def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-disconnect",
dest="writeDPS", action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.writeDPS:
writeDPS(db)
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.write_pathsample:
write_pathsample_db(db)
def main():
# add some program options
parser = OptionParser(usage = "usage: %prog [options] storage")
parser.add_option("--write-disconnect",
dest="writeDPS", action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_option("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_option("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_option("--cif",
dest="writeCIF", action="store_true",
help="export cif files")
parser.add_option("--cif-dir",
dest="cifDir", default=".", action="store",type="string",
help="directory to write cifs to")
(options, args) = parser.parse_args()
# print help if no input file is given
if(len(args) != 1):
parser.print_help()
exit(-1)
db = Database(db=args[0])
if(options.writeMinima):
print "List of minima:"
print "---------------"
for m in db.minima():
print "%f\t\tid %d"%(m.energy, m._id)
print "END\n"
if(options.writeTS):
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if(options.writeDPS):
writeDPS(db)
if(options.writeCIF):
GMIN.initialize()
i=0
for m in db.minima():
i+=1
filename = options.cifDir+"/lowest%03d.cif"%(i)
print "minimum",i, "energy",m.energy,"to",filename
GMIN.writeCIF(filename, m.coords, "E"+str(m.energy))
def main():
# add some program options
parser = OptionParser(usage="usage: %prog [options] storage")
parser.add_option(
"--write-disconnect",
dest="writeDPS",
action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_option("-m",
dest="writeMinima",
action="store_true",
help="dump minima to screen")
parser.add_option("-t",
dest="writeTS",
action="store_true",
help="dump transition states to screen")
parser.add_option("--coords",
dest="writeCoords",
action="store_true",
help="export coordinates files")
parser.add_option("--xyz",
dest="writeXYZ",
action="store_true",
help="export xyz files")
(options, args) = parser.parse_args()
# print help if no input file is given
if (len(args) != 1):
parser.print_help()
exit(-1)
db = Database(db=args[0])
if (options.writeMinima):
print "List of minima:"
print "---------------"
for m in db.minima():
print "%f\t\tid %d" % (m.energy, m._id)
print "END\n"
if (options.writeTS):
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if (options.writeDPS):
writeDPS(db)
if (options.writeCoords):
GMIN.initialize()
i = 0
for m in db.minima():
i += 1
filename = "lowest/lowest%03d.cif" % (i)
print "minimum", i, "energy", m.energy, "to", filename
GMIN.userpot_dump(filename, m.coords)
if (not TO_PDB is None):
os.system(TO_PDB % filename)
np.savetxt("lowest/coords_%03d.txt" % (i), m.coords)
if (options.writeXYZ):
traj = open("lowest/traj.xyz", "w")
i = 0
for m in db.minima():
i += 1
filename = "lowest/lowest%03d.xyz" % (i)
print "minimum", i, "energy", m.energy, "to", filename
export_xyz(open(filename, "w"), m.coords)
export_xyz(traj, m.coords)
traj.close()
def main():
# add some program options
parser = OptionParser(usage = "usage: %prog [options] storage")
parser.add_option("--write-disconnect",
dest="writeDPS", action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_option("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_option("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_option("--coords",
dest="writeCoords", action="store_true",
help="export coordinates files")
parser.add_option("--xyz",
dest="writeXYZ", action="store_true",
help="export xyz files")
(options, args) = parser.parse_args()
# print help if no input file is given
if(len(args) != 1):
parser.print_help()
exit(-1)
db = Database(db=args[0])
if(options.writeMinima):
print "List of minima:"
print "---------------"
for m in db.minima():
print "%f\t\tid %d"%(m.energy, m._id)
print "END\n"
if(options.writeTS):
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f"%\
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if(options.writeDPS):
writeDPS(db)
if(options.writeCoords):
GMIN.initialize()
i=0
for m in db.minima():
i+=1
filename = "lowest/lowest%03d.cif"%(i)
print "minimum",i, "energy",m.energy,"to",filename
GMIN.userpot_dump(filename, m.coords)
if(not TO_PDB is None):
os.system(TO_PDB%filename)
np.savetxt("lowest/coords_%03d.txt"%(i), m.coords)
if(options.writeXYZ):
traj=open("lowest/traj.xyz", "w")
i=0
for m in db.minima():
i+=1
filename = "lowest/lowest%03d.xyz"%(i)
print "minimum",i, "energy",m.energy,"to",filename
export_xyz(open(filename, "w"), m.coords)
export_xyz(traj, m.coords)
traj.close()
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("--write-dummy-db",
dest="write_pathsample_dummy", action="store_true",
help="generate a pathsample database without the points files - min.data and ts.data only")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("--minimum", type=int, default=0, help="print the coordinates of a particular minimum to the screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
parser.add_argument("-l",
dest="long_output", action="store_true",
help="Allow long output to be printed")
args = parser.parse_args()
if args.summary_long:
args.summary = True
suppress = not args.long_output
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db,suppress_long=suppress)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.minimum > 0:
m = db.getMinimum(args.minimum)
print m.energy, m._id
x = m.coords.reshape(-1,3)
print x
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.write_pathsample:
write_pathsample_db(db)
elif args.write_pathsample_dummy:
write_pathsample_db(db, False)