Package org.biojava.nbio.structure.chem

Class ChemComp

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<ChemComp>, CifBean
    public class ChemComp
extends java.lang.Object
implements CifBean, java.lang.Comparable<ChemComp>
    Properties of a chemical component.
    Since:
    6.0.0
    Author:
    Sebastian Bittrich
    See Also:
    Serialized Form

    • Constructor Detail

      • ChemComp

        public ChemComp()

    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • hasParent

        public boolean hasParent()

      • isStandard

        public boolean isStandard()

      • getId

        public java.lang.String getId()

      • setId

        public void setId​(java.lang.String id)

      • getName

        public java.lang.String getName()

      • setName

        public void setName​(java.lang.String name)

      • getType

        public java.lang.String getType()

      • setType

        public void setType​(java.lang.String type)

      • setResidueType

        public void setResidueType​(ResidueType residueType)

      • setPolymerType

        public void setPolymerType​(PolymerType polymerType)

      • getPdbxType

        public java.lang.String getPdbxType()

      • setPdbxType

        public void setPdbxType​(java.lang.String pdbxType)

      • getFormula

        public java.lang.String getFormula()

      • setFormula

        public void setFormula​(java.lang.String formula)

      • getMonNstdParentCompId

        public java.lang.String getMonNstdParentCompId()

      • setMonNstdParentCompId

        public void setMonNstdParentCompId​(java.lang.String monNstdParentCompId)

      • getPdbxSynonyms

        public java.lang.String getPdbxSynonyms()

      • setPdbxSynonyms

        public void setPdbxSynonyms​(java.lang.String pdbxSynonyms)

      • getPdbxFormalCharge

        public int getPdbxFormalCharge()

      • setPdbxFormalCharge

        public void setPdbxFormalCharge​(int pdbxFormalCharge)

      • getPdbxInitialDate

        public java.lang.String getPdbxInitialDate()

      • setPdbxInitialDate

        public void setPdbxInitialDate​(java.lang.String pdbxInitialDate)

      • getPdbxModifiedDate

        public java.lang.String getPdbxModifiedDate()

      • setPdbxModifiedDate

        public void setPdbxModifiedDate​(java.lang.String pdbxModifiedDate)

      • getPdbxAmbiguousFlag

        public java.lang.String getPdbxAmbiguousFlag()

      • setPdbxAmbiguousFlag

        public void setPdbxAmbiguousFlag​(java.lang.String pdbxAmbiguousFlag)

      • getPdbxReleaseStatus

        public java.lang.String getPdbxReleaseStatus()

      • setPdbxReleaseStatus

        public void setPdbxReleaseStatus​(java.lang.String pdbxReleaseStatus)

      • getPdbxReplacedBy

        public java.lang.String getPdbxReplacedBy()

      • setPdbxReplacedBy

        public void setPdbxReplacedBy​(java.lang.String pdbxReplacedBy)

      • getPdbxReplaces

        public java.lang.String getPdbxReplaces()

      • setPdbxReplaces

        public void setPdbxReplaces​(java.lang.String pdbxReplaces)

      • getFormulaWeight

        public double getFormulaWeight()

      • setFormulaWeight

        public void setFormulaWeight​(double formulaWeight)

      • getOneLetterCode

        public java.lang.String getOneLetterCode()

      • setOneLetterCode

        public void setOneLetterCode​(java.lang.String oneLetterCode)

      • getThreeLetterCode

        public java.lang.String getThreeLetterCode()

      • setThreeLetterCode

        public void setThreeLetterCode​(java.lang.String threeLetterCode)

      • getPdbxModelCoordinatesDetails

        public java.lang.String getPdbxModelCoordinatesDetails()

      • setPdbxModelCoordinatesDetails

        public void setPdbxModelCoordinatesDetails​(java.lang.String pdbxModelCoordinatesDetails)

      • getPdbxModelCoordinatesMissingFlag

        public java.lang.String getPdbxModelCoordinatesMissingFlag()

      • setPdbxModelCoordinatesMissingFlag

        public void setPdbxModelCoordinatesMissingFlag​(java.lang.String pdbxModelCoordinatesMissingFlag)

      • getPdbxIdealCoordinatesDetails

        public java.lang.String getPdbxIdealCoordinatesDetails()

      • setPdbxIdealCoordinatesDetails

        public void setPdbxIdealCoordinatesDetails​(java.lang.String pdbxIdealCoordinatesDetails)

      • getPdbxIdealCoordinatesMissingFlag

        public java.lang.String getPdbxIdealCoordinatesMissingFlag()

      • setPdbxIdealCoordinatesMissingFlag

        public void setPdbxIdealCoordinatesMissingFlag​(java.lang.String pdbxIdealCoordinatesMissingFlag)

      • getPdbxModelCoordinatesDbCode

        public java.lang.String getPdbxModelCoordinatesDbCode()

      • setPdbxModelCoordinatesDbCode

        public void setPdbxModelCoordinatesDbCode​(java.lang.String pdbxModelCoordinatesDbCode)

      • getPdbxSubcomponentList

        public java.lang.String getPdbxSubcomponentList()

      • setPdbxSubcomponentList

        public void setPdbxSubcomponentList​(java.lang.String pdbxSubcomponentList)

      • getPdbxProcessingSite

        public java.lang.String getPdbxProcessingSite()

      • setPdbxProcessingSite

        public void setPdbxProcessingSite​(java.lang.String pdbxProcessingSite)

      • getMonNstdFlag

        public java.lang.String getMonNstdFlag()

      • setMonNstdFlag

        public void setMonNstdFlag​(java.lang.String monNstdFlag)

      • setDescriptors

        public void setDescriptors​(java.util.List<ChemCompDescriptor> descriptors)

      • setBonds

        public void setBonds​(java.util.List<ChemCompBond> bonds)

      • setAtoms

        public void setAtoms​(java.util.List<ChemCompAtom> atoms)

      • compareTo

        public int compareTo​(ChemComp arg0)
        Specified by:
        compareTo in interface java.lang.Comparable<ChemComp>

      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • getEmptyChemComp

        public static ChemComp getEmptyChemComp()
        Creates a new instance of the dummy empty ChemComp.
        Returns:
        a ChemComp

      • isEmpty

        public boolean isEmpty()
        Indicates whether this compound was created with
        Returns:
        a boolean