Package com.actelion.research.chem
Class MarkushStructure
- java.lang.Object
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- com.actelion.research.chem.MarkushStructure
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- All Implemented Interfaces:
java.io.Serializable
public class MarkushStructure extends java.lang.Object implements java.io.Serializable
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description MarkushStructure()
MarkushStructure(StereoMolecule[] fragment, int coreCount)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCore(StereoMolecule core)
void
addRGroup(StereoMolecule substituents)
This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule.int
getCoreCount()
StereoMolecule
getCoreStructure(int no)
StereoMolecule
getNextEnumeration()
After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.StereoMolecule
getRGroup(int no)
int
getRGroupCount()
java.lang.String
validate()
Check the validity of a defined Markush structure.
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Constructor Detail
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MarkushStructure
public MarkushStructure()
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MarkushStructure
public MarkushStructure(StereoMolecule[] fragment, int coreCount)
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Method Detail
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getCoreStructure
public StereoMolecule getCoreStructure(int no)
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getCoreCount
public int getCoreCount()
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getRGroup
public StereoMolecule getRGroup(int no)
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getRGroupCount
public int getRGroupCount()
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addCore
public void addCore(StereoMolecule core)
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addRGroup
public void addRGroup(StereoMolecule substituents)
This adds a substituent list representing one R-group as multiple fragments within one StereoMolecule. Every fragment is supposed to contain one atom with atomicNo=0 that is considered the attachment point. Fragments may contain atoms representing other R-groups (R1-R16). The first call of this method adds R1, the second R2, etc.- Parameters:
substituents
- multiple fragments representing R-group substituents
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validate
public java.lang.String validate() throws java.lang.Exception
Check the validity of a defined Markush structure. This method must be called before the enumeration.- Returns:
- a warning if defined R-groups are unreferenced
- Throws:
java.lang.Exception
- if an error prevents proper enumeration
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getNextEnumeration
public StereoMolecule getNextEnumeration()
After calling validate() this method may be called until null is returned to construct one by one a new representation of the Markush structure.
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