File size: 2,278 Bytes
9ae74ae | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | #!/usr/bin/env python
import distutils.spawn
import os
import sys
sys.path.append(os.path.dirname(distutils.spawn.find_executable("silent_tools.py")))
import silent_tools
from silent_tools import eprint
import re
# Don't throw an error when someone uses head
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)
if (len(sys.argv) == 1):
eprint("")
eprint('silentdropcorruptmodels by bcov - drop models with wrong number of residues')
eprint("Usage:")
eprint(" silentdropcorruptmodels myfile.silent > fixed.silent")
eprint("")
eprint("Note: Like the other oops series tools, this script performs a one-pass operation")
eprint(" on your file without building an index. Currently only BINARY supported.")
sys.exit(1)
silent_file = sys.argv[1]
scoreline, f = silent_tools.assert_is_silent_and_get_scoreline(silent_file, return_f=True, accept_garbage=True)
sys.stdout.write( silent_tools.silent_header_fix_corrupt_slim( "A", scoreline, "BINARY" ) )
sys.stdout.flush()
first_line = None
try:
first_line = next(f)
except:
pass
while (not first_line is None):
# try:
structure, first_line = silent_tools.rip_structure_by_lines_arbitrary_start(f, first_line)
# except:
# break
tag = structure[0].split()[-1]
try:
sequence_chunks = silent_tools.get_sequence_chunks( structure, tag )
except:
eprint("silentoopsdropcorruptmodels: Error reading sequence: %s"%(tag))
continue
if ( sequence_chunks is None ):
continue
sequence = "".join(sequence_chunks)
seqlen = len(sequence)
is_binary = True
is_protein = False
num_res_lines = 0
for line in structure:
if ( is_binary ):
if ( len(line) == 0 ):
continue
if ( line[0] in "HEL" ):
num_res_lines += 1
if ( is_protein ):
if ( len(line) < 6 ):
continue
if ( line[5] in "HEL" ):
num_res_lines += 1
if ( seqlen != num_res_lines ):
eprint("silentoopsdropcorruptmodels: Found %5i res expected %5i res: %s"%
(num_res_lines, seqlen, tag))
else:
sys.stdout.write("".join(structure))
sys.stdout.flush()
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