def test_connect_via_distances():
"""
Test whether the created bond list is equal to the bonds deposited
in the MMTF file.
"""
file = mmtf.MMTFFile.read(join(data_dir("structure"), "1l2y.mmtf"))
atoms = mmtf.get_structure(file, include_bonds=True, model=1)
# Remove termini to solve the issue that the reference bonds do not
# contain proper bonds for the protonated/deprotonated termini
atoms = atoms[(atoms.res_id > 1) & (atoms.res_id < 20)]
ref_bonds = atoms.bonds
# Convert all bonds to BondType.ANY
ref_bonds = struc.BondList(ref_bonds.get_atom_count(),
ref_bonds.as_array()[:, :2])
test_bonds = struc.connect_via_distances(atoms)
assert test_bonds == ref_bonds
import numpy as np
from matplotlib.colors import to_rgb
import biotite
import biotite.structure as struc
import ammolite
PNG_SIZE = (1000, 300)
# Define colors
for color_name, color_value in biotite.colors.items():
ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
# Convert to PyMOL
atom_array.bonds = struc.connect_via_distances(atom_array)
pymol_obj = ammolite.PyMOLObject.from_structure(atom_array)
# Visualize as stick model
pymol_obj.show_as("sticks")
pymol_obj.color("biotite_lightgreen",
(atom_array.res_id % 2 == 0) & (atom_array.element == "C"))
pymol_obj.color("biotite_dimgreen",
(atom_array.res_id % 2 != 0) & (atom_array.element == "C"))
ammolite.cmd.set("depth_cue", 0)
# Adjust camera
pymol_obj.orient()
pymol_obj.zoom(buffer=-9)
# Save image
ammolite.cmd.ray(*PNG_SIZE)
ammolite.cmd.png(__image_destination__)
import ammolite
PNG_SIZE = (1000, 700)
# General configuration
ammolite.cmd.set("sphere_scale", 1.5)
ammolite.cmd.set("depth_cue", 0)
# Define colors
for color_name, color_value in biotite.colors.items():
ammolite.cmd.set_color("biotite_" + color_name, to_rgb(color_value))
# Remove hydrogen and water and convert to PyMOL
structure = structure[(structure.element != "H")
& (structure.res_name != "TIP")]
structure.bonds = struc.connect_via_distances(structure)
pymol_obj = ammolite.PyMOLObject.from_structure(structure)
# Configure lipid tails
pymol_obj.color("biotite_lightgreen", structure.chain_id == "A")
pymol_obj.color("biotite_brightorange", structure.chain_id == "B")
pymol_obj.show("sticks", np.isin(structure.chain_id, ("A", "B")))
# Configure lipid heads
pymol_obj.color("biotite_darkgreen",
(structure.chain_id == "A") & (structure.atom_name == "P"))
pymol_obj.color("biotite_dimorange",
(structure.chain_id == "B") & (structure.atom_name == "P"))
pymol_obj.show(
"spheres",
np.isin(structure.chain_id, ("A", "B")) & (structure.atom_name == "P"))