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 rmsd import rmsd
mol1 = ksr.constructMolecule(geometry=compare[0])
nat1 = mol1.get_number_of_atoms()
mol2 = ksr.constructMolecule(geometry=compare[1])
nat2 = mol2.get_number_of_atoms()
# for RMSD comparison both coordinates need the same atom count
if nat1 != nat2:
click.echo(
"Error: number of atoms do not match in {} and in {}".format(
compare[0], compare[1]
),
file=out, # type: ignore
)
errorbye(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 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)
bonds = molecule.get_bonds()
nat = molecule.get_number_of_atoms()
# construct graph
from sort import Graph
g = Graph(inp)
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 bonds(config, inp: str, partner: int, constrain: bool, out: click.File):
"""Get information about covalent bonding partner."""
import os
molecule = ksr.constructMolecule(geometry=inp)
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()
pass
return bonds
def eeq(config, inp: str, out: click.File, chrg: int):
"""Electronegativity equilibration atomic partial charges."""
molecule = ksr.constructMolecule(geometry=inp)
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)
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)
nat = molecule.get_number_of_atoms()
vdw = np.zeros(shape=(nat,), dtype=np.float64)
if angstrom:
from units import Bohr
scale = Bohr
else:
scale = 1.0
vdw = np.zeros(shape=(nat,), dtype=np.float64)
vdw = molecule.get_vdw(chrg, vdwtype, scale)
for i in range(nat):
verbosePrinter(config.verbose, vdw[i], out)
return vdw
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)
nat = ref.get_number_of_atoms()
# get all covalent bonding partner in reference complex
covbonds = config.context.invoke(bonds, inp=inp)
from 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
