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 sort(config, inp: str, start: str, out: click.File):
"""Sort input geoemtry according to connectivity.
start defines on which atom we start the sorting process.
"""
molecule = ksr.constructMolecule(geometry=inp, out=out)
bonds = molecule.get_bonds()
nat = molecule.get_number_of_atoms()
# construct graph
from kallisto.sort import Graph
g = Graph(inp, out)
for i in range(nat):
partners = bonds[i]
for j in partners:
# add edges
g.addEdge(j, i)
if start == "X":
# start at #0
g.BFS(0)
else:
# start at atom #start
g.BFS(int(start))
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 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
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 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)
# write constrain file in xtb format
if constrain:
nat = molecule.get_number_of_atoms()
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()
return bonds
def __init__(self, inp: str, out: click.File):
self.inp = inp
self.graph = defaultdict(list) # type: ignore
self.molecule = ksr.constructMolecule(geometry=self.inp, out=out)
self.nat = self.molecule.get_number_of_atoms()
self.at = self.molecule.get_atomic_numbers()
self.coordinates = self.molecule.get_positions()
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 exs(
config,
inp: str,
center: int,
subnr: int,
name: str,
exclude: bool,
rotate: int,
out: click.File,
):
"""Exchange a substrate within a transition metal complex with another
substrate. Use an root mean squared deviation (RMSD) measure to rotate
and shift new substrate to the position of the old substrate.
Calculate the RMSD between two structures using quaternions."""
# setup reference molecular structure
ref = ksr.constructMolecule(geometry=inp[0], out=out)
substrate = ksr.constructMolecule(geometry=inp[1], out=out)
nat = ref.get_number_of_atoms()
# get all covalent bonding partner in reference complex
covBonds = ref.get_bonds()
# get covalent bonds in new substrate
newSubBonds = substrate.get_bonds()
newSubBonds = np.array(newSubBonds, dtype=object)
from kallisto.rmsd import exchangeSubstructure
mol = exchangeSubstructure(
nat,
center,
subnr,
covBonds, # type: ignore
ref,
substrate,
newSubBonds,
name,
rotate,
exclude,
)
return mol
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 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 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
