if sub.conf_num > 1:
s += "%-20s" % name
# if (i + 1) % 3 == 0:
if (i + 1) % 1 == 0:
s += "\n"
print(s.strip())
sys.exit(0)
detect_subs = False
s = ""
skipped = 0
for infile in glob_files(args.infile, parser=makeconf_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format[0], infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format[0], infile))
else:
f = FileReader(("from stdin", "xyz", infile))
geom = Geometry(f)
target_list = []
explicit_subnames = []
help="print all diastereomers for selected chiral centers")
changechiral_parser.add_argument(
"-m",
"--minimize",
action="store_true",
default=False,
dest="minimize",
help="rotate substituents to mitigate steric clashing",
)
args = changechiral_parser.parse_args()
s = ""
for infile in glob_files(args.infile, parser=changechiral_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format[0], infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format[0], stdin))
else:
f = FileReader(("from stdin", "xyz", stdin))
geom = Geometry(f)
target_list = []
if args.targets is None:
)
args = maplig_parser.parse_args()
if args.list_avail is not False:
s = ""
for i, name in enumerate(sorted(get_matching_ligands(args.list_avail))):
s += "%-35s" % name
if (i + 1) % 3 == 0:
# if (i + 1) % 1 == 0:
s += "\n"
print(s.strip())
sys.exit(0)
for infile in glob_files(args.infile, parser=maplig_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format[0], infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format[0], infile))
else:
f = FileReader(("from stdin", "xyz", infile))
cat = Geometry(f)
if args.center:
cat.detect_components(center=args.center)
def main(argv):
vbur_parser = argparse.ArgumentParser(
description=
"calculate Boltzmann-weighted percent buried volume parameters",
formatter_class=argparse.RawTextHelpFormatter)
vbur_parser.add_argument("infiles",
metavar="input files",
type=str,
nargs="+",
help="file containing coordinates and energy")
vbur_parser.add_argument("-if",
"--input-format",
type=str,
default=None,
choices=["log", "out", "dat"],
dest="input_format",
help="file format of input")
vbur_parser.add_argument("-o",
"--output",
type=str,
default=False,
required=False,
metavar="output destination",
dest="outfile",
help="output destination\n" + "Default: stdout")
vbur_parser.add_argument(
"-l",
"--ligand-atoms",
default=None,
required=False,
dest="targets",
help=
"atoms to consider in calculation\nDefault: use all atoms except the center",
)
vbur_parser.add_argument(
"-e",
"--exclude-atoms",
default=None,
required=False,
dest="exclude_atoms",
help=
"atoms to exclude from the calculation\nDefault: exclude no ligand atoms",
)
vbur_parser.add_argument(
"-c",
"--center",
action="append",
default=None,
required=False,
dest="center",
help="atom the sphere is centered on\n" +
"Default: detect metal center (centroid of all metals if multiple are present)",
)
vbur_parser.add_argument(
"-r",
"--radius",
default=3.5,
type=float,
dest="radius",
help="radius around center\nDefault: 3.5 Ångström")
vbur_parser.add_argument(
"-vdw",
"--vdw-radii",
type=str,
default="bondi",
choices=["bondi", "umn"],
dest="radii",
help="VDW radii to use in calculation\n" +
"umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812\n"
+ " (DOI: 10.1021/jp8111556)\n" +
" transition metals are crystal radii from Batsanov, S.S. Van der Waals\n"
+ " Radii of Elements. Inorganic Materials 37, 871–885 (2001).\n" +
" (DOI: 10.1023/A:1011625728803)\n" +
"bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)\n"
+ "Default: bondi")
vbur_parser.add_argument(
"-s",
"--scale",
default=1.17,
type=float,
dest="scale",
help="scale VDW radii by this amount\nDefault: 1.17",
)
vbur_parser.add_argument("-t",
"--temperature",
type=str,
default=298.15,
required=False,
dest="temperature",
help="temperature in K\nDefault: 298.15")
vbur_parser.add_argument(
"-f",
"--frequency",
action="store_true",
default=False,
required=False,
dest="frequency",
help="input files are frequency job output files\n"
"additional average values will be calculated for ZPE, H, G, etc.")
