def do_work(bgf_file, out_file, simple, silent=True):
#initialize
myPEI = bgf.BgfFile()
n_H = []
# open BGF
myBGF = bgf.BgfFile(bgf_file)
# remove hydrogens
pei = bgftools.getBackbone(myBGF, 0)
# convert connection into dictionary
d_graph = bgftools.getConnectionDict(pei)
# convert dictionary into Graph
G = nx.Graph(d_graph)
# calculate the all shortest length path
#d_dist = nx.floyd_warshall(G) # seems a problem
d_dist = nx.all_pairs_shortest_path_length(G)
# get Wiener Index
index = 0
for key in d_dist.iterkeys():
for key2 in d_dist[key].iterkeys():
index += d_dist[key][key2]
index = index / 2.0
return index
def copy_bgf_info(bgf_file, out_file=""):
"""
Generates an empty BGF file with same information.
copy_bgf_info(bgf_file): return new bgf file, DON'T SAVE
copy_bgf_info(bgf_file, out_file="filename"): return new bgf file, DO SAVE
"""
if isinstance(bgf_file, bgf.BgfFile):
orig = bgf_file
else:
orig = bgf.BgfFile(bgf_file)
new = bgf.BgfFile()
new.BIOGRF = orig.BIOGRF
new.DESCRP = orig.DESCRP
new.REMARK = orig.REMARK
new.FF = orig.FF
new.FORMAT = orig.FORMAT
new.PERIOD = orig.PERIOD
new.AXES = orig.AXES
new.SGNAME = orig.SGNAME
new.CRYSTX = orig.CRYSTX
new.OTHER = orig.OTHER
new.CELLS = orig.CELLS
if out_file:
new.saveBGF(out_file)
return new
def check_isomorphism(l):
if simple:
# open BGF
myBGF1 = bgf.BgfFile(bgf_file1)
myBGF2 = bgf.BgfFile(bgf_file2)
# remove hydrogens only in carbon atoms
remove_aNo1 = []
remove_aNo2 = []
for atom in myBGF1.a:
if "C_" in atom.ffType:
n_H = []
for aNo in atom.CONECT:
if myBGF1.getAtom(aNo).is_hydrogen():
n_H.append(myBGF1.a2i[aNo])
if len(n_H) != 3:
n_H.sort()
n_H.reverse()
myBGF1.delAtoms(n_H)
myBGF1.renumber()
for atom in myBGF2.a:
if "C_" in atom.ffType:
n_H = []
for aNo in atom.CONECT:
if myBGF2.getAtom(aNo).is_hydrogen():
n_H.append(myBGF2.a2i[aNo])
if len(n_H) != 3:
n_H.sort()
n_H.reverse()
myBGF2.delAtoms(n_H)
myBGF2.renumber()
# toss reduced BGFs to networkx
pei1 = myBGF1
pei2 = myBGF2
else:
# toss whole structures
pei1 = bgf_file1
pei2 = bgf_file2
# convert connection into dictionary
d_graph1 = bgftools.getConnectionDict(pei1)
d_graph2 = bgftools.getConnectionDict(pei2)
# convert dictionary into Graph
G1 = nx.Graph(d_graph1)
G2 = nx.Graph(d_graph2)
# check isomorphism
GM = isomorphism.GraphMatcher(G1, G2)
result = GM.is_isomorphic()
return bgf_file1, bgf_file2, result
def randomDisperse(bgf_file, size, number, out_file, silent=False):
"""
def randomDisperse():
Create a randomly distributed cubic with full of the monomers
Function Parameters:
bgf_file A string which contains a monomer information in a BGF format.
size
number
out_file
"""
# initialize
# open bgf
if not silent: print("reading monomer..")
cubicBGF = bgf.BgfFile()
#for atom in cubicBGF.a:
# cubicBGF.delAtom(cubicBGF.a2i[atom.aNo])
# repeat up to number:
if not silent: print("generating cubic box..")
