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
silentPrinter(config.silent,
"Write out substructures for {}".format(center), out)
substructures = recursiveGetSubstructures(nat, covbonds, center)
k = 0
for path in substructures:
silentPrinter(
config.silent,
"Substructure {}: {}".format(k, path),
out,
)
k += 1
def vdw(config, inp: str, out: click.File, chrg: int, vdwtype: str, angstrom: bool):
"""Charge-dependent atomic van der Waals radii in Bohr."""
# Available VDWs
availableVDW = ("rahm", "truhlar")
if vdwtype not in availableVDW:
errorbye(
'VDW definition "{}" is not implemented. Please use "rahm" or "truhlar"'.format(
vdwtype
)
)
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):
silentPrinter(config.silent, vdw[i], out)
return vdw
def rms(config, inp: 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=inp[0], out=out)
nat1 = mol1.get_number_of_atoms()
mol2 = ksr.constructMolecule(geometry=inp[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(
inp[0], inp[1]), )
coord1 = mol1.get_positions()
coord2 = mol2.get_positions()
# get RMSD error and rotation matrix u
error, u = rmsd(nat1, coord1, coord2)
silentPrinter(config.silent, "RMSD {} Angstrom".format(error), out)
silentPrinter(config.silent, "Rotation Matrix", out)
click.echo(u, file=out) # type: ignore
return error, u
def bonds(config, inp: str, partner: int, constrain: bool, out: click.File):
"""Get information about covalent bonding partner."""
import os
molecule = ksr.constructMolecule(geometry=inp, out=out)
if partner == "X":
# Get index table of covalent bonding partners
bonds = molecule.get_bonds(partner=partner)
else:
# Get all covalent bonding partners of atom #partner
bonds = molecule.get_bonds(partner=partner)
nat = molecule.get_number_of_atoms()
# write constrain file in xtb format
if constrain:
f = open("constrain.inp", "w")
s = os.linesep
f.write("$constrain" + s)
for i in range(nat):
for partner in bonds[i]:
f.write(" distance: {}, {}, auto".format(
i + 1 + config.shift, partner + 1 + config.shift) + s)
f.write("$end" + s)
f.close()
if partner != "X":
silentPrinter(config.silent, str(bonds), out)
else:
for i in range(nat):
silentPrinter(config.silent, str(bonds[i]), out)
return bonds
def prox(config, inp: str, size: Tuple[int, int], out: click.File):
"""Atomic proximity shells."""
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
prox = molecule.get_prox(size)
for i in range(nat):
silentPrinter(config.silent, prox[i], out)
return prox
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)
nat = molecule.get_number_of_atoms()
for i in range(nat):
silentPrinter(config.silent, cns[i], out)
return cns
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):
silentPrinter(config.silent, 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:
silentPrinter(config.silent, np.sum(alp), out)
else:
for i in range(nat):
silentPrinter(config.silent, alp[i], out)
return alp
def prox(config, inp: str, size: Tuple[int, int], out: click.File):
"""Atomic proximity shells."""
# Stop if outer border is smaller than inner one
if size[0] > size[1]:
errorbye("Outer border is smaller than inner one. Switch them and try again!")
molecule = ksr.constructMolecule(geometry=inp, out=out)
nat = molecule.get_number_of_atoms()
prox = molecule.get_prox(size)
for i in range(nat):
silentPrinter(config.silent, prox[i], out)
return prox
def cns(config, inp: str, out: click.File, cntype: str):
"""Atomic coordination numbers."""
# Available CNs
availableCN = ("erf", "cov", "exp")
if cntype not in availableCN:
errorbye(
'CN definition "{}" is not implemented. Please use "erf", "cov", or "exp"'
.format(cntype))
molecule = ksr.constructMolecule(geometry=inp, out=out)
cns = molecule.get_cns(cntype)
nat = molecule.get_number_of_atoms()
for i in range(nat):
silentPrinter(config.silent, cns[i], out)
return cns
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):
silentPrinter(config.silent, vdw[i], out)
return vdw
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)
# print origin and partner
silentPrinter(
config.silent,
"Calculated for atom {0} (origin) and atom {1} (partner)".format(
origin, partner
),
out,
)
# descriptors in Bohr
silentPrinter(
config.silent,
"L, Bmin, Bmax / au: {:8.6f} {:8.6f} {:8.6f}".format(L, bmin, bmax),
out,
)
# descriptors in Angstrom
from kallisto.units import Bohr
silentPrinter(
config.silent,
"L, Bmin, Bmax / A: {:8.6f} {:8.6f} {:8.6f}".format(
L * Bohr, bmin * Bohr, bmax * Bohr
),
out,
)
return L, bmin, bmax
