diff --git a/docs/source/conf.py b/docs/source/conf.py index bf30ef5..6525b09 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -45,7 +45,7 @@ # EXTRA CONF # ============================================================================= # nbsphinx -nbsphinx_execute = 'always' +nbsphinx_execute = "always" autodoc_member_order = "bysource" diff --git a/docs/source/tests_book/display.py b/docs/source/tests_book/display.py index 7843359..8dbe8e3 100644 --- a/docs/source/tests_book/display.py +++ b/docs/source/tests_book/display.py @@ -11,11 +11,12 @@ # path tests project_root = os.path.abspath( - os.path.join(os.path.dirname(__file__), '../../../tests/') + os.path.join(os.path.dirname(__file__), "../../../tests/") ) sys.path.append(project_root) + # Display function def display_case_module(cases: list): for case in cases: @@ -24,9 +25,9 @@ def display_case_module(cases: list): drawer = rdMolDraw2D.MolDraw2DSVG(400, 200) drawer.DrawMolecule(mol) drawer.FinishDrawing() - + svg = drawer.GetDrawingText().replace("svg:", "") - + # HTML block case_html = f"""
diff --git a/reminder.md b/reminder.md index 2790895..6732ea7 100644 --- a/reminder.md +++ b/reminder.md @@ -1,45 +1,3 @@ -Constantinou Gani secondary test: +Joback good examples: -CHn=CHm-CHp=CHk ---------------- -CH0=CH0-CH0=CH0|[CH0]=[CH0]-[CH0]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH0=CH1-CH1=CH0|[CH0]=[CH1]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH0=CH0-CH1=CH0|[CH0]=[CH0]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH0-CH0=CH0|[CH1]=[CH0]-[CH0]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH1-CH1=CH0|[CH1]=[CH1]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH0-CH1=CH0|[CH1]=[CH0]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH1-CH0=CH0|[CH1]=[CH1]-[CH0]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH0=CH0|[CH2]=[CH0]-[CH0]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH1-CH1=CH0|[CH2]=[CH1]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH1=CH0|[CH2]=[CH0]-[CH1]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH1-CH0=CH0|[CH2]=[CH1]-[CH0]=[CH0]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH0-CH0=CH1|[CH1]=[CH0]-[CH0]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH1-CH1=CH1|[CH1]=[CH1]-[CH1]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH1=CH0-CH1=CH1|[CH1]=[CH0]-[CH1]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH0=CH1|[CH2]=[CH0]-[CH0]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH1-CH1=CH1|[CH2]=[CH1]-[CH1]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH1=CH1|[CH2]=[CH0]-[CH1]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH1-CH0=CH1|[CH2]=[CH1]-[CH0]=[CH1]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH0=CH2|[CH2]=[CH0]-[CH0]=[CH2]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH1-CH1=CH2|[CH2]=[CH1]-[CH1]=[CH2]|""{"CHn=CHm-CHp=CHk": 1}"" -CH2=CH0-CH1=CH2|[CH2]=[CH0]-[CH1]=[CH2]|""{"CHn=CHm-CHp=CHk": 1}"" - - -CH3-CHm=CHn ------------ -CH3-CH0=CH0 -CH3-CH0=CH1 -CH3-CH0=CH2 -CH3-CH1=CH0 -CH3-CH1=CH1 -CH3-CH1=CH2 - - -CH2-CHm=CHn ------------ -CH2-CH0=CH0 -CH2-CH0=CH1 -CH2-CH0=CH2 -CH2-CH1=CH0 -CH2-CH1=CH1 -CH2-CH1=CH2 \ No newline at end of file +"CCOC(O)=O" multiple solutions \ No newline at end of file diff --git a/tests/cases/acids.py b/tests/cases/acids.py index 55f1699..555eed8 100644 --- a/tests/cases/acids.py +++ b/tests/cases/acids.py @@ -9,8 +9,6 @@ identifier="OC(O)=O", identifier_type="smiles", cases_module="acids", - r=None, - q=None, unifac_result={"OH": 1, "COOH": 1}, psrk_result={"OH": 1, "COOH": 1}, joback_result={"-OH (alcohol)": 1, "-COOH (acid)": 1}, @@ -19,23 +17,17 @@ identifier="CCOC(O)=O", identifier_type="smiles", cases_module="acids", - r=None, - q=None, unifac_result={"CH3": 1, "CH2O": 1, "COOH": 1}, psrk_result={"CH3": 1, "CH2O": 1, "COOH": 1}, - joback_result={ - "-CH3": 1, - "-CH2-": 1, - "-O- (non-ring)": 1, - "-COOH (acid)": 1, - }, + joback_result=[ + {"-CH3": 1, "-CH2-": 1, "-O- (non-ring)": 1, "-COOH (acid)": 1}, + {"-CH3": 1, "-CH2-": 1, "-OH (alcohol)": 1, "-COO- (ester)": 1}, + ], ), Case( identifier="C(CN)C(C(=O)O)N", identifier_type="smiles", cases_module="acids", - r=None, - q=None, unifac_result={"CH2": 1, "CH2NH2": 1, "CHNH2": 1, "COOH": 1}, psrk_result={"CH2": 1, "CH2NH2": 1, "CHNH2": 1, "COOH": 1}, joback_result={"-CH2-": 2, ">CH-": 1, "-COOH (acid)": 1, "-NH2": 2}, @@ -44,8 +36,6 @@ identifier="CC(=O)O", identifier_type="smiles", cases_module="acids", - r=None, - q=None, unifac_result={"CH3": 1, "COOH": 1}, psrk_result={"CH3": 1, "COOH": 1}, joback_result={"-CH3": 1, "-COOH (acid)": 1}, @@ -54,8 +44,6 @@ identifier="C(=O)O", identifier_type="smiles", cases_module="acids", - r=None, - q=None, unifac_result={"HCOOH": 1}, psrk_result={"HCOOH": 1}, joback_result={}, diff --git a/tests/cases/alcohols.py b/tests/cases/alcohols.py index 4817d19..8c853fe 100644 --- a/tests/cases/alcohols.py +++ b/tests/cases/alcohols.py @@ -11,8 +11,6 @@ identifier="C(CO)O", identifier_type="smiles", cases_module="alcohols", - r=None, - q=None, unifac_result={"DOH": 1}, psrk_result={"DOH": 1}, joback_result={"-CH2-": 2, "-OH (alcohol)": 2}, @@ -21,8 +19,6 @@ identifier="CCOCCO", identifier_type="smiles", cases_module="alcohols", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "C2H5O2": 1}, psrk_result={"CH3": 1, "CH2": 1, "C2H5O2": 1}, joback_result={ @@ -36,8 +32,6 @@ identifier="CCOC(C)CO", identifier_type="smiles", cases_module="alcohols", - r=None, - q=None, unifac_result={"CH3": 2, "C2H4O2": 1, "CH2": 1}, psrk_result={"CH3": 2, "C2H4O2": 1, "CH2": 1}, joback_result={ @@ -53,8 +47,6 @@ "smiles", "alcohols", "1,2-Cyclohexanediol, 4-tert-butyl-1-phenyl-, stereoisomer", - r=None, - q=None, unifac_result={ "CH3": 3, "CH2": 3, @@ -89,8 +81,6 @@ "smiles", "alcohols", "(2S,3S)-2-Methyl-1,3-hexanediol", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 3, "CH": 2, "OH": 2}, psrk_result={"CH3": 