def create_top(o, struct, posres):
print("attempting to auto-generate a topology...")
top = md.topology(struct=struct, protein="protein", posres=posres, dirname=o)
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'posres': 'protein_posres.itp',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
print("succesfully auto-generated topology")
print('pwd', os.getcwd())
print('top', top)
"""
def create_top(o, struct, posres):
print("attempting to auto-generate a topology...")
top = md.topology(struct=struct,
protein="protein",
posres=posres,
dirname=o)
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'posres': 'protein_posres.itp',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
print("succesfully auto-generated topology")
print('pwd', os.getcwd())
print('top', top)
"""
# try to create an integrator
attr(INTEGRATOR, str, integrator)
attr(INTEGRATOR_ARGS, list, integrator_args)
try:
integrator_type = util.get_class(conf[INTEGRATOR])
integrator_type(None, *conf[INTEGRATOR_ARGS])
print("succesfully created integrator {}".format(integrator))
except Exception, e:
print("error creating integrator {}".format(integrator))
raise e
# make a top if we don't have one
if top is None:
print("attempting to auto-generate a topology...")
with md.topology(struct=struct, protein="protein") as top:
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
print("succesfully auto-generated topology")
print('pwd', os.getcwd())
print('top', top)
filedata_fromfile(TOPOL_TOP, top["top"])
filedata_fromfile(STRUCT_PDB, top["struct"])
include_dirs = [os.path.abspath(top.dirname)]
read_includes(top["top"])
# try to create an integrator
attr(INTEGRATOR, str, integrator)
attr(INTEGRATOR_ARGS, list, integrator_args)
try:
integrator_type = util.get_class(conf[INTEGRATOR])
integrator_type(None, *conf[INTEGRATOR_ARGS])
print("succesfully created integrator {}".format(integrator))
except Exception, e:
print("error creating integrator {}".format(integrator))
raise e
# make a top if we don't have one
if top is None:
print("attempting to auto-generate a topology...")
with md.topology(struct=struct, protein="protein") as top:
# topology returns:
# {'top': '/home/andy/tmp/Au/top/system.top',
# 'dirname': 'top',
# 'struct': '/home/andy/tmp/Au/top/protein.pdb'}
print("succesfully auto-generated topology")
print('pwd', os.getcwd())
print('top', top)
filedata_fromfile(TOPOL_TOP, top["top"])
filedata_fromfile(STRUCT_PDB, top["struct"])
include_dirs = [os.path.abspath(top.dirname)]
read_includes(top["top"])
