def main():
utils.TITLE("Proximity Analysis")
FILENAME = input("Enter .pdb file path...\t\t")
PRT = utils.PDB(FILENAME).prot
SEL_CHAIN = input("Select chain...\t\t\t")
SEL_RSN = input("Select residue...\t\t")
print("\nDetected Atom Type in", SEL_RSN, PRT[SEL_CHAIN][SEL_RSN][0][2],
":\n")
for i in PRT[SEL_CHAIN][SEL_RSN]:
print(">> ", i[1])
SEL_AT = input("\nSelect Atom Type:\t\t")
TGT = [i for i in PRT[SEL_CHAIN][SEL_RSN] if i[1] == SEL_AT][0]
DIST_TGT = {}
for i in PRT[SEL_CHAIN]:
for j in PRT[SEL_CHAIN][i]:
distance = utils.dist([TGT[5], TGT[6], TGT[7]], [j[5], j[6], j[7]])
if j[4] not in DIST_TGT:
DIST_TGT[j[4]] = distance
elif j[4] in DIST_TGT:
if distance < float(DIST_TGT[j[4]]):
DIST_TGT[j[4]] = distance
else:
print("ERROR!")
RES = []
try:
THR_DIST = float(input("Select cutoff distance...\t"))
for i in DIST_TGT:
if DIST_TGT[i] <= THR_DIST and PRT[SEL_CHAIN][i][0][2] in POS_AA:
RES.append(i)
print("{}\t{:.3f}\t{}\t+1".format(i, DIST_TGT[i],
PRT[SEL_CHAIN][i][0][2]))
elif DIST_TGT[i] <= THR_DIST and PRT[SEL_CHAIN][i][0][2] in NEG_AA:
RES.append(i)
print("{}\t{:.3f}\t{}\t-1".format(i, DIST_TGT[i],
PRT[SEL_CHAIN][i][0][2]))
elif DIST_TGT[i] <= THR_DIST:
RES.append(i)
print("{}\t{:.3f}\t{}".format(i, DIST_TGT[i],
PRT[SEL_CHAIN][i][0][2]))
except KeyboardInterrupt:
print("Interrupted by user")
try:
sys.exit(0)
except SystemExit:
os._exit(0)
cps = input(
"\nPass the selected residues to the Catalytic Pocket Selector module? [y/n]:\t"
)
if cps == 'y':
pro_pru.main(FILENAME, SEL_CHAIN, RES)
else:
utils.NT()
def main():
def multiple_parser(inp_list):
"""Multiple input parser"""
out_list = []
for k in inp_list:
if "-" in k:
for li in range(int(k.split("-")[0]),
int(k.split("-")[1]) + 1):
if int(li) not in out_list:
out_list.append(int(li))
else:
if int(k) not in out_list:
out_list.append(int(k))
return out_list
utils.TITLE("Trajectory Pruning")
TRJ = utils.TRJ(input("Enter trajectory file path...\t"))
K_LIST = input("\nSnapshot groups to extract? (e.g. 1-5 6-10)\t").split()
K_LISTD = [multiple_parser([i]) for i in K_LIST]
for trj_n, sna_list in enumerate(K_LISTD):
with open("./TRJ_{}.xyz".format(str(trj_n)), 'a') as out:
for idx_i, val_i in enumerate(TRJ.trajectory):
if idx_i + 1 in sna_list:
out.write("{}\n".format(str(TRJ.natoms)))
out.write("Trajectory {}\n".format(idx_i + 1))
for j in val_i:
out.write("{} \t{:.10f}\t {:.10f}\t {:.10f} \n".format(
j[0], j[1], j[2], j[3]))
utils.NT()
def main(path):
utils.TITLE("NEB Visualizer (ORCA)")
fig = go.Figure()
with open(path) as file:
lines = file.readlines()
idx_pts = []
idx_int = []
for idx, val in enumerate(lines):
if "Images:" in val:
idx_pts.append(idx + 1)
elif "Interp.:" in val:
idx_int.append(idx + 1)
pts_n = idx_int[0] - 6
if len(idx_pts) != 1:
int_n = idx_pts[1] - idx_int[0] - 3
else:
int_n = len(lines) - idx_int[0]
for i in idx_pts:
if i == idx_pts[0]:
x = [float(lines[j].split()[0]) for j in range(i, i + pts_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + pts_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='markers', name='markers', marker=dict(color='darkorange')))
elif i == idx_pts[-1]:
x = [float(lines[j].split()[0]) for j in range(i, i + pts_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + pts_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='markers', name='markers', marker=dict(color='cornflowerblue')))