vbur_parser.add_argument(
"-w0",
"--frequency-cutoff",
type=float,
default=100.0,
required=False,
dest="w0",
help="cutoff frequency for quasi free energy corrections (1/cm)\n" +
"Default: 100 cm^-1")
vbur_parser.add_argument("-v",
"--verbose",
action="store_true",
default=False,
required=False,
dest="verbose",
help="also print population")
vbur_parser.add_argument(
"-m",
"--method",
default="Lebedev",
type=lambda x: x.capitalize() if x.lower() == "lebedev" else x.upper(),
choices=["MC", "Lebedev"],
dest="method",
help=
"integration method - Monte-Carlo (MC) or Lebedev quadrature (Lebedev)\nDefault: Lebedev"
)
grid_options = vbur_parser.add_argument_group(
"Lebedev integration options")
grid_options.add_argument(
"-rp",
"--radial-points",
type=int,
default=20,
choices=[20, 32, 64, 75, 99, 127],
dest="rpoints",
help="number of radial shells for Gauss-Legendre integration\n" +
"of the radial component\n" +
"lower values are faster, but at the cost of accuracy\nDefault: 20")
grid_options.add_argument(
"-ap",
"--angular-points",
type=int,
default=1454,
choices=[110, 194, 302, 590, 974, 1454, 2030, 2702, 5810],
dest="apoints",
help="number of angular points for Lebedev integration\n" +
"lower values are faster, but at the cost of accuracy\nDefault: 1454")
mc_options = vbur_parser.add_argument_group(
"Monte-Carlo integration options")
mc_options.add_argument(
"-i",
"--minimum-iterations",
type=int,
default=25,
metavar="ITERATIONS",
dest="min_iter",
help="minimum iterations - each is a batch of 3000 points\n" +
"MC will continue after this until convergence criteria are met\n" +
"Default: 25",
)
args = vbur_parser.parse_args(args=argv)
targets = None
if args.exclude_atoms and not args.targets:
targets = (NotAny(args.exclude_atoms))
elif args.exclude_atoms and args.targets:
targets = (NotAny(args.exclude_atoms), args.targets)
else:
targets = NotAny(args.center)
geoms = []
energies = {"E": []}
if args.frequency:
energies["E+ZPE"] = []
energies["H(RRHO)"] = []
energies["G(RRHO)"] = []
energies["G(Quasi-RRHO)"] = []
energies["G(Quasi-Harmonic)"] = []
for infile in glob_files(args.infiles, parser=vbur_parser):
if args.input_format is not None:
fr = FileReader((infile, args.input_format, infile),
just_geom=False)
else:
fr = FileReader(infile, just_geom=False)
geom = Geometry(fr)
geoms.append(geom)
nrg = fr.other["energy"]
energies["E"].append(nrg)
if args.frequency:
co = CompOutput(fr)
dE, dH, entropy = co.therm_corr(temperature=args.temperature)
rrho_dG = co.calc_G_corr(v0=0,
temperature=args.temperature,
method="RRHO")
qrrho_dG = co.calc_G_corr(v0=args.w0,
temperature=args.temperature,
method="QRRHO")
qharm_dG = co.calc_G_corr(v0=args.w0,
temperature=args.temperature,
method="QHARM")
energies["E+ZPE"].append(nrg + co.ZPVE)
energies["H(RRHO)"].append(nrg + dH)
energies["G(RRHO)"].append(nrg + rrho_dG)
energies["G(Quasi-RRHO)"].append(nrg + qrrho_dG)
energies["G(Quasi-Harmonic)"].append(nrg + qharm_dG)
s = ""
for nrg_type in energies:
energies_arr = np.array(energies[nrg_type])
energies_arr *= UNIT.HART_TO_KCAL
if args.verbose and nrg_type == "E":
s += "\t".join(["%Vbur", "file"])
s += "\n"
for f, geom in zip(args.infiles, geoms):
data = geom.percent_buried_volume(
targets=targets,
center=args.center,
radius=args.radius,
radii=args.radii,
scale=args.scale,
method=args.method,
rpoints=args.rpoints,
apoints=args.apoints,
min_iter=args.min_iter,
)
s += "%.1f%%\t%s\n" % (data, f)
s += "\n"
s += "weighted using %s:\n" % nrg_type
data = Geometry.weighted_percent_buried_volume(
geoms,
energies_arr,
args.temperature,
targets=targets,
center=args.center,
radius=args.radius,
radii=args.radii,
scale=args.scale,
method=args.method,
rpoints=args.rpoints,
apoints=args.apoints,
min_iter=args.min_iter,
)
if args.verbose:
coeff = boltzmann_coefficients(energies_arr, args.temperature)
coeff /= sum(coeff)
coeff *= 100
for f, c, e in zip(args.infiles, coeff, energies_arr):
s += "%s %.1f%% (%.1f kcal/mol)\n" % (f, c,
e - min(energies_arr))
s += "%%Vbur: %.2f\n\n" % data
if not args.outfile:
print(s)
else:
with open(args.outfile, "w") as f:
f.write(s)
)
args = substitute_parser.parse_args()
