def adjust_interior_water(self, n_water):
if not self._water_position_determined:
nu.warn("You have to run determine_water_position() first.")
return
if not n_water:
nu.warn(
"You must specify the number of water molecules inside the Nanotube."
)
return
self.bgfmodel = bgftools.renumberMolecules(self.bgfmodel, 0, False)
waters = set()
for atom in self.bgfmodel.a:
if atom.chain == 'I':
waters.add(atom.rNo)
waters = list(waters)
print("\tFound %d interior water molecules." % len(waters))
if len(waters) < n_water:
nu.warn("Too few solvent molecules to choose %d molecules." %
n_water)
return
rNos = random.sample(waters, n_water)
print("%d water molecules are randomly chosen. Others are removed." %
n_water)
delist = []
for atom in self.bgfmodel.a:
if atom.chain == 'I' and not atom.rNo in rNos:
delist.append(self.bgfmodel.a2i[atom.aNo])
delist.sort()
self.bgfmodel.delAtoms(delist, False)
self.bgfmodel.renumber()
self.bgfmodel = bgftools.renumberMolecules(self.bgfmodel, 0, False)
self.update()
def determine_water_position(self, *args):
print("Marking water molecules whether internal or external..")
if self.isRadiusCalc == False:
nu.warn("Nanotube radius not calculated.")
return 0
tempBGF = bgf.BgfFile()
tempBGF = bgftools.make_periodic(tempBGF, self.pbc)
self.make_pbc(self.pbc, self.bgfmodel.CRYSTX)
# copy Nanotube atoms
for atom in self.NTatoms + self.otheratoms:
atom2 = copy.deepcopy(atom)
tempBGF.addAtom(atom2)
tempBGF.renumber()
# mark rNames to Oxygen atoms
n_oxygen_inside = 0
n_oxygen_outside = 0
for atom in self.WATatoms:
if "H" in atom.ffType:
continue
xyz = np.array([atom.x, atom.y, atom.z])
r = np.sqrt(
((xyz * self.axis - self.center * self.axis)**2).sum(axis=-1))
h = (xyz * self.axismask).sum()
if r < self.radius:
# inside O
atom.chain = "I"
n_oxygen_inside += 1
else:
# outside O
atom.chain = "O"
n_oxygen_outside += 1
print("Interior oxygens: " + str(n_oxygen_inside) +
", exterior oxygens: " + str(n_oxygen_outside))
self.n_inside_water = n_oxygen_inside
self.n_outside_water = n_oxygen_outside
# write water molecules
chain = ["I", "O"]
for cname in chain:
print("Passing " + cname)
for atom in self.WATatoms:
if cname in atom.chain and "O" in atom.ffType:
tempBGF.addAtom(atom) #
l_Hatoms = atom.CONECT
for index, ano in enumerate(l_Hatoms):
atom2 = self.bgfmodel.getAtom(ano)
atom2.chain = cname
tempBGF.addAtom(atom2) #
self.bgfmodel = tempBGF
self.bgfmodel.renumber()
self.bgfmodel = bgftools.renumberMolecules(self.bgfmodel, 0, False)
self.update()
print(
"Water molecules are identified into interior(I) and exterior(O).")
if len(args) == 0:
nu.warn(
"Residue name and coords for water molecules are modified.")
elif len(args) == 1:
print("Modified BGF file is saved to " + str(args[0]))
self.bgfmodel.saveBGF(args[0])
self._water_position_determined = True
def renumberResNum(bgf_file, out_file, silent=True):
bgftools.renumberMolecules(bgf_file, out_file, False)
if len(sys.argv) < 3:
print(usage)
sys.exit(0)
mybgf = bgf.BgfFile(sys.argv[1])
out_file = sys.argv[2]
selection = sys.argv[3]
n_del = int(sys.argv[4])
resid = set()
for atom in mybgf.a:
if eval(selection):
resid.add(atom.rNo)
resid = list(resid)
if len(resid) < n_del:
nu.die("Not enough molecules to choose %d molecules to delete." % n_del)
rnos = random.sample(resid, n_del)
delist = []
for atom in mybgf.a:
if atom.rNo in rnos:
delist.append(mybgf.a2i[atom.aNo])
mybgf.delAtoms(delist)
mybgf.renumber()
mybgf.saveBGF(out_file)
bt.renumberMolecules(out_file, out_file)
for atom in newBGF.a:
atom.aTag = 0 # change into ATOM
atom.rName = "WAT"
