def xyz2bgf(xyz_file, bgf_file, silent=False):
"""
Converts xyz to bgf
"""
### open xyz
f_xyz = open(xyz_file, 'r')
### create bgf
myBGF = bgf.BgfFile()
myBGF.BIOGRF = '200'
myBGF.DESCRP = xyz_file
### read and create atoms for bgf file
while 1:
line = f_xyz.readline()
if not line: break
words = string.split(line)
if not words: break
natoms = int(words[0])
myBGF.REMARK = [cleansym(f_xyz.readline())]
for i in range(natoms):
line = f_xyz.readline()
words = string.split(line)
sym = words[0]
sym = cleansym(sym)
x, y, z = float(words[1]), float(words[2]), float(words[3])
### add atoms
atom = bgf.BgfAtom()
atom.x = x
atom.y = y
atom.z = z
atom.ffType = sym
atom.aNo = i
atom.aName = sym + str(i)
atom.rNo = 1
atom.chain = "A"
atom.rName = "RES"
myBGF.addAtom(atom)
### save bgf
myBGF.OTHER = []
myBGF.saveBGF(bgf_file)
def convertBGF(self):
myBGF = bgf.BgfFile()
natom = 0
for index, i in enumerate(self._atom_numbers):
name = self._atom_types[index]
name = raw_input("- assign the force field type for " + name +
" (default: " + name +
") ?? ") or self._atom_types[index]
for j in xrange(i):
atom = bgf.BgfAtom()
atom.x = self._coords[natom][0]
atom.y = self._coords[natom][1]
atom.z = self._coords[natom][2]
atom.aTag = 1
atom.aNo = natom + 1
atom.aName = self._atom_types[index] + str(j + 1)
atom.rName = "RES"
atom.rNo = 100
atom.chain = "A"
atom.ffType = name
myBGF.addAtom(atom)
natom += 1
# assign remarks
myBGF.BIOGRF = 200
myBGF.DESCRP = "From " + self._filename + " at " + time.asctime(
time.gmtime(
)) + " on " + os.environ["HOSTNAME"] + " by " + os.environ["USER"]
myBGF.PERIOD = "111"
myBGF.AXES = "ZYX"
myBGF.SGNAME = "P 1 1 1"
myBGF.CELLS = [-1, 1, -1, 1, -1, 1]
myBGF.CRYSTX = self._latticeParams
self._bgf = myBGF
def add_ions_inside_nanotube(self, n_ion):
"""
Add Na+ and Cl- ions inside nanotube.
"""
if not self.isRadiusCalc == True:
nu.warn("Nanotube radius not defined. Exiting.")
return 0
### find the last atom before resname WAT
aNo_lastatom = 0
for i in self.bgfmodel.a:
aNo = i.aNo
if not "WAT" in i.rName:
if aNo > aNo_lastatom:
aNo_lastatom = aNo
### add
n_add = 0
while n_add < n_ion:
x = random.uniform(0, self.pbc[0])
y = random.uniform(0, self.pbc[1])
z = random.uniform(0, self.pbc[2])
xyz = np.array([x, y, z])
r = np.sqrt(
((xyz * self.axis - self.center * self.axis)**2).sum(axis=-1))
h = (xyz * self.axismask).sum()
if r < self.radius and self.zlo < h < self.zhi:
# Na+ ion
atom_Na = bgf.BgfAtom()
atom_Na.x = x
atom_Na.y = y
atom_Na.z = z
atom_Na.aTag = 1 # HETATM
atom_Na.ffType = "Na"
atom_Na.rName = "ION"
atom_Na.aName = "Na"
atom_Na.charge = 1.00
atom_Na.rNo = 0
atom_Na.chain = "X"
# Cl- ion
atom_Cl = bgf.BgfAtom()
atom_Cl.x = x + 2
atom_Cl.y = y + 2
atom_Cl.z = z + 2
atom_Cl.aTag = 1 # HETATM
atom_Cl.ffType = "Cl"
atom_Cl.rName = "ION"
atom_Cl.aName = "Cl"
atom_Cl.charge = -1.00
atom_Cl.rNo = 0
atom_Cl.chain = "X"
self.bgfmodel.addAtom(atom_Na,
self.bgfmodel.a2i[aNo_lastatom + 1])
self.bgfmodel.addAtom(atom_Cl,
self.bgfmodel.a2i[aNo_lastatom + 2])
n_add += 1
self.bgfmodel.renumber()
print("%d atoms added to the nanotube." % n_add)
def countWater(bgf_file, trj_file, n_step, watercopy, ff_file, silent=False):
### const
PI = math.pi
vdw_r_C = 1.7
### init
timestep = 0
l_timestep = []
line = []
n_header = 0
t1 = 0
t2 = 0
# clock
myBGF = bgf.BgfFile(bgf_file)
myTRJ = open(trj_file)
myTRJ.seek(0)
global out_file
if out_file == "": out_file = "countWater5.profile"
print("The result will be recorded to the file " + out_file + " ...")