if args.list_avail:
s = ""
for i, name in enumerate(sorted(Substituent.list())):
s += "%-20s" % name
# if (i + 1) % 3 == 0:
if (i + 1) % 1 == 0:
s += "\n"
print(s.strip())
sys.exit(0)
for infile in glob_files(args.infile, parser=substitute_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format, infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format, infile))
else:
f = FileReader(("from stdin", "xyz", infile))
geom = Geometry(f)
target_list = []
for sub in args.substitutions:
def main(argv):
sterimol_parser = argparse.ArgumentParser(
description=
"calculate B1-B5, and L sterimol parameters for ligands - see Verloop, A. and Tipker, J. (1976), Use of linear free energy related and other parameters in the study of fungicidal selectivity. Pestic. Sci., 7: 379-390.",
formatter_class=argparse.RawTextHelpFormatter)
sterimol_parser.add_argument("infile",
metavar="input file",
type=str,
nargs="*",
default=[sys.stdin],
help="a coordinate file")
sterimol_parser.add_argument(
"-if",
"--input-format",
type=str,
default=None,
choices=read_types,
dest="input_format",
help="file format of input\nxyz is assumed if input is stdin")
sterimol_parser.add_argument(
"-k",
"--key-atoms",
type=str,
required=True,
dest="key",
help="1-indexed position of the ligand's coordinating atoms")
sterimol_parser.add_argument("-c",
"--center-atom",
type=str,
required=True,
dest="center",
help="atom the ligand is coordinated to")
sterimol_parser.add_argument(
"-r",
"--radii",
type=str,
default="bondi",
choices=["bondi", "umn"],
dest="radii",
help="VDW radii to use in calculation\n"
"umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812\n"
" (DOI: 10.1021/jp8111556)\n"
" transition metals are crystal radii from Batsanov, S.S. Van der Waals\n"
" Radii of Elements. Inorganic Materials 37, 871–885 (2001).\n"
" (DOI: 10.1023/A:1011625728803)\n"
"bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451\n(DOI: 10.1021/j100785a001)\n"
"Default: bondi")
sterimol_parser.add_argument(
"-bl",
"--bisect-L",
action="store_true",
required=False,
dest="bisect_L",
help="L axis will bisect (or analogous for higher denticity\n"
"ligands) the L-M-L angle\n"
"Default: center to centroid of key atoms")
sterimol_parser.add_argument(
"-al",
"--at-L",
default=[None],
dest="L_value",
type=lambda x: [float(v) for v in x.split(",")],
help="get widths at specific L values (comma-separated)\n"
"can be used for Sterimol2Vec parameters\n"
"Default: use the entire ligand",
)
sterimol_parser.add_argument(
"-v",
"--vector",
action="store_true",
required=False,
dest="vector",
help=
"print Chimera/ChimeraX bild file for vectors instead of parameter values"
)
sterimol_parser.add_argument("-o",
"--output",
type=str,
default=False,
required=False,
metavar="output destination",
dest="outfile",
help="output destination\n" +
"Default: stdout")
args = sterimol_parser.parse_args(args=argv)
s = ""
if not args.vector:
s += "B1\tB2\tB3\tB4\tB5\tL\tfile\n"
for infile in glob_files(args.infile, parser=sterimol_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format, infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format, infile))
else:
f = FileReader(("from stdin", "xyz", infile))
geom = Geometry(f, refresh_ranks=False)
comp = Component(
geom.get_fragment(args.key, stop=args.center),
to_center=geom.find(args.center),
key_atoms=args.key,
detect_backbone=False,
)
for val in args.L_value:
data = comp.sterimol(
to_center=geom.find(args.center),
return_vector=args.vector,
radii=args.radii,
bisect_L=args.bisect_L,
at_L=val,
)
if args.vector:
for key, color in zip(
["B1", "B2", "B3", "B4", "B5", "L"],
["black", "green", "purple", "orange", "red", "blue"]):
start, end = data[key]
s += ".color %s\n" % color
s += ".note Sterimol %s\n" % key
s += ".arrow %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n" % (
*start, *end)
else:
s += "%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%s\n" % (
data["B1"],
data["B2"],
data["B3"],
data["B4"],
data["B5"],
data["L"],
infile,
)
if not args.outfile:
print(s)
else:
with open(args.outfile, "w") as f:
f.write(s)
help=
"CSV file containing observed spectrum data, which will be plotted on top\n"