else:
x = [float(lines[j].split()[0]) for j in range(i, i + pts_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + pts_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='markers', name='markers', marker=dict(color='gainsboro')))
for i in idx_int:
if i == idx_int[0]:
x = [float(lines[j].split()[0]) for j in range(i, i + int_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + int_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='lines', name='lines', line=dict(color='darkorange')))
elif i == idx_int[-1]:
x = [float(lines[j].split()[0]) for j in range(i, i + int_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + int_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='lines', name='lines', line=dict(color='cornflowerblue')))
else:
x = [float(lines[j].split()[0]) for j in range(i, i + int_n)]
y = [float(lines[j].split()[2]) * utils.ha2kcal for j in range(i, i + int_n)]
fig.add_trace(go.Scatter(x=x, y=y, mode='lines', name='lines', line=dict(color='gainsboro')))
fig.update_layout(
title="ORCA Nudged Elastic Band ",
xaxis_title="Iteration",
yaxis_title="E / kcal mol<sup>-1</sup>",
template="plotly_white",
showlegend=False
)
fig.show()
utils.NT()
def main():
utils.TITLE("Trajectory Analyzer/Freezer")
cat_d = [[], [], [], []]
TRJ = utils.TRJ(input("Enter trajectory file path...\t"))
print("\nATOM\tELEM\tSTD\t\tSTATUS\n")
for i in range(0, TRJ.natoms):
tmp = []
for j in range(0, TRJ.nspas):
tmp.append(TRJ.trajectory[j][i][1:])
atom_std = np.std(tmp, axis=0)
if np.sum(atom_std) < 0.001:
FRZ_STATUS = "FROZEN"
cat_d[0].append(i + 1)
elif np.sum(atom_std) >= 0.001 and np.sum(atom_std) < 0.3:
FRZ_STATUS = "+"
cat_d[1].append(i + 1)
elif np.sum(atom_std) >= 0.3 and np.sum(atom_std) < 0.5:
FRZ_STATUS = "++"
cat_d[2].append(i + 1)
elif np.sum(atom_std) >= 0.5:
FRZ_STATUS = "+++"
cat_d[3].append(i + 1)
print("{}\t{}\t{:.5f}\t\t{}".format(i + 1, TRJ.trajectory[j][i][0],
np.sum(atom_std), FRZ_STATUS))
print("\nDISPLACEMENTS\tATOMS\n")
print("FROZEN:\t\t{}".format(" ".join([str(i) for i in cat_d[0]])))
print("LOW:\t\t{}".format(" ".join([str(i) for i in cat_d[1]])))
print("MEDIUM:\t\t{}".format(" ".join([str(i) for i in cat_d[2]])))
print("HIGH:\t\t{}".format(" ".join([str(i) for i in cat_d[3]])))
FRZ_LIST = input(
"\nDo you want to CONSTRAIN some particular atom along the TRJ?\n\n"
).split()
FRZ_LIST = [int(i) for i in FRZ_LIST]
with open("./newTRAJ.xyz", 'a') as out:
for idx_i, val_i in enumerate(TRJ.trajectory):
out.write("{}\n".format(str(TRJ.natoms)))
out.write("Trajectory {}\n".format(idx_i + 1))
for idx_j, val_j in enumerate(val_i):
if idx_j + 1 in FRZ_LIST:
out.write("{} \t{:.10f}\t {:.10f}\t {:.10f} \n".format(
TRJ.trajectory[0][idx_j][0],
TRJ.trajectory[0][idx_j][1],
TRJ.trajectory[0][idx_j][2],
TRJ.trajectory[0][idx_j][3]))
else:
out.write("{} \t{:.10f}\t {:.10f}\t {:.10f} \n".format(
val_j[0], val_j[1], val_j[2], val_j[3]))
utils.NT()
def main():
def multiple_parser(inp_list):
"""Multiple input parser"""
out_list = []
for k in inp_list:
if "-" in k:
for li in range(int(k.split("-")[0]),
int(k.split("-")[1]) + 1):
if int(li) not in out_list:
out_list.append(int(li))
else:
if int(k) not in out_list:
out_list.append(int(k))
return out_list
utils.TITLE("CONSTRAINTS GENERATOR")