ftemp = open(out_file, 'w')
ftemp.write(str(sys.argv) + "\n")
ftemp.write("t" + '\t' + "n_O" + '\t' + "r_CNT" + '\t' + "std_r" + '\t' +
"min_x" + '\t' + "max_x" + '\t' + "min_y" + '\t' + "max_y" +
'\t' + "min_z" + '\t' + "max_z" + '\t' + "l_NT" + '\t' +
"replNum" + '\t' + "copyNum" + '\t' + "n_WAT" + '\t' +
"remark" + '\n')
curr_dir = os.path.abspath(".")
temp_dir = curr_dir + "/countWAT5/"
print(temp_dir)
if not os.path.isdir(temp_dir): os.makedirs(temp_dir)
### how many steps to go?
n_timestep = len(lt.getTrjInfo(trj_file))
if n_step == 0:
n_step = n_timestep
print(" ..The trajectory contains " + str(n_timestep) + " timesteps.")
print("The script will proceed for the first " + str(n_step) +
" timesteps.")
### read mass from ff_file
atominfo = dict()
try:
parse = ff_file.split(" ")
except:
nu.die(
"Error occurred when reading the force field file.. Check your " +
str(ff_file))
else:
if not silent:
print("Found " + str(len(parse)) + " Cerius2 Force Fields.")
for i in parse:
FF = dreiding.loadFF(i)
temp_atominfo = dreiding.loadAtomTypes(FF)
atominfo.update(temp_atominfo)
### extract aNos of CNT in the BGF file
aNo_CNT = []
aNo_WAT_O = []
aNo_WAT_all = []
mass_CNT = []
for atom in myBGF.a:
# Carbons in CNT or atoms in BNNT
if "NT" in atom.rName:
aNo_CNT.append(atom.aNo)
ffType = string.strip(atom.ffType)
try:
aMass = atominfo[ffType]['MASS']
except:
nu.die("Cannot read the atom type " + str(atom.ffType) +
" in the data file.")
mass_CNT.append(aMass)
# Oxygen in water
if "WAT" in atom.rName and "O" in atom.aName:
aNo_WAT_O.append(atom.aNo)
N_CNT = len(aNo_CNT) # the number of CNT atoms
### check if there exists water properly
if len(aNo_WAT_O) == 0:
nu.die("No water molecules in the BGF file.")
if len(aNo_CNT) == 0:
nu.die("No CNT molecules in the BGF file.")
### Find header of the trajectory file
while 1:
templine = myTRJ.readline()
line.append(templine.strip('\n').strip('ITEM: '))
n_header += 1
if "ITEM: ATOMS" in templine:
break
### INITIAL trajectory information
timestep = int(line[1])
natoms = int(line[3])
boxsize = [
line[5].split(' ')[0], line[5].split(' ')[1], line[6].split(' ')[0],
line[6].split(' ')[1], line[7].split(' ')[0], line[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
keywords = line[8].strip('ATOMS ')
# for every shot in the trajectory file update BGF and manipulate
dumpatom = get_line(trj_file)
processed_step = 0
t1 = t2 = 0
elapsed_time = 0
while 1:
### Show progress
t1 = time.time()
remaining_time = elapsed_time * (n_step - processed_step)
sys.stdout.write('\r' + "Reading timestep.. " + str(timestep) +
" (Remaining time: " +
"{0:4.1f}".format(remaining_time) + " seconds, " +
"{0:4.1f} minutes".format(remaining_time / 60) + ")")
sys.stdout.flush()
if processed_step == n_step:
break
### Read
myBGF = bgf.BgfFile(bgf_file)
try:
chunk = [next(dumpatom) for i in range(natoms + n_header)]
except StopIteration:
break
timestep = int(chunk[1])
natoms = int(chunk[3])
boxsize = [
chunk[5].split(' ')[0], chunk[5].split(' ')[1],
chunk[6].split(' ')[0], chunk[6].split(' ')[1],
chunk[7].split(' ')[0], chunk[7].split(' ')[1]
]
boxsize = [float(i) for i in boxsize]
boxsize = [(boxsize[1] - boxsize[0]), (boxsize[3] - boxsize[2]),
(boxsize[5] - boxsize[4])]
keywords = chunk[8].split('ATOMS ')[1].strip('\n').split(' ')
mode = 'unwrapped' # assume that "dump 1 all custom 100 ${sname}${rtemp}K.nvt.lammps id type xu yu zu vx vy vz" in lammps input
# actual coordinate
coordinfo = chunk[9:]
# load atom coordinates from chunk
for atomline in coordinfo:
atomcoord = atomline.split(' ')
atom = myBGF.getAtom(int(atomcoord[0]))
atom.x = float(atomcoord[2])
atom.y = float(atomcoord[3])
atom.z = float(atomcoord[4])
### convert atom coordinates to lists
CNT = []
WATER = []
for atom in myBGF.a:
if "NT" in atom.rName:
CNT.append([atom.x, atom.y, atom.z])
if "WAT" in atom.rName and "O" in atom.ffType:
WATER.append([atom.x, atom.y, atom.z])
CNT = np.array(CNT)