for i in xrange(number):
# create three random numbers
x1 = random.uniform(0, size)
y1 = random.uniform(0, size)
z1 = random.uniform(0, size)
# move the monomer
addBGF = bgf.BgfFile(bgf_file)
headAtom = addBGF.a[0]
#delta = (headAtom.x - x1, headAtom.y - y1, headAtom.z - z1)
delta = (x1 - headAtom.x, y1 - headAtom.y, z1 - headAtom.z)
bgf.moveBGF(addBGF, delta[0], delta[1], delta[2])
# merge
cubicBGF = cubicBGF.merge(addBGF, True)
# make it periodic
cubicBGF.BIOGRF = "200"
cubicBGF.DESCRP = bgf_file[:-4]
cubicBGF.REMARK.insert(0, "Cubic generated by " + os.path.basename(sys.argv[0]) + " by " + os.environ["USER"] + " on " + time.asctime(time.gmtime()))
cubicBGF.FF = "FORCEFIELD DREIDING"
cubicBGF.PERIOD = "111"
cubicBGF.CRYSTX = [ size, size, size, 90.0, 90.0, 90.0 ]
cubicBGF.AXES = "ZYX"
cubicBGF.SGNAME = "P 1 1 1\n"
cubicBGF.CELLS = [-1, 1, -1, 1, -1, 1]
# save
if not silent: print("saving.. " + out_file)
cubicBGF.saveBGF(out_file)
def test_isomorphism(bgf_file1, bgf_file2, simple, silent=True):
"""
def test_isomorphism():
Function Parameters:
bgf_file A string of filename or BgfFile class.
"""
# initialize
pei1 = 0
pei2 = 0
# open BGF
if isinstance(bgf_file1, bgf.BgfFile):
myBGF = bgf_file1
else:
if not silent: print("opening bgf file 1.. " + str(bgf_file1))
myBGF = bgf.BgfFile(bgf_file1)
if isinstance(bgf_file2, bgf.BgfFile):
myBGF = bgf_file2
else:
if not silent: print("opening bgf file 2.. " + str(bgf_file2))
myBGF = bgf.BgfFile(bgf_file2)
if simple:
# reduce hydrogens
pei1 = bgftools.getBackbone(bgf_file1)
pei2 = bgftools.getBackbone(bgf_file2)
else:
pei1 = bgf_file1
pei2 = bgf_file2
# convert connection into dictionary
d_graph1 = bgftools.getConnectionDict(pei1)
d_graph2 = bgftools.getConnectionDict(pei2)
if not silent: print("structures are converted to graph.")
G1 = nx.Graph(d_graph1)
G2 = nx.Graph(d_graph2)
if not silent: print("graphs are loaded.")
# check isomorphism
if not silent: print("now comparing two graphs..")
GM = isomorphism.GraphMatcher(G1, G2)
result = GM.is_isomorphic()
if not silent:
print(result)
else:
return result
def selectResName(bgf_file, resName, out_file, silent=False):
"""
selectResName(bgf_file, resName, out_file, silent=False):
return a BgfFile class which contains the same residue name as designated.
"""
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = copy.deepcopy(bgf_file)
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
l_notSelected_aNo = []
# delete unwanted atoms
for atom in myBGF.a:
if not resName in atom.rName:
l_notSelected_aNo.append(atom.aNo)
l_notSelected_aNo.sort()
l_notSelected_aNo.reverse()
myBGF.delAtoms(l_notSelected_aNo)
if not silent: print(str(len(myBGF.a)) + " atoms are selected.")
# 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 getShortestPath(bgf_file, ano1, ano2, silent=True):
"""
def getShortestPath(bgf_file, ano1, ano2):
Get a list of the shortest path between two atoms of the given BGF structure using findShortestPath()
Function Parameters:
bgf_file: a filename or BgfFile class
ano1: atom number of the starting atom
ano2: atom number of the ending atom
"""
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
### REMARK: be sure that the hydrogen branches of bgf_file are taken off.
## cut off all hydrogen branches
#myBGF = getBackbone(myBGF)
# prepare the connection information
graph = getConnectionDict(myBGF)
# run and return
return findShortestPath(graph, ano1, ano2)
def template(bgf_file, out_file, silent=False):
"""
def template():
Write what this function does.
Function Parameters:
bgf_file A string of filename or BgfFile class.
out_file A string of filename or BgfFile class.
"""
# 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)
# Write down the Template function here
# 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 getMoleculeList(bgf_file, recursion_limit=10000, silent=True):
"""
def getMoleculeList(bgf_file, silent=True):
Get a list of atom numbers (aNo) of the molecules of the given BGF file.
