def __init__(self, data) :
"""
data -- contents of an .xyz file as a str
"""
data = data.split('\n')
self.natom = int(data[0])
self.units = data[1]
self.labels = []
self.masses = []
self.charges = []
self.geom = []
for atom in data[2:] :
atom = atom.split()
if len(atom) != 4 :
continue # Throw Error?
self.labels.append(atom[0])
self.masses.append(m.get_mass(atom[0]))
self.charges.append(m.get_charge(atom[0]))
self.geom.append(atom[1:])
self.geom = [[float(coord) for coord in atom] for atom in self.geom]
def __init__(self, xyzfile):
with open(xyzfile, "r") as f:
lines = f.readlines() #opening the xyz file for reading
self.xyz = xyzfile
self.natom = int(lines[0]) #first line = num of atoms
if len(lines) != (self.natom + 2):
print("Error: incorrectly formatted xyz file")
return
self.units = lines[1].rstrip() #second line = Angstroms or Bohr
if self.units != "Angstrom" and self.units != "Bohr":
print("Error: unspecified units or units we are currently unequipped to handle.")
return
self.labels = []
for line in lines[2:]: #from the third line to the end
self.labels = self.labels + [line[0]] #append the first character
self.masses = [masses.get_mass(i) for i in self.labels] #creates a list of the masses
self.charges = [masses.get_charge(i) for i in self.labels] #creates a list of the charges
fgeoms = []
for line in lines[2:]: #from the third line to the end
line = line.split()
newline = line[1:] #leave out the atom name, have list of xyz's
for i in range(len(newline)):
newline[i] = float(newline[i]) #converting to float
fgeoms = fgeoms + [newline] #a list of lists of the xyz values
self.geoms = np.array(fgeoms) #making an array out of the list of lists
def __init__(self, geom):
"""
Creates a molecule with a geometry and corresponding units
"""
lines = geom.strip().split("\n")
units = lines[1].lower()
natom = int(lines[0])
atoms = []
geom = []
for line in lines[2:]:
atom, x, y, z = line.split()
atoms.append(atom)
geom.append([float(x), float(y), float(z)])
self.units = units
self.natom = natom
self.atoms = atoms
self.geom = np.array(geom)
mass = []
charges =[]
for atom in atoms:
mass.append(float(masses.get_mass(atom)))
charges.append(int(masses.get_charge(atom))) #might want to include symbols
self.mass = mass
self.charges = charges
def __init__(self,data):
#checking if input string is filename or xyzstring by determining number of lines
if data.endswith('.xyz'):
with open(data, 'r') as moleculefile:
self.moleculelines = moleculefile.readlines()
else:
self.moleculelines = data.split('\n')
#units are supplied on line 2
self.units = self.moleculelines[1].rstrip()
#number of atoms is supplied on line 1
self.natom = int((self.moleculelines[0]).rstrip())
#create empty lists of atom labels, masses, charge, and geometry matrix for later population
self.labels = []
self.masses = []
self.charges = []
self.geom = np.zeros((self.natom,3))
#loop through atoms and populate information into empty lists
for atom in range(self.natom):
#+2 because atoms start at line 3
element,x,y,z = self.moleculelines[atom+2].split()
self.labels.append(element)
self.charges.append(masses.get_charge(element))
self.masses.append(masses.get_mass(element))
self.geom[atom] = [x,y,z]
def __init__(self,TextFile):
# Empty arrays defined to be later appended to
self.current = 0
self.textfile = TextFile
labels = []
geom = []
charges = []
mass = []
# open text file, read in the values, and store them as the desired units
with open(TextFile,'r') as my_file:
data = my_file.read().replace('\n',' ')
data = data.split()
self.natom = int(data[0])
del data[0]
self.units = data[0]
del data[0]
# reading in rest of the data
for i in range(self.natom):
# Store the first line of the column as a label
labels.append(data[4*i])
# Temporary list defined to store subarray of geom
temp = []
# Cycle through the x,y,z coordinates
for j in range(3):
temp.append(float(data[4 * i + j + 1]))
# Append 1x3 subarray to geom array
geom.append(temp)
self.labels = labels
self.geom = np.array(geom)
for i in range(self.natom):
mass.append(masses.get_mass(str(labels[i])))
charges.append(masses.get_charge(str(labels[i])))
self.charges = charges
self.masses = mass
def mass_charge(self):
sys.path.insert(0, '../../extra-files')
import masses as M
mass = [float(M.get_mass(self.labels[i])) for i in range(self.natom)]
charge = [M.get_charge(self.labels[i]) for i in range(self.natom)]
return (mass, charge)
def generate_sto3g_data(atoms, geom):
"""Create the sto3g_data."""