if "O" in atom.ffType:
atom.aName = "O"
atom.ffType = water_O_ffType
l_Hatoms = atom.CONECT
for index, ano2 in enumerate(l_Hatoms):
atom2 = newBGF.getAtom(ano2)
atom2.aName = "H" + str(index + 1)
atom2.ffType = water_H_ffType
# merge myBGF and newBGF
myBGF = myBGF.merge(newBGF, True)
myBGF.renumber()
# save
myBGF = bgftools.renumberMolecules(myBGF, 0)
myBGF.renumber()
try:
bgf_file = sys.argv[2]
except:
myBGF.saveBGF(sys.argv[1].split(".bgf")[0] + "_mod.bgf")
else:
myBGF.saveBGF(bgf_file)
### end
mybgf, 'atom.z', selection="'S_3a' in atom.ffType and atom.rNo == 2")
avg_s3b_z2 = bt.atoms_average(
mybgf, 'atom.z', selection="'S_3b' in atom.ffType and atom.rNo == 2")
# prepare water box
solvent = bgf.BgfFile('/home/noische/scripts/dat/WAT/spc_box.bgf')
solvent = bt.stress_cell(solvent, str(1 / math.pow(1.7, 0.3333)))
solvent.saveBGF('_solvent.bgf')
addsolv_reg_cmd = "/qcfs/noische/scripts/BGF_addSolvent_region.py -b _temp.bgf -f %s -o _temp.bgf -m '0 0 %f' -M '%f %f %f' -n %d -t _solvent.bgf -v I" % (
ff_file, avg_s3a_z1 + 1.5, result.CRYSTX[0], result.CRYSTX[1],
avg_s3b_z2 - 1.0, n_wat)
print("** Adding confined water..")
print(addsolv_reg_cmd)
os.system(addsolv_reg_cmd)
bt.renumberMolecules('_temp.bgf', '_temp.bgf')
if len(sys.argv) == 8:
os.system("mv _temp.bgf %s" % out_file)
sys.exit(0)
# add water outside mos2: bottom
addsolv_reg_cmd = "/qcfs/noische/scripts/BGF_addSolvent_region.py -b _temp.bgf -f %s -o _temp.bgf -M '%f %f %f' -v O" % (
ff_file, result.CRYSTX[0], result.CRYSTX[1], avg_s3b_z1 - 0.5)
print("** Adding bottom water..")
print(addsolv_reg_cmd)
os.system(addsolv_reg_cmd)
bt.renumberMolecules('_temp.bgf', '_temp.bgf')
# add water outside mos2: top
addsolv_reg_cmd = "/qcfs/noische/scripts/BGF_addSolvent_region.py -b _temp.bgf -f %s -m '0 0 %f' -o %s -v O" % (
def addsolvent(bgf_file,
solvent_bgf,
min,
max,
n_solvent,
out_file,
ff_file,
margin,
mark,
silent=True):
### initialize
water = False
default_margin = 1.0
x_margin = 0.0
y_margin = 0.0
z_margin = 0.0
if "x" in margin.lower():
x_margin = default_margin
if "y" in margin.lower():
y_margin = default_margin
if "z" in margin.lower():
z_margin = default_margin
### load the solute bgf file
if not silent: print("Initializing..")
myBGF = bgf.BgfFile(bgf_file) # str
myBGF.renumber()
if not silent: print("Loading the solvent file " + solvent_bgf + " ..")
solventBGF = bgf.BgfFile(solvent_bgf)
### Generate error when the solvent box is not periodic:
if not solventBGF.PERIOD:
nu.die(
"addSolvent: The solvent file is not periodic. Use a box full of solvent."
)
### Check the type of solvent
if not silent:
print("(the solvent box seems to be full of " +
os.path.basename(solvent_file)[:-4] + " )")
if "f3c" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
if "spc" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
if "tip" in solvent_bgf:
water = True # this flag is used to remove the bad contacts with the molecule.
### calculate the box size
if not silent: print("Analyzing box information..")
if not min:
min = [0.0, 0.0, 0.0]
if not max:
max = myBGF.CRYSTX[:3]
strsize = [
max[0] - min[0] - x_margin, max[1] - min[1] - y_margin,
max[2] - min[2] - z_margin
]
waterboxsize = solventBGF.CRYSTX[:3] # REMARK: This is a kind of constant.
copyNumber = [0, 0, 0]
for index, i in enumerate(copyNumber):
copyNumber[index] = math.ceil(
strsize[index] /
waterboxsize[index]) # how many times to replicate the water box
if not silent: print("Creating box information: " + str(strsize))
### replicate the solvent box
if not silent: print("Creating box.. this may take some time.")
