def stm(config, inp: str, origin: int, partner: int, out: click.File):
"""Calculate sterimol descriptors using kallisto van der Waals radii."""
# setup molecular structure
mol = ksr.constructMolecule(geometry=inp, out=out)
# calculate Sterimol descriptors: L, bmin, bmax
from kallisto.sterics import getClassicalSterimol
L, bmin, bmax = getClassicalSterimol(mol, origin, partner)
if config.verbose:
# print values in Bohr
verbosePrinter(
config.verbose,
"L, Bmin, Bmax / au: {:5.2f} {:5.2f} {:5.2f}".format(
L, bmin, bmax),
out,
)
# print values in Angstrom
from kallisto.units import Bohr
verbosePrinter(
config.verbose,
"L, Bmin, Bmax / A: {:5.2f} {:5.2f} {:5.2f}".format(
L * Bohr, bmin * Bohr, bmax * Bohr),
out,
)
return L, bmin, bmax
def lig(config, inp: str, center: int, out: click.File):
"""Get all substructures (or ligands) that are bound to the center atom."""
# setup reference molecular structure
ref = ksr.constructMolecule(geometry=inp, out=out)
nat = ref.get_number_of_atoms()
# get all covalent bonding partner in reference complex
covbonds = config.context.invoke(bonds, inp=inp)
from kallisto.rmsd import recursiveGetSubstructures
verbosePrinter(config.verbose,
"Write out substructures for {}".format(center), out)
substructures = recursiveGetSubstructures(nat, covbonds, center)
if config.verbose:
k = 0
for path in substructures:
verbosePrinter(
config.verbose,
"Substructure {}: {}".format(k, path),
out,
)
k += 1
def rms(config, compare: Tuple[str, str], out: click.File):
"""Calculate the root mean squared deviation between two structures using quaternions.
Based on a Fortran implementation by Chaok Seok, Evangelos
Coutsias, and Ken Dill."""
from kallisto.rmsd import rmsd
mol1 = ksr.constructMolecule(geometry=compare[0], out=out)
nat1 = mol1.get_number_of_atoms()
mol2 = ksr.constructMolecule(geometry=compare[1], out=out)
nat2 = mol2.get_number_of_atoms()
# for RMSD comparison both coordinates need the same atom count
if nat1 != nat2:
errorbye(
"Error: number of atoms do not match in {} and in {}".format(
compare[0], compare[1]),
out,
)
coord1 = mol1.get_positions()
coord2 = mol2.get_positions()
# get RMSD error and rotation matrix u
error, u = rmsd(nat1, coord1, coord2)
verbosePrinter(config.verbose, "RMSD {} Angstrom".format(error), out)
verbosePrinter(config.verbose, "Rotation Matrix", out)
click.echo(u, file=out) # type: ignore
return error, u
def cns(config, inp: str, out: click.File, cntype: str):
"""Atomic coordination numbers."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
cns = molecule.get_cns(cntype)
verbosePrinter(config.verbose, cns, out)
return cns
def cnsp(config, inp: str, out: click.File, cntype: str):
"""Atomic coordination number spheres."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
cnsp = molecule.get_cnspheres(cntype)
for i in range(nat):
verbosePrinter(config.verbose, cnsp[i], out)
return cnsp
def eeq(config, inp: str, out: click.File, chrg: int):
"""Electronegativity equilibration atomic partial charges."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
eeq = molecule.get_eeq(chrg)
for i in range(nat):
verbosePrinter(config.verbose, eeq[i], out)
return eeq
def alp(config, inp: str, out: click.File, chrg: int, molecular: bool):
"""Static atomic polarizabilities in Bohr^3."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
alp = molecule.get_alp(charge=chrg)
if molecular:
verbosePrinter(config.verbose, np.sum(alp), out)
else:
for i in range(nat):
verbosePrinter(config.verbose, alp[i], out)
return alp
def vdw(config, inp: str, out: click.File, chrg: int, vdwtype: str,
angstrom: bool):
"""Charge-dependent atomic van der Waals radii in Bohr."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
if angstrom:
from kallisto.units import Bohr
scale = Bohr
else:
scale = 1.0
vdw = molecule.get_vdw(chrg, vdwtype, scale)
for i in range(nat):
verbosePrinter(config.verbose, vdw[i], out)
return vdw