def test_molecule_is_not_none():
atoms = []
for i in range(2):
atoms.append(Atom(symbol="H", position=(0, 0, i)))
molecule = Molecule(atoms)
atom = Atom(symbol="H", position=(0, 0, 4), molecule=molecule)
assert atom.molecule is not None
def pyridine_mH():
"""Create a pyridine molecule minus Hydrogen on carbon #0 and return as Molecule."""
coords = [
[1.3603, 0.0256, 0.0],
[0.6971, -1.202, 0.0],
[-0.6944, -1.2184, 0.0],
[-1.3895, -0.0129, 0.0],
[-0.6712, 1.1834, 0.0],
[0.6816, 1.196, 0.0],
[1.2665, -2.1365, 0.0],
[-1.2365, -2.1696, 0.0],
[-2.4837, 0.0011, 0.0],
[-1.1569, 2.1657, 0.0],
]
coords = [[float(j) / Bohr for j in i] for i in coords]
symbols = [
"C",
"C",
"C",
"C",
"C",
"N",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def read(fileObject):
"""Method to read Turbomole coord files.
coord in Bohr, atom types in lowercase, format:
$coord
x y z atomType
x y z atomType
$end
"""
lines = fileObject.readlines()
atoms = []
start = 0
# find "$coord" marker
for index, line in enumerate(lines):
if line.strip().startswith("$coord"):
start = index
break
for line in lines[start + 1:]:
# check if new section begins
if line.startswith("$"):
break
else:
x, y, z, symbolRaw = line.split()[:4]
symbolShort = symbolRaw.strip()
atomSymbol = symbolShort[0].upper() + symbolShort[1:].lower()
atomPosition = [float(x), float(y), float(z)]
atom = Atom(symbol=atomSymbol, position=atomPosition)
atoms.append(atom)
return atoms
def read(fileObject):
"""Method to read XYZ files.
atomic coord in Angstroem, atom types in lowercase, format:
<number of atoms>
<comment line>
<atomType x y z>
<atomType x y z>
"""
lines = fileObject.readlines()
atoms = []
# by convention the first thing in the xyz is the number of atoms
nat = int(lines[0])
# loop over the nat lines
for line in lines[2:nat + 2]:
symbolRaw, x, y, z = line.split()[:4]
symbolShort = symbolRaw.strip()
atomSymbol = symbolShort[0].upper() + symbolShort[1:].lower()
atomPosition = [float(x) / Bohr, float(y) / Bohr, float(z) / Bohr]
atom = Atom(symbol=atomSymbol, position=atomPosition)
atoms.append(atom)
return atoms
def getSubstructureFromPath(refmol: Molecule, path: np.ndarray) -> Molecule:
"""Create a molecules object from a substructure of given molecule."""
# initialize
refat = refmol.get_atomic_numbers()
refxyz = refmol.get_positions()
# atoms from complex excluding old substrate
atoms = []
for elem in path:
atom = Atom(symbol=refat[elem], position=refxyz[elem, :])
atoms.append(atom)
# create molecule from atoms
return Molecule(symbols=atoms)
def acetylene():
"""Create an acetylene molecule and return as Molecule."""
coords = [
[0.0, 0.0, -1.06176434496059],
[0.0, 0.0, 1.06176434496059],
]
symbols = [
"C",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def neopentane():
"""Create a neopentane molecule and return as Molecule."""
coords = [
[0.000000, 0.0, 0.0],
[0.881905, 0.881905, 0.881905],
[-0.881905, -0.881905, 0.881905],
[0.881905, -0.881905, -0.881905],
[-0.881905, 0.881905, -0.881905],
[-1.524077, 0.276170, -1.524077],
[1.524077, 1.524077, 0.276170],
[1.524077, -0.276170, -1.524077],
[1.524077, 0.276170, 1.524077],
[-1.524077, -0.276170, 1.524077],
[1.524077, -1.524077, -0.276170],
[-0.276170, 1.524077, -1.524077],
[0.276170, 1.524077, 1.524077],
[0.276170, -1.524077, -1.524077],
[-0.276170, -1.524077, 1.524077],
[-1.524077, 1.524077, -0.276170],
[-1.524077, -1.524077, 0.276170],
]
coords = [[float(j) / Bohr for j in i] for i in coords]
symbols = [
"C",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def toluene():
"""Create a toluene molecule and return as Molecule."""
