def get_xtc_time(filename):
""" Returns the starting time and first timestep of the given xtc traj """
f = xtc.XTCFile()
f.read(filename, start=0, stop=2)
time = f.get_time()
time[1] -= time[0]
return time
def test_PDBx_consistency(format):
pdbx_file = pdbx.PDBxFile()
pdbx_file.read(join(data_dir, "1l2y.cif"))
array1 = pdbx.get_structure(pdbx_file)
template = pdbx.get_structure(pdbx_file, model=1)
if format == "trr":
traj_file = trr.TRRFile()
traj_file.read(join(data_dir, "1l2y.trr"))
if format == "xtc":
traj_file = xtc.XTCFile()
traj_file.read(join(data_dir, "1l2y.xtc"))
array2 = traj_file.get_structure(template)
for cat in array1. get_annotation_categories():
assert array1.get_annotation(cat).tolist() == \
array2.get_annotation(cat).tolist()
assert array1.coord == pytest.approx(array2.coord)
# The structure still has water and ions, that are not needed for our
# calculations, we are only interested in the protein itself
# These are removed for the sake of computational speed using a boolean
# mask
protein_mask = struc.filter_amino_acids(protein)
template = protein[protein_mask]
# We could have loaded the trajectory also with
# 'strucio.load_structure()', but in this case we only want to load
# those coordinates that belong to the already selected atoms of the
# template structure.
# Hence, we use the 'XTCFile' class directly to load the trajectory
# This gives us the additional option that allows us to select the
# coordinates belonging to the amino acids.
print(" .. loading trajectory ...")
xtc_file = xtc.XTCFile()
#xtc_file.read(traj_file_path, 0, 10, atom_i=np.where(protein_mask)[0])
xtc_file.read(traj_file_path, atom_i=np.where(protein_mask)[0])
#xtc_file.read(traj_file_path)
trajectory = xtc_file.get_structure(template)
print(" ... done ... ")
#trajectory = struc.remove_pbc(trajectory)
print(trajectory[0].coord)
trajectory_kinase_left = trajectory[:, trajectory.chain_id == "A"]
trajectory_kinase_right = trajectory[:, trajectory.chain_id == "D"]
print(trajectory_kinase_left.coord.shape[0])
def write_to_xtc(array_stack, outfile):
"""
"""
xtcfile = bxtc.XTCFile()
xtcfile.set_coord(array_stack)
xtcfile.write(outfile)
active_sites = traj[:,mask_active_site,:]
active_sites = np.mean(active_sites,axis = 1)
coords_exit = traj[:,mask_exit,:]
coords_exit = np.mean(coords_exit,axis = 1)
density = np.empty((traj.shape[0],len(radius)))
for j,r in enumerate(radius):
for i in range(traj.shape[0]):
n_atoms = np.where(in_cylinder(coords_exit[i],active_sites[i],r,traj[i]))[0].shape
volume = np.linalg.norm(coords_exit[i] - active_sites[i]) * np.pi * r**2
density[i,j] = n_atoms / volume
return density
radius = [6,8,9,10,11,12,13,14,15,16]
struct = PDB.PDBFile()
struct.read("../md_simulations/kinase_dimer.pdb")
struct = struct.get_structure()[0]
traj = XTC.XTCFile()
traj.read("../md_simulations/kinase_dimer_nopbc_cluster_fit.xtc")
traj = traj.get_coord()
density_a = calculate_densities(struct,traj,"A",radius)
density_data_a = pd.DataFrame(data=density_a,columns = [str(i) for i in radius])
density_data_a.to_csv("density_data_kinase_a.csv")
density_d = calculate_densities(struct,traj,"D",radius)
density_data_d = pd.DataFrame(data=density_d,columns = [str(i) for i in radius])
density_data_d.to_csv("density_data_kinase_d.csv")
# These can be extracted as :class:`ndarray` with the
# :func:`get_coord()` method.
import requests
import biotite
import biotite.structure.io.xtc as xtc
# Download 1L2Y as XTC file for demonstration purposes
xtc_file_path = biotite.temp_file("xtc")
with open(xtc_file_path, "bw") as file:
response = requests.get(
"https://raw.githubusercontent.com/biotite-dev/biotite/master/"
"tests/structure/data/1l2y.xtc")
file.write(response.content)
traj_file = xtc.XTCFile()
traj_file.read(xtc_file_path)
coord = traj_file.get_coord()
print(coord.shape)
########################################################################
# If only an excerpt of frames is desired, the behavior of
# :func:`read()` function can be customized with the `start`, `stop` and
# `step` parameters.
traj_file = xtc.XTCFile()
# Read only every second frame
traj_file.read(xtc_file_path, step=2)
coord = traj_file.get_coord()
print(coord.shape)
distance_matrices = None
with Pool() as p:
distance_matrices = p.map(f_worker, lines)
return np.array(distance_matrices)
if __name__ == "__main__":
# take first output structure as structure to align to
template_dimer = strucio.load_structure(
"dimer_refined/pk_mono_sur_di_0001_000001_0001.pdb")
print(" ... loading XTC files ... ")
xtc_dimer = xtc.XTCFile()
xtc_dimer.read("dimers_ordered_by_cleaned.xtc") #, 1, 10)
print(" ... done ... ")
print("")
print("")
trajectory_dimer = xtc_dimer.get_structure(template_dimer)
pkcs_start = trajectory_dimer[0][trajectory_dimer[0].chain_id == 'A']
pkcs_start = pkcs_start[pkcs_start.atom_name == "CA"]
trajectory_dimer, transform = struc.superimpose(
trajectory_dimer[0], trajectory_dimer,
(trajectory_dimer[0].chain_id == 'A')
& (trajectory_dimer[0].atom_name == 'CA'))
trajectory_dimer_ca = trajectory_dimer[:,