"frequency job files should not come directly after this flag")
args = ir_parser.parse_args()
exp_data = None
if args.exp_data:
exp_data = []
for f in args.exp_data:
data = np.loadtxt(f, delimiter=",")
for i in range(1, data.shape[1]):
exp_data.append((data[:, 0], data[:, i], None))
for f in glob_files(args.infiles, parser=ir_parser):
fr = FileReader(f, just_geom=False)
freq = fr.other["frequency"]
fig = plt.gcf()
fig.clear()
freq.plot_ir(
fig,
centers=args.centers,
widths=args.widths,
plot_type=args.plot_type,
peak_type=args.peak_type,
reverse_x=args.reverse_x,
fwhm=args.fwhm,
help="print all symmetry elements",
)
pg_parser.add_argument(
"-b",
"--bild",
action="store_true",
default=False,
dest="print_bild",
help="print Chimera(X) bild file to display various symmetry elements",
)
args = pg_parser.parse_args()
s = ""
for f in glob_files(args.infile, parser=pg_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None), just_geom=True)
else:
infile = FileReader(f, just_geom=True)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f),
just_geom=True)
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f), just_geom=True)
geom = Geometry(infile)
pg = PointGroup(
if args.csv:
if args.csv == "comma":
sep = ","
elif args.csv == "tab":
sep = "\t"
elif args.csv == "semicolon":
sep = ";"
else:
sep = " "
s = ""
np.set_printoptions(precision=5)
for f in glob_files(args.infile, parser=info_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None),
just_geom=False)
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f),
just_geom=False)
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f), just_geom=False)
if args.list:
help="also try swapping target order when minimizing")
args = ring_parser.parse_args()
if args.list_avail:
s = ""
for i, name in enumerate(sorted(Ring.list())):
s += "%-20s" % name
# if (i + 1) % 3 == 0:
if (i + 1) % 1 == 0:
s += "\n"
print(s.strip())
exit(0)
for infile in glob_files(args.infile, parser=ring_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format, infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format, stdin))
else:
f = FileReader(("from stdin", "xyz", stdin))
geom = Geometry(f)
targets = {}
help=
"put structures in specified directory\nDefault: don't output structures",
)
args = unique_parser.parse_args()
if args.energy_filter is None:
args.energy_filter = 0.2
mirror_mat = np.eye(3)
mirror_mat[0][0] *= -1
# dictionary of structures, which will be ordered by number of atoms, elements, etc.
structures = {}
for f in glob_files(args.infile, parser=unique_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None), just_geom=False)
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f),
just_geom=False)
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f), just_geom=False)
geom = Geometry(infile)
geom.other = infile.other
if args.angle is None and args.num is None:
raise ValueError("must specified one of ('--angle', '--number')")
elif args.num is None and args.angle is not None:
args.num = 1
args.angle = args.angle
elif args.num is not None and args.angle is None:
args.num = args.num
args.angle = 360.0 / args.num
elif args.num is not None and args.angle is not None:
args.num = args.num
args.angle = args.angle
if not args.radians:
args.angle = np.deg2rad(args.angle)
for f in glob_files(args.infile, parser=rotate_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
center = args.center
if args.fragment is not None:
dest="comment",
help="comment line"
)
xyz_parser.add_argument(
"-a", "--append",
action="store_true",
default=False,
required=False,
dest="append",
help="append structures to output file if it already exists\nDefault: false"
)
args = xyz_parser.parse_args()
for f in glob_files(args.infile, parser=xyz_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile, refresh_connected=False, refresh_ranks=False)
if args.comment:
geom.comment = args.comment
angle_parser.add_argument(
"-o",
"--output",
type=str,
default=False,
required=False,
dest="outfile",
metavar="output destination",
help="output destination\n" +
"$INFILE will be replaced with the name of the input file\n" +
"Default: stdout")
args = angle_parser.parse_args()
