def run_me(self, inputs=None):
import os
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
# unique to run
runname = 'test_crysol'
dcdpath = './'
dcdfile = 'test_crysol.dcd'
pdbpath = './'
pdbfile = 'new_dsDNA60.pdb'
# system defaults
# cryexe='/share/apps/bin/crysol.exe'
cryexe = '/home/programs/sassie_bin/crysol.exe'
delafs = '1'
# my defaults
# maxh='5'
# fib='5'
maxh = '15'
fib = '18'
maxs = '0.199'
numpoints = '200'
# program defaults
option = '0'
contrast = '0.03'
edensolv = '0.334'
hydrogens = 'N'
# END USER EDIT
# END USER EDIT
# END USER EDIT
if inputs:
in_vars = inputs
else:
in_vars = parse()
if in_vars.dcdfile != None and in_vars.pdbfile != None:
print 'loading parameters from command line'
runname = in_vars.runname
dcdpath = in_vars.dcdpath
dcdfile = in_vars.dcdfile
pdbpath = in_vars.pdbpath
pdbfile = in_vars.pdbfile
maxh = in_vars.maxh
fib = in_vars.fib
maxs = in_vars.maxs
numpoints = in_vars.numpoints
else:
print 'using default parameters from driver script'
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['dcdpath'] = (dcdpath, 'string')
svariables['dcdfile'] = (dcdfile, 'string')
svariables['pdbpath'] = (pdbpath, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['cryexe'] = (cryexe, 'string')
svariables['delafs'] = (delafs, 'int')
svariables['option'] = (option, 'string')
svariables['maxh'] = (maxh, 'string')
svariables['fib'] = (fib, 'string')
svariables['maxs'] = (maxs, 'string')
svariables['numpoints'] = (numpoints, 'string')
svariables['contrast'] = (contrast, 'string')
svariables['edensolv'] = (edensolv, 'string')
svariables['hydrogens'] = (hydrogens, 'string')
error, self.variables = input_filter.type_check_and_convert(svariables)
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
if(len(error) > 0):
print 'error = ', error
sys.exit()
runname = self.variables['runname'][0]
import multiprocessing
# import sassie.tools.center as center
txtQueue = multiprocessing.JoinableQueue()
gcrysol.gcrysol(self.variables, txtQueue)
svariables['low_rg_cutoff'] = (low_rg_cutoff, 'float')
svariables['high_rg_cutoff'] = (high_rg_cutoff, 'float')
svariables['z_flag'] = (z_flag, 'boolean')
svariables['z_cutoff'] = (z_cutoff, 'float')
svariables['constraint_flag'] = (constraint_flag, 'boolean')
svariables['constraint_file'] = (constraint_file, 'string')
svariables['nonbondflag'] = (nonbondflag, 'int')
svariables['seed'] = (seed, 'int_array')
error, variables = input_filter.type_check_and_convert(svariables)
if len(error) > 0:
print 'error = ', error
sys.exit()
#import pprint; pprint.pprint(variables); exit()
txtQueue = multiprocessing.JoinableQueue()
simulation = monte_carlo.simulation()
simulation.main(variables, txtQueue)
this_text = txtQueue.get(True, timeout=0.1)
#print 'in GUI and txtOutput = ', this_text, '\n'
def run_me(self):
import os
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
runname = 'dsDNA60bps'
infile = './140904_094120_new_dsDNA60.dcd'
# this is the atom info file (for use with a dcd)
pdbfile = './new_dsDNA60.pdb'
outfile = 'dsDNA60_100s_min.dcd'
psffile = './new_dsDNA60.psf'
nsteps = '2000'
parmfile = '/usr/local/bin/toppar/par_all27_prot_na.inp'
ncpu = '4'
keepout = '1'
dcdfreq = '20'
# 'dcd' # need to change this to dcd if I input a dcd file
infiletype = infile[-3:]
md = '0'
mdsteps = '100'
dielect = '80.0'
temperature = '300.0'
# END USER EDIT
# END USER EDIT
# END USER EDIT
uname = os.popen("whoami").read()
if 'schowell\n' == uname:
ARGS = parse()
runname = ARGS.runname
infile = ARGS.infile
infiletype = ARGS.infile[-3:]
pdbfile = ARGS.pdbfile
outfile = ARGS.outfile
nsteps = ARGS.nsteps
parmfile = ARGS.parmfile
psffile = ARGS.psffile
ncpu = ARGS.ncpu
keepout = ARGS.keepout
dcdfreq = ARGS.dcdfreq
md = ARGS.md
mdsteps = ARGS.mdsteps
dielect = ARGS.dielect
temperature = ARGS.temperature
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['infile'] = (infile, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['outfile'] = (outfile, 'string')
