def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
line = file.readline()
title = line.strip()
line = file.readline()
title2 = line.strip()
line = file.readline()
title3 = line.strip()
line = file.readline()
natoms = int(line[:3])
nbonds = int(line[3:6])
# Note: I'm skipping the H information here, which is
# typically given in fields 5-
for i in range(natoms):
line = file.readline()
words = line.split()
xyz = array(map(float, words[:3]))
sym = cleansym(words[3])
atno = sym2no[sym]
material.add_atom(Atom(atno, xyz, sym, sym + str(i)))
atoms = material.get_atoms()
for i in range(nbonds):
line = file.readline()
words = line.split()
# bond order is the third field, which I'm ignoring
iat, jat, iorder = map(int, words[:3])
material.add_bond(Bond(atoms[iat - 1], atoms[jat - 1], iorder))
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material = Material(fileprefix)
file = open(fullfilename, 'r')
line = file.readline()
title = line.strip()
line = file.readline()
natoms, nbonds = map(int, line.split())
for i in range(natoms):
line = file.readline()
words = line.split()
xyz = array(map(float, words[:3]))
sym = cleansym(words[3])
atno = sym2no[sym]
material.add_atom(Atom(atno, xyz, sym, sym + str(i)))
atoms = material.get_atoms()
for i in range(nbonds):
line = file.readline()
words = line.split()
# I think order is the third one, but I'm not sure
iat, jat, iorder = map(int, words[:3])
material.add_bond(Bond(atoms[iat - 1], atoms[jat - 1], iorder))
return material
def load(fullfilename):
filedir, fileprefix, fileext = path_split(fullfilename)
material=Material(fileprefix)
file=open(fullfilename, 'r')
hatpat = re.compile('HETATM')
atpat = re.compile('^ATOM')
conpat = re.compile('^CONECT')
ordpat = re.compile('^ORDER')
endpat = re.compile('^END')
ucpat = re.compile('^CRYSTX')
bonds = {}
orders = {}
iat = 0
for line in open(fullfilename):
if hatpat.search(line) or atpat.search(line):
d1,i,d2,d3,d4,d5,x,y,z,attype,d6,d7,q = read(line,atom_format)
xyz = array([x,y,z])
sym = cleansym(attype)
atno = sym2no[sym]
atom = Atom(atno,xyz,sym,sym+str(iat))
atom.fftype = attype # save just in case
material.add_atom(atom)
iat += 1
elif conpat.search(line):
ats = map(int,line[6:].split())
index = ats[0]-1
bonds[index] = [atj-1 for atj in ats[1:]]
orders[index] = [1]*(len(ats)-1)
elif ordpat.search(line):
ords = map(int,line[6:].split())
index = ords[0]-1
orders[index] = ords[1:]
elif ucpat.search(line):
words = line.split()
a,b,c,alpha,beta,gamma = map(float,words[1:7])
axyz,bxyz,cxyz = abcabg2abc(a,b,c,alpha,beta,gamma)
cell = Cell(axyz,bxyz,cxyz)
material.set_cell(cell)
atoms = material.get_atoms()
#print len(atoms)," atoms loaded"
for iat in bonds.keys():
bond_partners = bonds[iat]
bond_orders = orders[iat]
for jat,ij_order in zip(bond_partners,bond_orders):
if jat > iat: material.add_bond(Bond(atoms[iat],atoms[jat],
ij_order))
return material