n_CNT = len(CNT) # CNT coordinates
WATER = np.array(WATER) # Water coordinates
WATERONLY = np.copy(WATER)
boxsize = np.array(boxsize)
### initialize for the moment of inertia and the center of mass calculation
U = 0
Ut = 0
Uv = 0
Ixx = 0
Ixy = 0
Ixz = 0
Iyx = 0
Iyy = 0
Iyz = 0
Izx = 0
Izy = 0
Izz = 0
Mx = 0
My = 0
Mz = 0
### transpose "all atoms in BGF": move COM of CNT as origin
Mx, My, Mz = np.average(CNT, axis=0, weights=mass_CNT) # CoM of CNT
COM = np.array([[Mx, My, Mz]])
CNT = CNT - COM + boxsize / 2.0 # move
WATER = WATER - COM + boxsize / 2.0
### apply PBC
WATER = np.mod(WATER, boxsize)
### save coordinates to BGF before rotation
myBGF2 = bgf.BgfFile()
for index, i in enumerate(CNT):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index
newatom.aName = 'C' + str(index)
newatom.rName = 'CNT'
newatom.ffType = 'C_'
newatom.chain = 'A'
newatom.rNo = 1
myBGF2.addAtom(newatom)
for index, i in enumerate(WATER):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index + n_CNT
newatom.aName = 'O'
newatom.rName = 'WAT'
newatom.ffType = 'OW'
newatom.chain = 'O'
newatom.rNo = 100
myBGF2.addAtom(newatom)
myBGF2.REMARK.append('TIMESTEP ' + str(timestep))
myBGF2.PERIOD = "111"
myBGF2.AXES = "ZYX"
myBGF2.SGNAME = "P 1 1 1"
myBGF2.CELLS = [-1, 1, -1, 1, -1, 1]
myBGF2.CRYSTX = [boxsize[0], boxsize[1], boxsize[2], 90.0, 90.0, 90.0]
myBGF2.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".bgf")
### move CM of CNT to origin
CNT = CNT - boxsize / 2.0
WATER = WATER - boxsize / 2.0
### how the CNT is lying across the periodic box?
for atom in CNT:
min_x_CNT, min_y_CNT, min_z_CNT = CNT.min(axis=0)
max_x_CNT, max_y_CNT, max_z_CNT = CNT.max(axis=0)
margin = 5.0
### copy water molecules
max_x_axis = int(round((max_x_CNT + margin) / boxsize[0]))
min_x_axis = int(round((min_x_CNT - margin) / boxsize[0]))
max_y_axis = int(round((max_y_CNT + margin) / boxsize[1]))
min_y_axis = int(round((min_y_CNT - margin) / boxsize[1]))
max_z_axis = int(round((max_z_CNT + margin) / boxsize[2]))
min_z_axis = int(round((min_z_CNT - margin) / boxsize[2]))
replNum = (min_x_axis, max_x_axis, min_y_axis, max_y_axis, min_z_axis,
max_z_axis)
copyNum = 0
remark = ""
if watercopy:
for x in range(min_x_axis, max_x_axis + 1):
remark += "x: "
if x != 0:
WATER2 = np.copy(WATERONLY)
dx = np.array([[boxsize[0] * x, 0, 0]])
WATER2 = WATER2 + dx
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(x) + " "
for y in range(min_y_axis, max_y_axis + 1):
remark += "y: "
if y != 0:
WATER2 = np.copy(WATERONLY)
dy = np.array([[0, boxsize[1] * y, 0]])
WATER2 = WATER2 + dy
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(y) + " "
for z in range(min_z_axis, max_z_axis + 1):
remark += "z: "
if z != 0:
WATER2 = np.copy(WATERONLY)
dz = np.array([[0, 0, boxsize[2] * z]])
WATER2 = WATER2 + dz
WATER = np.concatenate((WATER, WATER2))
copyNum += 1
remark += str(z) + " "
'''
### WATER distribution check
x_axis = np.linspace(WATER[:,0].min(), WATER[:,0].max(), 10)
y_axis = np.linspace(WATER[:,1].min(), WATER[:,1].max(), 10)
z_axis = np.linspace(WATER[:,2].min(), WATER[:,2].max(), 10)
x_hist, _ = np.histogram(WATER[:,0], x_axis, normed=True)
y_hist, _ = np.histogram(WATER[:,1], y_axis, normed=True)
z_hist, _ = np.histogram(WATER[:,2], z_axis, normed=True)
remark += " xdist: "
for i in x_hist:
remark += "{0:6.3f}".format(i)
remark += " ydist: "
for i in y_hist:
remark += "{0:6.3f}".format(i)
remark += " zdist: "
for i in z_hist:
remark += "{0:6.3f}".format(i)
'''
### MI of CNT calculation
for atom in CNT:
Ixx += (atom[1]**2 + atom[2]**2) / N_CNT
Iyy += (atom[0]**2 + atom[2]**2) / N_CNT
Izz += (atom[0]**2 + atom[1]**2) / N_CNT
Ixy -= (atom[0] * atom[1]) / N_CNT
Ixz -= (atom[0] * atom[2]) / N_CNT
Iyz -= (atom[1] * atom[2]) / N_CNT
I = np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz],
[Ixz, Iyz, Izz]]) # the moment of inertia tensor
eigval, eigvec = np.linalg.eig(
I) # eigval[0] is the minimum among the values.