2, "CH2": 3, "CH": 2, "OH": 2}, joback_result={"-CH3": 2, "-CH2-": 3, ">CH-": 2, "-OH (alcohol)": 2}, @@ -100,8 +90,6 @@ "smiles", "alcohols", "2-propanol", - r=None, - q=None, unifac_result={"CH3": 2, "CH": 1, "OH": 1}, psrk_result={"CH3": 2, "CH": 1, "OH": 1}, joback_result={"-CH3": 2, ">CH-": 1, "-OH (alcohol)": 1}, @@ -111,8 +99,6 @@ "smiles", "alcohols", "methanol", - r=None, - q=None, unifac_result={"CH3OH": 1}, psrk_result={"CH3OH": 1}, joback_result={"-CH3": 1, "-OH (alcohol)": 1}, @@ -122,8 +108,6 @@ "smiles", "alcohols", "ethanol", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "OH": 1}, psrk_result={"CH3": 1, "CH2": 1, "OH": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "-OH (alcohol)": 1}, @@ -133,8 +117,6 @@ "smiles", "alcohols", "1-propanol", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 2, "OH": 1}, psrk_result={"CH3": 1, "CH2": 2, "OH": 1}, joback_result={"-CH3": 1, "-CH2-": 2, "-OH (alcohol)": 1}, @@ -144,8 +126,6 @@ "smiles", "alcohols", "Phenanthrene-3,4-diol", - r=None, - q=None, unifac_result={"ACH": 8, "AC": 4, "ACOH": 2}, psrk_result={"ACH": 8, "AC": 4, "ACOH": 2}, joback_result={"ring=CH-": 8, "ring=C<": 6, "-OH (phenol)": 2}, @@ -155,8 +135,6 @@ "smiles", "alcohols", "3-(tert-butyl)benzene-1,2-diol", - r=None, - q=None, unifac_result={"ACH": 3, "AC": 1, "ACOH": 2, "CH3": 3, "C": 1}, psrk_result={"ACH": 3, "AC": 1, "ACOH": 2, "CH3": 3, "C": 1}, joback_result={ @@ -172,8 +150,6 @@ "smiles", "alcohols", "[1,1'-Biphenyl]-2,3',4-triol", - r=None, - q=None, unifac_result={"ACH": 7, "AC": 2, "ACOH": 3}, psrk_result={"ACH": 7, "AC": 2, "ACOH": 3}, joback_result={"ring=CH-": 7, "ring=C<": 5, "-OH (phenol)": 3}, diff --git a/tests/cases/aldehydes.py b/tests/cases/aldehydes.py index 8a9995c..0e00141 100644 --- a/tests/cases/aldehydes.py +++ b/tests/cases/aldehydes.py @@ -10,8 +10,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="", - r=None, - q=None, unifac_result={"HCO": 2}, psrk_result={"HCO": 2}, joback_result={"O=CH- (aldehyde)": 2}, @@ -21,8 +19,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="salicylaldehyde", - r=None, - q=None, unifac_result={"ACH": 4, "ACOH": 1, "AC": 1, "HCO": 1}, psrk_result={"ACH": 4, "ACOH": 1, "AC": 1, "HCO": 1}, joback_result={ @@ -37,8 +33,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="2-Methyl-3-butenal", - r=None, - q=None, unifac_result={"CH3": 1, "CH": 1, "CH2=CH": 1, "HCO": 1}, psrk_result={"CH3": 1, "CH": 1, "CH2=CH": 1, "HCO": 1}, joback_result={ @@ -54,8 +48,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="Cinnamaldehyde", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "CH=CH": 1, "HCO": 1}, psrk_result={"ACH": 5, "AC": 1, "CH=CH": 1, "HCO": 1}, joback_result={ @@ -70,8 +62,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="benzaldehyde", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "HCO": 1}, psrk_result={"ACH": 5, "AC": 1, "HCO": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "O=CH- (aldehyde)": 