Objects

This section describes how chemical data is handled in ChemShell.

• Fragment objects
  • Fragment
  • Fragment properties
    • totalcharge
    • connect_mode
    • connect_scale
    • connect_toler
    • cell
    • natoms
    • nbqs
    • nshells
    • names
    • coords
    • znums
    • charges
    • masses
    • bqs
    • shells
  • Fragment enquiry
    • Fragment.centroid()
    • Fragment.radius()
    • Fragment.angle()
    • Fragment.dihedral()
    • Fragment.hascharges()
  • Fragment functions
    • Fragment.save()
    • Fragment.connect()
    • Fragment.connIJ()
    • Fragment.delete()
    • Fragment.insert()
    • Fragment.merge()
    • Fragment.addCharges()
    • Fragment.addShells()
  • Atoms selecting methods
    • Fragment.select()
    • Fragment.selectByAtoms()
    • Fragment.selectByBackbone()
    • Fragment.selectByCommonNames()
    • Fragment.selectByIndices()
    • Fragment.selectByIons()
    • Fragment.selectByRadius()
    • Fragment.selectByRegions()
    • Fragment.selectByShell()
    • Fragment.selectByNeighbours()
  • Cell object
    • Fragment.ndimensions
    • Fragment.cell.consts
    • Fragment.cell.vectors
    • Fragment.cell.fractional
  • BQs object
    • Fragment.bqs.names
    • Fragment.bqs.coords
    • Fragment.bqs.charges
  • Shells object
    • Fragment.shells.coreatoms
    • Fragment.shells.names
    • Fragment.shells.coords
    • Fragment.shells.displace
    • Fragment.shells.charges
• Field objects
  • Field properties
    • Field.grid
    • Field.pot
    • Field.efield
• Result objects
  • Result properties
    • Result.energy
    • Result.gradients
• Restraints
  • Abstract base
    • Restraint
      • Restraint.accumulate()
  • Harmonic restraints
    • Bond
      • Bond
        • Bond.r0
        • Bond.k
        • Bond.__init__()
        • Bond.accumulate()
        • Bond.indices
    • Angle
      • Angle
        • Angle.k
        • Angle.__init__()
        • Angle.accumulate()
        • Angle.indices
        • Angle.theta0
    • Torsion
      • Torsion
        • Torsion.k
        • Torsion.__init__()
        • Torsion.accumulate()
        • Torsion.indices
        • Torsion.phi0
        • Torsion.torsion_angle()
        • Torsion.torsion_angle_and_derivative()
    • Distance-difference restraints
      • BondDifference2
        • BondDifference2.r0
        • BondDifference2.k
        • BondDifference2.__init__()
        • BondDifference2.accumulate()
        • BondDifference2.indices
      • BondDifference3
        • BondDifference3.r0
        • BondDifference3.k
        • BondDifference3.__init__()
        • BondDifference3.accumulate()
        • BondDifference3.indices
      • BondDifference4
        • BondDifference4.r0
        • BondDifference4.k
        • BondDifference4.__init__()
        • BondDifference4.accumulate()
        • BondDifference4.indices
    • Type aliases