def attach(self, object, attachname, desc=''):
"""
Attach an object to this replica. This will create a pickle of the object
with a temporary filename and store the pickle file name with a *name* and *description*
in current replica attribute :attr:`Replica.attached` dictionary.
:arg any object: Object to pickle and link to the replica
:arg str attachname: Name to assign to the attachment
:arg str desc: Description. Optional.
"""
# Go to replica folder if not there
T.BROWSER.gotoReplica(self)
# If attachname present, remove it first
if self.attached.has_key(attachname): self.dettach(attachname)
# Obtain temp name, save pickle and store info in self.attached
attachfile = fname = os.path.basename(
tempfile.mktemp(prefix=self.name + '_%s_' % attachname))
T.dump(object, attachfile)
self.attached[attachname] = {'file': attachfile, 'desc': desc}
if self.__folderscreated: self.write()
# Goback to previous folder
T.BROWSER.goback()
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser(self.finp,
self.fref,
box=True,
rnAmber=True,
log=self.log,
verbose=self.local)
self.t = self.p.crd2traj()
self.t.removeAtoms(
lambda a: a['residue_name'] in ['WAT', 'Na+', 'Cl-'])
self.t.removeAtoms(lambda a: a['element'] == 'H')
if self.local:
print "Dumping result to ", self.fout
T.dump(self.t, T.absfile(self.fout))
if self.local:
print "Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() )
self.assertEqual(len(self.t), 10)
self.assertEqual(self.t.lenAtoms(), 440)
def write(self):
"Save object __dict__ to pickled file."
self.log.debug("Writing pickle")
with FileLock(self.replFilePath) as lock:
d = self.__dict__.copy()
del d['log']
del d['grids']
T.dump(d, self.replFilePath)
def write(self):
"Save object __dict__ to pickled file."
with FileLock(self.projFilePath) as lock:
d = self.__dict__.copy()
del d['log']
d['systems'] = {} # Empty systems and replicas
d['replicas'] = {}
T.dump(d, self.projFilePath)
def write(self, outfile=None):
"Save object __dict__ to pickled file."
outfile = outfile or self.sysFilePath
with FileLock(outfile) as lock:
d = self.__dict__.copy()
d['create'] = None #Dont pickle Amber class if loaded
# del d['log']
T.dump(d, outfile)
self.sysFilePath = osp.abspath(outfile)
self.__sysfile = True
def saveSolvent(self, solvent, db=None, createEmpty=False):
"""
Save a Solvent isntance in the database :attr:`db` or default DB locations.
Selection of database is done in :meth:`self.__getDatabase`.
:arg solvent: Solvent object to save.
:type solvent: :class:`Solvent`
:arg str db: Database where to save the solvent.
If None, default ones will be used (package DB if
the user can write there, or user DB otherwise).
:arg bool createEmpty: If new database, create empty.
If False, copy data from package DB to the new DB.
"""
db = self.__getDatabase(db, createEmpty)
solvLib = T.load(db)
solvLib[solvent.name] = solvent
T.dump(solvLib, db)
self.log.info("Solvent %s saved to database %s" % (solvent.name, db))
def __getDatabase(self, db=None, createEmpty=False):
"""
Select and return database (which is actually a dictionary type) for which the user has writing permisions.
By default, the package database will be used but if the user cannot write there,
a new database will be created under the users home directory: $HOME/.mdmix/SOLVENTS.db
which will also contain all solvents from the package db.
:arg None|str db: If *db* != None:
- Check if this DB filename is writtable and return full path. Create it otherwise.
If None:
- Check if user has writing permisions in package DB and return the path.
- If not, create a user-spacific database and return the path.
:arg bool createEmpty: If the database has to be created, ignore solvents from the package DB.
Will create an empty DB.
:return: Path to a db for which the user should have writting permisions.
:type: string
"""
import shutil
# Try to use specified db
if db:
if osp.exists(db) and T.filePermission(db)['WRITE']:
return T.absfile(db)
else:
if createEmpty: T.dump({}, db)
else: shutil.copy(S.SOLVENTDB, db)
return T.absfile(db)
else:
# USE USER DATABASE IF IT EXISTS
if osp.exists(S.USER_SOLVENT_DB):
return T.absfile(S.USER_SOLVENT_DB)
else:
db = S.SOLVENTDB
# Create USER DB from package if user cannot write to package directory
if not T.filePermission(db)['WRITE']:
# User cannot write to package DB so create a custom one
if createEmpty: T.dump({}, S.USER_SOLVENT_DB)
else:
shutil.copy(db, S.USER_SOLVENT_DB
) # Make a copy to user's home mdmix folder
db = S.USER_SOLVENT_DB
return T.absfile(db)
def removeSolvent(self, solvName, db=None):
"""
Remove solvent from database
Same as saveSolvent, :attr:`db` will be chosen automatically if None.