svariables['nsteps'] = (nsteps, 'int')
svariables['parmfile'] = (parmfile, 'string')
svariables['psffile'] = (psffile, 'string')
svariables['ncpu'] = (ncpu, 'int')
#svariables['energyfile'] = (energyfile,'string')
svariables['keepout'] = (keepout, 'int')
svariables['dcdfreq'] = (dcdfreq, 'int')
svariables['infiletype'] = ('dcd', 'string')
svariables['md'] = (md, 'int')
svariables['mdsteps'] = (mdsteps, 'int')
svariables['dielect'] = (dielect, 'float')
svariables['temperature'] = (temperature, 'float')
error, variables = input_filter.type_check_and_convert(svariables)
if(len(error) != 0):
print 'error = ', error
sys.exit()
else:
error = minimize_filter.check_minimize(variables)
if(len(error) != 0):
print 'error = ', error
sys.exit()
runname = variables['runname'][0]
import multiprocessing
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
txtQueue = multiprocessing.JoinableQueue()
minimize.minimize(variables, txtQueue)
def run_me(self):
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
runname = 'run_0'
dcdfile = './data/generate/run_0.dcd'
pdbfile = './data/generate/min3.pdb'
nsegments = '1'
ofile = 'test'
xlength = '350.0'
gridsp = '6.0'
ylength = '350.0'
basis = 'calpha'
zlength = '350.0'
nregions = '5'
lowregions = '1, 124, 143, 355, 380'
highregions = '123, 142, 353, 379, 420'
equalweights = '1'
weightfile = './data/filter/x2lowweights.txt'
save_occupancy = 'N'
# END USER EDIT
# END USER EDIT
# END USER EDIT
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['nsegments'] = (nsegments, 'int')
svariables['dcdfile'] = (dcdfile, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['ofile'] = (ofile, 'string')
svariables['xlength'] = (xlength, 'float')
svariables['gridsp'] = (gridsp, 'float')
svariables['ylength'] = (ylength, 'float')
svariables['basis'] = (basis, 'string')
svariables['zlength'] = (zlength, 'float')
svariables['nregions'] = (nregions, 'int')
svariables['lowregions'] = (lowregions, 'int_array')
svariables['highregions'] = (highregions, 'int_array')
svariables['equalweights'] = (equalweights, 'int')
svariables['weightsfile'] = (weightfile, 'string')
svariables['save_occupancy'] = (save_occupancy, 'string')
error, self.variables = input_filter.type_check_and_convert(svariables)
if(len(error) > 0):
print 'error = ', error
sys.exit()
runname = self.variables['runname'][0]
import multiprocessing
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
txtQueue = multiprocessing.JoinableQueue()
segvariables = [
['5', '1,124,143,355,380', '123,142,353,379,420', 'CA', 'GAG']]
density.density(self.variables, segvariables, txtQueue)
def run_me(self):
import os
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
runname = 'dsDNA60bps'
infile = './140904_094120_new_dsDNA60.dcd'
# this is the atom info file (for use with a dcd)
pdbfile = './new_dsDNA60.pdb'
outfile = 'dsDNA60_100s_min.dcd'
psffile = './new_dsDNA60.psf'
nsteps = '2000'
parmfile = '/usr/local/bin/toppar/par_all27_prot_na.inp'
ncpu = '4'
keepout = '1'
dcdfreq = '20'
# 'dcd' # need to change this to dcd if I input a dcd file
infiletype = infile[-3:]
md = '0'
mdsteps = '100'
dielect = '80.0'
temperature = '300.0'
# END USER EDIT
# END USER EDIT
# END USER EDIT
uname = os.popen("whoami").read()
if 'schowell\n' == uname:
ARGS = parse()
runname = ARGS.runname
infile = ARGS.infile
infiletype = ARGS.infile[-3:]
pdbfile = ARGS.pdbfile
outfile = ARGS.outfile
nsteps = ARGS.nsteps
parmfile = ARGS.parmfile
psffile = ARGS.psffile
ncpu = ARGS.ncpu
keepout = ARGS.keepout
dcdfreq = ARGS.dcdfreq
md = ARGS.md
mdsteps = ARGS.mdsteps
dielect = ARGS.dielect
temperature = ARGS.temperature
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['infile'] = (infile, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['outfile'] = (outfile, 'string')
svariables['nsteps'] = (nsteps, 'int')
svariables['parmfile'] = (parmfile, 'string')
svariables['psffile'] = (psffile, 'string')
