def add_h(b, centers, cn):
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
n_cut = 10
for i in range(len(cn)):
n = int(cn[i])
print "processing %d"%(n*1.0/8183*100)
if n < n_cut:
a = Atom()
a.name = "H"
a.element = "H"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + 1.5
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a.x[0] = x
a.x[1] = y
a.x[2] = z
b1.atoms.append(a)
toPdb(b1, "add_h.pdb")
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s
def parser(self):
s = System()
s.pbc = v2lattice(self.a, self.b, self.c)
s.atomtypes = self.atomtypes
s.n_atoms = self.n_atoms
s.n_bonds = self.n_bonds
s.n_angles = self.n_angles
s.n_dihedrals = self.n_dihedrals
s.n_impropers = self.n_impropers
s.n_atomtypes = self.n_atomtypes
s.n_bondtypes = self.n_bondtypes
s.n_angletypes = self.n_angletypes
s.n_dihedraltypes = self.n_dihedraltypes
s.n_impropertypes = self.n_impropertypes
s.bonds = self.bonds
s.angles = self.angles
s.dihedrals = self.dihedrals
s.ffparams = self.ffparams
for i in self.coords:
# n is used to distinguish the type of data file
n = 0
for j in i:
# ignore the comments
if "#" in j:
break
n += 1
atom = Atom()
atom.an = int(i[0])
if n == 7:
# n = 7 is full type
atom.resn = int(i[1])
atom.name = self.elements[int(i[2]) - 1]
atom.element = self.elements[int(i[2]) - 1]
atom.type2 = int(i[2])
atom.charge = float(i[3])
atom.x[0] = float(i[4])
atom.x[1] = float(i[5])
atom.x[2] = float(i[6])
s.atoms.append(atom)
return s
def add_o(b, centers, cn):
"""add o
"""
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
n_cut = 10
for i in range(len(cn)):
print "processing %d"%(i*1.0/8183*100)
n = int(cn[i])
token = random.random()
if n < n_cut and token > 0.9:
a = Atom()
a.name = "O"
a.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + 2.0
s = r/r1
x = s*(x0-x1) + x1 + 1.0
y = s*(y0-y1) + y1 + 1.0
z = s*(z0-z1) + z1
a.x[0] = x
a.x[1] = y
a.x[2] = z
b1.atoms.append(a)
toPdb(b1, "add_o.pdb")
def add_oh(b, centers, cn, n_ignore, ndx):
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
a = Atom()
a.name = "O"
a.element = "O"
b2.atoms.append(a)
a = Atom()
a.name = "H"
a.element = "H"
b2.atoms.append(a)
n_cut = 10
r_pt_oh = 2.0
r_oh = 1.0
for i in range(len(cn)):
#print "processing %d"%(i*1.0/len(cn)*100)
token = random.random()
n = int(cn[i])
if n < n_cut and token >= 0.0:
a1 = Atom()
a1.name = "O"
a1.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + r_pt_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a1.x[0] = x
a1.x[1] = y
a1.x[2] = z
b1.atoms.append(a1)
b2.atoms[-2].x[0] = x
b2.atoms[-2].x[1] = y
b2.atoms[-2].x[2] = z
a2 = Atom()
a2.name = "H"
a2.element = "H"
r = r1 + r_pt_oh + r_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a2.x[0] = x
a2.x[1] = y
a2.x[2] = z
b1.atoms.append(a2)
b2.atoms[-1].x[0] = x
b2.atoms[-1].x[1] = y
b2.atoms[-1].x[2] = z
if i >= n_ignore - 1:
toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))
toPdb(b1, "add_oh.pdb")
def add_oh(b, centers, cn, n_ignore, ndx):
"""add oh
"""
dx = DELTA_X
zl = b.pbc[2]
b1 = copy.deepcopy(b)
b2 = copy.deepcopy(b)
a = Atom()
a.name = "O"
a.element = "O"
b2.atoms.append(a)
a = Atom()
a.name = "H"
a.element = "H"
b2.atoms.append(a)
n_cut = 10
r_pt_oh = 2.0
r_oh = 1.0
for i in range(len(cn)):
#print "processing %d"%(i*1.0/len(cn)*100)
token = random.random()
n = int(cn[i])
if n < n_cut and token >= 0.0:
a1 = Atom()
a1.name = "O"
a1.element = "O"
x0 = b.atoms[i].x[0]
y0 = b.atoms[i].x[1]
z0 = b.atoms[i].x[2]
z0 = z0 - int(z0/zl)*zl
n_sl = int(z0/dx)
x1 = centers[n_sl][0]
y1 = centers[n_sl][1]
z1 = centers[n_sl][2]
r2 = (x0-x1)*(x0-x1)
r2 += (y0-y1)*(y0-y1)
r2 += (z0-z1)*(z0-z1)
r1 = math.sqrt(r2)
r = r1 + r_pt_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a1.x[0] = x
a1.x[1] = y
a1.x[2] = z
b1.atoms.append(a1)
b2.atoms[-2].x[0] = x
b2.atoms[-2].x[1] = y
b2.atoms[-2].x[2] = z
a2 = Atom()
a2.name = "H"
a2.element = "H"
r = r1 + r_pt_oh + r_oh
s = r/r1
x = s*(x0-x1) + x1
y = s*(y0-y1) + y1
z = s*(z0-z1) + z1
a2.x[0] = x
a2.x[1] = y
a2.x[2] = z
b1.atoms.append(a2)
b2.atoms[-1].x[0] = x
b2.atoms[-1].x[1] = y
b2.atoms[-1].x[2] = z
if i >= n_ignore - 1:
toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))
toPdb(b1, "add_oh.pdb")
