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)
def ligandSterimol(session,
selection,
radii="UMN",
showVectors=True,
showRadii=True,
at_L=None,
bisect_L=False,
return_values=False):
models, center, key_atoms = avoidTargets(session.logger, selection)
radii = radii.lower()
targets = []
coord_atoms = []
datas = []
info = "<pre>model\tcoord. atoms\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)
comp_atoms = [AtomSpec(at.atomspec) for at in models[model]]
key_atomspec = [AtomSpec(at.atomspec) for at in key_atoms[model]]
center_atomspec = [AtomSpec(at.atomspec) for at in center[model]]
if len(center_atomspec) != 1:
session.logger.error(
"ligand sterimol requires one central atom to which " + \
"the ligand is coordinated\n" + \
"%i were found on model %s:\n" % (len(center_atomspec), model.atomspec) + \
"\n".join([at.atomspec for at in center[model]])
)
continue
comp = Component(
rescol.find(comp_atoms),
to_center=rescol.find(center_atomspec),
key_atoms=rescol.find(key_atomspec),
)
data = comp.sterimol(
return_vector=True,
radii=radii,
at_L=at_L,
to_center=rescol.find(center_atomspec),
bisect_L=bisect_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 comp.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)
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" % (
name, ", ".join(at.atomspec
for at in key_atoms[model]), b1, b2, b3, b4, b5, l)
targets.append(name)
coord_atoms.append([at.atomspec for at in key_atoms[model]])
datas.append(data)
info = info.strip()
info += "</pre>"
if not return_values:
session.logger.info(info, is_html=True)
if return_values:
return targets, coord_atoms, datas