def freesasa_cb(prody_parsed, probe_radius=1.4):
cb_sele = prody_parsed.select(
'protein and (backbone or name CB) and not element H D')
coords = list(x for y in cb_sele.getCoords() for x in y)
radii = list(freesasa.Classifier().radius(x, y) for x, y in zip(cb_sele.getResnames(), \
cb_sele.getNames()))
return freesasa.calcCoord(
coords, radii, freesasa.Parameters({'probe-radius': probe_radius}))
def analyze_sasa(u: mda.Universe) -> np.ndarray:
"""Extract SASA value for each trajectory frame."""
atoms = u.select_atoms(STANDARD_SELECTION)
positions = u.trajectory.timeseries(asel=atoms)
trajectory_sasa = []
atom_radius = list(map(get_atom_radius, atoms))
for frame in np.swapaxes(positions, 0, 1):
sasa = freesasa.calcCoord(frame.reshape(-1), atom_radius).totalArea()
trajectory_sasa.append(sasa)
return np.array(trajectory_sasa)
def compute_accessibility(pdbname, pdb_path, pdb_dca_resids, backmap_table,
allowed_residues, vmd_path, results_folder,
accessibilities_by_domain):
print("SASA:")
radii_d = {}
this_path = os.path.dirname(os.path.abspath(__file__)) + '/'
with open(this_path + 'support_files/radii.txt') as radii_file:
for line in radii_file:
fields = line.split()
radii_d[fields[0]] = float(fields[1])
alaxala = {}
with open(this_path + 'support_files/alaxala_sasa.txt') as alaxala_file:
for line in alaxala_file:
fields = line.split()
alaxala[fields[0]] = float(fields[1])
residues_linear = []
coords = []
names = []
radii = []
parser = Bio.PDB.PDBParser(QUIET=True)
structure = parser.get_structure(pdbname, pdb_path)
chains = [x.get_id() for x in structure[0].get_chains()]
residues = {}
for c in chains:
residues[c] = [
int(x.get_id()[1]) for x in structure[0][c].get_residues()
]
distance_threshold = 20
if accessibilities_by_domain:
for pfam_acc, mapping, unip in backmap_table:
loc_coords = []
loc_names = []
loc_radii = []
for c, r in [
x for x in pdb_dca_resids if x[0] == mapping[0]
and x[1] >= mapping[1][0] and x[1] <= mapping[1][1]
]:
if (c not in chains) or (r not in residues[c]):
continue
res = structure[0][c][r]
resname = res.get_resname()
for atom in res:
atname = atom.get_name()[0]
if atname not in radii_d:
continue
loc_names.append((c, (r, resname), atname))
loc_coords.append(atom.get_coord())
loc_radii.append(radii_d[atname])
coords.append(loc_coords)
names.append(loc_names)
radii.append(loc_radii)
else:
loc_coords = []
loc_names = []
loc_radii = []
for model in structure:
for chain1 in allowed_residues:
c1 = model[chain1]
for r1 in c1:
resid1 = r1.id[1]
resname = r1.get_resname()
if resid1 not in allowed_residues[chain1]:
continue
if (chain1, resid1) not in residues_linear:
residues_linear.append((chain1, resid1))
for a1 in r1:
atname1 = a1.get_name()[0]
if atname1 not in radii_d:
continue
loc_names.append((chain1, (resid1, resname), atname1))
loc_coords.append(a1.get_coord())
loc_radii.append(radii_d[atname1])
coords.append(loc_coords)
names.append(loc_names)
radii.append(loc_radii)
sasas = []
for i in range(len(coords)):
loc_coords = coords[i]
loc_names = names[i]
loc_radii = radii[i]
N = len(residues_linear)
loc_coords = np.array(loc_coords).flatten()
loc_radii = np.array(loc_radii)
# print(loc_coords)
Results = freesasa.calcCoord(loc_coords, loc_radii)
sasas.append([Results.atomArea(i) for i in range(Results.nAtoms())])
# print(names)
SASA = {}
if accessibilities_by_domain:
