def centerbgffileclass(myBGF, method="com_origin"):
new_x, new_y, new_z = bgftools.getCom(myBGF, "")
if len(myBGF.CRYSTX) > 2:
boxcenter = [(i / 2.0) for i in myBGF.CRYSTX[0:3]]
else:
boxsize = bgf.getBGFSize(myBGF, 0)
boxcenter = [(boxsize[1] - boxsize[0]) / 2,
(boxsize[3] - boxsize[2]) / 2,
(boxsize[5] - boxsize[4]) / 2]
if method == "com_origin":
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
elif method == "com_center":
dx = boxcenter[0] - new_x
dy = boxcenter[1] - new_y
dz = boxcenter[2] - new_z
bgf.moveBGF(myBGF, dx, dy, dz)
elif method == "box_origin":
dx = boxcenter[0]
dy = boxcenter[1]
dz = boxcenter[2]
bgf.moveBGF(myBGF, dx, dy, dz)
else:
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
return myBGF
def centerbgf(bgf_file, out_file, ff_file, method="com_origin", silent=False):
if silent == 1:
nu.shutup()
boxcenter = []
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
if not silent:
print("Moving the origin of the coordinate in " + bgf_file +
" and saving to " + out_file + ".")
if method != "box_origin":
new_x, new_y, new_z = bgftools.getCom(myBGF, ff_file)
if len(myBGF.CRYSTX) > 2:
boxcenter = [(i / 2.0) for i in myBGF.CRYSTX[0:3]]
else:
boxsize = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
boxcenter = [(boxsize[1] - boxsize[0]) / 2,
(boxsize[3] - boxsize[2]) / 2,
(boxsize[5] - boxsize[4]) / 2]
if method == "com_origin":
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
elif method == "com_center":
dx = boxcenter[0] - new_x
dy = boxcenter[1] - new_y
dz = boxcenter[2] - new_z
bgf.moveBGF(myBGF, dx, dy, dz)
elif method == "box_origin":
dx = boxcenter[0]
dy = boxcenter[1]
dz = boxcenter[2]
bgf.moveBGF(myBGF, dx, dy, dz)
else:
bgf.moveBGF(myBGF, (-new_x), (-new_y), (-new_z))
# save
if isinstance(out_file, str):
if not silent: print("Saving information to " + out_file + " ..")
myBGF.saveBGF(out_file)
return 1
else:
return myBGF
def addsolvent(bgf_file,
solvent_bgf,
size,
margin,
out_file,
ff_file,
silent=True):
### initialize
water = False
### load the solute bgf file
if not silent: print("Initializing..")
myBGF = bgf.BgfFile(bgf_file) # str
#solventBGF = bgf.BgfFile("/home/noische/scripts/dat/WAT/f3c_box.bgf") # F3C waterbox
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 len(myBGF.CRYSTX) > 2:
strsize = [myBGF.CRYSTX[0], myBGF.CRYSTX[1], myBGF.CRYSTX[2]]
else:
box = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
strsize = [box[1] - box[0], box[3] - box[2], box[5] - box[4]]
###
if size == "" and margin != "":
strsize = [
strsize[0] + 2 * margin[0], strsize[1] + 2 * margin[1],
strsize[2] + 2 * margin[2]
] # add margin on str size
elif size != "" and margin == "":
strsize = size
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
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)))
### trim the water box
if water:
if not silent:
print("Generating water box.. Calculating water molecules")
delatom = []
delwater = []
delwaterindex = []
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)
delwater.sort()
delwater.reverse()
for aNo in delwater:
delwaterindex.append(bigboxBGF.getAtomIndex(aNo))
del (delwater)
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")
delatom = []
delsolvent = []
delsolventindex = []
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:
molecule_list = []
molecule = bgftools.getmolecule(bigboxBGF, bigboxBGF.getAtom(aNo),
molecule_list)
for number in molecule_list:
if not number in delsolvent: delsolvent.append(number)
delsolvent = nu.flatten(delsolvent)
delsolvent = nu.removeRepeat(delsolvent)
delsolvent.sort()
delsolvent.reverse()
for aNo in delsolvent:
delsolventindex.append(bigboxBGF.getAtomIndex(aNo))
if not silent: print("Generating solvent box.. Trimming")
bigboxBGF.delAtoms(delsolventindex, False)
bigboxBGF.renumber()
### merge two structure
# 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.
if not silent: print("\nAdding trimmed solvent box to the structure..")
