Class AtomType

java.lang.Object
org.jmol.minimize.forcefield.AtomType

public class AtomType extends Object
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    (package private) boolean
    MMFF aromatic types 37, 38, 39, 44, 58, 59, 63, 64, 65, 66, 69, 78, 79, 81, 82
    (package private) String
     
    (package private) int
     
    (package private) float
     
    (package private) float
     
    (package private) int
     
    (package private) int
    MMFF multiple bond type "specifies cases in which double (2) or triple (3) bonds are expected to be made to an atom having the listed atom type" [https://hpc.nih.gov/apps/charmm/c39b2html/mmff_params.html]
    (package private) int
     
    (package private) boolean
    MMFF pi lone pair type, i.e.
    (package private) boolean
    MMFF special bond types 2, 3, 4, 9, 30, 37, 39, 54, 57, 58, 63, 64, 67, 75, 78, 80, 81 for which a=b-c=d bc bond should be considered single, not double
    (package private) String
     
    (package private) int
    valence (number of bonds, generally 4 for neutral carbon, regardless of bonding, but 3 in the case of isonitrile)
  • Constructor Summary

    Constructors
    Constructor
    Description
    AtomType(int elemNo, int mmType, int hType, float formalCharge, int val, String descr, String smartsCode)
     
  • Method Summary

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • elemNo

      int elemNo
    • descr

      String descr
    • smartsCode

      String smartsCode
    • mmType

      int mmType
    • hType

      int hType
    • formalCharge

      float formalCharge
    • fcadj

      float fcadj
    • sbmb

      boolean sbmb
      MMFF special bond types 2, 3, 4, 9, 30, 37, 39, 54, 57, 58, 63, 64, 67, 75, 78, 80, 81 for which a=b-c=d bc bond should be considered single, not double
    • arom

      boolean arom
      MMFF aromatic types 37, 38, 39, 44, 58, 59, 63, 64, 65, 66, 69, 78, 79, 81, 82
    • pilp

      boolean pilp
      MMFF pi lone pair type, i.e. "those atom types which have a pi lone pair capable of partaking in resonance interactions with, say, an adjacent multiple bond" [https://hpc.nih.gov/apps/charmm/c39b2html/mmff_params.html] 6, 8, 10, 11, 12, 13, 14, 15, 26, 32, 35, 39, 40, 43, 44, 59, 62, 70, 72, 76
    • mltb

      int mltb
      MMFF multiple bond type "specifies cases in which double (2) or triple (3) bonds are expected to be made to an atom having the listed atom type" [https://hpc.nih.gov/apps/charmm/c39b2html/mmff_params.html]
    • val

      int val
      valence (number of bonds, generally 4 for neutral carbon, regardless of bonding, but 3 in the case of isonitrile)
  • Constructor Details

    • AtomType

      AtomType(int elemNo, int mmType, int hType, float formalCharge, int val, String descr, String smartsCode)