U = np.matrix(eigvec)
Ut = U.T
### box rotation
for atom in CNT:
v = np.matrix([atom[0], atom[1], atom[2]]).T
Uv = Ut * v
atom[0] = float(Uv[2])
atom[1] = float(Uv[1])
atom[2] = float(Uv[0]) # CNT rotation
for atom in WATER:
v = np.matrix([atom[0], atom[1], atom[2]]).T
Uv = Ut * v
atom[0] = float(Uv[2])
atom[1] = float(Uv[1])
atom[2] = float(Uv[0]) # water rotation
### save coordinates to BGF after rotation
myBGF2 = bgf.BgfFile()
for index, i in enumerate(CNT):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index
newatom.aName = 'C' + str(index)
newatom.rName = 'CNT'
newatom.ffType = 'C_'
newatom.chain = 'A'
newatom.rNo = 1
myBGF2.addAtom(newatom)
for index, i in enumerate(WATER):
newatom = bgf.BgfAtom()
newatom.x, newatom.y, newatom.z = i
newatom.aNo = index + n_CNT
newatom.aName = 'O'
newatom.rName = 'WAT'
newatom.ffType = 'OW'
newatom.chain = 'O'
newatom.rNo = 100
myBGF2.addAtom(newatom)
myBGF2.REMARK.append('TIMESTEP ' + str(timestep))
myBGF2.PERIOD = "111"
myBGF2.AXES = "ZYX"
myBGF2.SGNAME = "P 1 1 1"
myBGF2.CELLS = [-1, 1, -1, 1, -1, 1]
myBGF2.CRYSTX = [boxsize[0], boxsize[1], boxsize[2], 90.0, 90.0, 90.0]
myBGF2.saveBGF(temp_dir + bgf_file.split(".bgf")[0] + "." +
str(timestep) + ".rot.bgf")
### CNT height
_, _, min_z_CNT = CNT.min(axis=0)
_, _, max_z_CNT = CNT.max(axis=0)
height_CNT = max_z_CNT - min_z_CNT
### CNT radius
x_CNT, y_CNT, z_CNT = np.mean(CNT, axis=0)
x_std_CNT, y_std_CNT, z_std_CNT = np.std(CNT, axis=0)
if x_std_CNT > 1.0 or y_std_CNT > 1.0:
remark += ""
### radius of CNT
l_r_CNT = []
for atom in CNT:
l_r_CNT.append(
math.sqrt((atom[0] - x_CNT)**2 + (atom[1] - y_CNT)**2))
r_CNT = np.mean(l_r_CNT)
std_r_CNT = np.std(l_r_CNT)
### get water molecules in CNT
# inside the CNT := min_z_CNT <= z <= max_z_CNT and (x - (x_diff/2))**2 + (y - (y_diff/2))**2 < r_CNT**2
# aNo_WAT_O_atoms: molecules which O atom is within CNT
# we don't need to calculate H atoms. Let's consider only O atoms
#####
margin = 0.0
# water molecules far from the margin will be only considered
WAT_in_CNT = []
for atom in WATER:
dist_sq = (atom[0] - x_CNT)**2 + (atom[1] - y_CNT)**2
if min_z_CNT + margin <= atom[2] and atom[
2] <= max_z_CNT - margin and dist_sq < r_CNT**2:
WAT_in_CNT.append(atom)
n_WAT_in_CNT = len(WAT_in_CNT)
'''
### WATER bad contact check: copy-failure-proof: NEED CORRECTION
WAT1 = []; WAT2 = [];
for index1, i in enumerate(WAT_in_CNT):
for j in WATER[index1:]:
WAT1.append(i); WAT2.append(j);
WAT1 = np.array(WAT1); WAT2 = np.array(WAT2)
min_dists = np.min(np.dstack(((WAT1 - WAT2) % boxsize, (WAT2 - WAT1) % boxsize)), axis = 2)
dists = np.sqrt(np.sum(min_dists ** 2, axis = 1))
for d in dists:
if d > 0 and d < 1.0:
remark += "Bad contacts" + str(d)
continue;
'''
d = "{0:8.3f}"
e = "{0:6.1f}"
output = "{0:<10}".format(timestep) + str(
n_WAT_in_CNT
) + ' | ' + d.format(r_CNT) + d.format(std_r_CNT) + ' | ' + e.format(
boxsize[0]
) + e.format(boxsize[1]) + e.format(boxsize[2]) + ' | ' + e.format(
min_x_CNT) + e.format(max_x_CNT) + e.format(min_y_CNT) + e.format(
max_y_CNT) + e.format(min_z_CNT) + e.format(
max_z_CNT) + ' | ' + e.format(height_CNT) + ' | ' + str(
