def do_workflow_parse(arguments, help_text, md_time="", cphmd_barrier=""):
"""
Args:
arguments:
help_text:
md_time:
cphmd_barrier:
"""
output_folder = "undefined"
comand_line_options = {}
try:
try:
for i, x in enumerate(arguments):
if (x == "-o" and len(arguments) > i + 1
and not str(arguments[i + 1]).startswith("-")):
output_folder = arguments[i + 1]
elif (str(x).startswith("-") and len(arguments) > i + 1
and not str(arguments[i + 1]).startswith("-")):
if (x.replace("-", "") in comand_line_options):
raise Exception("command_line option is given twice")
else:
comand_line_options.update(
{x.replace("-", ""): arguments[i + 1]})
elif ("-f" in arguments):
comand_line_options.update({"Ff": ""}) # flages
except Exception as err:
print(bash.increment_error_level("IO-Problem", err))
except Exception as err:
print(bash.increment_error_level("IO-Problem", err))
print("\n\n\n" + help_text)
exit()
return output_folder, comand_line_options
def md(self,
workdir,
gro_file,
top_file,
ndx_file,
in_protocol,
out_prefix=False,
restriction_gro=False,
gromacs_run="gmx mdrun",
gromacs_grompp="gmx grompp"):
"""This starts an initial run for a simulation "step". very crude and
easy ;) :param workdir: absolute path to folder with step prefix as last
part ("absolutePath/prefix") :param gromacs_run: contains the string,
executing the gromacs command: "gmx mdrun" "gmx_mpi mdrun" ... :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
gro_file:
top_file:
ndx_file:
in_protocol:
out_prefix:
restriction_gro:
gromacs_run:
gromacs_grompp:
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(in_protocol))[0] # prefix of the step
if (not restriction_gro):
restriction_gro = gro_file
output = workdir + "/" + step_name
# Formulate commands
grompp_command = gromacs_grompp + " -f " + output + ".mdp -c " + gro_file + " -p " + top_file + " -n " + ndx_file + " -r " + restriction_gro + " -o " + output + ".tpr 1> " + output + "_grompp.log 2>" + output + "_grompp.err\n"
mdrun_command = gromacs_run + " -s " + output + ".tpr -deffnm " + output + " 1> " + output + "_mdrun.log 2>" + output + "_mdrun.err\n"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
bash.copy_file(in_protocol, output + ".mdp")
print("\tgrompp command: " + step_name)
bash.execute("cd " + workdir + "\n" + grompp_command)
print("\trun_sim: " + step_name)
bash.execute("cd " + workdir + "\n" + mdrun_command)
except Exception as err:
raise bash.increment_error_level("simple sim failed!\n", err)
return output
def grompp(self,
workdir,
gro_file,
top_file,
ndx_file,
in_protocol,
gromacs_grompp="grompp_mpi",
out_prefix=False):
"""This starts grompp to build a tpr file. :param workdir: absolute path
to folder with step prefix as last part ("absolutePath/prefix") :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
gro_file:
top_file:
ndx_file:
in_protocol:
gromacs_grompp:
out_prefix:
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(in_protocol))[0] # prefix of the step
output = workdir + "/" + step_name
# Formulate commands
grompp_command = gromacs_grompp + " -f " + output + ".mdp -c " + gro_file + " -p " + top_file + " -n " + ndx_file + " -o " + output + ".tpr 1> " + output + "_grompp.log 2>" + output + "_grompp.err\n"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
bash.copy_file(in_protocol, output + ".mdp")
print("\tgrompp command: " + step_name)
bash.execute("cd " + workdir + "\n" + grompp_command)
except Exception as err:
raise bash.increment_error_level("grompp failed!\n", err)
return output
def mdrun(self,
workdir,
tpr_file,
out_prefix=False,
gromacs="gmx ",
additional_options: str = " "):
"""This starts an initial run for a simulation "step". very crude and
easy ;) :param workdir: absolute path to folder with step prefix as last
part ("absolutePath/prefix") :param gromacs_run: contains the string,
executing the gromacs command: "gmx mdrun" "gmx_mpi mdrun" ... :param
gro_file:absolute path to .gro file input (build input or previous
simulation step) :param top_file: absolute path to .top file input
(build input folder) :param ndx_file: absolute path to .ndx file input
(build input folder) :return: stepcounter (updates the gro_file for next
step)
Args:
workdir:
tpr_file:
out_prefix:
gromacs:
additional_options (str):
"""
if (out_prefix):
step_name = out_prefix
else:
step_name = os.path.splitext(
os.path.basename(tpr_file))[0] # prefix of the step
output = workdir + "/" + step_name
# Formulate commands
mdrun_command = gromacs + " mdrun -s " + tpr_file + " -deffnm " + output + " " + additional_options + " 1> " + output + "_mdrun.log 2>" + output + "_mdrun.err"
try:
# execute commands:
print("\tCopy_protocol: " + step_name)
if (not os.path.exists(output + ".tpr")):
bash.copy_file(tpr_file, output + ".tpr")
print("\trun_sim: " + step_name)
bash.execute("cd " + workdir + " && " + mdrun_command)
except Exception as err:
raise bash.increment_error_level("mdrun failed!\n", err)
return output