def get_cmd_run_initial(self, target):
"""
Create a compute unit description to be run
Parameters
----------
target : str
location of the created target trajectory
Returns
-------
"""
cmd = self.cluster.link(self.conf_file_link)
cmd += self.cluster.link(self.pdb_file_link)
cmd += BashCommand(
'acemd',
[
self.conf_file
])
cmd += self.cluster.move('output.xtc', target)
return cmd
def link(self, source, target=None, stage=None):
st = get_type(source)
tt = get_type(target)
if target is None:
target = ''
if os.path.basename(target) == '':
target = target + os.path.basename(source)
if st in ['shared'] and tt in ['unit']:
source = source.replace('shared://', self.path_to_shared)
target = target.replace('shared://', self.path_to_shared)
return BashCommand('ln', ['-l', source, target])
elif st in ['staging'] and tt in ['unit']:
stage = stage or rp.STAGING_INPUT
return StagingCommand(
{
'source': source,
'target': target,
'action': rp.LINK
}, stage)
else:
raise NotImplementedError(
'linking from `%s` to `%s` is not implemented yet.' % (st, tt))
def makedir(self, source):
st = get_type(source)
if st in ['shared', 'unit']:
source = source.replace('shared://', self.path_to_shared)
return BashCommand('mkdir', [source])
else:
raise NotImplementedError(
'makedir in `%s` is not implemented yet.' % st)
def remove(self, source):
st = get_type(source)
if st in ['shared', 'unit']:
source = source.replace('shared://', self.path_to_shared)
return BashCommand('rm', [source])
else:
raise NotImplementedError(
'deleting from `%s` is not implemented yet.' % st)
def get_cmd_trajectory_frame(self, source, frame, target):
"""
Create a command that runs from a fram in a trajectory
Parameters
----------
source : str
location of the input trajectory, usually starts with `shared://`
and lists the location on the shared space
frame : int
the integer index starting from 0 in the input trajectory
target : str
location of the target trajectory, usually starts with `shared://`
Returns
-------
Command
"""
# todo: add the extraction of a single frame using a little python tool
# question: how to run multiple commands with MPU
cmd = self.cluster.link(self.conf_file_link)
cmd += self.cluster.link(self.pdb_file_link)
cmd += self.cluster.link(source, 'input.xtc')
# might use mdconvert from mdtraj for now
cmd += BashCommand(
'mdconvert',
[
'-o', 'initial.pdb',
'-i', '%d' % frame,
'input.xtc',
self.pdb_file,
])
cmd += BashCommand(
'acemd',
[
self.conf_file
])
cmd += self.cluster.move('output.xtc', target)
return cmd
def mv(self, source, target=None):
st = get_type(source)
tt = get_type(target)
if target is None:
target = ''
if os.path.basename(target) == '':
target = target + os.path.basename(source)
if st in ['shared', 'unit'] and tt in ['shared', 'unit']:
source = source.replace('shared://', self.path_to_shared)
target = target.replace('shared://', self.path_to_shared)
return BashCommand('cp', [source, target])
else:
raise NotImplementedError(
'moving from `%s` to `%s` is not implemented yet.' % (st, tt))
def get_cmd_pdb(self, pdb_file):
"""
Create a compute unit description to be run
Parameters
----------
Returns
-------
"""
cmd = self.cluster.link(self.conf_file)
cmd += self.cluster.copy(pdb_file)
cmd += BashCommand(
'acemd',
[
self.conf_file
])
return cmd