replNum) + '\t' + str(copyNum) + '\t' + str(
len(WATER)) + '\t' + str(remark) + '\n'
ftemp.write(output)
sys.stdout.flush()
t2 = time.time() # time mark
elapsed_time = t2 - t1
processed_step += 1
print('')
ftemp.close()
print("Numbers of water molecules are written in " + out_file + " ..Done.")
return 1
def main():
if len(sys.argv) < 2:
print usage
sys.exit(0)
head = bgf.BgfFile(sys.argv[1])
head_mon = bgf.BgfFile(sys.argv[2])
monomer = bgf.BgfFile(sys.argv[3])
tail_mon = bgf.BgfFile(sys.argv[4])
tail = bgf.BgfFile(sys.argv[5])
target_mw = float(sys.argv[6])
ff_file = sys.argv[7]
# number of required monomers to make a PEGDE chain
mw_head = bgftools.getMoleculeMass(head, ff_file)
print("** Mw of Molecule head: " + "{0:5.3f}".format(mw_head))
mw_tail = bgftools.getMoleculeMass(tail, ff_file)
print("** Mw of Molecule tail: " + "{0:5.3f}".format(mw_tail))
mw_monomer = bgftools.getMoleculeMass(monomer, ff_file)
print("** Mw of Molecule monomer: " + "{0:5.3f}".format(mw_monomer))
print("** Requested Mw: " + str(target_mw))
# number of required monomers
n_monomers = round((target_mw - mw_head - mw_tail) / mw_monomer)
print("** Required number of monomers: " + str(int(n_monomers)))
actual_mw = mw_head + mw_tail + mw_monomer * n_monomers
print("** Actual Mw: " + "{0:5.3f}".format(actual_mw))
### overall structure
### head -- head_mon -- monomer -- tail_mon -- tail
### connect blocks
m1 = copy.deepcopy(
head_mon) # start adding monomers from the head_near monomer
for atom in m1.a:
atom.rNo = 1
atom.rName = 'MON'
print("* attaching head_monomer")
n_monomers = int(n_monomers)
### monomer - monomer: 1H_T -- 2H_H
for i in range(n_monomers - 1):
# if the last monomer, attach tail_monomer
# else prepare monomer 2
if i == n_monomers - 2:
print("* attaching tail_monomer")
m2 = copy.deepcopy(tail_mon)
else:
print("* attaching monomer " + str(i))
m2 = copy.deepcopy(monomer)
# renumber residue numbers
for atom in m2.a:
atom.rNo = i + 2
atom.rName = 'MON'
# move H_H of m2 to H_T of m1 position
h_t = 0
h_h = 0
for atom in m1.a:
if atom.ffType == "H_T" and atom.rNo == i + 1:
h_t = atom
for atom in m2.a:
if atom.ffType == "H_H" and atom.rNo == i + 2:
h_h = atom
for atom in m2.a:
atom.x += h_t.x
atom.y += h_t.y
atom.z += h_t.z
# delete H_T in monomer
m1.delAtom(m1.a2i[h_t.aNo])
m1.renumber()
# delete H_H in monomer2
m2.delAtom(m2.a2i[h_h.aNo])
m2.renumber()
# merge
m1 = m1.merge(m2, True)
m1.renumber()
# find tag in the merged molecule
atomH = bgf.BgfAtom()
atomT = bgf.BgfAtom()
for atom in m1.a:
if 'T' in atom.chain and atom.rNo == i + 1:
atomT = atom
if 'H' in atom.chain and atom.rNo == i + 2:
atomH = atom
# update chain
atomT.chain = "A"
atomH.chain = "A"
# connect
m1.connect(m1.a2i[atomH.aNo], m1.a2i[atomT.aNo])
#m1.saveBGF('temp_monomer.bgf')
### head - monomer: H_EG -- H_H
# head
h1 = copy.deepcopy(head)
for atom in h1.a:
atom.rNo = 100
atom.rName = 'HED'
h_eg = 0
h_h = 0
for atom in h1.a:
if atom.ffType == "H_EG":
h_eg = atom
for atom in m1.a:
if atom.ffType == "H_H":
h_h = atom
for atom in m1.a:
atom.x += h_eg.x
atom.y += h_eg.y
atom.z += h_eg.z
h1.delAtom(h1.a2i[h_eg.aNo])
