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more joback test (aldehydes, esters, ketones), first problematic stru…
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…ctures for Joback detected and added to list
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@SalvadorBrandolin
SalvadorBrandolin committed Nov 7, 2023
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81 changes: 79 additions & 2 deletions tests/joback/test_alcohols.py
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# Gastrodigenin
# ("C1=CC(=CC=C1CO)O", {"ring=CH-": 4, "ACOH": 1, "ACCH2": 1, "OH": 1}, "smiles"),
import pytest

import ugropy as ug


# =============================================================================
# -OH (alcohol), -OH (phenol)
# =============================================================================
# Joback
trials = [
# 1,2-Cyclohexanediol, 4-tert-butyl-1-phenyl-, stereoisomer
(
"CC(C)(C)C1CCC(C(C1)O)(C2=CC=CC=C2)O",
{
"-CH3": 3,
">C<": 1,
"ring-CH2-": 3,
"ring>CH-": 2,
"ring>C<": 1,
"-OH (alcohol)": 2,
"ring=C<": 1,
"ring=CH-": 5,
},
"smiles",
),
# (2S,3S)-2-Methyl-1,3-hexanediol
(
"CCCC(C(C)CO)O",
{"-CH3": 2, "-CH2-": 3, ">CH-": 2, "-OH (alcohol)": 2},
"smiles",
),
# 2-propanol
("CC(C)O", {"-CH3": 2, ">CH-": 1, "-OH (alcohol)": 1}, "smiles"),
("OC(O)=O", {"-COOH (acid)": 1, "-OH (alcohol)": 1}, "smiles"),
# Phenanthrene-3,4-diol
(
"C1=CC=C2C(=C1)C=CC3=C2C(=C(C=C3)O)O",
{"ring=CH-": 8, "ring=C<": 6, "-OH (phenol)": 2},
"smiles",
),
# 3-(tert-butyl)benzene-1,2-diol
(
"CC(C)(C)C1=C(C(=CC=C1)O)O",
{"ring=CH-": 3, "ring=C<": 3, "-OH (phenol)": 2, "-CH3": 3, ">C<": 1},
"smiles",
),
# [1,1'-Biphenyl]-2,3',4-triol
(
"C1=CC(=CC(=C1)O)C2=C(C=C(C=C2)O)O",
{"ring=CH-": 7, "ring=C<": 5, "-OH (phenol)": 3},
"smiles",
),
# phenol
(
"C1=CC=C(C=C1)O",
{"ring=CH-": 5, "ring=C<": 1, "-OH (phenol)": 1},
"smiles",
),
# methanol
("CO", {"-CH3": 1, "-OH (alcohol)": 1}, "smiles"),
# Gastrodigenin
(
"C1=CC(=CC=C1CO)O",
{
"ring=CH-": 4,
"ring=C<": 2,
"-OH (phenol)": 1,
"-CH2-": 1,
"-OH (alcohol)": 1,
},
"smiles",
),
]


@pytest.mark.Joback
@pytest.mark.parametrize("identifier, result, identifier_type", trials)
def test_joback_alcohols(identifier, result, identifier_type):
assert ug.get_joback_groups(identifier, identifier_type) == result
72 changes: 72 additions & 0 deletions tests/joback/test_aldehydes.py
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import pytest

import ugropy as ug


# =============================================================================
# O=CH- (aldehyde)
# =============================================================================
# Joback
trials = [
("C(=O)C=O", {"O=CH- (aldehyde)": 2}, "smiles"),
# salicylaldehyde
(
"C1=CC=C(C(=C1)C=O)O",
{
"ring=CH-": 4,
"-OH (phenol)": 1,
"ring=C<": 2,
"O=CH- (aldehyde)": 1,
},
"smiles",
),
# 2-Methyl-3-butenal
(
"CC(C=C)C=O",
{"-CH3": 1, ">CH-": 1, "CH2=CH-": 1, "O=CH- (aldehyde)": 1},
"smiles",
),
# Cinnamaldehyde
(
"C1=CC=C(C=C1)C=CC=O",
{"ring=CH-": 5, "ring=C<": 1, "-CH=CH-": 1, "O=CH- (aldehyde)": 1},
"smiles",
),
# benzaldehyde
(
"C1=CC=C(C=C1)C=O",
{"ring=CH-": 5, "ring=C<": 1, "O=CH- (aldehyde)": 1},
"smiles",
),
# cyclohexanecarbaldehyde
(
"C1CCC(CC1)C=O",
{
"ring-CH2-": 5,
"ring>CH-": 1,
"O=CH- (aldehyde)": 1,
},
"smiles",
),
# pentanal
("CCCCC=O", {"-CH3": 1, "-CH2-": 3, "O=CH- (aldehyde)": 1}, "smiles"),
# 3-methylbutanal
(
"CC(C)CC=O",
{"-CH3": 2, "-CH2-": 1, ">CH-": 1, "O=CH- (aldehyde)": 1},
"smiles",
),
# acetaldehyde
("CC=O", {"-CH3": 1, "O=CH- (aldehyde)": 1}, "smiles"),
(
r"CCCCCC\C(C=O)=C/C1=CC=CC=C1",
{},
"smiles",
),
]


