def test_pubchem_4a():
subject = subject4
fullans = copy.deepcopy(fullans4)
fullans["provenance"] = _string_prov_stamp
final, intermed = qcelemental.molparse.from_string(subject, return_processed=True)
assert compare_molrecs(ans4, intermed, tnm() + ": intermediate")
assert compare_molrecs(fullans, final["qm"], tnm() + ": full")
def test_pubchem_13i():
subject = "PubChem:223"
fullans = copy.deepcopy(fullans13)
fullans['provenance'] = _string_prov_stamp
final, intermed = qcelemental.molparse.from_string(subject,
return_processed=True)
assert compare_molrecs(ans13, intermed, tnm() + ': intermediate')
assert compare_molrecs(fullans, final['qm'], tnm() + ': full')
def test_pubchem_13i():
subject = "PubChem:223"
fullans = copy.deepcopy(fullans13)
fullans["provenance"] = _string_prov_stamp
with xfail_on_pubchem_busy():
final, intermed = qcelemental.molparse.from_string(subject, return_processed=True)
assert compare_molrecs(ans13, intermed, tnm() + ": intermediate")
assert compare_molrecs(fullans, final["qm"], tnm() + ": full")
def test_pubchem_4c():
subject = """
pubchem : 241
"""
ans = copy.deepcopy(ans4)
ans["name"] = "benzene"
fullans = copy.deepcopy(fullans4)
fullans["name"] = "benzene"
fullans["provenance"] = _string_prov_stamp
final, intermed = qcelemental.molparse.from_string(subject, return_processed=True, name="benzene", verbose=2)
assert compare_molrecs(ans, intermed, tnm() + ": intermediate")
assert compare_molrecs(fullans, final["qm"], tnm() + ": full")
def test_2_14b():
fullans = copy.deepcopy(schema14_2)
fullans['provenance'] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject14)
kmol = qcelemental.molparse.to_schema(final['qm'], dtype=2)
assert compare_molrecs(fullans, kmol)
fullans = copy.deepcopy(schema14_psi4)
fullans['provenance'] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_1_14a():
fullans = copy.deepcopy(schema14_1)
fullans["molecule"]["provenance"] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject14)
kmol = qcelemental.molparse.to_schema(final["qm"], dtype=1)
assert compare_molrecs(fullans["molecule"], kmol["molecule"])
fullans = copy.deepcopy(schema14_psi4)
fullans["provenance"] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_2_14b(request):
fullans = copy.deepcopy(schema14_2)
fullans["provenance"] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject14)
kmol = qcelemental.molparse.to_schema(final["qm"], dtype=2)
drop_qcsk(kmol, request.node.name, "Molecule")
assert compare_molrecs(fullans, kmol)
fullans = copy.deepcopy(schema14_psi4)
fullans["provenance"] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_tofro_16b(dtype):
fullans = copy.deepcopy(schema16_psi4)
fullans['provenance'] = _schema_prov_stamp
roundtrip = qcelemental.molparse.from_schema(qcelemental.molparse.to_schema(schema16_psi4, dtype=dtype))
assert compare_molrecs(fullans, roundtrip)
def test_psi4_14c():
fullans = copy.deepcopy(schema14_psi4)
fullans['provenance'] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject14)
kmol = qcelemental.molparse.to_schema(final['qm'], dtype='psi4')
assert compare_molrecs(fullans, kmol)
def test_pubchem_4c():
subject = """
pubchem : 241
"""
ans = copy.deepcopy(ans4)
ans['name'] = 'benzene'
fullans = copy.deepcopy(fullans4)
fullans['name'] = 'benzene'
fullans['provenance'] = _string_prov_stamp
final, intermed = qcelemental.molparse.from_string(subject,