FILENAME = input("Enter .xyz file path...\t\t")
XMOL = molecule.MOL(FILENAME)
INPUT_INDEX = input(
"\nEnter the element(s) to constrain.\nMultiple elements constraints are possible (e.g.: C O).\nDifferent elements must be separated by a SPACE.\nSpecial tokens are allowed (e.g.: All)\n\nSelection\n"
).split()
CONST_INDEX = []
for idx, val in enumerate(XMOL.element):
if val in INPUT_INDEX:
CONST_INDEX.append(idx + 1)
if "All" in INPUT_INDEX:
CONST_INDEX = [i for i in range(1, XMOL.natoms + 1)]
INPUT_INDEX = input(
"\nDo you want to CONSTRAIN some particular atom?\n\n").split()
for i in multiple_parser(INPUT_INDEX):
if int(i) not in CONST_INDEX:
CONST_INDEX.append(int(i))
INPUT_INDEX = input(
"\nDo you want to UN-CONSTRAIN some particular atom?\n\n").split()
for i in multiple_parser(INPUT_INDEX):
if int(i) in CONST_INDEX:
CONST_INDEX.remove(int(i))
FREE_INDEX = list({int(i)
for i in range(1, XMOL.natoms + 1)} - set(CONST_INDEX))
SOFT = input("\nSelect software:\n1)\tORCA\n2)\tGaussian\n3)\txTB\n")
if SOFT == "1":
print("\nFROZEN ATOMS:", " ".join([str(x - 1) for x in CONST_INDEX]))
print("\n%GEOM")
print(" Constraints")
for i in CONST_INDEX:
print(" {C", i - 1, "C}")
print(" End")
print("END")
CONST_INDEX[:] = [x - 1 for x in CONST_INDEX]
FREE_INDEX[:] = [x - 1 for x in FREE_INDEX]
print(
"\nTo project-out the immaginary frequencies due to frozen atoms in a vibrational analysis use:\n"
)
print("%FREQ")
print(" AnFreq False")
print(" NumFreq True")
print(" Partial_Hess")
print(" {", " ".join(map(str, CONST_INDEX)), "}")
print(" End")
print("END")
elif SOFT == "2":
print("\nFROZEN ATOMS:", " ".join([str(x) for x in CONST_INDEX]))
print(
"\nModredundant syntax is available below but it is suggested to use the classical frozen syntax (Atom 0/-1 X Y Z) at the end of this report:\n"
)
for i in CONST_INDEX:
print("X", i, "F")
print(
"\nTo project-out the immaginary frequencies due to frozen atoms in a vibrational analysis change the coordinates using the frozen syntax (Atom 0/-1 X Y Z):\n"
)
for idx, val in enumerate(XMOL.element):
if idx + 1 in FREE_INDEX:
print("{} {} \t{:.10f}\t {:.10f}\t {:.10f}".format(
val, "0", XMOL.xyz[idx][0], XMOL.xyz[idx][1],
XMOL.xyz[idx][2]))
elif idx + 1 in CONST_INDEX:
print("{} {} \t{:.10f}\t {:.10f}\t {:.10f}".format(
val, "-1", XMOL.xyz[idx][0], XMOL.xyz[idx][1],
XMOL.xyz[idx][2]))
else:
print("ERROR!!! Something wrong just happened... :(")
elif SOFT == "3":
print("\nFROZEN ATOMS:", " ".join([str(x) for x in CONST_INDEX]))
XTB_OPT = input(
"\nDo you like to freeze atoms in hessian calculation? (All immaginary mode due to frozen atoms will be projected out) [y/n]\n"
)
print("\n$fix")
for i in CONST_INDEX:
print("atoms:", i)
if XTB_OPT == "y":
for i in CONST_INDEX:
print("freeze:", i)
print("end")
utils.NT()
def main(FILENAME='', CHN='', RES=''):
def multiple_parser(inp_list):
"""Multiple input parser"""
out_list = []
for k in inp_list:
if "-" in k:
for li in range(int(k.split('-')[0]),
int(k.split('-')[1]) + 1):
if int(li) not in out_list:
out_list.append(int(li))
else:
if int(k) not in out_list:
out_list.append(int(k))
return out_list
def group_ranges(L):
"""
Collapses a list of integers into a list of the start and end of
consecutive runs of numbers. Returns a generator of generators.