"""
sys.setrecursionlimit(recursion_limit)
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# build all ano list
l_all_atom = []
for atom in myBGF.a:
l_all_atom.append(atom.aNo)
# for every atoms, get connected atoms
l_all_molecules = []
l_molecule = []
while len(l_all_atom) > 0:
l_temp = []
l_molecule = getmolecule(
myBGF, myBGF.getAtom(l_all_atom[0]), l_temp, recursion_limit
) # l_molecule is kind of dummy.. no items in there.
l_all_molecules.append(l_temp)
for i in l_temp:
l_all_atom.remove(i)
return l_all_molecules
def rotate(bgf_file, v, out_file, silent=True):
"""
rotate BGF to v2 to z axis.
"""
# Initialization
# 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)
# rotation 1 to x axis
v1_dot_v2 = v[0]
mag_v1 = 1.0
mag_v2 = math.sqrt(v[0]**2 + v[1]**2)
theta = math.acos(v1_dot_v2 / (mag_v1 * mag_v2))
theta = -theta
print(theta)
rot1 = np.array([[math.cos(theta), -math.sin(theta), 0],
[math.sin(theta), math.cos(theta), 0], [0, 0, 1]])
# rotation 2 to y axis
v1_dot_v2 = v[1]
mag_v1 = 1.0
mag_v2 = math.sqrt(v[1]**2 + v[2]**2)
rho = math.acos(v1_dot_v2 / (mag_v1 * mag_v2))
rho = -rho
print(rho)
rot2 = np.array([[1, 0, 0], [0, math.cos(rho),
math.sin(rho)],
[0, -math.sin(rho), math.cos(rho)]])
# rotation 3 to z axis
v1_dot_v2 = v[2]
mag_v1 = 1.0
mag_v2 = math.sqrt(v[0]**2 + v[2]**2)
phi = math.acos(v1_dot_v2 / (mag_v1 * mag_v2))
phi = -phi
print(phi)
rot3 = np.array([[math.cos(phi), 0, math.sin(phi)], [0, 1, 0],
[-math.sin(phi), 0, math.cos(phi)]])
for atom in myBGF.a:
coord = [atom.x, atom.y, atom.z]
newcoord = np.dot(rot1, coord)
newcoord = np.dot(rot2, newcoord)
newcoord = np.dot(rot3, newcoord)
atom.x = newcoord[0]
atom.y = newcoord[1]
atom.z = newcoord[2]
# 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 check_monomer(monomer, ff_file):
"""
Check whether monomer has proper number of branching points
:str monomer:
:str ff_file:
:bool : object
"""
try:
f = bgf.BgfFile(monomer)
except IOError:
return False
branch = 0
head = 0
for atom in f.a:
atom.rNo = 0 # this residue number will be the key to distinguish body and the new block
if atom.chain == "B":
branch += 1
if atom.chain == "H":
head += 1
if branch != 1:
raise ValueError('More than two branch atoms inside ' + str(monomer))
return False
if head != 1:
raise ValueError('More than two head atoms inside ' + str(monomer))
return False
mass = bgftools.getMass(f, ff_file)
f.saveBGF(monomer)
return mass
def analyze(bgf_file, trj_file, ff_file='', out_file=''):
'''analyze something within a timestep in a series of lammps trajectory.
'''
# variables
# inner functions
def get_line(file):
with open(file, 'r') as f:
for line in f:
yield line
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
# 2. Read LAMMPS Trajectory
#timesteps, N_HEADER, N_ATOMS = lt.getTrjInfo(trj_file)
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_HEADER = mytrj.nheader
N_ATOMS = mytrj.natoms[0]
N_BUFFER = N_HEADER + N_ATOMS
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 3. Determine dump style
dump_keywords = mytrj.dumpstyle
yes_scale = False
if 'xs' in dump_keywords:
yes_scale = True
# 4. Update coordinates from the snapshot
dump = get_line(trj_file)
for t in tqdm.tqdm(timesteps, ncols=120, desc="Analyzing"):
chunk = [next(dump) for i in range(N_BUFFER)]
t = int(chunk[1])
mybgf.CRYSTX = mytrj.pbc[t] + [90.0, 90.0, 90.0]
coords = chunk[9:]
for c in coords:
c = c.split(' ')
atom = mybgf.getAtom(int(c[0]))
if yes_scale:
atom.x = float(c[2]) * pbc[0]
atom.y = float(c[3]) * pbc[1]
atom.z = float(c[4]) * pbc[2]
else:
atom.x = float(c[2])
atom.y = float(c[3])
atom.z = float(c[4])
mybgf = bt.periodicMoleculeSort(mybgf,
mybgf.CRYSTX,
ff_file=ff_file,
silent=True)
def dat2bgf(bgf_file, dat_file, out_file):
# init
mybgf = bgf.BgfFile(bgf_file)
f_dat_file = open(dat_file)
temp = f_dat_file.read().split('\n')
f_dat_file.close()
temp = [i.partition('#')[0].rstrip() for i in temp if i != ""]
# PBC
for i in temp:
if 'xlo' in i:
line = i.split()
mybgf.CRYSTX[0] = float(line[1]) - float(line[0])
if 'ylo' in i:
line = i.split()
mybgf.CRYSTX[1] = float(line[1]) - float(line[0])
if 'zlo' in i:
line = i.split()
mybgf.CRYSTX[2] = float(line[1]) - float(line[0])
# Coordinates
dat_atom_start = temp.index('Atoms')
dat_atom_end = temp.index('Bonds')
if 'Velocities' in temp:
dat_atom_end = temp.index('Velocities') # if data file is from write_restart command, Velocities are also written in the file.:w
temp = temp[dat_atom_start + 1:dat_atom_end]
n_dat_atoms = len(temp)
n_bgf_atoms = len(mybgf.a)
if n_dat_atoms != n_bgf_atoms:
nu.die("Number of atoms mismatch between bgf and LAMMPS data file.")