bigboxcenter = [strsize[0] / 2, strsize[1] / 2, strsize[2] / 2]
a, b, c = bgftools.getCom(myBGF, ff_file)
bgf.moveBGF(myBGF, bigboxcenter[0] - a, bigboxcenter[1] - b,
bigboxcenter[2] - c)
## remove bad contacts between solutes and solvents
if not silent: print("Atom distance calculation for contacts..")
delatom = []
delsolvent = []
delsolventindex = []
for atom1 in myBGF.a:
for atom2 in bigboxBGF.a:
# if the distance between atom1 and atom2 is less than 2.8, add to a delete list
dist_sq = (atom1.x - atom2.x)**2 + (atom1.y - atom2.y)**2 + (
atom1.z - atom2.z)**2
if dist_sq < 7.84:
delatom.append(atom2.aNo)
# delete bad atoms!
if not silent: print("Removing bad contacts..")
for aNo in delatom:
molecule_list = []
molecule = bgftools.getmolecule(bigboxBGF, bigboxBGF.getAtom(aNo),
molecule_list)
for number in molecule_list:
if not number in delsolvent: delsolvent.append(number)
delsolvent = nu.flatten(delsolvent)
delsolvent = nu.removeRepeat(delsolvent)
delsolvent.sort()
delsolvent.reverse()
for aNo in delsolvent:
delsolventindex.append(bigboxBGF.getAtomIndex(aNo))
bigboxBGF.delAtoms(delsolventindex, False)
bigboxBGF.renumber()
## 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)
if not silent: print("Total atoms in the file: " + str(len(bigboxBGF.a)))
## some paperworking for periodic box
bigboxBGF.OTHER = solventBGF.OTHER
bigboxBGF.PERIOD = solventBGF.PERIOD
bigboxBGF.AXES = solventBGF.AXES
bigboxBGF.SGNAME = solventBGF.SGNAME
bigboxBGF.CRYSTX = solventBGF.CRYSTX
bigboxBGF.CELLS = solventBGF.CELLS
## adjust the size of the box
bigboxBGF.CRYSTX = [
strsize[0], strsize[1], strsize[2], solventBGF.CRYSTX[3],
solventBGF.CRYSTX[4], solventBGF.CRYSTX[5]
]
"""
### remove bad contacts and save
if water:
if not silent: print("Removing bad contacts: distance criteria is 2.8 A")
bigboxBGF = removebadcontacts(bigboxBGF, bigboxBGF, 2.8)
### renumber residue numbers
# RULE: all rNos for water molecules will be renumbered from 2. (for createLammpsInput.pl)
if not silent: print("Renumbering water molecules..")
max_rNo_in_hetatm = 0;
oxygen_list = bgftools.listOxygenAtoms(bigboxBGF)
### find the biggest rNo among HETATM
for atom in bigboxBGF.a:
if atom.aTag == 1:
if max_rNo_in_hetatm < atom.rNo: max_rNo_in_hetatm = atom.rNo
### update rNo in water molecules
rNo_for_water = max_rNo_in_hetatm + 500;
for aNo in oxygen_list:
water_aNo = bgftools.is_water(bigboxBGF, aNo) # get aNo in a water molecule by checking the oxygen atom
if water_aNo != []:
for atom_aNo in water_aNo:
bigboxBGF.getAtom(atom_aNo).rNo = rNo_for_water
rNo_for_water += 1
"""
### record BGF remarks
bigboxBGF.REMARK.insert(
0, "Solvents added by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
bigboxBGF.REMARK.insert(0, "Solvents: " + str(solvent_file))
### save BGF
if not silent: print("Saving the file.. see " + str(out_file))
bigboxBGF.saveBGF(out_file)
return 1
def replicateCell(myBGF, multiplication, spaceFilling=True):
"""
replicateCell():
Requires a BgfFile class.