sto3g_data = []
for atom, geom in zip(atoms, geom):
for subshell, coefficient in zip(subshells[atom], coefficient_tuple):
atom_index = masses.get_charge(atom) - 1
for orbital in subshell_to_orbitals(subshell):
# A full function will be needed for this if I extend into d
# block elements.
subshell_index = int(orbital[0]) - 1
sto3g_data.append({
"a":
exponential_tuple[atom_index][subshell_index],
"d":
coefficient,
"r":
geom.tolist()[0],
"l":
1 if orbital == "2px" else 0,
"m":
1 if orbital == "2py" else 0,
"n":
1 if orbital == "2pz" else 0,
})
return sto3g_data
def __init__(self, geom):
"""
Creates a molecule with a geometry and corresponding units
"""
lines = geom.strip().split("\n")
units = lines[1].lower()
natom = int(lines[0])
atoms = []
geom = []
for line in lines[2:]:
atom, x, y, z = line.split()
atoms.append(atom)
geom.append([float(x), float(y), float(z)])
self.units = units
self.natom = natom
self.atoms = atoms
self.geom = np.array(geom)
mass = []
charges = []
for atom in atoms:
mass.append(float(masses.get_mass(atom)))
charges.append(int(
masses.get_charge(atom))) #might want to include symbols
self.mass = mass
self.charges = charges
def __init__(self, data):
"""
data -- contents of an .xyz file as a str
"""
data = data.split('\n')
self.natom = int(data[0])
self.units = data[1]
self.labels = []
self.masses = []
self.charges = []
self.geom = []
for atom in data[2:]:
atom = atom.split()
if len(atom) != 4:
continue # Throw Error?
self.labels.append(atom[0])
self.masses.append(m.get_mass(atom[0]))
self.charges.append(m.get_charge(atom[0]))
self.geom.append(atom[1:])
self.geom = [[float(coord) for coord in atom] for atom in self.geom]
def read(self, geom_str):
#Read in the file containing the geometry of the molecule in question
#print("\n" + "MOLECULE INFORMATION" + "\n")
geom = []
self.labels = []
self.masses = []
self.charges = []
lines = geom_str.strip().splitlines()
self.natom = int(lines[0])
#print("Number of atoms: " + str(self.natom) + "\n")
#print("Units are currently in: " + self.units + "\n")
for line in lines[2:]:
atom, x, y, z = line.split()
self.labels.append(atom)
geom.append([float(x), float(y), float(z)])
self.geom = np.array(geom)
#print("Atoms: " + str(self.labels)+ "\n")
#Reading in the masses and charges of the atoms from the .xyz file
for x in self.labels:
self.masses.append(get_mass(x))
self.charges.append(get_charge(x))
y = 0
for x in self.labels:
#print("Mass of " + x + " is: " + str(self.masses[y]))
#print("Charge of " + x + " is: " + str(self.charges[y]))
y += 1
#print("\n")
#print("Molecular Geometry in: " + self.units + "\n")
#print(self.geom)
return self.geom, self.natom, self.labels
def __init__(self, TextFile):
# Empty arrays defined to be later appended to
self.textfile = TextFile
labels = []
geom = []
charges = []
mass = []
# open text file, read in the values, and store them as the desired units
with open(TextFile, 'r') as my_file:
data = my_file.read().replace('\n', ' ')
data = data.split()
self.natom = int(data[0])
del data[0]
self.units = data[0]
del data[0]
# reading in rest of the data
for i in range(self.natom):
# Store the first line of the column as a label
labels.append(data[4 * i])
# Temporary list defined to store subarray of geom
temp = []
# Cycle through the x,y,z coordinates
for j in range(3):
temp.append(float(data[4 * i + j + 1]))
# Append 1x3 subarray to geom array
geom.append(temp)
self.labels = labels
self.geom = np.array(geom)
for i in range(self.natom):
mass.append(masses.get_mass(str(labels[i])))
charges.append(masses.get_charge(str(labels[i])))
self.charges = charges
self.masses = mass
def __init__(self,inputString,lengthUnits="Angstrom",angleUnits="Degree"): self.inputString = inputString self.lengthUnits = lengthUnits self.angleUnits = angleUnits self.read(inputString) self.masses = [ float(get_mass(i)) for i in self.atoms ] self.charges = [ int(get_charge(i)) for i in self.atoms ]
def nuclear_attraction_matrix(sto3g_data, labels, geom):
"""Compute the nuclear attraction matrix."""