for f in glob_files(args.infile, parser=angle_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
#set angle to specified value
for angle in args.set_ang:
stat_parser.add_argument("-o",
"--output",
type=str,
nargs="+",
default=None,
required=False,
dest="outfile",
help="output destination\nDefault: stdout")
args = stat_parser.parse_args()
s = ""
header_vals = [None]
for f in glob_files(args.infile, parser=stat_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None),
just_geom=False)
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f),
just_geom=False)
else:
stat_parser.print_help()
raise RuntimeError(
"when no input file is given, stdin is read and a format must be specified"
)
kwargs[pos].extend(opt)
for pos in [PSI4_BEFORE_GEOM, PSI4_AFTER_JOB, PSI4_BEFORE_JOB, GAUSSIAN_POST]:
opt = getattr(args, pos)
if opt:
if pos not in kwargs:
kwargs[pos] = []
kwargs[pos].extend([" ".join(word) for word in opt])
if args.comments:
kwargs["comments"] = [" ".join(comment) for comment in args.comments]
# Theory() is made for each file because we might be using things from the input file
for f in glob_files(args.infile, parser=theory_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None),
just_geom=False,
get_all=True)
else:
infile = FileReader(f, just_geom=False, get_all=True)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f),
just_geom=False,
get_all=True)
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f),
anharm_header = delim.join([
"E", "E+ZPE", "E+ZPE(anh)", "H(RRHO)", "G(RRHO)", "G(Quasi-RRHO)",
"G(Quasi-harmonic)", "ZPE", "ZPE(anh)", "dH(RRHO)", "dG(RRHO)",
"dG(Quasi-RRHO)", "dG(Quasi-harmonic)", "SP_File", "Thermo_File"
])
harm_header = delim.join([
"E", "E+ZPE", "H(RRHO)", "G(RRHO)", "G(Quasi-RRHO)",
"G(Quasi-harmonic)", "ZPE", "dH(RRHO)", "dG(RRHO)", "dG(Quasi-RRHO)",
"dG(Quasi-harmonic)", "SP_File", "Thermo_File"
])
header = None
output = ""
if args.pattern is None:
infiles = glob_files(args.infile, parser=thermo_parser)
else:
infiles = []
if args.infile == [sys.stdin]:
directories = [os.getcwd()]
else:
directories = []
for directory in args.infile:
directories.extend(glob(directory))
for directory in directories:
for root, dirs, files in os.walk(directory, topdown=True):
for pattern in args.pattern:
full_glob = os.path.join(root, pattern)
infiles.extend(glob(full_glob))
eye = np.identity(3)
if args.yz_plane:
eye[0, 0] *= -1
if args.xz_plane:
eye[1, 1] *= -1
if args.xy_plane:
eye[2, 2] *= -1
if np.sum(eye) == 3:
eye[0, 0] *= -1
for f in glob_files(args.infile, parser=mirror_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
geom.update_geometry(np.dot(geom.coords, eye))
help="translate the centroid of the targets to the destination")
translate_parser.add_argument(
"-o",
"--output",
type=str,
default=False,
required=False,
dest="outfile",
help="output destination\n" +
"$INFILE will be replaced with the name of the input file\n" +
"Default: stdout")
args = translate_parser.parse_args()
for f in glob_files(args.infile, parser=translate_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
# targets to move
targets = []
mc_options.add_argument(
"-i", "--minimum-iterations",
type=int,
default=25,
metavar="ITERATIONS",
dest="min_iter",
help="minimum iterations - each is a batch of 3000 points\n" +
"MC will continue after this until convergence criteria are met\n" +
"Default: 25",
)
args = vbur_parser.parse_args()
s = ""
for f in glob_files(args.infile, parser=vbur_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None))
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
targets = None
"Default: umn",
)
cone_parser.add_argument(
"-b", "--cone-bild",
action="store_true",
default=False,
dest="print_cones",
help="print Chimera/ChimeraX bild file containing cones",
)
args = cone_parser.parse_args()
s = ""
for f in glob_files(args.infile, parser=cone_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None))
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
ligand = geom.get_fragment(args.key_atoms, stop=args.center)
def main(argv):
sterimol_parser = argparse.ArgumentParser(
description=
"calculate Boltzmann-weighted Sterimol parameters - see doi 10.1021/acscatal.8b04043",