bigboxBGF = bgftools.replicateCell(solventBGF, copyNumber, True)
bigboxBGF.saveBGF("_replicate.bgf")
if not silent:
print("- Number of atoms in the created box: " + str(len(bigboxBGF.a)))
delatom = []
delsolvent = []
delsolventindex = []
delwater = []
delwaterindex = []
bigboxBGF = bgf.BgfFile("_replicate.bgf")
bigboxBGF.renumber()
### trim the water box
if water:
if not silent:
print("Generating water box.. Calculating water molecules")
for atom in bigboxBGF.a:
if atom.x > strsize[0] or atom.y > strsize[1] or atom.z > strsize[
2]:
delatom.append(atom.aNo)
for aNo in delatom:
water_molecule = bgftools.is_water(bigboxBGF, aNo)
if not water_molecule in delwater:
delwater.append(water_molecule)
delwater = nu.flatten(delwater)
delwater = nu.removeRepeat(delwater)
for aNo in delwater:
delwaterindex.append(bigboxBGF.a2i[aNo])
if not silent: print("Generating water box.. Trimming")
bigboxBGF.delAtoms(delwaterindex, False)
bigboxBGF.renumber()
elif not water:
if not silent:
print("Generating solvent box.. Extracting solvent molecules")
for atom in tqdm.tqdm(bigboxBGF.a, desc='Iterating', ncols=120):
if atom.x > strsize[0] or atom.y > strsize[1] or atom.z > strsize[
2]:
delatom.append(atom.aNo)
molecule = bgftools.getMoleculeList(bigboxBGF)
for aNo in tqdm.tqdm(delatom,
desc='Appending atoms to remove',
ncols=120):
for i in molecule:
if aNo in i:
delsolvent += i
break
delsolvent = list(set(delsolvent))
for aNo in delsolvent:
delsolventindex.append(bigboxBGF.a2i[aNo])
if not silent: print("Generating solvent box.. Trimming")
delsolventindex.sort()
#delsolventindex.reverse()
bigboxBGF.delAtoms(delsolventindex, False)
bigboxBGF.renumber()
bigboxBGF.saveBGF("_temp.bgf") ## debug
### remain n molecules and delete residues
bigboxBGF = bgftools.renumberMolecules(bigboxBGF, 0, False) # renumber rNo
if n_solvent:
residues = set()
for atom in bigboxBGF.a:
residues.add(atom.rNo) # scan molecule rNo
residues = list(residues)
if not silent: print("Found %d water molecules." % len(residues))
if len(residues) < n_solvent:
nu.die("Too few solvent molecules to choose %d molecules." %
n_solvent)
rNos = random.sample(residues, n_solvent) # select n molecules
if not silent: print("%d water molecules are chosen." % n_solvent)
# delete molecules
delist = []
for atom in bigboxBGF.a:
if not atom.rNo in rNos:
delist.append(bigboxBGF.a2i[atom.aNo]) # if not chosen, delete
delist.sort()
bigboxBGF.delAtoms(delist, False)
bigboxBGF.renumber()
bigboxBGF = bgftools.renumberMolecules(bigboxBGF, 0, False)
### move the water box to min position
for atom in bigboxBGF.a:
atom.x += min[0] + x_margin / 2
atom.y += min[1] + y_margin / 2
atom.z += min[2] + z_margin / 2
### add mark to the solvents
if mark:
for atom in bigboxBGF.a:
atom.chain = mark
bigboxBGF.saveBGF('_temp.bgf')
# REMARK: it is natural to have the periodic information of water box for the output BGF file.
# REMARK: HETATOM should be located on the first of the BGF file. So use dummy for merging.
## compute stats for adding solvents
if not silent: print("\nComputing stats..")
mol_list = bgftools.getMoleculeList(bigboxBGF)
n_mol = len(mol_list)
n_atom = len(nu.flatten(mol_list))
if not silent:
print(
str(n_mol) + " molecules (" + str(n_atom) +
" atoms) will be added.")
## merge
#bigboxBGF = myBGF.merge(bigboxBGF, True)
myBGF = bgf.BgfFile(bgf_file)
bigboxBGF = bgf.BgfFile("_temp.bgf")
bigboxBGF2 = myBGF.merge(bigboxBGF)
if not silent: print("Total atoms in the file: " + str(len(bigboxBGF.a)))
## some paperworking for periodic box
bigboxBGF2.OTHER = myBGF.OTHER
bigboxBGF2.PERIOD = myBGF.PERIOD
bigboxBGF2.AXES = myBGF.AXES
bigboxBGF2.SGNAME = myBGF.SGNAME
bigboxBGF2.CRYSTX = myBGF.CRYSTX
bigboxBGF2.CELLS = myBGF.CELLS
### record BGF remarks
bigboxBGF2.REMARK.insert(
0, "Solvents added by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
bigboxBGF2.REMARK.insert(0, "Solvents: " + str(solvent_file))
### save BGF
if not silent: print("Saving the file.. see " + str(out_file))
bigboxBGF2.saveBGF(out_file)
return 1