@pytest.mark.Joback
@pytest.mark.parametrize("identifier, result, identifier_type", trials)
def test_joback_aldehydes(identifier, result, identifier_type):
assert ug.get_joback_groups(identifier, identifier_type) == result
76 changes: 76 additions & 0 deletions tests/joback/test_esters.py
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import pytest

import ugropy as ug


# =============================================================================
# -COO- (ester)
# =============================================================================
# Joback
trials = [
# Ascorbic acid
(
"OCC(O)C1OC(=O)C(O)=C1O",
{
"-COO- (ester)": 1,
"ring=C<": 2,
"-OH (alcohol)": 4,
">CH-": 1,
"ring>CH-": 1,
"-CH2-": 1,
},
"smiles",
),
# Procaine
(
"CCN(CC)CCOC(=O)C1=CC=C(N)C=C1",
{
"-NH2": 1,
"ring=CH-": 4,
"ring=C<": 2,
"-COO- (ester)": 1,
"-CH2-": 4,
"-CH3": 2,
">N- (non-ring)": 1,
},
"smiles",
),
# Cocaine
(
"COC(=O)C1C2CCC(CC1OC(=O)C1=CC=CC=C1)N2C",
{},
"smiles",
),
# Methyl acrylate
("COC(=O)C=C", {"-CH3": 1, "CH2=CH-": 1, "-COO- (ester)": 1}, "smiles"),
# Aspirin
(
"CC(=O)OC1=CC=CC=C1C(=O)O",
{
"-CH3": 1,
"-COO- (ester)": 1,
"ring=C<": 2,
"ring=CH-": 4,
"-COOH (acid)": 1,
},
"smiles",
),
# Tert-butyl acetate
("CC(=O)OC(C)(C)C", {"-COO- (ester)": 1, "-CH3": 4, ">C<": 1}, "smiles"),
# triacetin
(
"CC(=O)OCC(COC(=O)C)OC(=O)C",
{"-CH3": 3, "-COO- (ester)": 3, "-CH2-": 2, ">CH-": 1},
"smiles",
),
# butyl propanoate
("CCCCOC(=O)CC", {"-CH3": 2, "-CH2-": 4, "-COO- (ester)": 1}, "smiles"),
# butyl acetate
("CCCCOC(=O)C", {"-CH3": 2, "-CH2-": 3, "-COO- (ester)": 1}, "smiles"),
]


@pytest.mark.Joback
@pytest.mark.parametrize("identifier, result, identifier_type", trials)
def test_joback_esters(identifier, result, identifier_type):
assert ug.get_joback_groups(identifier, identifier_type) == result
128 changes: 128 additions & 0 deletions tests/joback/test_ethers.py
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import pytest