coords = [] # coords = id type molid charge x y z ix iy iz
for i in temp:
line = i.split()
coords.append(line)
for i in coords:
id = int(i[0])
atom = mybgf.a[mybgf.a2i[id]] # getAtom
atom.x = float(i[4])
atom.y = float(i[5])
atom.z = float(i[6])
if out_file == "": out_file = bgf_file.split(".bgf")[0] + "_mod.bgf"
mybgf.REMARK.append("Coordinates updated on %s" % time.asctime(time.gmtime()))
mybgf.REMARK.append("Coordinates updated with data file %s" % os.path.abspath(dat_file))
mybgf.saveBGF(out_file)
print('Done. Check %s ' % out_file)
return 1
def assignWaterResidue(bgf_file, out_file, silent=True):
mybgf = bgf.BgfFile(bgf_file)
for atom in mybgf.a:
for i in bgftools.is_water(mybgf, atom.aNo):
mybgf.getAtom(i).rName = "WAT"
mybgf.saveBGF(out_file)
def removebadcontacts(bgf_file, out_file, thresh, silent=True):
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent:
print(sys.argv[0] + ": Removing bad contacts from " + bgf_file +
" with distance threshold " + str(thresh) +
" A and saving to " + out_file + ".")
myBGF = bgf.BgfFile(bgf_file)
delete_list = []
if not silent:
print("removeBadContacts will remove water molecules within " +
str(thresh) + " Angstrom from the solute.")
for solute_aNo in bgftools.listSoluteAtoms(myBGF):
solute = myBGF.getAtom(solute_aNo)
for oxygen_aNo in bgftools.listOxygenAtoms(myBGF):
water = bgftools.is_water(myBGF, oxygen_aNo)
if water != [] or type(water) != NoneType:
if len(water) == 3: # if water is a water molecule,
# calculate the distance between solute atoms and the molecule
O = myBGF.getAtom(water[0])
H1 = myBGF.getAtom(water[1])
H2 = myBGF.getAtom(water[2])
dist_O_sol = bgf.distance(solute, O)
dist_H1_sol = bgf.distance(solute, H1)
dist_H2_sol = bgf.distance(solute, H2)
if dist_O_sol < thresh or dist_H1_sol < thresh or dist_H2_sol < thresh:
if oxygen_aNo not in delete_list:
delete_list.append(oxygen_aNo)
delete_list.sort()
##if water not in delete_list:
##delete_list.append(water)
if delete_list != []:
delete_list.reverse() # reverse sort for delAtoms
for oxygen_index in delete_list:
bgftools.deleteWaterAtoms(myBGF, oxygen_index)
myBGF.renumber()
if not silent:
print("removeBadContacts: " + str(len(delete_list)) +
" water molecules are removed.")
else:
if not silent:
print(
"There are no water molecules that corresponds to the criteria."
)
if isinstance(out_file, bgf.BgfFile):
return myBGF
else:
myBGF.saveBGF(out_file)
return 1
def setAmineGroupInfo(bgf_file, out_file, silent=True):
"""
setAmineGroupInfo(bgf_file, silent=True):
get a BGF file or BgfFile class object
returns a BgfFile or 1 with primary, secondary, and tertiary amines information corrected.