Returns a BgfFile class of the replicated structure of the given structure.
Options:
spaceFilling = True
Just copy the cell (x, y, z) times to the (x, y, z) coordinateas. Negative multiplication indices are allowed.
(1, 1, 1) with a cell gives 4 cells (i.e. replication to x, y, and z coordinates).
spaceFilling = False
Fill the space as a Cuboid form for a given times. Negative multiplication indices are NOT allowed.
(2, 1, 3) with a cell gives the 6 cells (i.e. cubiod). (1, 1, 1) with a cell gives the identical structure (nothing happens).
"""
copyTime = [
int(multiplication[0]),
int(multiplication[1]),
int(multiplication[2])
]
# the number of cells that will be copied
myBGFx = bgf.BgfFile()
myBGFy = bgf.BgfFile()
myBGFz = bgf.BgfFile()
boxsize = [0, 0, 0]
if len(myBGF.CRYSTX) > 2:
boxsize = [myBGF.CRYSTX[0], myBGF.CRYSTX[1], myBGF.CRYSTX[2]]
else:
box = bgf.getBGFSize(myBGF, 0) # [xlo, xhi, ylo, yhi, zlo, zhi]
boxsize = [box[1] - box[0], box[3] - box[2], box[5] - box[4]]
if spaceFilling:
if copyTime[0] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[0] - 1):
bgf.moveBGF(myBGF2, boxsize[0], 0, 0)
myBGF = myBGF.merge(myBGF2, True)
if copyTime[1] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[1] - 1):
bgf.moveBGF(myBGF2, 0, boxsize[1], 0)
myBGF = myBGF.merge(myBGF2, True)
if copyTime[2] != 0:
myBGF2 = copy.deepcopy(myBGF)
for n in range(0, copyTime[2] - 1):
bgf.moveBGF(myBGF2, 0, 0, boxsize[2])
myBGF = myBGF.merge(myBGF2, True)
# update the CRYSTX information
if len(myBGF.CRYSTX) > 2:
for index, number in enumerate(copyTime):
myBGF.CRYSTX[index] *= copyTime[index]
else:
# replication
if copyTime[0] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[0])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, boxsize[0] * (n + 1) * sign, 0, 0)
myBGFx = myBGFx.merge(myBGF2, True)
if copyTime[1] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[1])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, boxsize[1] * (n + 1) * sign, 0)
myBGFy = myBGFy.merge(myBGF2, True)
if copyTime[2] != 0:
if copyTime[0] < 0: sign = -1
else: sign = 1
for n in range(0, abs(copyTime[2])):
if copyTime[0] < 0: n -= 1
myBGF2 = copy.deepcopy(myBGF)
bgf.moveBGF(myBGF2, 0, 0, boxsize[2] * (n + 1) * sign)
myBGFz = myBGFz.merge(myBGF2, True)
myBGF = myBGF.merge(myBGFx, True)
myBGF = myBGF.merge(myBGFy, True)
myBGF = myBGF.merge(myBGFz, True)
# update the CRYSTX information
if len(myBGF.CRYSTX) > 2:
for index, number in enumerate(copyTime):
myBGF.CRYSTX[index] += myBGF.CRYSTX[index] * copyTime[index]
return myBGF
def poresize(bgf_file, out_file, grid=0.25, thresh=0.25, silent=False):
"""
def poresize():
Calculates pore sizes in the BGF molecule
Function Parameters:
bgf_file A string which contains a PEI information in a BGF format.
(e.g. "file1.bgf file2.bgf file3.bgf ...")
