public abstract class MDLReaderBase
extends org.openscience.cdk.io.DefaultChemObjectReader
Modifier and Type | Field and Description |
---|---|
protected SuperAtomContainer |
superAtomContainer |
Constructor and Description |
---|
MDLReaderBase() |
Modifier and Type | Method and Description |
---|---|
protected void |
createAtomProperty(org.openscience.cdk.interfaces.IAtomContainer molecule,
java.lang.String line,
int linecount) |
protected void |
createGroupOldVersion(java.io.BufferedReader input,
org.openscience.cdk.interfaces.IAtomContainer outputContainer,
org.openscience.cdk.interfaces.IAtomContainer molecule,
java.lang.String line,
int linecount) |
protected void |
createPseudoAtomProperty(org.openscience.cdk.interfaces.IAtomContainer molecule,
org.openscience.cdk.interfaces.IAtomContainer outputContainer,
java.lang.String line,
int RGroupCounter,
int aliasAtomNumber) |
protected void |
createRGroupAtomProperties(java.lang.String line,
java.util.Map<java.lang.Integer,org.openscience.cdk.interfaces.IPseudoAtom> rAtoms,
int Rnumber) |
protected void |
createSgroupProperty(org.openscience.cdk.interfaces.IAtomContainer molecule,
org.openscience.cdk.interfaces.IAtomContainer outputContainer,
java.lang.String line,
int linecount) |
abstract void |
customizeJob() |
float |
extractFloat(java.lang.String string,
int start,
int stop)
Returns the float value of the specified substring.
|
int |
extractInt(java.lang.String string,
int start,
int stop)
Returns the integer value of the specified substring.
|
java.lang.String |
extractString(java.lang.String string,
int start,
int stop)
Returns the specified substring, trimming of whitespace.
|
static void |
replaceAtom(org.openscience.cdk.interfaces.IAtomContainer molecule,
org.openscience.cdk.interfaces.IAtom prevAtom,
org.openscience.cdk.interfaces.IPseudoAtom pseudoAtom) |
fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
protected SuperAtomContainer superAtomContainer
public static void replaceAtom(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtom prevAtom, org.openscience.cdk.interfaces.IPseudoAtom pseudoAtom)
molecule
- prevAtom
- pseudoAtom
- protected void createAtomProperty(org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String line, int linecount) throws org.openscience.cdk.exception.CDKException
molecule
- line
- linecount
- org.openscience.cdk.exception.CDKException
protected void createGroupOldVersion(java.io.BufferedReader input, org.openscience.cdk.interfaces.IAtomContainer outputContainer, org.openscience.cdk.interfaces.IAtomContainer molecule, java.lang.String line, int linecount) throws java.io.IOException, org.openscience.cdk.exception.CDKException
input
- outputContainer
- molecule
- line
- linecount
- java.io.IOException
org.openscience.cdk.exception.CDKException
protected void createSgroupProperty(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer outputContainer, java.lang.String line, int linecount) throws org.openscience.cdk.exception.CDKException
molecule
- outputContainer
- line
- linecount
- org.openscience.cdk.exception.CDKException
protected void createPseudoAtomProperty(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer outputContainer, java.lang.String line, int RGroupCounter, int aliasAtomNumber)
molecule
- outputContainer
- line
- RGroupCounter
- aliasAtomNumber
- protected void createRGroupAtomProperties(java.lang.String line, java.util.Map<java.lang.Integer,org.openscience.cdk.interfaces.IPseudoAtom> rAtoms, int Rnumber)
line
- rAtoms
- Rnumber
- public abstract void customizeJob()
public float extractFloat(java.lang.String string, int start, int stop)
string
- the stringstart
- the start indexstop
- the end indexpublic int extractInt(java.lang.String string, int start, int stop)
string
- the stringstart
- the start indexstop
- the end indexpublic java.lang.String extractString(java.lang.String string, int start, int stop)
string
- the stringstart
- the start indexstop
- the end index