:arg str solvName: Solvent name.
:arg str db: Database path. If None, automatically detect.
:raises SolventManagerError: if *db* does not contain *solvName*.
"""
solvents = self.listSolvents(db)
if solvName in solvents:
solvLib.pop(solvName)
T.dump(solvLib, db)
self.log.info("Removed solvent %s from database %s" %
(solvName, db))
return True
else:
raise SolventManagerError, "DB %s does not contain solvent name %s" % (
db, solvName)
def tracking_request(string_from, string_to, DEBUG_MODE=False):
gmaps = googlemaps.Client(key='API-ID-googlemaps')
tools.dprint("from:"+string_from+" to:"+string_to, DEBUG_MODE)
# Putting them into the calculator
now = datetime.now()
directions_result = gmaps.directions(string_from, string_to, mode="driving", departure_time=now)
# dump
tools.dump(directions_result, DEBUG_MODE)
duration = directions_result[0]["legs"][0]["duration_in_traffic"]["text"]
eta = directions_result[0]["legs"][0]["duration_in_traffic"]["value"]
# debug trace
tools.dprint(eta, DEBUG_MODE)
# Outputting the result
return (duration, eta)
def test_AmberCrdParser(self):
"""AmberCrdParser test"""
self.p = AmberCrdParser( self.finp, self.fref, box=True, rnAmber=True,
log=self.log, verbose=self.local )
self.t = self.p.crd2traj()
self.t.removeAtoms(lambda a: a['residue_name'] in ['WAT','Na+','Cl-'] )
self.t.removeAtoms(lambda a: a['element'] == 'H' )
if self.local:
print "Dumping result to ", self.fout
T.dump( self.t, T.absfile(self.fout) )
if self.local:
print "Dumped Trajectory with %i frames and %i atoms." % \
(len(self.t), self.t.lenAtoms() )
self.assertEqual( len(self.t), 10 )
self.assertEqual( self.t.lenAtoms(), 440 )
import GNUScreen as sc
from ScreenSaver import ScreenSaver
import tools
if __name__=='__main__':
session=sys.argv[1]
showpid=sys.argv[2]
reverse=sys.argv[3]
sort=sys.argv[4]
try:
groupids=sys.argv[5:]
except:
groupids=[]
if showpid=='0':
showpid=False
else:
showpid=True
if reverse=='0':
reverse=True
else:
reverse=False
if sort=='0':
sort=False
else:
sort=True
ss=ScreenSaver(session)
tools.dump(ss,showpid,reverse,sort,groupids)
def dump(self, file):
"Write pickle to file *file*"
T.dump(self, file)
import sys
import GNUScreen as sc
from ScreenSaver import ScreenSaver
import tools
import util
if __name__ == '__main__':
session = (sys.argv)[1]
showpid = (sys.argv)[2]
reverse = (sys.argv)[3]
sort = (sys.argv)[4]
windows = util.expand_numbers_list((sys.argv)[5:])
if showpid == '0':
showpid = False
else:
showpid = True
if reverse == '0':
reverse = True
else:
reverse = False
if sort == '0':
sort = False
else:
sort = True
ss = ScreenSaver(session)
tools.dump(ss, tools.require_dumpscreen_window(session, True), showpid,
reverse, sort, windows)
tools.cleanup()
import sys
import GNUScreen as sc
from ScreenSaver import ScreenSaver
import tools
import util
if __name__ == '__main__':
session = (sys.argv)[1]
showpid = (sys.argv)[2]
reverse = (sys.argv)[3]
sort = (sys.argv)[4]
windows = util.expand_numbers_list((sys.argv)[5:])
if showpid == '0':
showpid = False
else:
showpid = True
if reverse == '0':
reverse = True
else:
reverse = False
if sort == '0':
sort = False
else:
sort = True
ss = ScreenSaver(session)
tools.dump(ss, tools.require_dumpscreen_window(session, True),
showpid, reverse, sort, windows)
tools.cleanup()