def pdb_from_file(path, hydrogenate=True, clean=True) -> Pdb:
"""Construct Pdb object from a PDB file
Args:
path: Path to PDB file
hydrogenate: Whether to add hydrogens
clean: Whether to remove unwanted molecules
Returns:
Protein databank entry
"""
pdb = atomium.pdb_from_file(path)
return pdb_from_atomium_pdb(pdb, hydrogenate, clean)
def test_model_saving(self):
model = Model()
atom1 = Atom("N", 12.0, 11.5, 1.5)
atom2 = Atom("C", 12.5, 10, 2, id=102, bfactor=22.1)
model.add_atom(atom1)
model.add_atom(atom2)
model.save("tests/integration/files/model.xyz",
description="Some atoms")
new = atomium.xyz_from_file("tests/integration/files/model.xyz")
self.assertEqual(new.title, "Some atoms")
self.assertEqual(len(new.model.atoms()), 2)
self.assertEqual(new.model.atom(element="N").location, (12, 11.5, 1.5))
self.assertEqual(new.model.atom(element="C").location, (12.5, 10, 2))
model.save("tests/integration/files/model.pdb",
description="Some atoms")
new = atomium.pdb_from_file("tests/integration/files/model.pdb")
self.assertEqual(new.title, "Some atoms")
self.assertEqual(len(new.model.atoms()), 2)
self.assertEqual(new.model.atom(0).location, (12, 11.5, 1.5))
self.assertEqual(new.model.atom(102).bfactor, 22.1)
#! /usr/bin/env python3
import atomium
import biometal
import sys
import matplotlib.pyplot as plt
if len(sys.argv) == 1:
print("Please provide a PDB and ion")
sys.exit()
pdbs = []
for arg in sys.argv[1:-2]:
pdb, atom_id = arg.split(":")
model = atomium.pdb_from_file(pdb + ".pdb").model
pdbs.append({"model": model, "atom": model.atom(id=int(atom_id))})
radius = float(sys.argv[-2])
step = float(sys.argv[-1])
x = [0.5]
while x[-1] < radius:
x.append(round(x[-1] + step, 6))
ys = []
for pdb in pdbs:
ys.append([
biometal.hydrophobic_contrast(
pdb["model"], *pdb["atom"].location, radius, metal=False, pc=False)
/ 1000 for radius in x
])
files = os.listdir(location)
scores = [f for f in files if f.endswith("_scores.dat")]
os.chdir(location)
print("There are {} PDBs with scores".format(len(scores)))
print("PDB\tPoints\tIon\tRank\tDev.\tScore\tRange")
for scores_file in scores:
pdb_file = scores_file.replace("_scores.dat", ".pdb")
with open(scores_file) as f:
lines = f.read().splitlines()
lines = [[float(val) for val in line.split()] for line in lines[1:]]
point_count = len(lines) - 1
model = atomium.pdb_from_file(pdb_file).model
metals = model.atoms() - model.atoms(metal=False)
for i, metal in enumerate(metals):
point = [line for line in lines if metal.distance_to(line[:3]) <= 3][-1]
deviation = metal.distance_to(point[:3])
print("{}\t{}\t{}\t{}\t{}\t{}\t{}{}{}".format(
pdb_file[:-4] if i == 0 else "",
point_count if i == 0 else "",
metal.element,
len(lines) - lines.index(point),
round(deviation, 1),
round(point[-1] / 1000, 1),
round(max([l[-1] for l in lines]) / 1000, 1) if i == 0 else "",
"/" if i == 0 else "",
round(min([l[-1] for l in lines]) / 1000, 1) if i == 0 else ""
import sys
sys.path.insert(0, ".")
import atomium
pdb = atomium.pdb_from_file("tests/time/{}.pdb")
pdb.save("tests/time/temp.pdb")