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()