Note that corrections WILL BE applied to the original BGF file.
"""
n_pri = 0
n_sec = 0
n_ter = 0
n_garbage = 0
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# get nitrogen ano lists
l_nitrogen_ano = []
for atom in myBGF.a:
if "N_" in atom.ffType: l_nitrogen_ano.append(atom.aNo)
# for every nitrogen
for aNo in l_nitrogen_ano:
n_carbon = 0
connected_ano = myBGF.getAtom(aNo).CONECT
## for every connection
for aNo2 in connected_ano:
if "C_" in myBGF.getAtom(aNo2).ffType:
n_carbon += 1
### no carbon: primary, 1 carbons: secondary, 2 carbons: tertiary
if n_carbon == 1:
myBGF.getAtom(aNo).rName = "PRI"
elif n_carbon == 2:
myBGF.getAtom(aNo).rName = "SEC"
elif n_carbon == 3:
myBGF.getAtom(aNo).rName = "TER"
else:
n_garbage += 1
# what are you??
if n_garbage != 0:
nu.warn("Suspicious amine groups are found!")
return 0
# save
if isinstance(out_file, str):
if not silent: print("Saving information to " + out_file + " ..")
myBGF.saveBGF(out_file)
return getAmineGroupInfo(myBGF)
else:
return getAmineGroupInfo(myBGF)
def get_head_ano_of_monomer(monomer):
"""
"""
ano = 0
f = bgf.BgfFile(monomer)
for atom in f.a:
if atom.chain == "B":
ano = atom.aNo
return ano
def removeFragments(bgf_file, resname, n_frag, out_file, silent=True):
"""
"""
# variables
l_delatoms = []
n_molecules = 0
n_atoms = 0
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# get lists of molecules
l_molecule = getMoleculeList(bgf_file)
if not silent:
print("Molecules which is less atoms than " + str(n_frag) +
" among the residue name " + str(resname) + " will be removed.")
# for every molecule
for molecule in l_molecule:
if len(molecule) < n_frag:
for ano in molecule:
# check rName
atom = myBGF.getAtom(ano)
if resname in atom.rName:
l_delatoms.append(myBGF.a2i[ano]) # remove index, not ano!
#l_delatoms.append(ano) # remove index, not ano!
n_molecules += 1
# delete and compute stats
n_atoms = len(l_delatoms)
l_delatoms.sort()
l_delatoms.reverse()
myBGF.renumber()
myBGF.delAtoms(l_delatoms)
myBGF.renumber()
if not silent:
print(
str(n_molecules) + " molecules (" + str(n_atoms) +
" atoms) are deleted.")
# 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 __init__(self, max_branch=2):
super(RandomPolymer, self).__init__()
self.monomers = {}
self.num_monomer = 0
self.max_num_branch = max_branch # number of allowed branchs per a node
self.target_mw = 0 # target molecular weight
self.num_target_node = 0 # number of nodes required to build a random polymer
self.Terminal = ""
self.Linear = ""
self.Dendron = ""
self.bgfmodel = bgf.BgfFile()
self.ff = ""
def evaporate(bgf_file, out_file=False, safemode=False, silent=True):
"""
evaporate(bgf_file, out_file):
bgf_file A string for input file.
out_file A string for output file.
safemode A boolean for safe mode determination.
To-do:
None
"""
# Initialization
temp = []
# 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)
# Delete water molecules
if safemode:
for atom in myBGF.a:
temp.append(atom.aNo)
for aNo in temp:
bgftools.deleteWaterAtoms(myBGF, aNo)
else:
if not silent: print("listing water molecules..")
for atom in myBGF.a:
if "WAT" in atom.rName:
temp.append(myBGF.a2i[atom.aNo])
n_delatoms = len(temp)
if not silent:
print("found " + str(n_delatoms) + " atoms for water molecules..")
if n_delatoms % 3 != 0:
nu.die(
"ERROR: the number of atoms to be deleted is not divided in 3. Check the structure."