number_ao = len(sto3g_data)
V = np.zeros((number_ao, number_ao))
for label, geom in zip(labels, geom):
Z = masses.get_charge(label)
V_temp = np.zeros((number_ao, number_ao))
for index in np.ndindex(V.shape):
orbitals = [sto3g_data[i] for i in index]
n_attract = functools.partial(attraction_term, Z, geom.tolist()[0])
gaussian_recursion(orbitals, [], n_attract, V_temp, index)
V += V_temp
return V
def nuclear_attraction_matrix(sto3g_data, labels, geom):
"""Compute the nuclear attraction matrix."""
number_ao = len(sto3g_data)
V = np.zeros((number_ao, number_ao))
for label, geom in zip(labels, geom):
Z = masses.get_charge(label)
V_temp = np.zeros((number_ao, number_ao))
for index in np.ndindex(V.shape):
orbitals = [sto3g_data[i] for i in index]
n_attract = functools.partial(attraction_term, Z, geom.tolist()[0])
gaussian_recursion(orbitals, [], n_attract, V_temp, index)
V += V_temp
return V
def __init__(self, geom_str):
lines=geom_str.splitlines() # splitting lines of input file
self.natom = int(lines[0]) # number of atoms in the input
self.units = lines[1] # units of geometry
self.labels = [] # atoms in the input file
self.mass = [] # mass of each atom
self.charge = [] # charge of each atom
self.geom = [] # geometry of molecule in xyz coordinates
for line in lines[2:]:
atom,x,y,z = line.split()
self.labels.append(str(atom))
self.mass.append(float(masses.get_mass(atom)))
self.charge.append(int(masses.get_charge(atom)))
self.geom.append([float(x),float(y),float(z)])
self.geom = np.array(self.geom) # matrix of xyz coordinates
def __init__(self, geom_str):
lines = geom_str.splitlines() # splitting lines of input file
self.natom = int(lines[0]) # number of atoms in the input
self.units = lines[1] # units of geometry
self.labels = [] # atoms in the input file
self.mass = [] # mass of each atom
self.charge = [] # charge of each atom
self.geom = [] # geometry of molecule in xyz coordinates
for line in lines[2:]:
atom, x, y, z = line.split()
self.labels.append(str(atom))
self.mass.append(float(masses.get_mass(atom)))
self.charge.append(int(masses.get_charge(atom)))
self.geom.append([float(x), float(y), float(z)])
self.geom = np.array(self.geom) # matrix of xyz coordinates
def __init__(self, xyzstring, units="angstrom"):
labels = []
geom = []
try:
lines = xyzstring.strip().splitlines()
natom = int(lines[0])
for line in lines[2:]:
l, x, y, z = line.split()
labels.append(l.upper())
geom.append([float(x), float(y), float(z)])
except:
raise Exception("Invalid .xyz string\n'''\n{:s}\n'''\npassed to Molecule constructor.".format(xyzstring))
self.units = units
self.natom = natom
self.labels = labels
self.masses = [get_mass(label) for label in labels]
self.charges = [get_charge(label) for label in labels]
self.geom = np.array(geom)
def __init__(self, geom_path):
f = open(geom_path)
lines = f.readlines()
f.close()
self.natom = int(lines[0])
self.units = lines[1]
# initialize stuff
self.labels = []
self.charges = []
self.masses = []
self.xyz = []
# get geoms
for line in lines[2:]:
atom, x, y, z = line.split()
self.labels.append(atom)
self.charges.append(get_charge(atom))
self.masses.append(get_mass(atom))
self.xyz.append((float(x), float(y), float(z)))
self.geom = np.array(self.xyz) # make numpy array
def generate_sto3g_data(atoms, geom):
"""Create the sto3g_data."""