formatter_class=argparse.RawTextHelpFormatter)
sterimol_parser.add_argument("infiles",
metavar="input files",
type=str,
nargs="+",
help="file containing coordinates and energy")
sterimol_parser.add_argument("-if",
"--input-format",
type=str,
default=None,
choices=["log", "out", "dat"],
dest="input_format",
help="file format of input")
sterimol_parser.add_argument(
"-s",
"--substituent-atom",
type=str,
required=True,
dest="targets",
help="substituent atom\n" +
"1-indexed position of the starting position of the\n" +
"substituent of which you are calculating sterimol\nparameters")
sterimol_parser.add_argument(
"-a",
"--attached-to",
type=str,
required=True,
dest="avoid",
help="non-substituent atom\n" +
"1-indexed position of the starting position of the atom\n" +
"connected to the substituent of which you are calculating\n" +
"sterimol parameters")
sterimol_parser.add_argument(
"-r",
"--radii",
type=str,
default="bondi",
choices=["bondi", "umn"],
dest="radii",
help="VDW radii to use in calculation\n" +
"umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812\n"
+ " (DOI: 10.1021/jp8111556)\n" +
" transition metals are crystal radii from Batsanov, S.S. Van der Waals\n"
+ " Radii of Elements. Inorganic Materials 37, 871–885 (2001).\n" +
" (DOI: 10.1023/A:1011625728803)\n" +
"bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)\n"
+ "Default: bondi")
sterimol_parser.add_argument(
"-l",
"--old-l",
action="store_true",
required=False,
dest="old_L",
help="approximate FORTRAN Sterimol method for determining L\n"
"This is 0.4 + the ideal bond length for a target-H bond\n"
"to outer VDW radii of atoms projected onto L-axis\n"
"Default: L value is from VDW radii of target atom to outer\n"
"VDW radii of atoms projected onto L-axis")
sterimol_parser.add_argument("-t",
"--temperature",
type=float,
default=298.15,
required=False,
dest="temperature",
help="temperature in K\nDefault: 298.15")
sterimol_parser.add_argument(
"-f",
"--frequency",
action="store_true",
default=False,
required=False,
dest="frequency",
help="input files are frequency job output files\n"
"additional average values will be calculated for ZPE, H, G, etc.")
sterimol_parser.add_argument(
"-w0",
"--frequency-cutoff",
type=float,
default=100.0,
required=False,
dest="w0",
help="cutoff frequency for quasi free energy corrections (1/cm)\n" +
"Default: 100 cm^-1")
sterimol_parser.add_argument("-v",
"--verbose",
action="store_true",
default=False,
required=False,
dest="verbose",
help="also print population")
sterimol_parser.add_argument("-o",
"--output",
type=str,
default=False,
required=False,
metavar="output destination",
dest="outfile",
help="output destination\n" +
"Default: stdout")
args = sterimol_parser.parse_args(args=argv)
subs = []
energies = {"E": []}
if args.frequency:
energies["E+ZPE"] = []
energies["H(RRHO)"] = []
energies["G(RRHO)"] = []
energies["G(Quasi-RRHO)"] = []
energies["G(Quasi-Harmonic)"] = []
for infile in glob_files(args.infiles, parser=sterimol_parser):
if args.input_format is not None:
fr = FileReader((infile, args.input_format, infile),
just_geom=False)
else:
fr = FileReader(infile, just_geom=False)
geom = Geometry(fr)
target = args.targets
avoid = args.avoid
end = geom.find(avoid)[0]
frag = geom.get_fragment(target, stop=end)
sub = Substituent(frag, end=end, detect=False)
subs.append(sub)
nrg = fr.other["energy"]
energies["E"].append(nrg)
if args.frequency:
co = CompOutput(fr)
dE, dH, entropy = co.therm_corr(temperature=args.temperature)
rrho_dG = co.calc_G_corr(v0=0,
temperature=args.temperature,
method="RRHO")
qrrho_dG = co.calc_G_corr(v0=args.w0,
temperature=args.temperature,
method="QRRHO")
qharm_dG = co.calc_G_corr(v0=args.w0,
temperature=args.temperature,
method="QHARM")
energies["E+ZPE"].append(nrg + co.ZPVE)
energies["H(RRHO)"].append(nrg + dH)
energies["G(RRHO)"].append(nrg + rrho_dG)
energies["G(Quasi-RRHO)"].append(nrg + qrrho_dG)
energies["G(Quasi-Harmonic)"].append(nrg + qharm_dG)
s = ""
for nrg_type in energies:
energies_arr = np.array(energies[nrg_type])
energies_arr *= UNIT.HART_TO_KCAL
if args.verbose and nrg_type == "E":