"""
for w, z in itertools.groupby(
L, lambda x, y=itertools.count(): next(y) - x):
grouped = list(z)
yield (x for x in [grouped[0], grouped[-1]][:len(grouped)])
def saturate(C_tgt, ref_atom):
"""Saturate the valence of a carbon atom with hydrogen
Args:
C_tgt (list): Cartesian coordinate of C atom to saturate [X, Y, Z]
ref_atom (list): Cartesian coordinate of an atom directly bonded to C_tgt. This is used to create a vector for the rotation of hydrogen atoms [X, Y, Z]
Returns:
[type]: Distance between atom_a and atom_b
"""
MG = [['H', -0.510365374578, -0.883978759193, 0.399020000000],
['H', 1.020730749156, 0.000000000000, 0.399020000000],
['H', -0.510365374578, 0.883978759193, 0.399020000000]]
vec_MG = [0.0, 0.0, -1.4]
vec_TGT = [
ref_atom[0] - C_tgt[0],
ref_atom[1] - C_tgt[1],
ref_atom[2] - C_tgt[2],
]
rot_mat = utils.rot_mat_v(vec_MG, vec_TGT)
H_end = []
for i in MG:
MG_rot = np.matmul(rot_mat, np.array(i[1:4]))
MG_rot = MG_rot + C_tgt
H_end.append([i[0], MG_rot[0], MG_rot[1], MG_rot[2]])
return H_end
utils.TITLE("Catalytic Pocket Selector")
if FILENAME == '':
filename = input('Enter .PDB file name...\t\t')
PRO = utils.PDB(filename)
SelC = input('Select chain...\t\t')
SelRSN = multiple_parser(input('Select residues...\t\t').split())
else:
filename = FILENAME
PRO = utils.PDB(filename)
SelC = CHN
SelRSN = multiple_parser(RES)
SelRSN.sort()
GrpRSN = [list(x) for x in group_ranges(SelRSN)]
print('\nNumber of groups detected...\t{}'.format(len(GrpRSN)))
print('Number of terminations...\t{}'.format(2 * len(GrpRSN)))
for idx, val in enumerate(GrpRSN):
print('\n>> Group:\t{}'.format(str(idx + 1)))
for j in range(val[0], val[-1] + 1):
print('\t', PRO.prot[SelC][str(j)][0][2], str(j))
TGroup = input(
'\nSelect terminations:\n1) ACE/NME\n2) Marker Atom\n3) No Terminations\n\nSelection: '
)
if TGroup == '2':
Mk_Atom = input('\nWhich atom do you like to place as a marker?...\t')
MOL = []
for GRP in GrpRSN:
for AA in range(GRP[0], GRP[-1] + 1):
for ATOM in PRO.prot[SelC][str(AA)]:
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
# ACE
if AA == GRP[0] and TGroup == '1':
for ATOM in PRO.prot[SelC][str(AA - 1)]:
if ATOM[1] == 'O':
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
elif ATOM[1] == 'C':
C_atom = ATOM
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
elif ATOM[1] == 'CA':
CA_atom = ATOM
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
H_Met = saturate(CA_atom[5:8], C_atom[5:8])
for i in H_Met:
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
i[0], i[1], i[2], i[3]))
# NME
if AA == GRP[-1] and TGroup == '1':
for ATOM in PRO.prot[SelC][str(AA + 1)]:
if ATOM[1] == 'NH':
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
elif ATOM[1] == 'N':
C_atom = ATOM
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
elif ATOM[1] == 'CA':
CA_atom = ATOM
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
ATOM[8], ATOM[5], ATOM[6], ATOM[7]))
H_Met = saturate(CA_atom[5:8], C_atom[5:8])
for i in H_Met:
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
i[0], i[1], i[2], i[3]))
if AA == GRP[0] and TGroup == '2':
for ATOM in PRO.prot[SelC][str(AA - 1)]:
if ATOM[1] == 'C':
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
Mk_Atom, ATOM[5], ATOM[6], ATOM[7]))
if AA == GRP[-1] and TGroup == '2':
for ATOM in PRO.prot[SelC][str(AA + 1)]:
if ATOM[1] == 'N':
MOL.append("{} \t{:.3f}\t {:.3f}\t {:.3f}".format(
Mk_Atom, ATOM[5], ATOM[6], ATOM[7]))
with open(filename + '.' + SelC + '.pruned.xyz', 'w') as out:
out.write(str(len(MOL)) + '\n')
out.write('AA: ' + str(SelRSN) + ' Chain: ' + SelC + '\n')
for i in MOL:
out.write(i + '\n')
out.close()
print("\nPruned structure has been saven in: {}\n".format(filename + '.' +
SelC +
'.pruned.xyz'))
utils.NT()
def main():
utils.TITLE("TRJ 2 Synchronous Transit-Guided Quasi-Newton")
TRAJ = utils.TRJ(input("Enter trajectory file path...\t"))
R_SNAP = int(input("\nSnapshot number before TS...\t")) - 1
TS_SNAP = input("Snapshot number of TS guess...\t")
if TS_SNAP == "":
print("Switching to a QST2 input generation...")
else:
print("Switching to a QST3 input generation...")
