File size: 2,268 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 | #!/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")
sys.exit(1)
silent_file = sys.argv[1]
silent_index = silent_tools.get_silent_index( silent_file, accept_garbage=True)
is_binary = silent_index['silent_type'] == "BINARY"
is_protein = silent_index['silent_type'] == "PROTEIN"
if ( not is_binary and not is_protein ):
eprint("silentdropcorruptmodels: Unknown silent type. Trying BINARY")
is_binary = True
sys.stdout.write( silent_tools.silent_header_fix_corrupt( silent_index ) )
sys.stdout.flush()
with open(silent_file, errors='ignore') as sf:
for tag in silent_index['tags']:
structure = silent_tools.get_silent_structure_file_open( sf, silent_index, tag )
try:
sequence_chunks = silent_tools.get_sequence_chunks( structure, tag )
except:
eprint("silentdropcorruptmodels: Error reading sequence: %s"%(tag))
continue
if ( sequence_chunks is None ):
continue
sequence = "".join(sequence_chunks)
seqlen = len(sequence)
assert( is_binary ^ is_protein )
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("silentdropcorruptmodels: Found %5i res expected %5i res: %s"%
(num_res_lines, seqlen, tag))
else:
sys.stdout.write("".join(structure))
sys.stdout.flush()
|