svariables['ncpu'] = (ncpu, 'int')
#svariables['energyfile'] = (energyfile,'string')
svariables['keepout'] = (keepout, 'int')
svariables['dcdfreq'] = (dcdfreq, 'int')
svariables['infiletype'] = ('dcd', 'string')
svariables['md'] = (md, 'int')
svariables['mdsteps'] = (mdsteps, 'int')
svariables['dielect'] = (dielect, 'float')
svariables['temperature'] = (temperature, 'float')
svariables['use_external_input_file'] = ('False','boolean')
svariables['external_input_file'] = ('','string')
svariables['velocity_restart_file'] = ('','string')
svariables['extended_system_restart_file'] = ('','string')
error, variables = input_filter.type_check_and_convert(svariables)
if(len(error) != 0):
print 'error = ', error
sys.exit()
else:
error = minimize_filter.check_minimize(variables)
if(len(error) != 0):
print 'error = ', error
sys.exit()
runname = variables['runname'][0]
import multiprocessing
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
txtQueue = multiprocessing.JoinableQueue()
minimize.minimize(variables, txtQueue)
def run_me(self, inputs=None):
import os
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
# unique to run
runname = 'test_crysol'
dcdpath = './'
dcdfile = 'test_crysol.dcd'
pdbpath = './'
pdbfile = 'new_dsDNA60.pdb'
# system defaults
# cryexe='/share/apps/bin/crysol.exe'
cryexe = '/home/programs/sassie_bin/crysol.exe'
delafs = '1'
# my defaults
# maxh='5'
# fib='5'
maxh = '15'
fib = '18'
maxs = '0.199'
numpoints = '200'
# program defaults
option = '0'
contrast = '0.03'
edensolv = '0.334'
hydrogens = 'N'
# END USER EDIT
# END USER EDIT
# END USER EDIT
if inputs:
in_vars = inputs
else:
in_vars = parse()
if in_vars.dcdfile != None and in_vars.pdbfile != None:
print 'loading parameters from command line'
runname = in_vars.runname
dcdpath = in_vars.dcdpath
dcdfile = in_vars.dcdfile
pdbpath = in_vars.pdbpath
pdbfile = in_vars.pdbfile
maxh = in_vars.maxh
fib = in_vars.fib
maxs = in_vars.maxs
numpoints = in_vars.numpoints
else:
print 'using default parameters from driver script'
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['dcdpath'] = (dcdpath, 'string')
svariables['dcdfile'] = (dcdfile, 'string')
svariables['pdbpath'] = (pdbpath, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['cryexe'] = (cryexe, 'string')
svariables['delafs'] = (delafs, 'int')
svariables['option'] = (option, 'string')
svariables['maxh'] = (maxh, 'string')
svariables['fib'] = (fib, 'string')
svariables['maxs'] = (maxs, 'string')
svariables['numpoints'] = (numpoints, 'string')
svariables['contrast'] = (contrast, 'string')
svariables['edensolv'] = (edensolv, 'string')
svariables['hydrogens'] = (hydrogens, 'string')
error, self.variables = input_filter.type_check_and_convert(svariables)
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
if (len(error) > 0):
print 'error = ', error
sys.exit()
runname = self.variables['runname'][0]
import multiprocessing
# import sassie.tools.center as center
txtQueue = multiprocessing.JoinableQueue()
gcrysol.gcrysol(self.variables, txtQueue)
def run_me(self):
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
runname = 'run_0'
dcdfile = './data/generate/run_0.dcd'
pdbfile = './data/generate/min3.pdb'
nsegments = '1'
ofile = 'test'
xlength = '350.0'
gridsp = '6.0'
ylength = '350.0'
basis = 'calpha'
zlength = '350.0'
nregions = '5'
lowregions = '1, 124, 143, 355, 380'
highregions = '123, 142, 353, 379, 420'
equalweights = '1'
weightfile = './data/filter/x2lowweights.txt'
save_occupancy = 'N'
# END USER EDIT
# END USER EDIT
# END USER EDIT
svariables = {}
svariables['runname'] = (runname, 'string')
svariables['nsegments'] = (nsegments, 'int')
svariables['dcdfile'] = (dcdfile, 'string')
svariables['pdbfile'] = (pdbfile, 'string')
svariables['ofile'] = (ofile, 'string')
svariables['xlength'] = (xlength, 'float')
svariables['gridsp'] = (gridsp, 'float')
svariables['ylength'] = (ylength, 'float')
svariables['basis'] = (basis, 'string')
