtomicNum(int atomicNumber) |
gov.nih.ncats.molwitch.Bond |
addBond(gov.nih.ncats.molwitch.Atom atom1,
gov.nih.ncats.molwitch.Atom atom2,
gov.nih.ncats.molwitch.Bond.BondType type) |
gov.nih.ncats.molwitch.Bond |
addBond(gov.nih.ncats.molwitch.Bond b) |
void |
addChemical(gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl> other) |
gov.nih.ncats.molwitch.SGroup |
addSgroup(gov.nih.ncats.molwitch.SGroup.SGroupType type) |
void |
aromatize() |
Iterator<CdkChemicalImpl> |
connectedComponents() |
CdkChemicalImpl |
deepCopy() |
void |
expandSGroups() |
void |
flipChirality(gov.nih.ncats.molwitch.Stereocenter s) |
void |
generateCoordinates() |
gov.nih.ncats.molwitch.Atom |
getAtom(int i) |
int |
getAtomCount() |
gov.nih.ncats.molwitch.Bond |
getBond(int i) |
int |
getBondCount() |
gov.nih.ncats.molwitch.BondTable |
getBondTable() |
org.openscience.cdk.interfaces.IAtomContainer |
getContainer() |
List<gov.nih.ncats.molwitch.DoubleBondStereochemistry> |
getDoubleBondStereochemistry() |
List<gov.nih.ncats.molwitch.ExtendedTetrahedralChirality> |
getExtendedTetrahedrals() |
String |
getFormula() |
String |
getFormula(boolean includeImplicitHydrogen) |
gov.nih.ncats.molwitch.GraphInvariant |
getGraphInvariant() |
double |
getMass() |
String |
getName() |
String |
getProperty(String key) |
int |
getSGroupCount() |
List<gov.nih.ncats.molwitch.SGroup> |
getSGroups() |
int |
getSmallestRingSize() |
gov.nih.ncats.molwitch.ChemicalSource |
getSource() |
List<gov.nih.ncats.molwitch.TetrahedralChirality> |
getTetrahedrals() |
Object |
getWrappedObject()
Get the
IAtomContainer. |
boolean |
has2DCoordinates() |
boolean |
has3DCoordinates() |
boolean |
hasCoordinates() |
boolean |
hasImplicitHydrogens() |
boolean |
hasSGroups() |
int |
indexOf(gov.nih.ncats.molwitch.Atom a) |
int |
indexOf(gov.nih.ncats.molwitch.Bond b) |
boolean |
isAromatic() |
void |
kekulize() |
void |
makeHydrogensExplicit() |
void |
makeHydrogensImplicit() |
void |
prepareForBuild(gov.nih.ncats.molwitch.spi.ChemicalImpl.PreparationOptions options) |
Iterator<Map.Entry<String,String>> |
properties() |
gov.nih.ncats.molwitch.Atom |
removeAtom(gov.nih.ncats.molwitch.Atom a) |
gov.nih.ncats.molwitch.Atom |
removeAtom(int i) |
gov.nih.ncats.molwitch.Bond |
removeBond(gov.nih.ncats.molwitch.Atom a,
gov.nih.ncats.molwitch.Atom b) |
gov.nih.ncats.molwitch.Bond |
removeBond(gov.nih.ncats.molwitch.Bond b) |
gov.nih.ncats.molwitch.Bond |
removeBond(int i) |
void |
removeProperty(String name) |
void |
removeSGroup(gov.nih.ncats.molwitch.SGroup sgroup) |
protected void |
setImplicitHydrogens() |
protected int |
setImplicitHydrogens(org.openscience.cdk.interfaces.IAtom atom) |
void |
setName(String name) |
void |
setProperty(String key,
String value) |
CdkChemicalImpl |
shallowCopy() |
public CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
java.util.function.Supplier<? extends gov.nih.ncats.molwitch.ChemicalSource> source)
public CdkChemicalImpl(org.openscience.cdk.interfaces.IAtomContainer container,
gov.nih.ncats.molwitch.ChemicalSource source)
public void flipChirality(gov.nih.ncats.molwitch.Stereocenter s)
flipChirality in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.ChemicalSource getSource()
getSource in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int getSmallestRingSize()
getSmallestRingSize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public Object getWrappedObject()
IAtomContainer.getWrappedObject in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public CdkChemicalImpl shallowCopy()
shallowCopy in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public CdkChemicalImpl deepCopy()
deepCopy in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom addAtom(String symbol)
addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void addChemical(gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl> other)
addChemical in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom addAtom(gov.nih.ncats.molwitch.Atom a)
addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom addAtom(gov.nih.ncats.molwitch.isotopes.Isotope isotope)
addAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom addAtomByAtomicNum(int atomicNumber)
addAtomByAtomicNum in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int getSGroupCount()
getSGroupCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void makeHydrogensExplicit()
makeHydrogensExplicit in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public boolean hasImplicitHydrogens()
hasImplicitHydrogens in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void makeHydrogensImplicit()
makeHydrogensImplicit in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public boolean isAromatic()
