def get_sas(pdb, probe):
import modeller
# Read the PDB file
env = modeller.environ()
mdl = modeller.model(env)
mdl.read(file=pdb)
# Calculate atomic accessibilities (in Biso) with appropriate probe_radius
myedat = modeller.energy_data()
myedat.radii_factor = 1.6
mdl.write_data(edat=myedat, output="PSA ATOMIC_SOL", psa_integration_step=0.05, probe_radius=probe)
mdl.write(file=pdb.rsplit(".", 1)[0] + ".sas")
# read SAS
with open("%s.sas" % (pdb.rsplit(".", 1)[0],)) as data:
D = data.readlines()
Sas = {}
for d in D:
d = d.strip()
if d[:4] == "ATOM":
atom, res, resid, cid = d[12:16], d[17:20], int(d[22:26]), d[21]
if cid == " ":
cid = "A"
Sas[(atom, res, resid, cid)] = float(d[60:66])
return Sas
def get_sas(pdb,probe):
import modeller
# Read the PDB file
env = modeller.environ()
mdl = modeller.model(env)
mdl.read(file=pdb)
# Calculate atomic accessibilities (in Biso) with appropriate probe_radius
myedat = modeller.energy_data()
myedat.radii_factor = 1.6
mdl.write_data(edat=myedat, output='PSA ATOMIC_SOL',
psa_integration_step=0.05, probe_radius=probe)
mdl.write(file=pdb.rsplit('.',1)[0]+'.sas')
# read SAS
with open('%s.sas' % (pdb.rsplit('.',1)[0], )) as data:
D = data.readlines()
Sas = {}
for d in D:
d = d.strip()
if d[:4]=='ATOM':
atom, res, resid, cid = d[12:16], d[17:20], int(d[22:26]), d[21]
if cid == ' ':
cid='A'
Sas[(atom,res,resid,cid)] = float(d[60:66])
return Sas
def get_dope_energy_data(self):
"""Get ideal energy_data terms for DOPE potential evaluations"""
return energy_data(contact_shell=15.0,
dynamic_modeller=True,
dynamic_lennard=False,
dynamic_sphere=False,
excl_local=(False, False, False, False))
def _get_energy_data(self):
from modeller import energy_data
return energy_data(contact_shell=-999,
dynamic_sphere=False,
excl_local=[True, False, False, True])
def _get_energy_data(self):
from modeller import energy_data
return energy_data(contact_shell=-999, dynamic_sphere=False)