svariables['zlength'] = (zlength, 'float')
svariables['nregions'] = (nregions, 'int')
svariables['lowregions'] = (lowregions, 'int_array')
svariables['highregions'] = (highregions, 'int_array')
svariables['equalweights'] = (equalweights, 'int')
svariables['weightsfile'] = (weightfile, 'string')
svariables['save_occupancy'] = (save_occupancy, 'string')
error, self.variables = input_filter.type_check_and_convert(svariables)
if (len(error) > 0):
print 'error = ', error
sys.exit()
runname = self.variables['runname'][0]
import multiprocessing
import shutil
import os
if os.path.exists(runname + '/' + self.module):
shutil.rmtree(runname + '/' + self.module)
txtQueue = multiprocessing.JoinableQueue()
segvariables = [[
'5', '1,124,143,355,380', '123,142,353,379,420', 'CA', 'GAG'
]]
density.density(self.variables, segvariables, txtQueue)
svariables['highrg'] = (highrg, 'float')
svariables['zflag'] = (zflag, 'int')
svariables['zcutoff'] = (zcutoff, 'float')
svariables['nonbondflag'] = (nbflag, 'int')
svariables['nonbondscale'] = (nbscale, 'float')
svariables['psffilepath'] = (psffilepath, 'string')
svariables['psffilename'] = (psffilename, 'string')
svariables['parmfilepath'] = (parmfilepath, 'string')
svariables['parmfilename'] = (parmfilename, 'string')
svariables['plotflag'] = (plotflag, 'int')
svariables['seed'] = (seed, 'int_array')
import sassie.simulate.monte_carlo.monomer.dihedral as dihedral
import sassie.interface.input_filter as input_filter
#import sassie.interface.generate_filter as generate_filt
error, variables = input_filter.type_check_and_convert(svariables)
#eflag=0 ; monflag=1
# error=generate_filter.check_protein(variables,eflag,monflag)
if(len(error) > 0):
print 'error = ', error
sys.exit()
runname = variables['runname'][0]
import multiprocessing
txtQueue = multiprocessing.JoinableQueue()
dihedralgenerate(variables, txtQueue)
def run_me(self, inputs=None):
import os
# BEGIN USER EDIT
# BEGIN USER EDIT
# BEGIN USER EDIT
# unique to run
runname = "test_crysol"
dcdpath = "./"
dcdfile = "test_crysol.dcd"
pdbpath = "./"
pdbfile = "new_dsDNA60.pdb"
# system defaults
# cryexe='/share/apps/bin/crysol.exe'
cryexe = "/home/programs/sassie_bin/crysol.exe"
delafs = "1"
# my defaults
# maxh='5'
# fib='5'
maxh = "15"
fib = "18"
maxs = "0.199"
numpoints = "200"
# program defaults
option = "0"
contrast = "0.03"
edensolv = "0.334"
hydrogens = "N"
# END USER EDIT
# END USER EDIT
# END USER EDIT
try:
in_vars = inputs
except:
in_vars = parse()
if in_vars.dcdfile != None and in_vars.pdbfile != None:
print "loading parameters from command line"
runname = in_vars.runname
dcdpath = in_vars.dcdpath
dcdfile = in_vars.dcdfile
pdbpath = in_vars.pdbpath
pdbfile = in_vars.pdbfile
maxh = in_vars.maxh
fib = in_vars.fib
maxs = in_vars.maxs
numpoints = in_vars.numpoints
else:
print "using default parameters from driver script"
svariables = {}
svariables["runname"] = (runname, "string")
svariables["dcdpath"] = (dcdpath, "string")
svariables["dcdfile"] = (dcdfile, "string")
svariables["pdbpath"] = (pdbpath, "string")
svariables["pdbfile"] = (pdbfile, "string")
svariables["cryexe"] = (cryexe, "string")
svariables["delafs"] = (delafs, "int")
svariables["option"] = (option, "string")
svariables["maxh"] = (maxh, "string")
svariables["fib"] = (fib, "string")
svariables["maxs"] = (maxs, "string")
svariables["numpoints"] = (numpoints, "string")
svariables["contrast"] = (contrast, "string")
svariables["edensolv"] = (edensolv, "string")
svariables["hydrogens"] = (hydrogens, "string")
error, self.variables = input_filter.type_check_and_convert(svariables)
import shutil
import os
if os.path.exists(runname + "/" + self.module):
shutil.rmtree(runname + "/" + self.module)
if len(error) > 0:
print "error = ", error
sys.exit()
runname = self.variables["runname"][0]
import multiprocessing
# import sassie.tools.center as center
txtQueue = multiprocessing.JoinableQueue()
gcrysol.gcrysol(self.variables, txtQueue)
