def sterimol(
session,
selection,
radii="UMN",
showVectors=True,
showRadii=True,
LCorrection="FORTRAN",
return_values=False
):
models, attached = avoidTargets(session.logger, selection)
radii = radii.lower()
old_L = False
if LCorrection.upper() == "FORTRAN":
old_L = True
model_names = []
targets = []
datas = []
info = "<pre>model\tsubstituent atom\tB1\tB2\tB3\tB4\tB5\tL\n"
# if return_values:
# if len(models.keys()) > 1:
# raise RuntimeError("only one substituent may be selected")
# if any(len(models[key]) > 1 for key in models.keys()):
# raise RuntimeError("only one substituent may be selected")
for model in models:
rescol = ResidueCollection(model, refresh_ranks=False)
for res in models[model]:
for target in models[model][res]:
end_atomspec = AtomSpec(attached[target].atomspec)
start_atomspec = AtomSpec(target.atomspec)
sub_atoms = rescol.get_fragment(start_atomspec, end_atomspec)
sub = Substituent(
sub_atoms,
end=rescol.find_exact(end_atomspec)[0],
detect=False,
)
data = sub.sterimol(
return_vector=True,
radii=radii,
old_L=old_L,
)
l = np.linalg.norm(data["L"][1] - data["L"][0])
b1 = np.linalg.norm(data["B1"][1] - data["B1"][0])
b2 = np.linalg.norm(data["B2"][1] - data["B2"][0])
b3 = np.linalg.norm(data["B3"][1] - data["B3"][0])
b4 = np.linalg.norm(data["B4"][1] - data["B4"][0])
b5 = np.linalg.norm(data["B5"][1] - data["B5"][0])
if showVectors:
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)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream, "Sterimol %s" % key)
session.models.add(bild_obj, parent=model)
if showRadii:
s = ".note radii\n"
s += ".transparency 75\n"
color = None
for atom in sub.atoms:
chix_atom = atom.chix_atom
if radii == "umn":
r = VDW_RADII[chix_atom.element.name]
elif radii == "bondi":
r = BONDI_RADII[chix_atom.element.name]
if color is None or chix_atom.color != color:
color = chix_atom.color
rgb = [x/255. for x in chix_atom.color]
rgb.pop(-1)
s += ".color %f %f %f\n" % tuple(rgb)
s += ".sphere %f %f %f %f\n" % (*chix_atom.coord, r)
stream = BytesIO(bytes(s, "utf-8"))
bild_obj, status = read_bild(session, stream, "Sterimol radii")
session.models.add(bild_obj, parent=model)
model_name = get_filename(model.name, include_parent_dir=False)
info += "%-16s\t%-11s\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\t%.2f\n" % (
model_name,
target.atomspec,
b1, b2, b3, b4, b5, l
)
model_names.append(model_name)
targets.append(target.atomspec)
datas.append(data)
info = info.strip()
info += "</pre>"
if not return_values:
session.logger.info(info, is_html=True)
if return_values:
return model_names, targets, datas
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)
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)