coords = [
[1.2264, 0.0427, 0.0670],
[1.0031, -1.3293, 0.0600],
[-0.2945, -1.8256, -0.0060],
[-1.3704, -0.9461, -0.0646],
[-1.1511, 0.4266, -0.0578],
[0.1497, 0.9292, 0.0066],
[0.3871, 2.3956, -0.0022],
[2.2495, 0.4310, 0.1211],
[1.8510, -2.0202, 0.1071],
[-0.4688, -2.9062, -0.0109],
[-2.3926, -1.3347, -0.1157],
[-2.0006, 1.1172, -0.1021],
[0.5024, 2.7582, -1.0330],
[1.2994, 2.6647, 0.5466],
[-0.4475, 2.9470, 0.4506],
]
coords = [[float(j) / Bohr for j in i] for i in coords]
symbols = [
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def propanolIntermediate():
"""Create higher conformer of 1-propanol and return as Molecule."""
coords = [
[-1.60306996, 0.10333519, 0.50792736],
[-0.66904416, -0.46962566, -0.55371646],
[0.67345677, 0.26436258, -0.61179298],
[1.26292797, -0.10585085, -1.45392921],
[0.49744830, 1.34089332, -0.75955140],
[1.47742183, 0.05176805, 0.52349829],
[0.98773122, 0.34094585, 1.30125393],
[-0.48213061, -1.52528483, -0.34815476],
[-1.14165995, -0.39229359, -1.53423716],
[-2.56608070, -0.40007121, 0.47312929],
[-1.76619136, 1.16652831, 0.34003517],
[-1.19366144, -0.03197289, 1.50775619],
]
symbols = [
"C",
"C",
"C",
"H",
"H",
"O",
"H",
"H",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def propanolLowest():
"""Create lowest conformer of 1-propanol and return as Molecule."""
coords = [
[-1.9554949371, 0.1467391618, 0.0031595607],
[-0.5906278346, -0.5279387138, -0.0201649611],
[0.5440986558, 0.4958779663, 0.0283462055],
[0.4812068385, 1.1678478833, -0.8308000219],
[0.4590669813, 1.0993020658, 0.9450529713],
[1.8195161785, -0.0957487212, -0.0534239359],
[1.9103706588, -0.7338049177, 0.6631507673],
[-0.5004127933, -1.2028008461, 0.8364936998],
[-0.4854009629, -1.1250023438, -0.9282499098],
[-2.7476736372, -0.5972665554, -0.0242488945],
[-2.0700756998, 0.8040326560, -0.8554507953],
[-2.0722381370, 0.7410005769, 0.9069567477],
]
symbols = [
"C",
"C",
"C",
"H",
"H",
"O",
"H",
"H",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
def exchangeSubstructure(
n: int,
center: int,
subnr: int,
bonds,
ref: Molecule,
newsub: Molecule,
newSubBonds,
name: str,
rotate: int,
exclude: bool,
) -> Molecule:
"""Exchange substructure (subnr) from ref with substrate."""
# setup initial complex
refxyz = ref.get_positions()
refat = ref.get_atomic_numbers()
refnat = ref.get_number_of_atoms()
# match new and old substrate
newat = newsub.get_atomic_numbers()
newnat = newsub.get_number_of_atoms()
# extract coordinates of central atom
centralAtom = refxyz[center, :]
mol = Molecule()
for i in range(len(bonds[center])):
if i == subnr:
path = np.zeros(shape=(n, ), dtype=np.int32)
# set all elements to -1
path.fill(-1)
partner = bonds[center][i]
count = Counter() # type: ignore
count["step"] = -1
getSubstructures(n, bonds, center, partner, path, count=count)
# get rid of -1 elements
path = [x for x in path if x != -1]
path = np.array(path)
# create molecule from given path
oldsub = getSubstructureFromPath(ref, path)
# get all bonding partner
oldSubBonds = oldsub.get_bonds(partner="X")
outxyz = matchSubstrates(
bonds,
newsub,
newSubBonds,
oldsub,
oldSubBonds,
centralAtom,
)
# atoms from complex excluding old substrate
atoms = []
for j in range(refnat):
if j in path:
continue
atom = Atom(symbol=refat[j], position=refxyz[j, :])
atoms.append(atom)
