def __filter_simrna_trajectory():
f = (line for line in open(args.trajectory))
c = 0
while 1:
try:
header = f.next().strip()
except StopIteration: # not nice
break
c += 1
coords = f.next().strip()
traj = SimRNATrajectory()
traj.load_from_string(c, header + '\n' + coords)
frame = traj.frames[0]
print(c)
for h in restraints:
a = int(h[0].replace('A',
'')) - 1 # A1 -> 0 (indexing Python-like)
b = int(h[1].replace('A', '')) - 1
a_mb = frame.residues[a].get_center()
b_mb = frame.residues[b].get_center()
# print ' mb for A' + str(a+1), a_mb
# print ' mb for A' + str(b+1), b_mb
dist = get_distance(a_mb, b_mb)
logger.info(' '.join(' d:A' + str(a + 1) + "-A" + str(b + 1),
dist))
def parse_logic(restraints_fn, verbose):
"""Parse logic of restraints.
Args:
restraints_nf(string): path to a file with restraints in the rigth format (see below)
verbose (bool) : be verbose?
Format::
# ignore comments
(d:A1-A2 < 10.0 1)|(d:A2-A1 <= 10 1)
Returns:
list: parse restraints into a list of lists, e.g. [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
"""
txt = ''
with open(restraints_fn) as f:
for l in f:
if not l.startswith('#'):
txt += l.strip()
if verbose:
logger.info(txt)
restraints = re.findall(
'\(d:(?P<start>.+?)-(?P<end>.+?)\s*(?P<operator>\>\=|\=|\<|\<\=)\s*(?P<distance>[\d\.]+)\s+(?P<weight>.+?)\)',
txt)
return restraints
def parse_logic(restraints_fn, verbose):
"""Parse logic of restraints.
Args:
restraints_nf(string): path to a file with restraints in the rigth format (see below)
verbose (bool) : be verbose?
Format::
# ignore comments
(d:A1-A2 < 10.0 1)|(d:A2-A1 <= 10 1)
Returns:
list: parse restraints into a list of lists, e.g. [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
"""
txt = ''
with open(restraints_fn) as f:
for l in f:
if not l.startswith('#'):
txt += l.strip()
if verbose:
logger.info(txt)
restraints = re.findall(
'\(d:(?P<start>.+?)-(?P<end>.+?)\s*(?P<operator>\>\=|\=|\<|\<\=)\s*(?P<distance>[\d\.]+)\s+(?P<weight>.+?)\)', txt)
return restraints
def get_residues(pdb_fn, restraints, verbose):
residues = set()
for h in restraints:
a = h[0]
b = h[1]
a = a[0] + ':' + a[1:]
residues.add(a) # A19
b = b[0] + ':' + b[1:]
residues.add(b)
# set(['A:41', 'A:9', 'A:10', 'A:16'])
selection = ','.join(residues)
selection_parsed = select_pdb_fragment(selection,
separator=",",
splitting="[,:;]")
residues = parse_pdb(pdb_fn, selection_parsed)
# get mb
for r in residues:
if 'N9' in residues[r]: # A,G
residues[r]['mb'] = residues[r]['N9'] - (
(residues[r]['N9'] - residues[r]['C6']) / 2)
else: # A,G
residues[r]['mb'] = residues[r]['N1'] - (
(residues[r]['N1'] - residues[r]['C4']) / 2)
for r in residues:
if verbose:
logger.info(' '.join(['mb for ', str(r), str(residues[r]['mb'])]))
return residues
def get_residues(pdb_fn, restraints, verbose):
residues = set()
for h in restraints:
a = h[0]
b = h[1]
a = a[0] + ':' + a[1:]
residues.add(a) # A19
b = b[0] + ':' + b[1:]
residues.add(b)
# set(['A:41', 'A:9', 'A:10', 'A:16'])
selection = ','.join(residues)
selection_parsed = select_pdb_fragment(selection, separator=",", splitting="[,:;]")
residues = parse_pdb(pdb_fn, selection_parsed)
# get mb
for r in residues:
if 'N9' in residues[r]: # A,G
residues[r]['mb'] = residues[r]['N9'] - ((residues[r]['N9'] - residues[r]['C6']) / 2)
else: # A,G
residues[r]['mb'] = residues[r]['N1'] - ((residues[r]['N1'] - residues[r]['C4']) / 2)
for r in residues:
if verbose:
logger.info(' '.join(['mb for ', str(r), str(residues[r]['mb'])]))
return residues
def parse_logic_newlines(restraints_fn, offset=0, verbose=False):
"""Parse logic of restraints.
Args:
restraints_nf(string): path to a file with restraints in the rigth format (see below)
verbose (bool) : be verbose?
