def __init__(self,
infile,
finalOutputDir=None,
finalOutputName=None,
workdir=None,
verbose=True):
"""Initialize the class
REQUIRED INPUTS
infile the stating *.pdb, *.gro, etc. file to initialize the system
OPTIONAL INPUTS
finalOutputDir directory to save final *.trp, *.gro files for an MD simulation. Defaults to './out'
finalOutputName basename (*) to name the final *.trp, *.gro files for an MD simulation. Defaults to 'out'
workdir directory to perform gmx preprocessing. If not specified, work
will be done in a unique temporary directory.
"""
self.verbose = verbose
# finalOutDir
# the name of the directory to write the final prepared gmx files
if finalOutputDir == None:
self.finalOutputDir = os.path.abspath(
os.path.join(os.curdir, 'out'))
else:
self.finalOutputDir = os.path.abspath(finalOutputDir)
# finalOutDir
# the root name of the files written in the final prepared gmx files
if finalOutputName == None:
self.finalOutputName = 'out'
else:
self.finalOutputName = finalOutputName
# workdir
# The working directory for the simulation preparation
if workdir == None:
self.workdir = tempfile.mkdtemp()
else:
self.workdir = workdir
# files
# An object for keeping track of a series of filenames
self.files = PrepFilenames(infile, self.workdir)
# status
self.status = PrepStatus()
self.checkForFatalErrors = True # these will be set by the prepare method
self.mockrun = False
# A set of paths to look in for mdpfiles
self.mdpPaths = []
self.mdpPaths.append(
os.path.join(os.environ['MMTOOLSPATH'],
'gromacstools/devel/SimulationPreparation/mdp'))
#####################################
# Start Building the GROMACS project
print "GROMACS files %s.tpr and %s.gro, etc. will be written to directory %s..." % (
self.finalOutputName, self.finalOutputName, self.finalOutputDir)
print "Building GROMACS project in temporary directory %s..." % self.workdir
output = commands.getoutput(
'cp %s %s' %
(self.files.infile,
os.path.join(self.workdir, self.files.infile_basename)))
print output
# show a listing of all the current gmx files
if (self.verbose):
self.files.show()