public boolean hasCoordinates()
hasCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public boolean has2DCoordinates()
has2DCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public boolean has3DCoordinates()
has3DCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public String getName()
getName in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void setName(String name)
setName in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public double getMass()
getMass in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int getAtomCount()
getAtomCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int getBondCount()
getBondCount in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom getAtom(int i)
getAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom removeAtom(int i)
removeAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Atom removeAtom(gov.nih.ncats.molwitch.Atom a)
removeAtom in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond removeBond(int i)
removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond removeBond(gov.nih.ncats.molwitch.Bond b)
removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond removeBond(gov.nih.ncats.molwitch.Atom a,
gov.nih.ncats.molwitch.Atom b)
removeBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public org.openscience.cdk.interfaces.IAtomContainer getContainer()
public void aromatize()
aromatize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void expandSGroups()
expandSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void generateCoordinates()
throws gov.nih.ncats.molwitch.ChemkitException
generateCoordinates in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>gov.nih.ncats.molwitch.ChemkitExceptionpublic void prepareForBuild(gov.nih.ncats.molwitch.spi.ChemicalImpl.PreparationOptions options)
prepareForBuild in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void kekulize()
kekulize in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public String getFormula()
getFormula in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public String getFormula(boolean includeImplicitHydrogen)
getFormula in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public List<gov.nih.ncats.molwitch.ExtendedTetrahedralChirality> getExtendedTetrahedrals()
getExtendedTetrahedrals in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public List<gov.nih.ncats.molwitch.TetrahedralChirality> getTetrahedrals()
getTetrahedrals in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond addBond(gov.nih.ncats.molwitch.Bond b)
addBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public List<gov.nih.ncats.molwitch.SGroup> getSGroups()
getSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void removeSGroup(gov.nih.ncats.molwitch.SGroup sgroup)
removeSGroup in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.SGroup addSgroup(gov.nih.ncats.molwitch.SGroup.SGroupType type)
addSgroup in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public boolean hasSGroups()
hasSGroups in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond addBond(gov.nih.ncats.molwitch.Atom atom1,
gov.nih.ncats.molwitch.Atom atom2,
gov.nih.ncats.molwitch.Bond.BondType type)
addBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>protected void setImplicitHydrogens()
protected int setImplicitHydrogens(org.openscience.cdk.interfaces.IAtom atom)
public Iterator<CdkChemicalImpl> connectedComponents()
connectedComponents in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int indexOf(gov.nih.ncats.molwitch.Atom a)
indexOf in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public int indexOf(gov.nih.ncats.molwitch.Bond b)
indexOf in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.GraphInvariant getGraphInvariant()
getGraphInvariant in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.Bond getBond(int i)
getBond in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public gov.nih.ncats.molwitch.BondTable getBondTable()
getBondTable in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public List<gov.nih.ncats.molwitch.DoubleBondStereochemistry> getDoubleBondStereochemistry()
getDoubleBondStereochemistry in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public String getProperty(String key)
getProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void removeProperty(String name)
removeProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public void setProperty(String key, String value)
setProperty in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>public Iterator<Map.Entry<String,String>> properties()
properties in interface gov.nih.ncats.molwitch.spi.ChemicalImpl<CdkChemicalImpl>Copyright © 2019 NIH/NCATS. All rights reserved.