__author__ = 'fanzheng'
import os, argparse, sys
import subprocess, threading
import General
selfbin = os.path.dirname(os.path.realpath(sys.argv[0]))
ldir1 = General.createLocalSpace()
ldir2 = General.createLocalSpace() # data files are here
cmd_setup = ['perl -w', selfbin +'/mdNAMD.pl', '-p', 'dummy.pdb', '-n', '1000000', '--ns', '1000', '--ts', '2', '--pad', '9', '--Pext', '1.01325', '--mini', '5000', '--top', '/home/grigoryanlab/home/fzheng/PDZ.2014/MD/Dcmap/top_all22_prot_namd.inp', '--par', '/home/grigoryanlab/home/fzheng/PDZ.2014/MD/Dcmap/par_all22_prot.inp', '--psfopts', '"first nter; last cter|first ace; last ct3"', '--np', '6', '--pme', '--odir', ldir2, '--dry', '--tmp', ldir1]
cmd_setup = ' '.join(cmd_setup)
par = argparse.ArgumentParser()
par.add_argument('--p', required = True, help = 'input pdb')
par.add_argument('--v', action = 'store_true', help = 'if true, copy everything back from local directory')
par.add_argument('--change', nargs ='+', help = 'if want to change the settings in setup command, provide strings in pairs, before and after change respectively; \n Original command: ' + cmd_setup )
par.add_argument('--nc', default = 4, type = int, help = 'the number of cores to use')
par.add_argument('--hrs', default = 23, type = float, help = 'time allocated to run this job, in hours')
args = par.parse_args()
cmd_setup = cmd_setup.replace('dummy.pdb', args.p)
if args.change != None:
assert len(args.change) % 2 == 0
for i in range(0, len(args.change), 2):
cmd_setup.replace(args.change[i], args.change[i+1])
cmd_run = ['/home/grigoryanlab/library/bin/charmrun', '+p'+str(args.nc), '/home/grigoryanlab/library/bin/namd2', 'namdrun_run.ctl >& namdrun_run.out']
cmd_run = ' '.join(cmd_run)
odir = os.getcwd()
pepseq = args.pseq
pdz.normalMut('_start.pdb', range(pepstart, pepend+1), pepseq, 'start.pdb')
# clean up
os.system('rm -r _*')
os.chdir(odir)
# the fpd part
pepfrags = '/home/grigoryanlab/home/fzheng/PDZ.2014/pepfrags/'
fpddemo = '/home/grigoryanlab/home/fzheng/PDZ.2014/FlexPepDock_AbInitio/'
flag = fpddemo + 'input_files/flags'
pflag = fpddemo + 'input_files/prepack_flags'
rosetta_db = '/home/grigoryanlab/home/fzheng/rosetta2014/main/database'
rosetta_exe = '/home/grigoryanlab/home/fzheng/rosetta2014/main/source/bin'
ldir = General.createLocalSpace()
os.system('cp '+ mdir + '/start.pdb ' + ldir + '/start.pdb')
os.system('cp '+ mdir + '/start.pdb ' + ldir + '/native.pdb')
os.chdir(ldir)
if args.ab != 0: # not tested, now only work for natural aa
# make fragments
fragf = '/'.join([odir, args.pname, '.fragready'])
if args.ab == 2:
while os.path.isfile(fragf) == False:
sleep(10)
else:
os.system(fpddemo + 'scripts/prep_abinitio.sh 0000')
os.system('cp -dr frags '+pepfrags+args.pname)
os.system('touch '+fragf)
# copy stuff
cmd_confind = [CONFIND, '--p', pdbf, '--o', cmap_file, '--rLib', ROTLIB]
sub.call(cmd_confind)
else:
print 'Skip running Confind...'
# if using environment adjustment, need to have self contact degree and crowdness
if args.env:
env_file = changeExt(pdbf, 'env.db')
print 'Calculate environment for the query protein...'
envToShelve(cmap_file, env_file)
residues_env = shelve.open(env_file, 'r')
head = ['r1', 'ur1', 'r2', 'ur2']
# set up and create working directory paths
ldir = General.createLocalSpace('collin')
FRAGMENTS_OUT = ldir + '/' + base + '/fragments'
DESIGNSCORE_OUT = ldir + '/' + base + '/designscore'
ABUNDANCE_OUT = ldir + '/' + base + '/abundance'
for out in [FRAGMENTS_OUT, DESIGNSCORE_OUT, ABUNDANCE_OUT]:
if not os.path.isdir(out):
os.makedirs(out)
# read in PDB file
protein = parsePDB(pdbf).select('protein').copy()
residues = []
for res in protein.iterResidues():
residues.append(res)
resInTerm = {} # what residues are contained by the term of a residue?
# functions