)
if not silent: print("deleting water molecules..")
myBGF.delAtoms(temp, silent)
myBGF.renumber()
# Save BGF
if isinstance(out_file, str):
if not silent: print("\nsaving information to " + out_file + " ..")
myBGF.REMARK.insert(
0, "Evaporated by " + os.path.basename(sys.argv[0]) + " by " +
os.environ["USER"] + " on " + time.asctime(time.gmtime()))
myBGF.saveBGF(out_file)
return 1
else:
return myBGF
def __init__(self, fname, *args, **kwargs):
bgf_file = ""
if fname:
bgf_file = fname
if isinstance(bgf_file, bgf.BgfFile):
self.bgfmodel = bgf_file
self.model_filename = "" # if the model is directly from bgf object, no filename will be assigned.
else:
self.bgfmodel = bgf.BgfFile(bgf_file)
self.model_filename = bgf_file
#
# Determine nanotube type and atom types
#
self.NTatoms = self.find_NT_atoms()
self.WATatoms = self.find_WAT_atoms()
self.otheratoms = self.find_other_atoms()
self.find_type()
self.set_ff()
#
# Set number of atoms
#
self.n_allatoms = len(self.bgfmodel.a)
self.n_nanotube = len(self.NTatoms)
self.n_water = len(self.WATatoms)
#
# Properties of CNT: requires special treatment so not automatically calculated.
#
self.isAligned = False
self.isRadiusCalc = False
self.isPBCadjusted = False
self.orientation = None
self.radius = None
self.height = None
self.zhi = None
self.zlo = None
self.water_position_determined = False
# model check-up: total charge
chg = bgftools.charge(self.bgfmodel)
if chg != 0 and abs(chg) > 1e-10:
nu.warn("Charge is not neutral: " + str(chg))
if self.bgfmodel.CRYSTX != []:
self.pbc = self.bgfmodel.CRYSTX[:3]
else:
nu.warn("Nanotube class: An empty object created.")
def selectAtoms(bgf_file, selection, out_file, silent=True):
"""
selectAtoms(bgf_file, selection, out_file):
Extract some atoms from bgf_file.
IMPORTANT NOTE: Connection information are not returned.
If you want to select atoms because of direct manipulation (i.e. adding 10 to xcoord)
then you'd better use another function.
"""
# variables
myBGF = 0
myBGF2 = 0
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# find
myBGF2 = bgf.BgfFile()
executable = "if " + selection + ": " + "myBGF2.addAtom(atom)"
for atom in myBGF.a:
exec(executable)
# if more than one atom is selected:
# save
if len(myBGF2) > 0:
if isinstance(out_file, str):
if not silent: print("Saving information to " + out_file + " ..")
myBGF2.saveBGF(out_file)
return 1
else:
return myBGF2
else:
print("No atoms are selected. Quit.")
return 0
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 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 getAmineGroupInfo(bgf_file, silent=True):
"""
getAmineGroupInfo(bgf_file, silent=True):
get a BGF file or BgfFile class object
returns a triplet list of numbers of primary, secondary, and tertiary amines.
Note that any corrections are not applied to the original BGF file.
"""
n_pri = 0
n_sec = 0
n_ter = 0
n_garbage = 0
# open bgf
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# get nitrogen ano lists
l_nitrogen_ano = []
for atom in myBGF.a:
if "N_" in atom.ffType: l_nitrogen_ano.append(atom.aNo)
# for every nitrogen
for aNo in l_nitrogen_ano:
n_carbon = 0
connected_ano = myBGF.getAtom(aNo).CONECT
## for every connection
for aNo2 in connected_ano:
if "C_" in myBGF.getAtom(aNo2).ffType:
n_carbon += 1
### no carbon: primary, 1 carbons: secondary, 2 carbons: tertiary
if n_carbon == 1:
n_pri += 1
#myBGF.getAtom(aNo).rName = "PRI"
elif n_carbon == 2:
n_sec += 1
#myBGF.getAtom(aNo).rName = "SEC"
elif n_carbon == 3:
n_ter += 1
#myBGF.getAtom(aNo).rName = "TER"
else:
n_garbage += 1
# return the number of pri, sec, and ter
return [n_pri, n_sec, n_ter]
def alignBGF(bgf_file, atom1, atom2, out_file, silent=False):
# open
if isinstance(bgf_file, bgf.BgfFile):
myBGF = bgf_file
else:
if not silent: print("reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
a1 = myBGF.a[myBGF.a2i[atom1]];
a2 = myBGF.a[myBGF.a2i[atom2]];
v1 = (a1.x, a1.y, a1.z)
# move atom1 to origin
for atom in myBGF.a:
atom.x -= v1[0]
atom.y -= v1[1]
atom.z -= v1[2]
v21 = [ (a2.x - a1.x), (a2.y - a1.y), (a2.z - a1.z) ]
# rotate v21 to x axis
u1 = v21 / np.linalg.norm(v21) ##
v2 = [u1[1], -u1[0], 0]
u2 = v2 / np.linalg.norm(v2) ##
v3 = np.cross(u1, u2)
u3 = v3 / np.linalg.norm(v3) ##
U = np.array([[u1[0], u1[1], u1[2]], [u2[0], u2[1], u2[2]], [u3[0], u3[1], u3[2]]])
# rotate all atoms
for atom in myBGF.a:
a = np.matrix([atom.x, atom.y, atom.z]).T
b = U*a
atom.x = float(b[0])
atom.y = float(b[1])
atom.z = float(b[2])
## 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 get_residue_names(bgf_file):
"""
returns all residue names in the BGF file.