sto3g_data = []
for atom, geom in zip(atoms, geom):
for subshell, coefficient in zip(subshells[atom], coefficient_tuple):
atom_index = masses.get_charge(atom) - 1
for orbital in subshell_to_orbitals(subshell):
# A full function will be needed for this if I extend into d
# block elements.
subshell_index = int(orbital[0]) - 1
sto3g_data.append({
"a": exponential_tuple[atom_index][subshell_index],
"d": coefficient,
"r": geom.tolist()[0],
"l": 1 if orbital == "2px" else 0,
"m": 1 if orbital == "2py" else 0,
"n": 1 if orbital == "2pz" else 0,
})
return sto3g_data
def parse_molecule(self, mole_str):
"""
Parses data from .xyz file to change class attributes
:param mole_str: string (typically .xyz file) describing a molecule
"""
lines = mole_str.strip().split("\n")
self.natom = int(lines[0])
if lines[1].lower() == "angstrom":
self.units = "angstrom"
elif lines[1].lower() == "bohr":
self.units = "bohr"
self.labels = [i.strip().split(" ")[0].strip() for i in lines[2:]]
self.masses = [m.get_mass( l ) for l in self.labels ]
self.charges = [m.get_charge( l ) for l in self.labels ]
tempArray = [i.split(" ")[1:4] for i in lines[2:]]
for a in range(len(tempArray)):
for b in range(len(tempArray[a])):
tempArray[a][b] = float(tempArray[a][b]
)
self.geom = np.array(tempArray)
def __init__(self, xyz):
self.units = "Angstrom"
self.labels = []
self.masses = []
self.charges = []
xyz_lines = filename_to_lines(xyz)
# Get the number of atoms.
natom = get_elt_0(xyz_lines, "Line 1", "file {}".format(xyz))
self.natom = validate_int(natom, "Line 1")
# Validate the file length.
validate_array_length(self.natom + 2, xyz_lines, "XYZ input", "lines")
geom = numpy.empty([0, 3])
for i, line in enumerate(xyz_lines[2:]):
# Ensure a coordinate line is valid before processing it.
atom, matr_row = validate_coord_line(line, i + 3)
geom = numpy.vstack((geom, matr_row))
self.labels.append(atom)
self.charges.append(masses.get_charge(atom))
self.masses.append(masses.get_mass(atom))
self.geom = geom
def __init__(self, xyz):
self.units = "Angstrom"
self.labels = []
self.masses = []
self.charges = []
xyz_lines = filename_to_lines(xyz)
# Get the number of atoms.
natom = get_elt_0(xyz_lines, "Line 1", "file {}".format(xyz))
self.natom = validate_int(natom, "Line 1")
# Validate the file length.
validate_array_length(self.natom + 2, xyz_lines, "XYZ input", "lines")
geom = numpy.empty([0, 3])
for i, line in enumerate(xyz_lines[2:]):
# Ensure a coordinate line is valid before processing it.
atom, matr_row = validate_coord_line(line, i + 3)
geom = numpy.vstack((geom, matr_row))
self.labels.append(atom)
self.charges.append(masses.get_charge(atom))
self.masses.append(masses.get_mass(atom))
self.geom = geom
def parse_molecule(self, mole_str):
"""
Parses data from .xyz file to change class attributes
:param mole_str: string (typically .xyz file) describing a molecule
"""
lines = mole_str.strip().split("\n")
self.natom = int(lines[0])
if lines[1].lower() == "angstrom":
self.units = "angstrom"
elif lines[1].lower() == "bohr":
self.units = "bohr"
self.labels = [i.strip().split(" ")[0].strip() for i in lines[2:]]
self.masses = [m.get_mass( l ) for l in self.labels ]
self.charges = [m.get_charge( l ) for l in self.labels ]
self.molecular_charge = 0
tempArray = [i.split(" ")[1:4] for i in lines[2:]]
for a in range(len(tempArray)):
for b in range(len(tempArray[a])):
tempArray[a][b] = float(tempArray[a][b]
)
self.geom = np.array(tempArray)
def __init__(
self, xyz_file
): #Initializes member variables: natom, units, labels, masses, charges, geom
with open(xyz_file) as f:
geom = [line.split() for line in f]
try: #Tests formatting of .xyz file
self.natom = int(geom.pop(0)[0]) #Gets number of atoms
units = geom.pop(0) #Gets units of coordinates
for i in units:
if isinstance(i, str) == True:
i = str(i)
if i.upper() == "BOHR" or i.upper() == "ANGSTROM":
self.units = i
except:
sys.exit(
"Error: Check .xyz file to ensure correct format. \n Number of Atoms \n Unit of Length \n Atom with Coordinates \n . \n . \n ."