TS_SNAP = int(TS_SNAP) - 1
P_SNAP = int(input("Snapshot number after TS...\t")) - 1
CHARGE = int(input("Totale charge of the system...\t"))
MULT = int(input("Multiplicity of the system...\t"))
FROZ = input("List of frozen atoms (if any)...\t").split()
FROZ = [int(i) for i in FROZ]
if TS_SNAP == "":
print("\n#Opt(QST2)")
else:
print("\n#Opt(QST3)")
print("\nReactant Guess\n")
print(CHARGE, MULT)
for idx, val in enumerate(TRAJ.trajectory[R_SNAP]):
if FROZ != []:
if idx + 1 in FROZ:
FROZ_STAT = "-1"
else:
FROZ_STAT = "0"
else:
FROZ_STAT = ""
print("{} {} \t{:.10f}\t {:.10f}\t {:.10f}".format(
val[0], FROZ_STAT, val[1], val[2], val[3]))
if TS_SNAP == "":
print("\n\nProduct Guess\n")
else:
print("\nProduct Guess\n")
print(CHARGE, MULT)
for idx, val in enumerate(TRAJ.trajectory[P_SNAP]):
if FROZ != []:
if idx + 1 in FROZ:
FROZ_STAT = "-1"
else:
FROZ_STAT = "0"
else:
FROZ_STAT = ""
print("{} {} \t{:.10f}\t {:.10f}\t {:.10f}".format(
val[0], FROZ_STAT, val[1], val[2], val[3]))
if TS_SNAP != "":
print("\nTS Guess\n")
print(CHARGE, MULT)
for idx, val in enumerate(TRAJ.trajectory[TS_SNAP]):
if FROZ != []:
if idx + 1 in FROZ:
FROZ_STAT = "-1"
else:
FROZ_STAT = "0"
else:
FROZ_STAT = ""
print("{} {} \t{:.10f}\t {:.10f}\t {:.10f}".format(
val[0], FROZ_STAT, val[1], val[2], val[3]))
utils.NT()
def main():
def Displacement(ndim, nim, R):
"""
Computes straight line distances between adjacent pair of images
and then sums up the distances
"""
displ = np.zeros(shape=(nim, ))
for i in range(1, nim):
R0 = R[(i - 1) * ndim:(i) * ndim]
R1 = R[(i) * ndim:(i + 1) * ndim]
dR = R1 - R0
displ[i] = displ[i - 1] + np.sqrt(np.dot(dR.T, dR))
return displ
def LinearInterpolateData(nlen, xData, yData, xnew):
"""
Linear interpolation of data points (xData, yData) to point xnew
"""
i = 0
if (xnew >= xData[nlen - 2]):
i = nlen - 2
else:
while (xnew > xData[i + 1]):
i = i + 1
xL = xData[i]
yL = yData[i]
xR = xData[i + 1]
yR = yData[i + 1]
if (xnew < xL):
yR = yL
if (xnew > xR):
yL = yR
dydx = (yR - yL) / (xR - xL)
return yL + dydx * (xnew - xL)
def GenerateNewPath(ndim, nim, npoints, S, R):
"""
Generates new path, newR of npoints images, from path R with nim images
"""
newR = np.zeros(shape=(ndim * npoints, 1))
xi = np.linspace(S[0], S[-1], npoints)
for i in range(ndim):
Rdof = np.zeros(shape=(nim, 1))
dRdof = np.zeros(shape=(nim, 1))
for j in range(nim):
Rdof[j] = R[j * ndim + i]
for xpt in range(npoints):
new_y = LinearInterpolateData(nim, S, Rdof, xi[xpt])
newR[xpt * ndim + i] = new_y
return newR
def ReadFirstLineOfFile(fname):
with open(fname) as f:
first_line = f.readline()
return first_line
def WriteTraj(fname, ndim, nim, R, E, symb3, restart="n"):
if len(symb3) != ndim:
raise RuntimeError("Error in WriteTraj. Dimension mismatch: symb3")
if len(E) != nim:
raise RuntimeError("Error in WriteTraj. Dimension mismatch: E")
if len(R) != ndim * nim:
raise RuntimeError("Error in WriteTraj. Dimension mismatch: R")
f = open(fname, 'w')
natoms = ndim / 3
for i in range(nim):
hnit = R[i * ndim:(i + 1) * ndim]
f.write("%i \n" % natoms)
f.write('E=%12.8f \n' % E[i])
for j in range(0, len(hnit), 3):
f.write('%s %12.8f %12.8f %12.8f\n' %
(symb3[j].strip(), hnit[j], hnit[j + 1], hnit[j + 2]))
if restart == "y" and i + 1 != nim:
f.write('>\n')
f.close()
return None
def ReadTraj(fname):
if not os.path.isfile(fname):
raise RuntimeError("File %s not found " % fname)
extension = fname.split('.')[-1]
# Get first line of the file (i.e. number of atoms)
first_line = ReadFirstLineOfFile(fname)
try:
natoms = int(first_line)
except:
raise TypeError("%s is not correctly formatted trajectory file")
ndim = natoms * 3
# begin by reading the contents of the file to a list
contents = []
f = open(fname).readlines()
for i, line in enumerate(f):
contents.append(line)
if ">\n" in contents:
print('\n--ORCA Restart file detected!')