Format::
# ignore comments
d:Y23-Y69 < 25.0
d:Y22-Y69 < 25.0
# d:<chain><resi_A>-<resi_B> <operator> <distance> <weight>; each restraints in a new line
Raises:
__main__.RNAFilterErrorInRestraints: Please check the format of your restraints!
Returns:
list: parse restraints into a list of lists, e.g. [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
"""
restraints = []
with open(restraints_fn) as f:
for l in f:
if l.strip():
if not l.startswith('#'):
if verbose:
logger.info(l)
restraint = re.findall(
'd:(?P<start>.+?)-(?P<end>.+?)\s*(?P<operator>\>\=|\=|\<|\<\=)\s*(?P<distance>[\d\.]+)\s+(?P<weight>.+?)',
l)
if restraint:
# without [0] it is restraints [[('Y23', 'Y69', '<', '25.0', '1')], [('Y22', 'Y69', '<', '25.0', '1')]]
# why? to convert 'Y23', 'Y69', '<', '25.0', '1' -> 'Y23', 'Y69', '<', 25.0, 1
start = restraint[0][0][0] + str(
int(restraint[0][0][1:]) + offset)
end = restraint[0][1][0] + str(
int(restraint[0][1][1:]) + offset)
restraints.append([
start, end, restraint[0][1], restraint[0][2],
float(restraint[0][3]),
float(restraint[0][4])
])
if len(restraints) == 0:
raise RNAFilterErrorInRestraints(
'Please check the format of your restraints!')
return restraints # [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
def parse_logic_newlines(restraints_fn, offset=0, verbose=False):
"""Parse logic of restraints.
Args:
restraints_nf(string): path to a file with restraints in the rigth format (see below)
verbose (bool) : be verbose?
Format::
# ignore comments
d:Y23-Y69 < 25.0
d:Y22-Y69 < 25.0
# d:<chain><resi_A>-<resi_B> <operator> <distance> <weight>; each restraints in a new line
Raises:
__main__.RNAFilterErrorInRestraints: Please check the format of your restraints!
Returns:
list: parse restraints into a list of lists, e.g. [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
"""
restraints = []
with open(restraints_fn) as f:
for l in f:
if l.strip():
if not l.startswith('#'):
if verbose:
logger.info(l)
restraint = re.findall(
'd:(?P<start>.+?)-(?P<end>.+?)\s*(?P<operator>\>\=|\=|\<|\<\=)\s*(?P<distance>[\d\.]+)\s+(?P<weight>.+?)', l)
if restraint:
# without [0] it is restraints [[('Y23', 'Y69', '<', '25.0', '1')], [('Y22', 'Y69', '<', '25.0', '1')]]
# why? to convert 'Y23', 'Y69', '<', '25.0', '1' -> 'Y23', 'Y69', '<', 25.0, 1
start = restraint[0][0][0] + str(int(restraint[0][0][1:]) + offset)
end = restraint[0][1][0] + str(int(restraint[0][1][1:]) + offset)
restraints.append([start, end, restraint[0][1], restraint[0][2],
float(restraint[0][3]), float(restraint[0][4])])
if len(restraints) == 0:
raise RNAFilterErrorInRestraints('Please check the format of your restraints!')
return restraints # [('A9', 'A41', '10.0', '1'), ('A10', 'A16', '10', '1')]
def __filter_simrna_trajectory():
f = (line for line in open(args.trajectory))
c = 0
while 1:
try:
header = f.next().strip()
except StopIteration: # not nice
break
c += 1
coords = f.next().strip()
traj = SimRNATrajectory()
traj.load_from_string(c, header + '\n' + coords)
frame = traj.frames[0]
print(c)
for h in restraints:
a = int(h[0].replace('A', '')) - 1 # A1 -> 0 (indexing Python-like)
b = int(h[1].replace('A', '')) - 1
a_mb = frame.residues[a].get_center()
b_mb = frame.residues[b].get_center()
# print ' mb for A' + str(a+1), a_mb
# print ' mb for A' + str(b+1), b_mb
dist = get_distance(a_mb, b_mb)
logger.info(' '.join(' d:A' + str(a + 1) + "-A" + str(b + 1), dist))
a = int(h[0].replace('A',
'')) - 1 # A1 -> 0 (indexing Python-like)
b = int(h[1].replace('A', '')) - 1
a_mb = frame.residues[a].get_center()
b_mb = frame.residues[b].get_center()
# print ' mb for A' + str(a+1), a_mb
# print ' mb for A' + str(b+1), b_mb
dist = get_distance(a_mb, b_mb)
logger.info(' '.join(' d:A' + str(a + 1) + "-A" + str(b + 1),
dist))
# main
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
# score = 1
# print ((True|True)|(False|False)), score
restraints = parse_logic_newlines(args.restraints_fn, args.offset,
args.verbose)
if args.verbose:
logger.info('restraints' + str(restraints))
if args.structures:
calc_scores_for_pdbs(args.structures, restraints, args.verbose)
# if args.trajectory:
# __filter_simrna_trajectory()
frame = traj.frames[0]
print(c)
for h in restraints:
a = int(h[0].replace('A', '')) - 1 # A1 -> 0 (indexing Python-like)
b = int(h[1].replace('A', '')) - 1
a_mb = frame.residues[a].get_center()
b_mb = frame.residues[b].get_center()
# print ' mb for A' + str(a+1), a_mb
# print ' mb for A' + str(b+1), b_mb
dist = get_distance(a_mb, b_mb)
logger.info(' '.join(' d:A' + str(a + 1) + "-A" + str(b + 1), dist))
# main
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
# score = 1
# print ((True|True)|(False|False)), score
restraints = parse_logic_newlines(args.restraints_fn, args.offset, args.verbose)
if args.verbose:
logger.info('restraints' + str(restraints))
if args.structures:
calc_scores_for_pdbs(args.structures, restraints, args.verbose)
# if args.trajectory:
# __filter_simrna_trajectory()