h1.renumber()
m1.delAtom(m1.a2i[h_h.aNo])
m1.renumber()
h1 = h1.merge(m1, True)
h1.renumber()
atomH = bgf.BgfAtom()
atomT = bgf.BgfAtom()
for atom in h1.a:
if 'T' in atom.chain and 'HED' in atom.rName:
atomT = atom
if 'H' in atom.chain and 'MON' in atom.rName:
atomH = atom
h1.connect(h1.a2i[atomT.aNo], h1.a2i[atomH.aNo])
#h1.saveBGF('temp_h-m.bgf')
# monomer - tail: H_T -- H_EG
t1 = copy.deepcopy(tail)
for atom in t1.a:
atom.rNo = 200
atom.rName = 'TAL'
h_t = 0
h_eg = 0
for atom in h1.a:
if atom.ffType == "H_T":
h_t = atom
for atom in t1.a:
if atom.ffType == "H_EG":
h_eg = atom
for atom in t1.a:
atom.x += h_t.x
atom.y += h_t.y
atom.z += h_t.z
h1.delAtom(h1.a2i[h_t.aNo])
h1.renumber()
t1.delAtom(t1.a2i[h_eg.aNo])
t1.renumber()
h1 = h1.merge(t1, True)
h1.renumber()
atomH = bgf.BgfAtom()
atomT = bgf.BgfAtom()
for atom in h1.a:
if 'T' in atom.chain and 'MON' in atom.rName:
atomT = atom
if 'H' in atom.chain and 'TAL' in atom.rName:
atomH = atom
h1.connect(h1.a2i[atomT.aNo], h1.a2i[atomH.aNo])
# adding remarks
h1.REMARK.append("Polymer Generated at " +
str(time.asctime(time.gmtime())))
h1.REMARK.append("head: " + sys.argv[1] + ", head_mon: " + sys.argv[2] +
", monomer: " + sys.argv[3] + ", tail_mon: " +
sys.argv[4] + ", tail: " + sys.argv[5])
h1.REMARK.append("Target Mw: " + str(sys.argv[6]) + ", Actual Mw: " +
"{0:5.3f}".format(actual_mw))
h1.REMARK.append("Number of monomers: " + str(n_monomers))
h1.REMARK.append("ff: " + sys.argv[7])
h1.saveBGF('generated_charge.bgf')
def addIons(bgf_file, out_file, region, number, silent=False):
"""
def addIons():
Write what this function does.
Function Parameters:
-b bgf_file A string of filename or BgfFile class.
-o out_file A string of filename or BgfFile class.
-n number
-r region: "xlo xhi ylo yhi zlo zhi"
"""
# open BGF
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("opening bgf file.. " + str(bgf_file))
myBGF = bgf.BgfFile(bgf_file)
boxsize = [myBGF.CRYSTX[0], myBGF.CRYSTX[1], myBGF.CRYSTX[2]]
### find the last HETATM
aNo_lastHETAtom = 0
for i in myBGF.a:
aNo = i.aNo
if i.aTag == 1:
if aNo > aNo_lastHETAtom:
aNo_lastHETAtom = aNo
for i in range(number):
"""
randx = random.uniform(0, boxsize[0])
randy = random.uniform(0, boxsize[1])
randz = random.uniform(0, boxsize[2])
"""
randx = random.uniform(region[0], region[1])
randy = random.uniform(region[2], region[3])
randz = random.uniform(region[4], region[5])
# Na+ ion
atom_Na = bgf.BgfAtom()
atom_Na.x = randx
atom_Na.y = randy
atom_Na.z = randz
atom_Na.aTag = 1 # HETATM
atom_Na.ffType = "Na"
atom_Na.rName = "ION"
atom_Na.aName = "Na"
atom_Na.charge = 1.00
atom_Na.rNo = 0
atom_Na.chain = "X"
# Cl- ion
atom_Cl = bgf.BgfAtom()
atom_Cl.x = randx + 2
atom_Cl.y = randy + 2
atom_Cl.z = randz + 2
atom_Cl.aTag = 1 # HETATM
atom_Cl.ffType = "Cl"
atom_Cl.rName = "ION"
atom_Cl.aName = "Cl"
atom_Cl.charge = -1.00
atom_Cl.rNo = 0
atom_Cl.chain = "X"
myBGF.addAtom(atom_Na, myBGF.a2i[aNo_lastHETAtom + 1])
myBGF.addAtom(atom_Cl, myBGF.a2i[aNo_lastHETAtom + 2])
myBGF.renumber()
# save BGF
if isinstance(out_file, str):
if not silent: print("Saving information to " + out_file + " ..")
