def readfromtxt(mol, txt):
# print('!!!!', filename)
globs = globalvars()
en_dict = globs.endict()
mol.graph = []
for line in txt:
line_split = line.split()
if len(line_split) == 4 and line_split[0]:
# this looks for unique atom IDs in files
lm = re.search(r'\d+$', line_split[0])
# if the string ends in digits m will be a Match object, or None otherwise.
if lm is not None:
symb = re.sub('\d+', '', line_split[0])
# number = lm.group()
# # print('sym and number ' +str(symb) + ' ' + str(number))
# globs = globalvars()
atom = atom3D(symb, [float(line_split[1]), float(line_split[2]), float(line_split[3])],
name=line_split[0])
elif line_split[0] in en_dict.keys():
atom = atom3D(line_split[0], [float(line_split[1]), float(line_split[2]), float(line_split[3])])
else:
print('cannot find atom type')
sys.exit()
mol.addAtom(atom)
return mol
def readfromtxt(mol, txt):
# print('!!!!', filename)
globs = globalvars()
en_dict = globs.endict()
mol.graph = []
for line in txt:
line_split = line.split()
if len(line_split) == 4 and line_split[0]:
# this looks for unique atom IDs in files
lm = re.search(r'\d+$', line_split[0])
# if the string ends in digits m will be a Match object, or None otherwise.
if lm is not None:
symb = re.sub('\d+', '', line_split[0])
# number = lm.group()
# # print('sym and number ' +str(symb) + ' ' + str(number))
# globs = globalvars()
atom = atom3D(symb, [
float(line_split[1]),
float(line_split[2]),
float(line_split[3])
],
name=line_split[0])
elif line_split[0] in list(en_dict.keys()):
atom = atom3D(line_split[0], [
float(line_split[1]),
float(line_split[2]),
float(line_split[3])
])
else:
print('cannot find atom type')
sys.exit()
mol.addAtom(atom)
return mol
def pad_mol(mol,target_atoms):
## adds placeholder atoms
## with zero nuclear charge
## located at the origin
## in order to get consistent size
## coulomb matrix
this_natoms = mol.natoms
blank_atom = atom3D(Sym='X') # placeholder type
blank_atom.frozen=False
safe_stop = False
counter = 0;
while this_natoms < target_atoms and not safe_stop:
mol.addAtom(blank_atom)
this_natoms = mol.natoms
counter +=1
if counter > target_atoms:
safe_stop = True
print('error padding mol')
return mol
def pad_mol(mol, target_atoms):
## adds placeholder atoms
## with zero nuclear charge
## located at the origin
## in order to get consistent size
## coulomb matrix
this_natoms = mol.natoms
blank_atom = atom3D(Sym='X') # placeholder type
blank_atom.frozen = False
safe_stop = False
counter = 0
while this_natoms < target_atoms and not safe_stop:
mol.addAtom(blank_atom)
this_natoms = mol.natoms
counter += 1
if counter > target_atoms:
safe_stop = True
print('error padding mol')
return mol