# atoms from new substrate
# Should we rotate the substrate around covalent bond?
if rotate:
theta = rotate
origin = refxyz[center, :]
partner = outxyz[0, :]
outxyz2 = np.zeros(shape=outxyz.shape, dtype=np.float64)
# reference shift
refShift = getRodriguezRotation(partner, origin, partner,
theta)
shift = outxyz[0, :] - refShift
for j in range(newnat):
outxyz2[j, :] = getRodriguezRotation(
outxyz[j, :],
origin,
partner,
theta,
)
outxyz2[j, :] += shift
atom = Atom(symbol=newat[j], position=outxyz2[j, :])
atoms.append(atom)
else:
for j in range(newnat):
atom = Atom(symbol=newat[j], position=outxyz[j, :])
atoms.append(atom)
# create molecule from atoms
mol = Molecule(symbols=atoms)
# write new structure in xyz format
mol.writeMolecule(name + ".xyz")
# write constrain file
refnat = ref.get_number_of_atoms()
oldnat = oldsub.get_number_of_atoms()
nat = refnat - oldnat
writeTransitionMetalConstrains(nat, newnat, newSubBonds, exclude)
return mol
return mol
def test_user_can_get_an_atom_symbol():
atom = Atom(symbol="C", position=[0, 0, 0])
got = atom.get("symbol")
want = "C"
assert got == want
def test_user_can_create_an_atom():
symbol = "C"
atomPosition = [0, 0, 0]
atom = Atom(symbol=symbol, position=atomPosition)
assert atom.symbol == "C"
def test_user_can_modify_atom_via_element_number():
atom = Atom("H")
atom.number = 6
assert atom.symbol == "C"
def test_user_can_create_atom_from_element_string():
atom = Atom("H")
assert atom.symbol == "H"
def iridiumCatalyst():
"""Create an Iridium catalyst and return as Molecule."""
coords = [
[-1.3672999, -1.4398999, 0.1359000],
[-2.4911998, -0.6808999, 0.1396000],
[-3.6534996, -1.1211999, -0.5090000],
[-3.6468996, -2.3434998, -1.1725999],
[-2.4848998, -3.1187997, -1.1555999],
[-1.3670999, -2.6316997, -0.4883000],
[-0.4373000, -3.1872997, -0.4306000],
[-2.4432998, -4.0866996, -1.6463998],
[-4.5575996, -0.5223999, -0.4887000],
[-2.4206998, 0.5908999, 0.8954999],
[-1.2879999, 0.7903999, 1.6181998],
[-1.1378999, 1.9348998, 2.3084998],
[-2.1077998, 2.9319997, 2.3219998],
[-3.2770997, 2.7402997, 1.5819998],
[-3.4330997, 1.5600998, 0.8608999],
[-4.3267996, 1.4057999, 0.2659000],
[-1.9411998, 3.8419996, 2.8913997],
[-0.1872000, 2.0459998, 2.8181997],
[0.4009000, -0.6061999, 1.1172999],
[-1.2690999, -3.8143996, 3.7856996],
[-0.1664000, -4.5494996, 4.2269996],
[1.1218999, -4.0950996, 3.9273996],
[1.2993999, -2.9384997, 3.1675997],
[0.2001000, -2.2075998, 2.6786997],
[-1.0849999, -2.6466997, 3.0382997],
[-1.9573998, -2.0870998, 2.7090997],
[0.8509999, -0.7173999, 2.6636997],
[2.3007998, -2.5989997, 2.9226997],
[-0.3087000, -5.4547995, 4.8119995],
[0.6392999, 0.6220999, -0.5923999],
[-0.0586000, 0.3754000, -1.7751998],
[0.0637000, 1.5387999, -2.6275997],
[0.0955000, 1.0794999, -4.0821996],
[0.8716999, 0.3276000, -4.2397996],
[0.2802000, 1.9248998, -4.7547995],
[-0.8681999, 0.6330999, -4.3491996],
[-1.1760999, 2.4077998, -2.3666998],
[-1.2042999, 3.2867997, -3.0193997],
[-2.0717998, 1.8058998, -2.5499998],
[-1.2019999, 2.7410997, -1.3247999],
[1.3891999, 2.1923998, -2.1029998],
[1.3915999, 1.7859998, -0.7128999],
[2.6481997, 1.5975998, -2.7492997],
[2.6573997, 0.5124000, -2.6283997],
[2.7186997, 1.8556998, -3.8108996],
[3.5309997, 1.9918998, -2.2375998],
[1.4299999, 3.7172996, -2.1670998],
[0.6241999, 4.1645996, -1.5814998],
[2.3812998, 4.0763996, -1.7610998],
[1.3476999, 4.0651996, -3.2032997],
[2.0756998, 0.4378000, 1.7666998],
[3.3654997, -0.0810000, 1.8671998],