import ugropy as ug


# =============================================================================
# -O- (non-ring), -O- (ring)
# =============================================================================
# Joback
trials = [
# # 4-flavanol
# (
# "OC1CC(OC2=CC=CC=C12)C1=CC=CC=C1",
# {"ACH": 9, "AC": 2, "ACCH": 1, "CHO": 1, "CH2": 1, "OH": 1},
# "smiles",
# ),
# (
# "O[C@@H]1CO[C@H](O)[C@@H](O)[C@@H]1O",
# {"CH2O": 1, "CH": 4, "OH": 4},
# "smiles",
# ),
# ("C1COCCOCCOCCOC1", {"CH2O": 4, "CH2": 5}, "smiles"),
# ("C1COCCO1", {"CH2O": 2, "CH2": 2}, "smiles"),
# ("CCOCOCC", {"CH3": 2, "CH2O": 2, "CH2": 1}, "smiles"),
# ("C1COCO1", {"CH2O": 2, "CH2": 1}, "smiles"),
# ("C1COCCOCCOCCOCCOCCO1", {"CH2O": 6, "CH2": 6}, "smiles"),
# # tetrahydrofuran
# ("C1CCOC1", {"THF": 1}, "smiles"),
# # diisopropyl ether
# ("CC(C)OC(C)C", {"CH3": 4, "CH": 1, "CHO": 1}, "smiles"),
# # diethyl ether
# ("CCOCC", {"CH3": 2, "CH2": 1, "CH2O": 1}, "smiles"),
# # dimethyl ether
# ("COC", {"CH3": 1, "CH3O": 1}, "smiles"),
# # 2H-Pyran, 2-(cyclohexyloxy)tetrahydro-
# (
# "C1CCC(CC1)OC2CCCCO2",
# {"CH2": 8, "CH": 1, "CH2O": 1, "CHO": 1},
# "smiles",
# ),
# # Problematic ones
# (
# "COC(=O)OC1=CC=CC=C1",
# {"CH3O": 1, "COO": 1, "AC": 1, "ACH": 5},
# "smiles",
# ),
# (
# "CCOC(=O)OC1=CC=CC=C1",
# {"CH3": 1, "CH2O": 1, "COO": 1, "AC": 1, "ACH": 5},
# "smiles",
# ),
# (
# "CC(C)OC(=O)OC1=CC=CC=C1",
# {"CH3": 2, "CHO": 1, "COO": 1, "AC": 1, "ACH": 5},
# "smiles",
# ),
# ("CC(C)(C)OC(=O)OC1=CC=CC=C1", {}, "smiles"),
# # Benzyl 2-hydroxyethyl carbonate
# (
# "C1=CC=C(C=C1)COC(=O)OCCO",
# {"ACCH2": 1, "ACH": 5, "COO": 1, "C2H5O2": 1},
# "smiles",
# ),
# # tert-Butyl ethyl carbonate
# ("CCOC(=O)OC(C)(C)C", {"CH3": 4, "C": 1, "COO": 1, "CH2O": 1}, "smiles"),
# # Ethyl phenyl carbonate
# (
# "CCOC(=O)OC1=CC=CC=C1",
# {"CH3": 1, "AC": 1, "ACH": 5, "COO": 1, "CH2O": 1},
# "smiles",
# ),
# # Carbonic acid, ethyl 2,3,6-trimethylcyclohexyl ester
# (
# "CCOC(=O)OC1C(CCC(C1C)C)C",
# {"CH3": 4, "CH2": 2, "CH": 4, "COO": 1, "CH2O": 1},
# "smiles",
# ),
# # Diethyl carbonate
# ("CCOC(=O)OCC", {"CH3": 2, "CH2": 1, "COO": 1, "CH2O": 1}, "smiles"),
# # Methyl phenyl carbonate
# (
# "COC(=O)OC1=CC=CC=C1",
# {"AC": 1, "ACH": 5, "COO": 1, "CH3O": 1},
# "smiles",
# ),
# # tert-Butyl methyl carbonate
# ("CC(C)(C)OC(=O)OC", {"CH3": 3, "C": 1, "COO": 1, "CH3O": 1}, "smiles"),
# # Methyl isopropyl carbonate
# ("CC(C)OC(=O)OC", {"CH3": 2, "CH": 1, "COO": 1, "CH3O": 1}, "smiles"),
# # Ethyl methyl carbonate
# ("CCOC(=O)OC", {"CH3": 1, "CH2": 1, "COO": 1, "CH3O": 1}, "smiles"),
# # Dimethyl carbonate
# ("COC(=O)OC", {"CH3": 1, "COO": 1, "CH3O": 1}, "smiles"),
# # I hate ether group
# ("COCOC(C)OCOC", {"CH3O": 2, "CH2O": 2, "CH": 1, "CH3": 1}, "smiles"),
# (
# "CC(C)OCOC(C)OCOC(C)C",
# {"CH3": 5, "CH": 1, "HCO": 2, "CH2O": 2},
# "smiles",
# ),
# (
# "CC(C)OCOCC(OCOC(C)C)OCOC(C)C",
# {"CH3": 6, "CH": 2, "CH2O": 4, "HCO": 2},
# "smiles",
# ),
# (
# "CC(C)OCOC(OCOC(C)C)OCOC(C)C",
# {"CH3": 6, "HCO": 3, "CH2O": 3, "CH": 1},
# "smiles",
# ),
# ("CC(C)OCOC(C)C", {"CH3": 4, "HCO": 1, "CH2O": 1, "CH": 1}, "smiles"),
# ("CCOCOCC", {"CH3": 2, "CH2O": 2, "CH2": 1}, "smiles"),
# ("COCOC", {"CH3O": 2, "CH2": 1}, "smiles"),
# # Problematics with acids
# ("COC(O)=O", {"COOH": 1, "CH3O": 1}, "smiles"),
# ("CCOC(O)=O", {"COOH": 1, "CH2O": 1, "CH3": 1}, "smiles"),
# ("CC(C)OC(O)=O", {"COOH": 1, "CHO": 1, "CH3": 2}, "smiles"),
# ("CC(C)(C)OC(O)=O", {"OH": 1, "COO": 1, "C": 1, "CH3": 3}, "smiles"),
# ("OC(=O)OC1=CC=CC=C1", {"OH": 1, "COO": 1, "AC": 1, "ACH": 5}, "smiles"),
# # Impossibles
# ("C1COCON1", {}, "smiles"),
]


@pytest.mark.Joback
@pytest.mark.parametrize("identifier, result, identifier_type", trials)
def test_joback_ethers(identifier, result, identifier_type):
assert ug.get_joback_groups(identifier, identifier_type) == result
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