Molecular Nodes is designed and created first and foremost as an add-on for Blender, so the API can at times seem a bit quirky and for the time being is not to be considered stable.
Molecular Nodes is versioned to match Blender versions, so while we are currently up to “4.2.*“, the API should be not be consired to be that mature.
This is how we can use the API.
import molecularnodes as mn
import numpy as np
# we currently have to manually register a lot of the internals with Blende
mn.register()
# create a 'Molecule' object, by fetching a structure and parsing it into the scene
mol = mn.fetch("1cd3")
mol<Molecule object: 1cd3>The Molecule object has the original data, as well as the Blender object associated with.
The different methods that are associated mostly interact with the Blender object, which is accessible via the mol.object, and the data is accessible via mol.array, which is the biotite.AtomArrayStack object.
len(mol)=9755
mol.object=bpy.data.objects['1cd3']
mol.array[0][:10]=array([
Atom(np.array([ 36.186, -5.245, 149.457], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="N", element="N", atom_id=1, b_factor=78.67, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 35.595, -6.174, 148.447], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="CA", element="C", atom_id=2, b_factor=75.04, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.585, -7.298, 148.158], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="C", element="C", atom_id=3, b_factor=73.45, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.205, -8.36 , 147.645], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="O", element="O", atom_id=4, b_factor=73.82, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 35.268, -5.432, 147.139], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="CB", element="C", atom_id=5, b_factor=83.35, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.12 , -4.183, 146.87 ], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="CG", element="C", atom_id=6, b_factor=91.19, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.503, -4.031, 145.396], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="CD", element="C", atom_id=7, b_factor=95.85, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.338, -5.011, 144.624], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="OE1", element="O", atom_id=8, b_factor=98.57, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 36.969, -2.93 , 145.015], dtype=float32), chain_id="1", res_id=6, ins_code="", res_name="GLU", hetero=False, atom_name="OE2", element="O", atom_id=9, b_factor=100.0, occupancy=1.0, sec_struct=3, entity_id=0),
Atom(np.array([ 37.852, -7.057, 148.492], dtype=float32), chain_id="1", res_id=7, ins_code="", res_name="GLN", hetero=False, atom_name="N", element="N", atom_id=10, b_factor=68.0, occupancy=1.0, sec_struct=1, entity_id=0)
])