[4.2709996, 1.0315999, 2.0579998],
[5.4819995, 0.5533999, 2.8527997],
[5.1838995, 0.0640000, 3.7825996],
[6.0490994, -0.1689000, 2.2567998],
[6.1442994, 1.3928999, 3.0939997],
[4.6909995, 1.5017999, 0.6583999],
[5.4398995, 2.2997998, 0.7063999],
[5.1090995, 0.6483999, 0.1171000],
[3.8181996, 1.8505998, 0.1015000],
[3.3502997, 2.0656998, 2.7942997],
[2.0458998, 1.7442998, 2.2507998],
[3.6590996, 3.5300997, 2.4959998],
[3.5358997, 3.7464996, 1.4332999],
[2.9753997, 4.1760996, 3.0565997],
[4.6847995, 3.7776996, 2.7930997],
[3.2796997, 1.8273998, 4.3083996],
[3.0708997, 0.7747999, 4.5225996],
[4.2123996, 2.1093998, 4.8080995],
[2.4671998, 2.4302998, 4.7258995],
[1.7917998, -1.7489998, 0.1412000],
[1.8500998, -3.1467997, 0.2110000],
[3.0569997, -3.5802997, -0.4612000],
[4.1632996, -3.6178996, 0.6029999],
[4.3272996, -2.6173997, 1.0149999],
[3.8420996, -4.2739996, 1.4174999],
[5.1055995, -3.9992996, 0.1957000],
[2.8261997, -4.9693995, -1.0466999],
[2.6792997, -5.6906994, -0.2364000],
[3.6907996, -5.2904995, -1.6389998],
[1.9392998, -4.9911995, -1.6839998],
[3.2640997, -2.4330998, -1.5048999],
[2.7238997, -1.2952999, -0.7998999],
[4.7166995, -2.1413998, -1.8718998],
[5.1881995, -3.0188997, -2.3293998],
[4.7565995, -1.3170999, -2.5912997],
[5.2941995, -1.8488998, -0.9925999],
[2.4197998, -2.6279997, -2.7728997],
[1.3752999, -2.8206997, -2.5121998],
[2.4501998, -1.7101998, -3.3667997],
[2.7924997, -3.4536997, -3.3878997],
[-2.2764998, -4.1481996, 4.0262996],
[1.9905998, -4.6454995, 4.2840996],
[-4.5414996, -2.6926997, -1.6821998],
[-4.0522996, 3.5020997, 1.5576998],
]
coords = [[float(j) / Bohr for j in i] for i in coords]
symbols = [
"N",
"C",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"C",
"N",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"Ir",
"C",
"C",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"H",
"B",
"O",
"C",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"C",
"O",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"B",
"O",
"C",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"C",
"O",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"B",
"O",
"C",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"C",
"O",
"C",
"H",
"H",
"H",
"C",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
]
atoms = []
for i, _ in enumerate(coords):
atoms.append(Atom(symbols[i], position=coords[i]))
return Molecule(symbols=atoms)
import tempfile
import numpy as np
import pytest
from kallisto.atom import Atom
from kallisto.molecule import Molecule
import kallisto.reader.strucreader as ksr
# define global lineseperator
s = os.linesep
# Create global molecule
atoms = []
for i in range(3):
atoms.append(Atom(symbol="H", position=(0, 0, i)))
# turbomole coord files can be read
def test_a_user_can_compute_coordination_numbers_for_molecule():
with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8") as f:
f.write("$coord" + s)
f.write(" 1.87167924 -0.101043656 0.1596818582 c" + s)
f.write(" 4.43543289 -0.101043656 0.1596818582 f" + s)
f.write(" 1.20847986 -1.386321988 1.6312493924 h" + s)
f.write(" 1.20847986 -0.732816897 -1.6891694984 h" + s)
f.write(" 1.20846096 1.816007916 0.5369845779 h" + s)
f.write("$end")
f.flush()
fileObject = open(f.name, "r+")
atoms = ksr.read(fileObject)
def test_user_can_set_an_atom_symbol():
symbol = "C"
atomPosition = [0, 0, 0]
atom = Atom(symbol=symbol, position=atomPosition)
atom.set("symbol", "N")
assert atom.symbol == "N"