Package org.jmol.minimize.forcefield

Class AtomType

  • public class AtomType
extends java.lang.Object

    • Field Summary

      Fields 
      Modifier and Type Field Description
      (package private) boolean arom
      MMFF aromatic types 37, 38, 39, 44, 58, 59, 63, 64, 65, 66, 69, 78, 79, 81, 82
      (package private) java.lang.String descr  
      (package private) int elemNo  
      (package private) float fcadj  
      (package private) float formalCharge  
      (package private) int hType  
      (package private) 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]
      (package private) int mmType  
      (package private) boolean pilp
      MMFF pi lone pair type, i.e.
      (package private) 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
      (package private) java.lang.String smartsCode  
      (package private) int val
      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, java.lang.String descr, java.lang.String smartsCode)  

    • Method Summary

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • elemNo

        int elemNo

      • descr

        java.lang.String descr

      • smartsCode

        java.lang.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 Detail

      • AtomType

        AtomType​(int elemNo,
         int mmType,
         int hType,
         float formalCharge,
         int val,
         java.lang.String descr,
         java.lang.String smartsCode)