def nuc_sample_array():
"""
Sample structure.
"""
nuc_sample_array = strucio.load_structure(
join(data_dir("structure"), "4p5j.cif")
)
return nuc_sample_array[struc.filter_nucleotides(nuc_sample_array)]
def plot_rna(pdb_id, axes):
# Download the PDB file and read the structure
pdb_file_path = rcsb.fetch(pdb_id, "pdb", gettempdir())
pdb_file = pdb.PDBFile.read(pdb_file_path)
atom_array = pdb.get_structure(pdb_file)[0]
nucleotides = atom_array[struc.filter_nucleotides(atom_array)]
# Compute the base pairs and their pseudoknot order
base_pairs = struc.base_pairs(nucleotides)
base_pairs = struc.get_residue_positions(
nucleotides, base_pairs.flatten()
).reshape(base_pairs.shape)
pseudoknot_order = struc.pseudoknots(base_pairs)[0]
# Set the linestyle according to the pseudoknot order
linestyles = np.full(base_pairs.shape[0], '-', dtype=object)
linestyles[pseudoknot_order == 1] = '--'
linestyles[pseudoknot_order == 2] = ':'
# Indicate canonical nucleotides with an upper case one-letter-code
# and non-canonical nucleotides with a lower case one-letter-code
base_labels = []
for base in struc.residue_iter(nucleotides):
one_letter_code, exact = struc.map_nucleotide(base)
if exact:
base_labels.append(one_letter_code)
else:
base_labels.append(one_letter_code.lower())
# Color canonical Watson-Crick base pairs with a darker orange and
# non-canonical base pairs with a lighter orange
colors = np.full(base_pairs.shape[0], biotite.colors['brightorange'])
for i, (base1, base2) in enumerate(base_pairs):
name1 = base_labels[base1]
name2 = base_labels[base2]
if sorted([name1, name2]) in [["A", "U"], ["C", "G"]]:
colors[i] = biotite.colors["dimorange"]
# Plot the secondary structure
graphics.plot_nucleotide_secondary_structure(
axes, base_labels, base_pairs, struc.get_residue_count(nucleotides),
pseudoknot_order=pseudoknot_order, bond_linestyle=linestyles,
bond_color=colors,
# Margin to compensate for reduced axis limits in shared axis
border=0.13
)
# Use the PDB ID to label each plot
axes.set_title(pdb_id, loc="left")
# License: BSD 3 clause
from tempfile import gettempdir
import biotite
import biotite.structure.io.pdb as pdb
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.graphics as graphics
import matplotlib.pyplot as plt
import numpy as np
# Download the PDB file and read the structure
pdb_file_path = rcsb.fetch("6ZYB", "pdb", gettempdir())
pdb_file = pdb.PDBFile.read(pdb_file_path)
atom_array = pdb.get_structure(pdb_file)[0]
nucleotides = atom_array[struc.filter_nucleotides(atom_array)]
# Compute the base pairs and the Leontis-Westhof nomenclature
base_pairs = struc.base_pairs(nucleotides)
glycosidic_bonds = struc.base_pairs_glycosidic_bond(nucleotides, base_pairs)
edges = struc.base_pairs_edge(nucleotides, base_pairs)
base_pairs = struc.get_residue_positions(
nucleotides, base_pairs.flatten()).reshape(base_pairs.shape)
# Get the one-letter-codes of the bases
base_labels = []
for base in struc.residue_iter(nucleotides):
base_labels.append(base.res_name[0])
# Color canonical Watson-Crick base pairs with a darker orange and
# non-canonical base pairs with a lighter orange
# Code source: Patrick Kunzmann
# License: BSD 3 clause
import numpy as np
import matplotlib.pyplot as plt
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import biotite.structure.graphics as graphics
import biotite.database.rcsb as rcsb
# Structure of a DNA double helix
mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("1qxb", "mmtf"))
structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True)
nucleotides = structure[struc.filter_nucleotides(structure)]
# Choose one adenine-thymine and one guanine-cytosine base pair
base_pairs = struc.base_pairs(nucleotides)
for i, j in base_pairs:
if (nucleotides.res_name[i], nucleotides.res_name[j]) == ("DG", "DC"):
guanine, cytosine = [nucleotides[mask] for mask
in struc.get_residue_masks(nucleotides, [i, j])]
break
for i, j in base_pairs:
if (nucleotides.res_name[i], nucleotides.res_name[j]) == ("DA", "DT"):
adenine, thymine = [nucleotides[mask] for mask
in struc.get_residue_masks(nucleotides, [i, j])]
break
pairs = [(guanine, cytosine), (adenine, thymine)]
# License: CC0
import numpy as np
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import biotite.database.rcsb as rcsb
import ammolite
PNG_SIZE = (800, 800)
########################################################################
mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("3EGZ", "mmtf"))
structure = mmtf.get_structure(mmtf_file, model=1)
aptamer = structure[struc.filter_nucleotides(structure)]
# Coarse graining: Represent each nucleotide using its C3' atom
aptamer = aptamer[aptamer.atom_name == "C3'"]
# Connect consecutive nucleotides
indices = np.arange(aptamer.array_length())
aptamer.bonds = struc.BondList(
aptamer.array_length(),
np.stack((indices[:-1], indices[1:]), axis=-1)
)
pymol_obj = ammolite.PyMOLObject.from_structure(aptamer)
pymol_obj.show("sticks")
pymol_obj.show("spheres")
pymol_obj.color("black")
ammolite.cmd.set("stick_color", "red")