contents = [i for i in contents if i != ">\n"]
else:
print('\n--Normal TRJ file detected!')
# get number of lines and hence number of images
number_of_lines = i + 1
nim = int((number_of_lines) / (natoms + 2))
RPATH = []
ind = 0
for i in range(nim):
symb3 = []
ind = ind + 2
for j in range(natoms):
geom_line = contents[ind]
geom_line = geom_line.split()
symb3.append(geom_line[0].strip())
symb3.append(geom_line[0].strip())
symb3.append(geom_line[0].strip())
RPATH.append(float(geom_line[1]))
RPATH.append(float(geom_line[2]))
RPATH.append(float(geom_line[3]))
ind += 1
RPATH = np.reshape(RPATH, (nim * ndim, 1))
return RPATH, ndim, nim, symb3
utils.TITLE("Linear interpolation of a trajectory")
# ============================================
# default values
# ============================================
fname = input("Enter .xyz trajectory file path...\t")
TRJ = utils.TRJ(fname)
npts = int(input("\nNumber of final points...\t"))
# ============================================
# Get inp arguments
# ============================================
# Notice that the order of the arguments matters.
for i in range(len(sys.argv)):
if i == 1:
fname = sys.argv[1]
if i == 2:
try:
npts = int(sys.argv[2])
except:
raise TypeError("Int. expected as a second arg")
file_extension = fname.split('.')[1]
# ============================================
# Read trajectory file
# ============================================
name_string = fname.split('.')
basename = name_string[0]
file_extension = name_string[1]
R, ndim, nim, symb3 = ReadTraj(fname)
print('--Found %i images with %i atoms' % (nim, ndim / 3))
print('--Interpolating to %i points' % (npts))
restart = input("\nSave as a ORCA Restart file? [y/n]...\t")
if npts > nim:
fname_output = basename + '_exte.' + file_extension
elif npts == nim:
fname_output = basename + '_redistri.' + file_extension
else:
fname_output = basename + '_reduc.' + file_extension
if restart == "y":
fname_output = 'restart.allxyz'
print('--output file: %s' % fname_output)
# ============================================
# Perform interpolation
# ============================================
S = Displacement(ndim, nim, R)
newR = GenerateNewPath(ndim, nim, npts, S, R)
# ============================================
# Write new trajectory file
# ============================================
E = np.zeros(shape=(npts, 1))
if restart == "y":
WriteTraj(fname_output, ndim, npts, newR, E, symb3, restart)
else:
WriteTraj(fname_output, ndim, npts, newR, E, symb3)
RP_SAVE = input("\nSave R/P files? [y/n]...\t")
if RP_SAVE == 'y':
with open("./R.xyz", 'a') as out:
out.write("{}\n".format(str(TRJ.natoms)))
out.write("Reactants\n")
for i in TRJ.trajectory[0]:
out.write("{} \t{:.10f}\t {:.10f}\t {:.10f} \n".format(
i[0], i[1], i[2], i[3]))
with open("./P.xyz", 'a') as out:
out.write("{}\n".format(str(TRJ.natoms)))
out.write("Products\n")
for i in TRJ.trajectory[-1]:
out.write("{} \t{:.10f}\t {:.10f}\t {:.10f} \n".format(
i[0], i[1], i[2], i[3]))
utils.NT()