s += "\t".join(["B1", "B2", "B3", "B4", "B5", "L", "file"])
s += "\n"
for f, sub in zip(args.infiles, subs):
data = sub.sterimol(
radii=args.radii,
old_L=args.old_L,
)
s += "\t".join([
"%.2f" % data[x]
for x in ["B1", "B2", "B3", "B4", "B5", "L"]
])
s += "\t%s\n" % f
s += "weighted using %s:\n" % nrg_type
data = Substituent.weighted_sterimol(
subs,
energies_arr,
args.temperature,
radii=args.radii,
old_L=args.old_L,
)
if args.verbose:
coeff = boltzmann_coefficients(energies_arr, args.temperature)
coeff /= sum(coeff)
coeff *= 100
for f, c, e in zip(args.infiles, coeff, energies_arr):
s += "%s %.1f%% (%.1f kcal/mol)\n" % (f, c,
e - min(energies_arr))
s += "\t".join(["B1", "B2", "B3", "B4", "B5", "L"])
s += "\n"
s += "\t".join(
["%.2f" % data[x] for x in ["B1", "B2", "B3", "B4", "B5", "L"]])
s += "\n"
s += "\n"
if not args.outfile:
print(s)
else:
with open(args.outfile, "w") as f:
f.write(s)
if args.geometry:
new_vsepr = args.geometry.replace("_", " ")
if adjust_hs == 0 and new_vsepr is None:
adjust_structure = False
elif adjust_hs == 0 and new_vsepr:
goal = len(Atom.get_shape(new_vsepr)) - 1
def goal_func(atom, goal=goal):
return goal - len(atom.connected)
adjust_structure = (goal_func, new_vsepr)
elif adjust_hs is True:
adjust_structure = True
else:
adjust_structure = (adjust_hs, new_vsepr)
for f in glob_files(args.infile, parser=element_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
target_list = []
help="scale VDW radii by this amount\nDefault: 1.17")
args = steric_parser.parse_args()
oop_vector = args.oop_vector
if args.oop_vector is not None:
oop_vector = np.array(args.oop_vector)
ip_vector = args.ip_vector
if args.ip_vector is not None:
ip_vector = np.array(args.ip_vector)
if args.vbur is None:
args.vbur = "Lebedev"
for f in glob_files(args.infile, parser=steric_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format[0], None))
else:
infile = FileReader(f, just_geom=False)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
x, y, z, min_alt, max_alt, basis, targets = geom.steric_map(
dihedral_parser.add_argument(
"-o",
"--output",
type=str,
default=False,
required=False,
dest="outfile",
metavar="output destination",
help="output destination\n" +
"$INFILE will be replaced with the name of the input file\n" +
"Default: stdout")
args = dihedral_parser.parse_args()
for f in glob_files(args.infile, dihedral_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
# set dihedral to specified value
for dihedral in args.set_ang:
if args.chiral:
finders.append(ChiralCenters())
if args.delim == "comma":
delim = ","
elif args.delim == "space":
delim = " "
elif args.delim == "tab":
delim = "\t"
elif args.delim == "semicolon":
delim = ";"
s = ""
for f in glob_files(args.infile, parser=find_parser):
if isinstance(f, str):
if args.input_format is not None:
infile = FileReader((f, args.input_format, None))
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
geom_finders = [x for x in finders]
"atom on the molecule that is connected to the fragment being removed\nDefault: longest fragment",
)
remove_frag_parser.add_argument(
"-a",
"--add-hydrogen",
action="store_true",
required=False,
default=False,
dest="add_H",
help="add hydrogen to cap where the fragment was removed",
)
args = remove_frag_parser.parse_args()
for infile in glob_files(args.infile, parser=remove_frag_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format[0], infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format[0], infile))
else:
f = FileReader(("from stdin", "xyz", infile))
geom = Geometry(f)
for atom in geom.find(args.target):
if atom in geom.atoms:
dest="wait_last",
help="wait for the last job to finish before exiting",
)
submit_parser.add_argument(
"-we",
"--wait-each",
action="store_true",
default=False,
dest="wait_each",
help="wait for each job to finish before submitting the next",
)
args = submit_parser.parse_args()
for i, f in enumerate(glob_files(args.infile, parser=submit_parser)):
# TODO: if processors etc. is not specified, read the input file to see if
# processors were specified
processors = args.processors
memory = args.memory
walltime = args.time
template = args.template
