public class Reader
extends java.lang.Object
Constructor and Description |
---|
Reader() |
Modifier and Type | Method and Description |
---|---|
void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainerSet molSet) |
void |
addImplicitHydrogens(org.openscience.cdk.interfaces.IReaction reaction) |
org.openscience.cdk.interfaces.IReaction |
canonise(org.openscience.cdk.interfaces.IReaction reaction) |
void |
draw(DirectMoleculeDrawer molDrawer,
org.openscience.cdk.interfaces.IAtomContainer AtomContainer,
java.lang.String dirPath,
java.lang.String name) |
org.openscience.cdk.interfaces.IAtomContainer |
layout(org.openscience.cdk.interfaces.IAtomContainer AtomContainer) |
java.awt.image.BufferedImage |
makeBlankImage(int width,
int height) |
org.openscience.cdk.interfaces.IReaction |
map(org.openscience.cdk.interfaces.IReaction reaction) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
parseRXN(java.lang.String fileNames) |
org.openscience.cdk.interfaces.IAtomContainer |
readMDLMolecule(java.lang.String name,
java.lang.String dir) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
boolean reMap) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
java.lang.String dir) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
java.lang.String dir,
boolean reMap) |
org.openscience.cdk.interfaces.IReaction |
readReaction(java.lang.String name,
java.lang.String dir,
boolean reMap,
boolean removeHydrogens) |
protected void |
renumberMappingIDs(org.openscience.cdk.interfaces.IReaction reaction) |
void |
typeAtoms(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
void |
writeToFile(java.awt.Image image,
java.lang.String outputDirPath,
java.lang.String name) |
public org.openscience.cdk.interfaces.IAtomContainer layout(org.openscience.cdk.interfaces.IAtomContainer AtomContainer)
AtomContainer
- public java.awt.image.BufferedImage makeBlankImage(int width, int height)
width
- height
- public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name) throws java.io.IOException
name
- java.io.IOException
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, boolean reMap) throws java.io.IOException
name
- reMap
- java.io.IOException
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, java.lang.String dir, boolean reMap) throws java.io.IOException
name
- dir
- reMap
- java.io.IOException
protected java.util.List<org.openscience.cdk.interfaces.IReaction> parseRXN(java.lang.String fileNames)
fileNames
- public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, java.lang.String dir, boolean reMap, boolean removeHydrogens) throws java.io.IOException
name
- dir
- reMap
- removeHydrogens
- java.io.IOException
public org.openscience.cdk.interfaces.IReaction readReaction(java.lang.String name, java.lang.String dir) throws java.io.IOException
name
- dir
- java.io.IOException
public org.openscience.cdk.interfaces.IAtomContainer readMDLMolecule(java.lang.String name, java.lang.String dir) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
name
- dir
- java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
public org.openscience.cdk.interfaces.IReaction canonise(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- public org.openscience.cdk.interfaces.IReaction map(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- public void writeToFile(java.awt.Image image, java.lang.String outputDirPath, java.lang.String name) throws java.io.IOException
image
- outputDirPath
- name
- java.io.IOException
public void addImplicitHydrogens(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- public void addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainerSet molSet)
molSet
- public void addImplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- public void typeAtoms(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
atomContainer
- protected void renumberMappingIDs(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- public void draw(DirectMoleculeDrawer molDrawer, org.openscience.cdk.interfaces.IAtomContainer AtomContainer, java.lang.String dirPath, java.lang.String name) throws java.io.IOException
molDrawer
- AtomContainer
- dirPath
- name
- java.io.IOException