for ie, entry in enumerate(backmap_table):
pfam_acc, mapping, unip = entry
loc_names = names[ie]
SASA[pfam_acc] = {}
for i, name in enumerate(loc_names):
ch, res, at = name
r, rname = res
idx = [
i for i, x in enumerate(pdb_dca_resids[(ch, r)])
if x[0] == pfam_acc
][0]
dca_i = pdb_dca_resids[(ch, r)][idx][1]
if (dca_i, ch, r) not in SASA[pfam_acc]:
SASA[pfam_acc][(dca_i, ch, r)] = [0, 0]
SASA[pfam_acc][(dca_i, ch, r)][0] += sasas[ie][i]
rname1 = from3to1(rname)
if rname1 not in alaxala:
SASA[pfam_acc][(dca_i, ch, r)][1] = 0
else:
SASA[pfam_acc][(dca_i, ch,
r)][1] += sasas[ie][i] / alaxala[rname1]
else:
loc_names = names[0]
for ie, entry in enumerate(backmap_table):
pfam_acc, mapping, unip = entry
SASA[pfam_acc] = {}
for i, name in enumerate(loc_names):
ch, res, at = name
r, rname = res
idx_list = [
i for i, x in enumerate(pdb_dca_resids[(ch, r)])
if x[0] == pfam_acc
]
if idx_list:
idx = idx_list[0]
else:
continue
dca_i = pdb_dca_resids[(ch, r)][idx][1]
if not (ch == mapping[0] and r >= mapping[1][0]
and r <= mapping[1][1]):
continue
if (dca_i, ch, r) not in SASA[pfam_acc]:
SASA[pfam_acc][(dca_i, ch, r)] = [0, 0]
SASA[pfam_acc][(dca_i, ch, r)][0] += sasas[0][i]
rname1 = from3to1(rname)
if rname1 not in alaxala:
SASA[pfam_acc][(dca_i, ch, r)][1] = 0
else:
# print(dca_i, ch, r, rname, at, sasas[0][i]/alaxala[rname1])
SASA[pfam_acc][(dca_i, ch,
r)][1] += sasas[0][i] / alaxala[rname1]
acessibility_filename = results_folder + "{0}_SASA.txt".format(pdbname)
with open(acessibility_filename, 'w') as accessibility_file:
for ie, entry in enumerate(backmap_table):
pfam_acc, mapping, unip = entry
for dca_i, ch, r in sorted(list(SASA[pfam_acc].keys()),
key=lambda x: x[0]):
if SASA[pfam_acc][(dca_i, ch, r)][1] > 1:
SASA[pfam_acc][(dca_i, ch, r)][1] = 1
accessibility_file.write(
"{0}\t{1}\t{2}\t{3}\t{4}\t{5}\n".format(
pfam_acc, dca_i, ch, r,
SASA[pfam_acc][(dca_i, ch, r)][0],
SASA[pfam_acc][(dca_i, ch, r)][1]))
print(acessibility_filename)
return SASA
# print(residues_linear)
# print(allowed_residues)
if not os.path.exists(vmd_path):
print(
"CRITICAL: path {0} not found.\n\tIf it is an alias, please expand it."
.format(vmd_path))
exit(1)
else:
vmd_path = vmd_path.replace(" ", "\ ")
SASA = {}
for i1 in range(N):
c1, r1 = residues_linear[i1]
print(pdb_dca_resids[(c1, r1)])
for pfam_acc_ann1, dca_i1 in pdb_dca_resids[(c1, r1)]:
# if dca_i1 in accessibility_dca_resids:
pfam_acc1, cmult1 = pfam_acc_ann1.split('_')
os.system(
"sed 's/XXX/chain {0} and resid {1}/' {2}/support_files/fixed_sasa_template.tcl | sed 's=YYY={3}=g' > {2}/support_files/fixed_sasa.tcl"
.format(c1, r1, this_path, results_folder))
sp = subprocess.run([
vmd_path + " " + pdb_path +
" -dispdev text -e {0}/support_files/fixed_sasa.tcl > /dev/null 2>&1"
.format(this_path)
],
shell=True,
executable='/bin/bash')
with open(results_folder + "SASA_output.dat") as output_file:
for line in output_file:
if not dca_i1 in SASA:
SASA[dca_i1] = []
SASA[dca_i1].append(
(pfam_acc_ann1, pdbname + ' ' + c1 + ' ' + str(r1),
float(line.strip())))
break
os.remove(results_folder + "SASA_output.dat")
acessibility_filename = results_folder + "{0}_SASA.txt".format(pdbname)
with open(acessibility_filename, 'w') as accessibility_file:
for dca_i in SASA:
for x in SASA[dca_i]:
accessibility_file.write("{0}\t{1}\t{2}\t{3}\n".format(
dca_i, x[0], x[1], x[2]))
print(acessibility_filename)
return SASA