myBGF.saveBGF(out_file)
return 1
else:
return myBGF
def protonate(bgf_file, out_file, log_file, silent=False):
"""
protonate(bgf_file, out_file, log_file, silent=False):
Protonate (performs alkylation of primary amines) the given bgf file.
To-do:
"""
# initialization
# open bgffile
myBGF = bgf.BgfFile(bgf_file)
# find all inserted hydrogen
N_index = []
for atom in myBGF.a:
if "H+" in atom.aName:
N_index.append(atom.aNo)
N_number = len(N_index)
# the number of all inserted hydrogen atoms
if not silent: print(str(N_number) + " protonated sites are found.")
# find the last HETATM (insertion position)
last_hetatm_aNo = 0
for atom in myBGF.a:
if atom.aTag != 1:
last_hetatm_aNo = atom.aNo
break
# add Cl atoms
if len(N_index) > 0:
for index, aNo in enumerate(N_index):
if not silent:
print("*** Protonated Hydrogen " + str(aNo) + " ***")
atom_H = myBGF.getAtom(aNo)
# new Cl atom near atom_H
atom_Cl = bgf.BgfAtom()
atom_Cl.x = atom_H.x + 3
atom_Cl.y = atom_H.y + 3
atom_Cl.z = atom_H.z + 3
atom_Cl.aName = "Cl"
atom_Cl.rName = "ION"
atom_Cl.chain = "A"
atom_Cl.aTag = 1
atom_Cl.rNo = 0
atom_Cl.ffType = "Cl"
atom_Cl.aNo = last_hetatm_aNo
atom_Cl.charge = -1.0000
myBGF.addAtom(atom_Cl, last_hetatm_aNo - 1)
if not silent: print("Total charge: " + " : " + str(myBGF.charge()))
# renumber
myBGF.renumber()
# save
myBGF.REMARK.insert(
0, "Ion added by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
myBGF.saveBGF(out_file)
if not silent: print("saving file " + out_file)
else:
if not silent:
print("No amine groups to be counter-ionized")
sys.exit(0)
if not silent: print("Done.")
def protonate(bgf_file,
ff_file,
probability,
out_file,
log_file,
silent=False):
"""
protonate(bgf_file, ff_file, suffix, nodes, criteria, t, out_file):
Protonate (performs alkylation of primary amines) the given bgf file.
To-do:
clean temp file management
display appropriate messages
server environments
"""
# initialization
# open bgffile
myBGF = bgf.BgfFile(bgf_file)
# find all tertiary amines
N_index = []
last_hetatm_aNo = 0
for atom in myBGF.a:
if string.strip(atom.ffType) == "N_3":
if "PRI" in atom.rName:
N_index.append(atom.aNo)
N_number = len(N_index)
# the number of all tertiary amines
if not silent: print(str(N_number) + " primary amines are found.")
# find the last HETATM (insertion position)
for atom in myBGF.a:
if atom.aTag != 1:
last_hetatm_aNo = atom.aNo
break
print(last_hetatm_aNo)
# choose the primary amines randomly according to the probability
if not probability == 1.0:
N_choose = int(N_number * probability)
N_index = random.sample(N_index, N_choose)
if not silent:
print(str(len(N_index)) + " primary amines will be protonated.")
# add an hydrogen
if len(N_index) > 0:
for index, aNo in enumerate(N_index):
if not silent: print("*** Primary amine " + str(aNo) + " ***")
atom_Npri = myBGF.getAtom(aNo) # N from the N_index list
# new proton on primary amine
proton = bgf.BgfAtom()
proton.x = atom_Npri.x + 1
proton.y = atom_Npri.y + 1
proton.z = atom_Npri.z + 1
proton.aName = "H+_" + str(index)
proton.rName = "PRI"
proton.chain = "A"
proton.aTag = 1
proton.rNo = atom_Npri.rNo
proton.ffType = "H_"
proton.aNo = last_hetatm_aNo
myBGF.addAtom(proton, last_hetatm_aNo - 1)
proton = myBGF.getAtom(
last_hetatm_aNo) # since (proton) != (proton add in myBGF)
#proton.aName = "H++"