"""
# initialize
xyz = []
rvdw = dict()
ubound = 10
lbound = 0
# open bgf
myBGF = bgf.BgfFile(bgf_file)
# read van der waals radii
rvdw['H'] = 1.2
rvdw['C'] = 1.7
rvdw['N'] = 1.55
rvdw['O'] = 1.52
# copy positions: [ x y z vdw ]
for atom in myBGF.a:
atomtype = atom.ffType[:-1].strip("_")
xyz.append(
[float(atom.x),
float(atom.y),
float(atom.z), rvdw[atomtype]])
xyz = np.array(xyz)
# get bgf size
size = np.array(bgf.getBGFSize(myBGF))
np.around(size, decimals=1)
# make grid
grid_x = np.arange(size[0], size[1], grid)
grid_y = np.arange(size[2], size[3], grid)
grid_z = np.arange(size[4], size[5], grid)
len_grid_x = len(grid_x)
len_grid_y = len(grid_y)
len_grid_z = len(grid_z)
poresize = np.zeros((len_grid_x, len_grid_y, len_grid_z))
ix = 0
iy = 0
iz = 0
t1 = 0
t2 = 0
# for each grid
for ix, x in enumerate(grid_x):
t1 = time.time()
for iy, y in enumerate(grid_y):
for iz, z in enumerate(grid_z):
ubound = 10
lbound = 0
minubound = 10
while ubound - lbound > thresh:
test_r = random.uniform(lbound, ubound)
flag = True
for atom in xyz:
value = (x - atom[0])**2 + (y - atom[1])**2 + (
z - atom[2])**2 - atom[3]**2 - test_r**2
if value < 0:
flag = False
if minubound > test_r: minubound = test_r
if flag:
lbound = test_r
else:
ubound = minubound
poresize[ix, iy, iz] = test_r
t2 = time.time()
print(
str(ix) + " out of " + str(len_grid_x) +
"( elapsed time for the step: " + str(t2 - t1) + " sec)")
# store them as a matrix
scipy.io.savemat(out_file, {'m': poresize})
def poresize(bgf_file, out_file, grid=0.25, thresh=0.25, silent=False):
"""
def poresize():
Calculates pore sizes in the BGF molecule
Function Parameters:
bgf_file A string which contains a PEI information in a BGF format.
(e.g. "file1.bgf file2.bgf file3.bgf ...")
"""
# initialize
xyz = []
rvdw = dict()
ubound = 10
lbound = 0
# open bgf
myBGF = bgf.BgfFile(bgf_file)
# read van der waals radii
rvdw['H'] = 1.2
rvdw['C'] = 1.7
rvdw['N'] = 1.55
rvdw['O'] = 1.52
# copy positions: [ x y z vdw ]
for atom in myBGF.a:
atomtype = atom.ffType[:-1].strip("_")
xyz.append(
[float(atom.x),
float(atom.y),
float(atom.z), rvdw[atomtype]])
xyz = np.array(xyz)
# get bgf size
size = np.array(bgf.getBGFSize(myBGF))
np.around(size, decimals=1)
# make grid
grid_x = np.arange(size[0], size[1], grid)
grid_y = np.arange(size[2], size[3], grid)
grid_z = np.arange(size[4], size[5], grid)
len_grid_x = len(grid_x)
len_grid_y = len(grid_y)
len_grid_z = len(grid_z)
poresize = np.zeros((len_grid_x, len_grid_y, len_grid_z))
# for each grid
for ix, x in enumerate(grid_x):
print(str(ix) + " out of " + str(len_grid_x))
for iy, y in enumerate(grid_y):
for iz, z in enumerate(grid_z):
ubound = 10
lbound = 0
minubound = 10
while ubound - lbound > thresh:
test_r = random.uniform(lbound, ubound)
### check the distance
flag = True
for atom in xyz:
value = (x - atom[0])**2 + (y - atom[1])**2 + (
z - atom[2])**2 - atom[3]**2 - test_r**2
if value < 0:
flag = False
if minubound > test_r: minubound = test_r
if flag:
lbound = test_r
else:
ubound = minubound
poresize[ix, iy, iz] = test_r
# store them as a matrix
with file(out_file, 'w') as outfile:
for data in poresize:
outfile.write("# new shot\n")
np.savetxt(outfile, data, fmt='%8.2f')