)
self.labels = []
self.masses = []
self.charges = []
for i in geom: #Loops over the labels with coordinates of the file
a = i.pop(0)
self.labels.append(a) #Builds list of labels
try:
self.masses.append(
masses.get_mass(a)) #Builds list of atomic masses
self.charges.append(
masses.get_charge(a)) #Builds list of atom charges
except:
sys.exit("Error: Check that labels are written correctly.")
try:
geom = [list(map(float, j)) for j in geom]
self.geom = np.array(
geom) #Makes array out of list of lists containing coordinates
except:
sys.exit(
"Error: Check if coordinates are in numerical format with x, y, and z components."
)
f.close()
def __init__(self, xyzfile):
with open(xyzfile, "r") as f:
lines = f.readlines() #opening the xyz file for reading
self.xyz = xyzfile
self.natom = int(lines[0]) #first line = num of atoms
if len(lines) != (self.natom + 2):
print("Error: incorrectly formatted xyz file")
return
self.units = lines[1].rstrip() #second line = Angstroms or Bohr
if self.units != "Angstrom" and self.units != "Bohr":
print(
"Error: unspecified units or units we are currently unequipped to handle."
)
return
self.labels = []
for line in lines[2:]: #from the third line to the end
self.labels = self.labels + [line[0]] #append the first character
self.masses = [masses.get_mass(i)
for i in self.labels] #creates a list of the masses
self.charges = [masses.get_charge(i)
for i in self.labels] #creates a list of the charges
fgeoms = []
for line in lines[2:]: #from the third line to the end
line = line.split()
newline = line[1:] #leave out the atom name, have list of xyz's
for i in range(len(newline)):
newline[i] = float(newline[i]) #converting to float
fgeoms = fgeoms + [newline] #a list of lists of the xyz values
self.geoms = np.array(
fgeoms) #making an array out of the list of lists
def __init__(self,
filename='molecule.xyz',
units='Angstrom',
charge=0,
mult=1):
self.units = units
self.labels = []
self.charges = []
self.masses = []
self.geom_list = []
self.index = 0
self.charge = charge
self.mult = mult
with open(filename, 'r') as fn:
self.natom = int(fn.readline())
geom_lines = fn.readlines()[1:]
for line in geom_lines:
line_list = line.split()
self.labels.append(line_list[0].upper())
self.charges.append(masses.get_charge(line_list[0]))
self.masses.append(masses.get_mass(line_list[0]))
self.geom_list.append(
[line_list[1], line_list[2], line_list[3]])
self.geom = np.array(self.geom_list).astype(float)
def __init__(self,geom_str,units = "Angstrom"):
self.read(geom_str)
self.units = units
self.charge = [get_charge(i) for i in self.label]
self.mass = [get_mass(i) for i in self.label]
def __init__(self, xyz_file, units="Angstrom"):
self.units = units
self.read(xyz_file)
self.masses = [ float(get_mass(i)) for i in self.atoms ]
self.charges = [ int(get_charge(i)) for i in self.atoms ]
def __init__(self, geom_str, units="Angstrom"):
self.read(geom_str)
self.units = units
self.charge = [get_charge(i) for i in self.label]
self.mass = [get_mass(i) for i in self.label]
def __init__(self, xyz_file, units="Angstrom"):
self.units = units
self.read(xyz_file)
self.masses = [ float(get_mass(i)) for i in self.atoms ]
self.charges = [ int(get_charge(i)) for i in self.atoms ]
def __init__(self, geom, units = "Angstrom"):
self.read(geom)
self.units = units
self.charge = [get_charge(atom) for atom in self.atoms]
self.mass = [get_mass(atom) for atom in self.atoms]
def __init__(self, geom, units="Angstrom"):
self.read(geom)
self.units = units
self.charge = [get_charge(atom) for atom in self.atoms]
self.mass = [get_mass(atom) for atom in self.atoms]