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 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 constructMolecule(geometry: str, out: click.File) -> Molecule:
"""Helper function to construct a Molecule."""
try:
with open(geometry, "r+") as fileObject:
# read atoms from input file
atoms = read(fileObject)
# create molecule from atoms
molecule = Molecule(symbols=atoms)
except FileNotFoundError:
errorbye("Input file not found.")
return molecule
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 read(fileObject):
"""Method to first check the file type and then read
the structure accordingly
The returned atom coordinates will be in Bohr
"""
fname = fileObject.name.lower()
filetp = "unknown"
lines = fileObject.readlines()
if fname.endswith((".xyz")):
filetp = "xyz"
else:
for line in lines:
if line.strip().startswith("$coord"):
filetp = "turbomole"
break
fileObject.close()
atoms = []
newfile = open(fname, "r+")
if filetp == "turbomole":
atoms = tm.read(newfile)
elif filetp == "xyz":
atoms = xyz.read(newfile)
else:
errorbye("Input format erroneous or not implemented.")
newfile.close()
return atoms
