Atom¶

This class describes an atom in a structural model.

You can get a number of atom’s parameters on its topology (bonds), identity (type, lement name, atomic weight, etc), and other properties (chain, occupancy, serial number, formal charge, temperature factor, etc), for example:

# get the bond list of an atom
atom.getBondList

# atom's element name
atom.elementName

# atom's atomic weight
atom.atomicWeight

# atom's occupancy
atom.occupancy

# atom's temperature factor
if atom.hasTemperatureFactor:
        atom.temperatureFactor

# atom's water flag
if atom.hasWaterFlag:
        atom.waterFlag

# the name of a residue to which atom belongs
if atom.hasResidueName:
        atom.getResidueName()

Note

Parameters which are owned by an atom are accesible as properties (e.g. atom.partialCharge), but due to some limitations some parameters which are owned by atom’s parent node are accessible via getter and setter functions (if setter functions are available for a parameter) (e.g. atom.getChain()).

There is a number of constructors for an atom node, for example:

from samson.Modeling.StructuralModel import Atom
from samson.Modeling.Element import Element

# construct a Carbon atom at (0, 0, 0) position
atom1 = Atom(Element.Carbon)
atom1.setPosition(Type.position3(Quantity.nm(1), Quantity.nm(-1.5), Quantity.nm(0)))
print(atom1)

# construct a Carbon atom at (0, 0, 0) position
atom2 = Atom(Element.Carbon, Type.position3(Quantity.nm(1), Quantity.nm(-1.5), Quantity.nm(0)))
print(atom2)

You can further add an atom to e.g. a structural model, chain, backbone, or sidechain:

# turn the undo system on
SAMSON.beginHolding("Add new atom")
# hold the atom instance
SAMSON.hold(atom)

# create the atom
atom.create()

# add the atom to a chain
chain.addChild(atom)

# turn the undo system off
SAMSON.endHolding()