File size: 3,114 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 84 85 86 87 88 89 90 91 | #!/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
from multiprocessing import Pool
# Don't throw an error when someone uses head
from signal import signal, SIGPIPE, SIG_DFL
signal(SIGPIPE, SIG_DFL)
# This code assumes that the target backbone is fixed and will need major revisions if that is every changed - NRB
if (len(sys.argv) == 1):
eprint("")
eprint('silentappendwaters by Nate - a tool to allow you to add waters directly to a silent file')
eprint("Usage:")
eprint(" silentappendwaters solvated_centered_target.silent file_of_docks.silent > file_of_solvated_docks.silent")
eprint("")
eprint(" WARNING!!! This only works in the very specific context of adding waters to a miniprotein binder dock where" )
eprint(" the waters are assigned chain B (the target's chain). If you find the need to use this is another case, talk" )
eprint(" to Nate (nrbennet@uw.edu) ")
sys.exit(1)
water_file = sys.argv[1]
silent_file = sys.argv[2]
n_cores = 1
if len(sys.argv) > 3:
n_cores = int(sys.argv[3])
try:
available = int(silent_tools.cmd( "echo $SLURM_CPUS_ON_NODE" ))
except():
eprint("Parallel only available on a qlogin node")
sys.exit( 0 )
if n_cores > available:
eprint( "More cpus requested (%i) than available (%i)"%(n_cores, available) )
sys.exit( 0 )
silent_index = silent_tools.get_silent_index( silent_file )
( RT_lines, xyz_lines, ann_seq_append, seq_append, edge_list ) = silent_tools.get_water_info( water_file )
# I'm going to do this in 1000 struct chunks to minimize the amount of data being stored. this can easily be changed
seek_size = 1000
cur_struct = 0
ifile = 0
total_structures = len(silent_index['tags'])
header = silent_tools.silent_header( silent_index ).split('\n')
header[0] += seq_append
sys.stdout.write( '\n'.join(header) )
sys.stdout.flush()
parallel = n_cores > 1
if parallel:
pool = Pool( n_cores )
with open( silent_file ) as open_silent_file:
while cur_struct < total_structures:
if ( cur_struct + seek_size > total_structures ):
seek_size = total_structures - cur_struct
structures = silent_tools.get_silent_structures_true_slice( open_silent_file,
silent_index, cur_struct, cur_struct+seek_size, True )
for structure in structures:
if parallel:
retval = pool.apply_async( silent_tools.solvate, args = [structure.split('\n'), RT_lines, xyz_lines, ann_seq_append, seq_append, edge_list] )
solvated_structure = retval.get()
else:
solvated_structure = silent_tools.solvate( structure.split('\n'), RT_lines, xyz_lines, ann_seq_append, seq_append, edge_list )
sys.stdout.write("\n".join(solvated_structure))
sys.stdout.flush()
cur_struct += seek_size
if parallel:
pool.close()
pool.join()
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