return_processed=True,
name='benzene',
verbose=2)
assert compare_molrecs(ans, intermed, tnm() + ': intermediate')
assert compare_molrecs(fullans, final['qm'], tnm() + ': full')
def test_from_schema_2_14e(request):
schema = copy.deepcopy(schema14_1)
schema.update({"schema_name": "qcschema_molecule", "schema_version": 2})
drop_qcsk(schema, request.node.name, "Molecule")
ans = qcel.molparse.from_schema(schema)
assert compare_molrecs(schema14_psi4_np, ans, 4)
def test_2_15b():
fullans = copy.deepcopy(schema15_2)
fullans['provenance'] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject15)
final['qm']['comment'] = 'I has a comment'
kmol = qcelemental.molparse.to_schema(final['qm'], dtype=2)
assert compare_molrecs(fullans, kmol)
fullans = copy.deepcopy(schema15_psi4)
fullans['units'] = 'Bohr'
fullans['geom'] = [0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0]
fullans['provenance'] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_2_15b():
fullans = copy.deepcopy(schema15_2)
fullans["provenance"] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject15)
final["qm"]["comment"] = "I has a comment"
kmol = qcelemental.molparse.to_schema(final["qm"], dtype=2)
assert compare_molrecs(fullans, kmol)
fullans = copy.deepcopy(schema15_psi4)
fullans["units"] = "Bohr"
fullans["geom"] = [0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0]
fullans["provenance"] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_psi4_15c():
fullans = copy.deepcopy(schema15_psi4)
fullans['provenance'] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject15)
final['qm']['comment'] = 'I has a comment'
kmol = qcelemental.molparse.to_schema(final['qm'], dtype='psi4', units='Angstrom')
assert compare_molrecs(fullans, kmol)
def test_from_schema_1p5_14e():
# this is the oddball case where passing code has internally a dtype=2 molecule
# but it's still passing the outer data structure
schema = {"schema_name": "qc_schema", "schema_version": 1, "molecule": copy.deepcopy(schema14_1)}
schema["molecule"].update({"schema_name": "qcschema_molecule", "schema_version": 2})
ans = qcel.molparse.from_schema(schema)
assert compare_molrecs(schema14_psi4_np, ans, 4)
def test_from_schema_1_14e():
schema = {
"schema_name": "qc_schema",
"schema_version": 1,
"molecule": copy.deepcopy(schema14_1)
}
ans = qcel.molparse.from_schema(schema)
assert compare_molrecs(schema14_psi4_np, ans, 4)
def test_1_15a(request):
fullans = copy.deepcopy(schema15_1)
fullans["molecule"]["provenance"] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject15)
final["qm"]["comment"] = "I has a comment"
kmol = qcelemental.molparse.to_schema(final["qm"], dtype=1)
drop_qcsk(kmol["molecule"], request.node.name, "Molecule")
assert compare_molrecs(fullans["molecule"], kmol["molecule"])
fullans = copy.deepcopy(schema15_psi4)
fullans["units"] = "Bohr"
fullans["geom"] = [0.0, 0.0, 2.0, 0.0, 0.0, 0.0, 2.0, 0.0, 0.0]
fullans["provenance"] = _schema_prov_stamp
molrec = qcelemental.molparse.from_schema(kmol)
molrec = qcelemental.util.unnp(molrec)
assert compare_molrecs(fullans, molrec)
def test_psi4_15c():
fullans = copy.deepcopy(schema15_psi4)
fullans["provenance"] = _string_prov_stamp
final = qcelemental.molparse.from_string(subject15)
final["qm"]["comment"] = "I has a comment"
kmol = qcelemental.molparse.to_schema(final["qm"],
dtype="psi4",
units="Angstrom")
assert compare_molrecs(fullans, kmol)
