def coordinates_read(fname=None):
"""
1 COP C1 1 2.122800112 1.917699933 2.044047117
||||| ----- ||||| |||||||||||||||---------------|||||||||||||||
.123456789.123456789.123456789.123456789.123456789.123456789.123456789
"""
mol = qm3.mol.molecule()
f = qm3.fio.open_r(fname)
l = f.readline()
while (l.strip() != "POSITION"):
l = f.readline()
l = f.readline()
while (l.strip() != "END"):
mol.natm += 1
mol.segn.append("A")
mol.resi.append(int(l[0:5]))
mol.resn.append(l[6:11].strip())
mol.labl.append(l[12:17].strip())
mol.coor.append(float(l[24:39].strip()) * 10.0)
mol.coor.append(float(l[39:54].strip()) * 10.0)
mol.coor.append(float(l[54:69].strip()) * 10.0)
l = f.readline()
l = f.readline()
if (l.strip() == "BOX"):
mol.boxl = [float(i) * 10.0 for i in f.readline().strip().split()]
qm3.fio.close(f, fname)
mol.settle()
return (mol)
def psf_read(mol, fname):
global __topo
mol.type = []
mol.chrg = []
mol.mass = []
f = qm3.fio.open_r(fname)
if (f.readline().split()[0] == "PSF"):
f.readline()
for i in range(int(f.readline().split()[0]) + 1):
f.readline()
n = int(f.readline().split()[0])
if (mol.natm == 0):
mol.natm = n
mol.segn = []
mol.resi = []
mol.resn = []
mol.labl = []
for i in range(n):
t = f.readline().split()
mol.segn.append(t[1])
mol.resi.append(int(t[2]))
mol.resn.append(t[3])
mol.labl.append(t[4])
mol.type.append(t[5])
mol.chrg.append(float(t[6]))
mol.mass.append(float(t[7]))
mol.settle()
elif (mol.natm == n):
for i in range(mol.natm):
t = f.readline().split()
if (mol.segn[i] == t[1] and mol.resi[i] == int(t[2])
and mol.resn[i] == t[3] and mol.labl[i] == t[4]):
mol.type.append(t[5])
mol.chrg.append(float(t[6]))
mol.mass.append(float(t[7]))
else:
print("- Wrong PSF data (%d): %s/%s %d/%s %s/%s %s/%s" %
(i + 1, mol.segn[i], t[1], mol.resi[i], t[2],
mol.resn[i], t[3], mol.labl[i], t[4]))
mol.type = []
mol.chrg = []
mol.mass = []
return ([])
else:
print("- Invalid number of atoms in PSF!")
return ([])
bonds = []
__topo = f.readline()
l = f.readline()
n = int(l.strip().split()[0])
__topo += l
while (len(bonds) < n):
l = f.readline()
t = [int(i) - 1 for i in l.strip().split()]
for i in range(len(t) // 2):
bonds.append([t[2 * i], t[2 * i + 1]])
__topo += l
__topo += f.read()
qm3.fio.close(f, fname)
return (bonds)
def mol2_read(fname=None):
mol = qm3.mol.molecule()
f = qm3.fio.open_r(fname)
l = f.readline()
while (l != ""):
if (l.strip() == "@<TRIPOS>MOLECULE"):
f.readline()
t = f.readline().strip().split()
mol.natm = int(t[0])
nbnd = int(t[1])
bond = []
if (l.strip() == "@<TRIPOS>ATOM"):
for i in range(mol.natm):
t = f.readline().strip().split()
mol.labl.append(t[1])
mol.coor += [float(t[2]), float(t[3]), float(t[4])]
mol.type.append(t[5])
mol.resi.append(int(t[6]))
mol.resn.append(t[7][0:3])
mol.chrg.append(float(t[8]))
mol.segn.append("X")
if (l.strip() == "@<TRIPOS>BOND"):
for i in range(nbnd):
t = f.readline().split()
ii = int(t[1]) - 1
jj = int(t[2]) - 1
bond.append([ii, jj])
l = f.readline()
qm3.fio.close(f, fname)
mol.settle()
return (mol, bond)
def sdf_read(fname=None):
mol = qm3.mol.molecule()
f = qm3.fio.open_r(fname)
for i in range(4):
l = f.readline()
mol.natm = int(l.strip().split()[0])
for i in range(mol.natm):
t = f.readline().split()
mol.labl.append(t[3])
mol.resi.append(1)
mol.resn.append("XXX")
mol.segn.append("X")
mol.coor += [float(j) for j in t[0:3]]
qm3.fio.close(f, fname)
mol.settle()
return (mol)
def lammps_read( fname = None ):
mol = qm3.mol.molecule()
f = qm3.fio.open_r( fname )
l = f.readline().lower()
q = True
m = {}
while( l != "" and q ):
if( l.find( "xlo" ) > 0 and l.find( "xhi" ) > 0 ):
t = l.strip().split()
mol.boxl[0] = float( t[1] ) - float( t[0] )
elif( l.find( "ylo" ) > 0 and l.find( "yhi" ) > 0 ):
t = l.strip().split()
mol.boxl[1] = float( t[1] ) - float( t[0] )
elif( l.find( "zlo" ) > 0 and l.find( "zhi" ) > 0 ):
t = l.strip().split()
mol.boxl[2] = float( t[1] ) - float( t[0] )
elif( l.find( "masses" ) >= 0 ):
f.readline()
l = f.readline().strip()
while( l != "" ):
t = l.split()
m[t[0]] = float( t[1] )
l = f.readline().strip()
elif( l.find( "atoms" ) == 0 ):
q = False
f.readline()
l = f.readline().strip()
while( l != "" ):
t = l.split()
mol.segn.append( "XXX" )
mol.resn.append( "X" )
mol.resi.append( int( t[1] ) )
mol.labl.append( t[2] )
mol.mass.append( m[t[2]] )
mol.chrg.append( float( t[3] ) )
mol.coor += [ float( t[4] ), float( t[5] ), float( t[6] ) ]
mol.natm += 1
l = f.readline().strip()
l = f.readline().lower()
qm3.fio.close( f, fname )
mol.settle()
return( mol )