myBGF.connect(myBGF.a2i[atom_Npri.aNo],
myBGF.a2i[proton.aNo]) # connect
# charge change: NH3 - CH2 - CH2 - .....
# 1. NH3 part
N_CONECT_aNo = atom_Npri.CONECT
N_CONECT_C_aNo = []
N_CONECT_H_aNo = []
for ano in N_CONECT_aNo:
atom = myBGF.getAtom(ano)
if "C" in atom.ffType:
N_CONECT_C_aNo.append(atom.aNo)
elif "H" in atom.ffType:
N_CONECT_H_aNo.append(atom.aNo)
else:
nu.die(str(atom))
if len(N_CONECT_C_aNo) != 1:
nu.die("Number of C atoms connected with primary amine " +
str(atom_Npri.aNo) + " mismatch!")
if len(N_CONECT_H_aNo) != 3:
nu.die("Number of H atoms connected with primary amine " +
str(atom_Npri.aNo) + " mismatch!")
atom_C2 = myBGF.getAtom(N_CONECT_C_aNo[0])
atom_HN1 = myBGF.getAtom(N_CONECT_H_aNo[0])
atom_HN2 = myBGF.getAtom(N_CONECT_H_aNo[1])
atom_HN3 = myBGF.getAtom(N_CONECT_H_aNo[2])
# update charges
old_NH3_charge = atom_Npri.charge + atom_HN1.charge + atom_HN2.charge + atom_HN3.charge
atom_Npri.charge = -0.72540
atom_HN1.charge = 0.43330
atom_HN2.charge = 0.43330
atom_HN3.charge = 0.43330
new_NH3_charge = atom_Npri.charge + atom_HN1.charge + atom_HN2.charge + atom_HN3.charge
NH3_charge_change = new_NH3_charge - old_NH3_charge
if not silent:
print("NH3 site charge change: " + str(atom_Npri.aNo) + " : " +
str(NH3_charge_change))
# 2. first CH2 part
C2_CONECT_aNo = atom_C2.CONECT
C2_CONECT_C_aNo = []
C2_CONECT_H_aNo = []
for ano in C2_CONECT_aNo:
atom = myBGF.getAtom(ano)
if "H" in atom.ffType:
C2_CONECT_H_aNo.append(atom.aNo)
elif "C" in atom.ffType and ano != atom_C2.aNo:
C2_CONECT_C_aNo.append(atom.aNo)
if len(C2_CONECT_H_aNo) != 2:
nu.die("Number of H atoms connected with primary amine " +
str(atom_C2.aNo) + " mismatch!")
if len(C2_CONECT_C_aNo) != 1:
nu.die("Number of C atoms connected with primary amine " +
str(atom_C2.aNo) + " mismatch!")
atom_C3 = myBGF.getAtom(C2_CONECT_C_aNo[0])
atom_HC21 = myBGF.getAtom(C2_CONECT_H_aNo[0])
atom_HC22 = myBGF.getAtom(C2_CONECT_H_aNo[1])
old_CH2_charge = atom_C2.charge + atom_HC21.charge + atom_HC22.charge
#if not silent: print((atom_C2.charge, atom_HC21.charge, atom_HC22.charge))
#if not silent: print("old CH2 site charge change: " + str(atom_Npri.aNo) + " : " + str(old_CH2_charge))
atom_C2.charge = -0.20790
atom_HC21.charge = 0.24090
atom_HC22.charge = 0.24090
new_CH2_charge = atom_C2.charge + atom_HC21.charge + atom_HC22.charge
#if not silent: print("new CH2 site charge change: " + str(atom_Npri.aNo) + " : " + str(new_CH2_charge))
CH2_charge_change = new_CH2_charge - old_CH2_charge
if not silent:
print("CH2 site charge change: " + str(atom_Npri.aNo) + " : " +
str(CH2_charge_change))
delta_charge = NH3_charge_change + CH2_charge_change
if not silent:
print("Primary amine site charge change: " +
str(atom_Npri.aNo) + " : " + str(delta_charge))
# 3. second CH2 part
old_C3_charge = atom_C3.charge
if not silent: print("Old C3 charge: " + str(atom_C3.charge))
atom_C3.charge = atom_C3.charge + (1 - delta_charge)
if not silent: print("New C3 charge: " + str(atom_C3.charge))
if not silent:
print("Total charge: " + " : " + str(myBGF.charge()))
# renumber
myBGF.renumber()
# save
myBGF.REMARK.insert(
0, "Protonated by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
myBGF.saveBGF(bgf_file[:-4] + "_protonated.bgf")
if not silent:
print("saving file " + bgf_file[:-4] + "_protonated.bgf")
else:
if not silent:
print("No amine groups to be protonated")
sys.exit(0)
if not silent: print("Done.")