Package org.rcsb.mmtf.spark.data

Class AtomSelectObject

  • All Implemented Interfaces:
    java.io.Serializable
    public class AtomSelectObject
extends java.lang.Object
implements java.io.Serializable
    Class to make selections of atoms to be considered for inter-atom contacts.
    Author:
    Anthony Bradley
    See Also:
    Serialized Form

    • Constructor Detail

      • AtomSelectObject

        public AtomSelectObject​(java.lang.String[] atomNameList,
                        java.lang.String[] elementNameList,
                        java.lang.String[] groupNameList,
                        boolean charged,
                        java.lang.String groupType)
        Constructor for the atom select object that takes all the input
        Parameters:
        groupType - a string specifying the type of the group
        atomNameList - the list of atoms to consider
        groupNameList - the list of groups to consider (e.g. LYS)
        charged - whether to consider charged atoms only (true)
        elementNameList - the list of elements to consider

      • AtomSelectObject

        public AtomSelectObject()
        Empty constructor sets the defaults.

    • Method Detail

      • getAtomNameList

        public java.util.List<java.lang.String> getAtomNameList()
        Returns:
        the atomNameList

      • atomNameList

        public AtomSelectObject atomNameList​(java.util.List<java.lang.String> atomNameList)
        Set the list of atom names allowed.
        Parameters:
        atomNameList - the atomNameList to set
        Returns:
        the AtomSelectObject updated

      • atomNameList

        public AtomSelectObject atomNameList​(java.lang.String[] atomNameList)
        Set the array of atom names allowed.
        Parameters:
        atomNameList - the atomNameList to set
        Returns:
        the AtomSelectObject updated

      • getElementNameList

        public java.util.List<java.lang.String> getElementNameList()
        Returns:
        the elementNameList

      • elementNameList

        public AtomSelectObject elementNameList​(java.util.List<java.lang.String> elementNameList)
        Set the list of element names allowed.
        Parameters:
        elementNameList - the elementNameList to set
        Returns:
        the AtomSelectObject updated

      • elementNameList

        public AtomSelectObject elementNameList​(java.lang.String[] elementNameList)
        Set the array of element names allowed.
        Parameters:
        elementNameList - the elementNameList to set
        Returns:
        the AtomSelectObject updated

      • getGroupNameList

        public java.util.List<java.lang.String> getGroupNameList()
        Returns:
        the groupNameList

      • groupNameList

        public AtomSelectObject groupNameList​(java.util.List<java.lang.String> groupNameList)
        Set the list of group names allowed.
        Parameters:
        groupNameList - the groupNameList to set
        Returns:
        the AtomSelectObject updated

      • groupNameList

        public AtomSelectObject groupNameList​(java.lang.String[] groupNameList)
        Set the array of group names allowed.
        Parameters:
        groupNameList - the groupNameList to set
        Returns:
        the AtomSelectObject updated

      • isCharged

        public boolean isCharged()
        Returns:
        the charged

      • charged

        public AtomSelectObject charged​(boolean charged)
        Set whether charged elements spuld be found
        Parameters:
        charged - the charged to set
        Returns:
        the AtomSelectObject updated

      • getGroupType

        public java.lang.String getGroupType()
        Returns:
        the groupType

      • groupType

        public AtomSelectObject groupType​(java.lang.String groupType)
        Set the type of group allowed.
        Parameters:
        groupType - the groupType to set
        Returns:
        the AtomSelectObject updated