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")
from pygmin.storage.database import Database
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("-d",
dest="write_distances", action="store_true",
help="dump distances to screen")
(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.write_distances):
print "List of distances:"
print "--------------------------"
for d in db.distances():
print "%d\t<->\t%d\tid %d\tdistance %f"%\
(d._minimum1_id, d._minimum2_id, d._id, d.dist)
print "END\n"
if(options.writeDPS):
writeDPS(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("--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("--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()