def test_tofro_16b(dtype, request):
fullans = copy.deepcopy(schema16_psi4)
fullans["provenance"] = _schema_prov_stamp
roundtrip = qcelemental.molparse.from_schema(
qcelemental.molparse.to_schema(schema16_psi4, dtype=dtype))
qcsk = qcelemental.molparse.to_schema(schema16_psi4, dtype=dtype)
qcsk = qcsk["molecule"] if dtype == 1 else qcsk
drop_qcsk(qcsk, request.node.name, "Molecule")
assert compare_molrecs(fullans, roundtrip)
def test_relative_geoms_align_fixed(request):
s22_12 = qcel.models.Molecule.from_data(ss22_12 + "nocom\nnoreorient\n")
drop_qcsk(s22_12, request.node.name)
for trial in range(3):
cmol, _ = s22_12.scramble(
do_shift=False, do_rotate=False, do_resort=False, do_plot=False, verbose=2, do_test=True
)
rmolrec = qcel.molparse.from_schema(s22_12.dict())
cmolrec = qcel.molparse.from_schema(cmol.dict())
assert compare_molrecs(rmolrec, cmolrec, atol=1.0e-4, relative_geoms="align")
def test_relative_geoms_align_free():
s22_12 = qcel.models.Molecule.from_data(ss22_12)
for trial in range(3):
cmol, _ = s22_12.scramble(do_shift=True,
do_rotate=True,
do_resort=False,
do_plot=False,
verbose=2,
do_test=True)
rmolrec = qcel.molparse.from_schema(s22_12.dict())
cmolrec = qcel.molparse.from_schema(cmol.dict())
assert compare_molrecs(rmolrec,
cmolrec,
atol=1.0e-4,
relative_geoms="align")
def test_froto_2_16a():
basic = {
'schema_name': 'qcschema_molecule',
'schema_version': 2,
'geometry': [2, 2, 3],
'symbols': ['C'],
'connectivity': [(0.0, -0.0, 0)],
'provenance': {
'creator': 'Mystery Program',
'version': '2018.3',
'routine': 'molecule builder',
},
}
fullans = copy.deepcopy(schema16_2)
fullans['provenance'] = _schema_prov_stamp
roundtrip = qcelemental.molparse.to_schema(qcelemental.molparse.from_schema(basic), dtype=2)
assert compare_molrecs(fullans, roundtrip)
def test_froto_2_16a():
basic = {
"schema_name": "qcschema_molecule",
"schema_version": 2,
"geometry": [2, 2, 3],
"symbols": ["C"],
"connectivity": [(0.0, -0.0, 0)],
"provenance": {
"creator": "Mystery Program",
"version": "2018.3",
"routine": "molecule builder"
},
}
fullans = copy.deepcopy(schema16_2)
fullans["provenance"] = _schema_prov_stamp
roundtrip = qcelemental.molparse.to_schema(
qcelemental.molparse.from_schema(basic), dtype=2)
assert compare_molrecs(fullans, roundtrip)
def test_froto_1_16a(request):
basic = {
"schema_name": "qc_schema_output",
"schema_version": 1,
"molecule": {
"geometry": [2, 2, 3],
"symbols": ["C"],
"connectivity": [(0.0, -0.0, 0)],
"provenance": {
"creator": "Mystery Program",
"version": "2018.3",
"routine": "molecule builder"
},
},
}
fullans = copy.deepcopy(schema16_1)
fullans["molecule"]["provenance"] = _schema_prov_stamp
roundtrip = qcelemental.molparse.to_schema(
qcelemental.molparse.from_schema(basic), dtype=1)
drop_qcsk(roundtrip["molecule"], request.node.name, "Molecule")
assert compare_molrecs(fullans["molecule"], roundtrip["molecule"])
def test_contiguize_from_fragment_pattern(inp, expected):
ans = qcel.molparse.contiguize_from_fragment_pattern(**inp)
# compare_molrecs instead of compare_dicts handles some fragment_separators types issues
assert compare_molrecs(expected, ans, atol=1.e-6)
def test_from_schema_2_14e():
schema = copy.deepcopy(schema14_1)
schema.update({"schema_name": "qcschema_molecule", "schema_version": 2})
ans = qcel.molparse.from_schema(schema)
assert compare_molrecs(schema14_psi4_np, ans, 4)