"""
# bgf open
if isinstance(bgf_file, bgf.BgfFile):
mybgf = bgf_file
else:
mybgf = bgf.BgfFile(bgf_file)
result = set()
for atom in mybgf.a:
result.add(atom.rName)
return list(result)
def fixbgf(bgf_file, out_file, silent=False): """ fixbgf(bgf_file, out_file): bgf_file A string for input file. out_file A string for output file. To-do: None """ # Open BGF myBGF = bgf.BgfFile(bgf_file) # Save BGF myBGF.REMARK.insert(0, "Renumbered by " + os.path.basename(sys.argv[0]) + " by " + os.environ["USER"] + " on " + time.asctime(time.gmtime())) myBGF.renumber() myBGF.saveBGF(out_file)
def count_layer(bgf_file, trj_file, ff_file='', out_file=''):
'''counts number of O atoms in each layer.
'''
# variables
result = dict()
# 1. Load BGF
mybgf = bgf.BgfFile(bgf_file)
N_BGF_ATOMS = len(mybgf.a)
r_vdw_C = 3.38383824 / 2
# 2. Read LAMMPS Trajectory
mytrj = lt.lammpstrj(trj_file)
timesteps = mytrj.load()
N_ATOMS = mytrj.natoms[0]
if N_BGF_ATOMS != N_ATOMS:
nu.die(
"Number of atoms in trajectory file does not match with BGF file.")
# 4. Update coordinates from the snapshot
for t in tqdm.tqdm(timesteps,
ncols=120,
desc="Calculating graphene z positions"):
mybgf = get_timestep(mybgf, trj_file, t)
avg_gra_z1 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 1")
avg_gra_z2 = bt.atoms_average(
mybgf,
'atom.z',
selection="'C_2G' in atom.ffType and atom.rNo == 2")
dist = avg_gra_z2 - avg_gra_z1
eff_dist = avg_gra_z2 - avg_gra_z1 - 2 * r_vdw_C
result[t] = [avg_gra_z1, avg_gra_z2, dist, eff_dist]
# 5. Analyze
timesteps = sorted(result.keys())
with open('z_position.test.dat', 'w') as f:
output = ''
for t in timesteps:
output += "%d " % t
output += "%8.3f %8.3f %8.3f %8.3f\n" % result[t]
f.write(output)
def bgf2qcin(bgf_file, qchem_in_file, rem_file):
# bgf open
print("Reading " + bgf_file + " ..")
myBGF = bgf.BgfFile(bgf_file)
# output
output = [
"$comment\n",
"from " + bgf_file + " at " + time.asctime(time.gmtime()) + " on " +
os.environ["HOSTNAME"] + " by " + os.environ["USER"] + "\n", "$end\n"
]
# charge and multiplicity
output += ["\n$molecule\n"]
chg = myBGF.charge()
if abs(chg) < 0.000001:
output += ["0" + "\t" + "1" + "\n"]
else:
nu.warn("Charge is not neutral. Charge will be written as " +
"{0:<4.1f}".format(chg))
output += ["{0:<4.1f}".format(chg) + "\t" + "1" + "\n"]
# coordinates
for atom in myBGF.a:
output += [
atom.ffType.split("_")[0] + "\t" +
"{0:10.6f} {1:10.6f} {2:10.6f}".format(atom.x, atom.y, atom.z) +
"\n"
]
output += ["$end\n\n"]
# rem
remf = open(rem_file)
remline = remf.readlines()
output += remline
# target file
qcinf = open(qchem_in_file, 'w')
qcinf.writelines(output)
qcinf.close()
print("Generated " + qchem_in_file + " . Done.")