if args.section is not None:
if args.processors is None:
processors = config.getint(args.section,
"processors",
fallback=None)
if args.memory is None:
memory = config.getint(args.section, "memory", fallback=None)
def main(argv):
sterimol_parser = argparse.ArgumentParser(
description="calculate B1-B5, and L sterimol parameters for substituents - see Verloop, A. and Tipker, J. (1976), Use of linear free energy related and other parameters in the study of fungicidal selectivity. Pestic. Sci., 7: 379-390.",
formatter_class=argparse.RawTextHelpFormatter
)
sterimol_parser.add_argument(
"infile", metavar="input file",
type=str,
nargs="*",
default=[sys.stdin],
help="a coordinate file"
)
sterimol_parser.add_argument(
"-if", "--input-format",
type=str,
default=None,
choices=read_types,
dest="input_format",
help="file format of input\nxyz is assumed if input is stdin"
)
sterimol_parser.add_argument(
"-s", "--substituent-atom",
type=str,
required=True,
dest="targets",
help="substituent atom\n" +
"1-indexed position of the starting position of the\n" +
"substituent of which you are calculating sterimol\nparameters"
)
sterimol_parser.add_argument(
"-a", "--attached-to",
type=str,
required=True,
dest="avoid",
help="non-substituent atom\n" +
"1-indexed position of the starting position of the atom\n" +
"connected to the substituent of which you are calculating\n" +
"sterimol parameters"
)
sterimol_parser.add_argument(
"-r", "--radii",
type=str,
default="bondi",
choices=["bondi", "umn"],
dest="radii",
help="VDW radii to use in calculation\n" +
"umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812\n" +
" (DOI: 10.1021/jp8111556)\n" +
" transition metals are crystal radii from Batsanov, S.S. Van der Waals\n" +
" Radii of Elements. Inorganic Materials 37, 871–885 (2001).\n" +
" (DOI: 10.1023/A:1011625728803)\n" +
"bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)\n" +
"Default: bondi"
)
sterimol_parser.add_argument(
"-l", "--old-l",
action="store_true",
required=False,
dest="old_L",
help="approximate FORTRAN Sterimol method for determining L\n"
"This is 0.4 + the ideal bond length for a target-H bond\n"
"Default: L value is from VDW radii of target atom to outer\n"
"VDW radii of atoms projected onto L-axis"
)
sterimol_parser.add_argument(
"-al", "--at-L",
default=[None],
dest="L_value",
type=lambda x: [float(v) for v in x.split(",")],
help="get widths at specific L values (comma-separated)\n"
"Default: use the entire ligand",
)
sterimol_parser.add_argument(
"-v", "--vector",
action="store_true",
required=False,
dest="vector",
help="print Chimera/ChimeraX bild file for vectors instead of parameter values"
)
sterimol_parser.add_argument(
"-o", "--output",
type=str,
default=False,
required=False,
metavar="output destination",
dest="outfile",
help="output destination\n" +
"Default: stdout"
)
args = sterimol_parser.parse_args(args=argv)
s = ""
if not args.vector:
s += "B1\tB2\tB3\tB4\tB5\tL\tfile\n"
for infile in glob_files(args.infile, parser=sterimol_parser):
if isinstance(infile, str):
if args.input_format is not None:
f = FileReader((infile, args.input_format, infile))
else:
f = FileReader(infile)
else:
if args.input_format is not None:
f = FileReader(("from stdin", args.input_format, infile))
else:
f = FileReader(("from stdin", "xyz", infile))
geom = Geometry(f)
target = args.targets
avoid = args.avoid
end = geom.find(avoid)[0]
frag = geom.get_fragment(target, stop=end)
sub = Substituent(frag, end=end, detect=False)
for val in args.L_value:
data = sub.sterimol(
return_vector=args.vector,
radii=args.radii,
old_L=args.old_L,
at_L=val,
)
if args.vector:
for key, color in zip(
["B1", "B2", "B3", "B4", "B5", "L"],
["black", "green", "purple", "orange", "red", "blue"]
):
start, end = data[key]
s += ".color %s\n" % color
s += ".note Sterimol %s\n" % key
s += ".arrow %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n" % (*start, *end)
else:
s += "%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%s\n" % (
data["B1"],
data["B2"],
data["B3"],
data["B4"],
data["B5"],
data["L"],
infile,
)
if not args.outfile:
print(s)
else:
with open(args.outfile, "w") as f:
f.write(s)
