def saveelts( part, filename):
env.history.message( "save main part element symbols -- no, atomic numbers -- to file: " + filename )
def doit():
atoms = atom_array_of_part(part)
## elts = [atm.element.symbol for atm in atoms]
elts = [atm.element.eltnum for atm in atoms]
env.history.message( "%d element nums, first few are %r" % (len(elts), elts[:5] ) )
thing = array(elts)
save_obj(thing, filename)
call_func_with_timing_histmsg( doit)
return
def savebtypes( part, filename):
env.history.message( "save main part bond type v6 ints to file: " + filename )
def doit():
atoms = atom_array_of_part(part)
res = []
for atm in atoms:
for b in atm.bonds:
# don't worry for now about hitting each bond twice... well, do, and see if this makes it slower, as i guess.
if b.atom1 is atm:
res.append(b.v6) # a small int
env.history.message( "%d btype ints, first few are %r" % (len(res), res[:5] ) )
thing = array(res, UnsignedInt8) # tell it to use a smaller type; see numpy.pdf page 14 on typecodes.
# update, bruce 070612: we still use Numeric Python (not numarray or numpy). I am not sure what URL
# is referred to by "numpy.pdf" above, but it is probably (and should be) about Numeric Python.
save_obj(thing, filename)
call_func_with_timing_histmsg( doit)
return
def count_bonds_cmd( target):
win = target.topLevelWidget()
assy = win.assy
part = assy.tree.part
mols = part.molecules
env.history.message( "count bonds (twice each) in %d mols:" % len(mols) )
def doit():
return nbonds(mols)
nb = call_func_with_timing_histmsg( doit)
env.history.message("count was %d, half that is %d" % (nb, nb/2) )
return
def count_bonds_cmd( target):
win = target.topLevelWidget()
assy = win.assy
part = assy.tree.part
mols = part.molecules
env.history.message( "count bonds (twice each) in %d mols:" % len(mols) )
def doit():
return nbonds(mols)
nb = call_func_with_timing_histmsg( doit)
env.history.message("count was %d, half that is %d" % (nb, nb/2) )
return
def blerg_cmd( target):
win = target.topLevelWidget()
assy = win.assy
part = assy.tree.part
mols = part.molecules
env.history.message( "blorg in %d mols:" % len(mols) )
def doit():
return blerg(mols)
na, nb = call_func_with_timing_histmsg( doit)
env.history.message("count was %d, %d" % (na,nb,) )
return
def loadposns( part, filename): # doesn't move atoms (just a file-reading speed test, for now)
env.history.message( "load atom posns from file (discards them, doesn't move atoms): " + filename )
def doit():
return load_obj(filename)
posns = call_func_with_timing_histmsg( doit)
return
def saveposns(part, filename):
env.history.message( "save main part atom posns to file: " + filename )
def doit():
save_atpos_list(part, filename)
call_func_with_timing_histmsg( doit)
