def get_chi(residue_sele, atoms_list):
'''Take parsedvdm and a list of 4 atoms and calculate dihedral in prody
Helper function for rotamer()'''
prody_list = [residue_sele.select('name %s' % name) for name in atoms_list]
return pr.calcDihedral(prody_list[0], prody_list[1], prody_list[2],
prody_list[3])
def get_sec_struct_phipsi(self, parsed_pdb):
phipsi = []
for resn in self.sele.getResnums()[self._ind]:
try:
phi = pr.calcDihedral(parsed_pdb.prody_pdb.select(
'name C and bonded 1 to (resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name N)'),
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name N'),
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name CA'),
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name C'))[0]
except:
phi = None
try:
psi = pr.calcDihedral(
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name N'),
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name CA'),
parsed_pdb.prody_pdb.select(
'resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name C'),
parsed_pdb.prody_pdb.select(
'name N and bonded 1 to (resnum ' + str(resn)
+ ' segment A chain ' + self.chid + ' name C)'))[0]
except:
psi = None
if phi is not None and psi is not None:
phipsi.append('(' + '{0:.2f}'.format(phi) + ' ' + '{0:.2f}'.format(psi) + ')')
elif phi is None and psi is not None:
phipsi.append('(' + 'None' + ' ' + '{0:.2f}'.format(psi) + ')')
elif phi is not None and psi is None:
phipsi.append('(' + '{0:.2f}'.format(phi) + ' ' + 'None' + ')')
else:
phipsi.append('(None None)')
self.sec_struct_phi_psi = ' '.join(phipsi)
def read_dihedral(self):
dihedral_list = self.select_atoms()
dihedral_results = []
for dihedral in dihedral_list:
atoms = []
for atom in dihedral:
atoms.append(atom)
dihedral_angle = prody.calcDihedral(atoms[0], atoms[1], atoms[2],
atoms[3])
dihedral_results.append(dihedral_angle)
return dihedral_results
def get_dih3(vdm, ifg, comb):
return pr.calcDihedral(
vdm.ires_sele.select('name ' + dih3[vdm.resname][0]),
ifg.sele.select('name ' + comb.vandarotamer_dict['A1']),
ifg.sele.select('name ' + comb.vandarotamer_dict['A2']),
ifg.sele.select('name ' + comb.vandarotamer_dict['A3']))[0]
def process(self, args=None):
if not args:
args = self.args
# Sfn = args['Sfn']
# Open matrix file in parallel mode
# Sf = h5py.File(Sfn, 'r')
args['mpi'] = self.mpi
extractor = er.PepExtractor(**args)
lM = len(self.aplist)
dtype = np.dtype([
('name', 'S10'),
('pnum', '<i4'),
('rnum', '<i4'),
('dist', '<f8'),
('hdist1', '<f8'),
('hdist2', '<f8'),
('BD', '<f8'),
('FL', '<f8'),
('AT', '<f8'),
('dir', 'S3'),
('aln', 'S20')
])
if self.mpi.rank == 0:
m = self.aplist[0]
lm = len(m)
S = extractor.extract_result(m)
lS = S.numCoordsets()
Sf = h5py.File(args['out'], 'w')
out = Sf.create_dataset(
'out', (len(self.plist) * lS * lm, ), dtype=dtype)
Sf.close()
self.mpi.comm.Barrier()
Sf = h5py.File(args['out'], 'r+', driver='mpio', comm=self.mpi.comm)
out = Sf['out']
# Init storage for matrices
# Get file name
# tSfn = 'tmp.' + Sfn
# tSfn = args['output']
# stubs = {
# 'ACE': 'X',
# 'NME': 'Z',
# }
a = prody.parsePDB(args['receptor'])
OG = a.select('resnum 151 name SG')
Ob = a.select('resnum 168 and name O')
ND1 = a.select('resnum 46 and name NE2')
OXH = a.select("name N resnum 149 150 151")
t0 = time.time()
for cm in range(lM):
m = self.aplist[cm]
lm = len(m)
t1 = time.time()
dt = t1 - t0
t0 = t1
print('STEP: %d PERCENT: %.2f%% TIME: %s' % (
cm, float(cm) / lM * 100, dt))
try:
S = extractor.extract_result(m)
except:
print('ERROR: BAD PEPTIDE: %s' % m)
continue
lS = S.numCoordsets()
for S_ in range(lS):
S.setACSIndex(S_)
tC = S.select('name C')
dist = np.inf
rnum = None
for C in tC.iterAtoms():
rnum = C.getResnum()
if rnum == 1:
continue
O = S.select('resnum %i and name O' % rnum)
Nl = S.select('resnum %i and name N' % (rnum))
N = S.select('resnum %i and name N' % (rnum + 1))
C_ = C.getCoords()
O_ = O.getCoords()[0]
N_ = N.getCoords()[0]
dist = prody.calcDistance(C, OG)[0]
hdist1 = np.min(prody.calcDistance(OXH, O))
hdist2 = np.min(prody.calcDistance(Ob, Nl))
nC_ = np.cross((C_ - N_), (O_ - C_))
nC_ /= np.linalg.norm(nC_)
nC_ = nC_ + C_
nC_ = nC_.reshape(1, 3)
nC = C.copy()
nC.setCoords(nC_)
BD = prody.calcAngle(OG, C, O)
FL = prody.calcDihedral(OG, nC, C, O)
AT = prody.calcAngle(ND1, OG, C)
angle_ = prody.calcDihedral(ND1, OG, C, N)
# angle_ = prody.calcDistance(Od, N)[0] \
# - prody.calcDistance(Od, C)[0]
if angle_ < 0:
DIR = 'F'
else:
DIR = 'R'
s = 'X' + m + 'Z'
pref = ''
if DIR == 'F':
seq = s
pref = 6 - rnum
else:
seq = s[::-1]
pref = rnum
suf = 12 - (pref + len(seq))
seq = '-' * pref + seq + '-' * suf
# outfmt = "%-10s\t%d\t%6.2f\t%6.2f%6.2f\t%6.2f\t" \
# "%6.2f\t%6.2f\t%3s\t%12s\n"
# outstr = outfmt % (
# ('%s_%02d' % (m, S_ + 1),
# rnum, dist, hdist1, hdist2, BD, FL, AT,
# DIR, seq)
# )
outdata = (m, S_ + 1,
rnum, dist, hdist1, hdist2, BD, FL, AT,
DIR, seq)
ind = (self.tb + cm) * lS * lm + S_ * lm + rnum - 2
out[ind] = outdata
self.database.close()
Sf.close()