1}, @@ -81,8 +71,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="cyclohexanecarbaldehyde", - r=None, - q=None, unifac_result={"CH2": 5, "CH": 1, "HCO": 1}, psrk_result={"CH2": 5, "CH": 1, "HCO": 1}, joback_result={"ring-CH2-": 5, "ring>CH-": 1, "O=CH- (aldehyde)": 1}, @@ -92,8 +80,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="pentanal", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 3, "HCO": 1}, psrk_result={"CH3": 1, "CH2": 3, "HCO": 1}, joback_result={"-CH3": 1, "-CH2-": 3, "O=CH- (aldehyde)": 1}, @@ -103,8 +89,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="3-methylbutanal", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH": 1, "HCO": 1}, psrk_result={"CH3": 2, "CH2": 1, "CH": 1, "HCO": 1}, joback_result={ @@ -119,8 +103,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="acetaldehyde", - r=None, - q=None, unifac_result={"CH3": 1, "HCO": 1}, psrk_result={"CH3": 1, "HCO": 1}, joback_result={"-CH3": 1, "O=CH- (aldehyde)": 1}, @@ -130,8 +112,6 @@ identifier_type="smiles", cases_module="aldhydes", commentary="2-Hexyl-3-Phenyl-2-Propenal", - r=None, - q=None, unifac_result={ "ACH": 5, "AC": 1, diff --git a/tests/cases/aromatics.py b/tests/cases/aromatics.py index acc79e0..f620770 100644 --- a/tests/cases/aromatics.py +++ b/tests/cases/aromatics.py @@ -9,8 +9,6 @@ "C1=CC2=CC=CC=CC2=C1", "smiles", "aromatics", - r=None, - q=None, unifac_result={"ACH": 8, "AC": 2}, psrk_result={"ACH": 8, "AC": 2}, joback_result={"ring=CH-": 8, "ring=C<": 2}, @@ -19,8 +17,6 @@ "C1=CC=CC=CC=CC=CC=CC=CC=CC=C1", "smiles", "aromatics", - r=None, - q=None, unifac_result={"ACH": 18}, psrk_result={"ACH": 18}, joback_result={"ring=CH-": 18}, @@ -29,8 +25,6 @@ "C1=CC=CC=CC=CC=CC=CC=C1", "smiles", "aromatics", - r=None, - q=None, unifac_result={"ACH": 14}, psrk_result={"ACH": 14}, joback_result={"ring=CH-": 14}, @@ -40,8 +34,6 @@ "smiles", "aromatics", commentary="phenanthrene", - r=None, - q=None, unifac_result={"ACH": 10, "AC": 4}, psrk_result={"ACH": 10, "AC": 4}, joback_result={"ring=CH-": 10, "ring=C<": 4}, @@ -51,8 +43,6 @@ "smiles", "aromatics", commentary="anthracene", - r=None, - q=None, unifac_result={"ACH": 10, "AC": 4}, psrk_result={"ACH": 10, "AC": 4}, joback_result={"ring=CH-": 10, "ring=C<": 4}, @@ -62,10 +52,8 @@ "smiles", "aromatics", commentary="1,1-Diphenylethylene", - r=None, - q=None, unifac_result={"ACH": 10, "AC": 2, "CH2=C": 1}, - psrk_result={"ACH": 10, "AC": 2}, + psrk_result={"ACH": 10, "AC": 2, "CH2=C": 1}, joback_result={"=CH2": 1, "=C<": 1, "ring=CH-": 10, "ring=C<": 2}, ), Case( @@ -73,8 +61,6 @@ "smiles", "aromatics", commentary="biphenyl", - r=None, - q=None, unifac_result={"ACH": 10, "AC": 2}, psrk_result={"ACH": 10, "AC": 2}, joback_result={"ring=CH-": 10, "ring=C<": 2}, @@ -84,8 +70,6 @@ "smiles", "aromatics", commentary="benzene", - r=None, - q=None, unifac_result={"ACH": 6}, psrk_result={"ACH": 6}, joback_result={"ring=CH-": 6}, @@ -95,8 +79,6 @@ "smiles", "aromatics", commentary="styrene", - r=None, - q=None, unifac_result={"AC": 1, "CH2=CH": 1, "ACH": 5}, psrk_result={"AC": 1, "CH2=CH": 1, "ACH": 5}, joback_result={"=CH2": 1, "=CH-": 1, "ring=CH-": 5, "ring=C<": 1}, @@ -106,8 +88,6 @@ "smiles", "aromatics", commentary="Atrolactic acid", - r=None, - q=None, unifac_result={ "ACH": 5, "AC": 1, @@ -131,8 +111,6 @@ "smiles", "aromatics", commentary="1-Phenyl-2-methyl-1,3-butadiene", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "CH=C": 1, "CH2=CH": 1, "CH3": 1}, psrk_result={"ACH": 5, "AC": 1, "CH=C": 1, "CH2=CH": 1, "CH3": 1}, joback_result={ @@ -149,8 +127,6 @@ "smiles", "aromatics", commentary="9-(3-Butenyl)anthracene", - r=None, - q=None, unifac_result={"ACH": 9, "ACCH2": 1, "AC": 4, "CH2": 1, "CH2=CH": 1}, psrk_result={"ACH": 9, "ACCH2": 1, "AC": 4, "CH2": 1, "CH2=CH": 1}, joback_result={ @@ -166,8 +142,6 @@ "smiles", "aromatics", commentary="9-Methylanthracene", - r=None, - q=None, unifac_result={"ACH": 9, "ACCH3": 1, "AC": 4}, psrk_result={"ACH": 9, "ACCH3": 1, "AC": 4}, joback_result={"-CH3": 1, "ring=CH-": 9, "ring=C<": 5}, @@ -177,8 +151,6 @@ "smiles", "aromatics", commentary="3-Methylbiphenyl", - r=None, - q=None, unifac_result={"ACH": 9, "ACCH3": 1, "AC": 2}, psrk_result={"ACH": 9, "ACCH3": 1, "AC": 2}, joback_result={"-CH3": 1, "ring=CH-": 9, "ring=C<": 3}, @@ -188,8 +160,6 @@ "smiles", "aromatics", commentary="1,2,4-Trimethyl-3-Ethylbenzene", - r=None, - q=None, unifac_result={"ACH": 2, "ACCH3": 3, "ACCH2": 1, "CH3": 1}, psrk_result={"ACH": 2, "ACCH3": 3, "ACCH2": 1, "CH3": 1}, joback_result={"-CH3": 4, "-CH2-": 1, "ring=CH-": 2, "ring=C<": 4}, @@ -199,8 +169,6 @@ "smiles", "aromatics", commentary="1-t-Butyl-3-ethylbenzene", - r=None, - q=None, unifac_result={"ACH": 4, "ACCH2": 1, "CH3": 4, "AC": 1, "C": 1}, psrk_result={"ACH": 4, "ACCH2": 1, "CH3": 4, "AC": 1, "C": 1}, joback_result={ @@ -216,8 +184,6 @@ "smiles", "aromatics", commentary="1-Ethyl-2,3-dimethylbenzene", - r=None, - q=None, unifac_result={"ACH": 3, "ACCH2": 1, "ACCH3": 2, "CH3": 1}, psrk_result={"ACH": 3, "ACCH2": 1, "ACCH3": 2, "CH3": 1}, joback_result={"-CH3": 3, "-CH2-": 1, "ring=CH-": 3, "ring=C<": 3}, @@ -227,8 +193,6 @@ "smiles", "aromatics", commentary="1-Ethyl-2-methylbenzene", - r=None, - q=None, unifac_result={"ACH": 4, "ACCH3": 1, "ACCH2": 1, "CH3": 1}, psrk_result={"ACH": 4, "ACCH3": 1, "ACCH2": 1, "CH3": 1}, joback_result={"-CH3": 2, "-CH2-": 1, "ring=CH-": 4, "ring=C<": 2}, @@ -238,8 +202,6 @@ "smiles", "aromatics", commentary="Benzene, 1-ethyl-4-(1-methylethyl)-", - r=None, - q=None, unifac_result={"ACH": 4, "ACCH": 1, "ACCH2": 1, "CH3": 3}, psrk_result={"ACH": 4, "ACCH": 1, "ACCH2": 1, "CH3": 3}, joback_result={ @@ -255,8 +217,6 @@ "smiles", "aromatics", commentary="Gastrodigenin", - r=None, - q=None, unifac_result={"ACH": 4, "ACOH": 1, "ACCH2": 1, "OH": 1}, psrk_result={"ACH": 4, "ACOH": 1, "ACCH2": 1, "OH": 1}, joback_result={ @@ -272,8 +232,6 @@ "smiles", "aromatics", commentary="cumene", - r=None, - q=None, unifac_result={"CH3": 2, "ACH": 5, "ACCH": 1}, psrk_result={"CH3": 2, "ACH": 5, "ACCH": 1}, joback_result={"-CH3": 2, ">CH-": 1, "ring=CH-": 5, "ring=C<": 1}, @@ -283,8 +241,6 @@ "smiles", "aromatics", commentary="ethylbenzene", - r=None, - q=None, unifac_result={"CH3": 1, "ACH": 5, "ACCH2": 1}, psrk_result={"CH3": 1, "ACH": 5, "ACCH2": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "ring=CH-": 5, "ring=C<": 1}, @@ -294,8 +250,6 @@ "smiles", "aromatics", commentary="toluene", - r=None, - q=None, unifac_result={"ACH": 5, "ACCH3": 1}, psrk_result={"ACH": 5, "ACCH3": 1}, joback_result={"-CH3": 1, "ring=CH-": 5, "ring=C<": 1}, @@ -305,8 +259,6 @@ "smiles", "aromatics", commentary="phenol", - r=None, - q=None, unifac_result={"ACH": 5, "ACOH": 1}, psrk_result={"ACH": 5, "ACOH": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-OH (phenol)": 1}, diff --git a/tests/cases/case.py b/tests/cases/case.py index 48ed6bf..20c5d50 100644 --- a/tests/cases/case.py +++ b/tests/cases/case.py @@ -21,10 +21,6 @@ class Case: Commentary of the test case. Usually to disctint something hard about the case. Also if a user found a bug could be mention here with the issue tag, by default "". - r : Union[float, None], optional - R value of the molecule, by default None. - q : Union[float, None], optional - Q value of the molecule, by default None. unifac_result : Union[dict, None], optional Result of the UNIFAC model, by default None. psrk_result : Union[dict, None], optional @@ -39,8 +35,6 @@ def __init__( identifier_type: str, cases_module: str, commentary: str = "", - r: Union[float, None] = None, - q: Union[float, None] = None, unifac_result: Union[dict, None] = None, psrk_result: Union[dict, None] = None, joback_result: Union[dict, None] = None, @@ -49,8 +43,6 @@ def __init__( self.identifier_type = identifier_type self.cases_module = cases_module self.commentary = commentary - self.r = r - self.q = q self.unifac_result = unifac_result self.psrk_result = psrk_result self.joback_result = joback_result diff --git a/tests/cases/complex.py b/tests/cases/complex.py index 2c100dc..cdb22ae 100644 --- a/tests/cases/complex.py +++ b/tests/cases/complex.py @@ -9,8 +9,6 @@ identifier="CCCC1=C(COC(C)(C)COC(=O)OCC)C=C(CC2=CC=CC=C2)C=C1", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={ "CH3": 4, "C": 1, @@ -45,8 +43,6 @@ identifier="CC(C)CC1=CC=C(C=C1)C(C)OC(C)(C)C", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={ "CH3": 6, "C": 1, @@ -79,8 +75,6 @@ identifier="CCCC1=CC=C(CC(=O)OC)C=C1", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result=[ {"CH3": 2, "ACH": 4, "ACCH2": 1, "CH2COO": 1, "CH2": 1, "AC": 1}, {"CH3": 2, "ACH": 4, "ACCH2": 2, "CH2": 1, "COO": 1}, @@ -101,8 +95,6 @@ identifier="C1=CC(=CC=C1COC(C)(C)C)CCC", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={ "CH3": 4, "C": 1, @@ -134,8 +126,6 @@ identifier="C13=C(C=C(C=C1)CC2=CC=CC(=C2)CC)CCCC3", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 2, "ACH": 7, "ACCH2": 4, "AC": 1}, psrk_result={"CH3": 1, "CH2": 2, "ACH": 7, "ACCH2": 4, "AC": 1}, joback_result={ @@ -150,8 +140,6 @@ identifier="C13=C(C(=C(C(=C1C)C)CC2=C(C(=C(C(=C2C)CC)O[H])N([H])[H])C)C)CCCC3", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={ "CH3": 1, "CH2": 2, @@ -183,8 +171,6 @@ identifier="C1(=CC=CC=C1)COC(C)(C)C", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "ACH": 5, "CH2O": 1, "AC": 1}, psrk_result={"CH3": 3, "C": 1, "ACH": 5, "CH2O": 1, "AC": 1}, joback_result={ @@ -200,8 +186,6 @@ identifier="C1=CC=C(C=C1)CC2=CC=CC=C2", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={"ACH": 10, "ACCH2": 1, "AC": 1}, psrk_result={"ACH": 10, "ACCH2": 1, "AC": 1}, joback_result={"-CH2-": 1, "ring=CH-": 10, "ring=C<": 2}, @@ -210,8 +194,6 @@ identifier="C1(=CC=CC=C1)C(OC(C)(C)C)C", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "ACH": 5, "CHO": 1, "AC": 1}, psrk_result={"CH3": 4, "C": 1, "ACH": 5, "CHO": 1, "AC": 1}, joback_result={ @@ -227,8 +209,6 @@ identifier="C12=CC=CC=C1COC2", identifier_type="smiles", cases_module="complex", - r=None, - q=None, unifac_result={"ACH": 4, "ACCH2": 1, "CH2O": 1, "AC": 1}, psrk_result={"ACH": 4, "ACCH2": 1, "CH2O": 1, "AC": 1}, joback_result={ diff --git a/tests/cases/epoxides.py b/tests/cases/epoxides.py index 27dacf4..3a62c3d 100644 --- a/tests/cases/epoxides.py +++ b/tests/cases/epoxides.py @@ -5,12 +5,34 @@ epoxides_cases = [ + Case( + identifier="O1C2OC12", + identifier_type="smiles", + cases_module="epoxides", + unifac_result={"CHO": 2}, + psrk_result={"CHO": 2}, + joback_result={"-O- (ring)": 2, "ring>CH-": 2}, + ), + Case( + identifier="O1C23OC22OC132", + identifier_type="smiles", + cases_module="epoxides", + unifac_result={}, + psrk_result={}, + joback_result={"-O- (ring)": 3, "ring>C<": 3}, + ), + Case( + identifier="C1OC11CO1", + identifier_type="smiles", + cases_module="epoxides", + unifac_result={"CH2O": 2, "C": 1}, + psrk_result={"H2COC": 1, "CH2O": 1}, + joback_result={"-O- (ring)": 2, "ring>C<": 1, "ring-CH2-": 2}, + ), Case( identifier="CC1CO1", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH": 1, "CH2O": 1}, {"CH3": 1, "CH2": 1, "CHO": 1}, @@ -27,10 +49,11 @@ identifier="C1OC1C1=CC=CC=C1", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result={"ACH": 5, "ACCH": 1, "CH2O": 1}, - psrk_result={"ACH": 5, "H2COCH": 1, "AC": 1}, + psrk_result=[ + {"ACH": 5, "AC": 1, "H2COCH": 1}, + {"ACH": 5, "ACCH": 1, "CH2O": 1}, + ], joback_result={ "ring-CH2-": 1, "ring>CH-": 1, @@ -43,8 +66,6 @@ identifier="CC1C(O1)C", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result={"CH3": 2, "CH": 1, "CHO": 1}, psrk_result={"CH3": 2, "HCOCH": 1}, joback_result={"-CH3": 2, "ring>CH-": 2, "-O- (ring)": 1}, @@ -53,8 +74,6 @@ identifier="CC1OC1(C)C", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "CHO": 1}, psrk_result={"CH3": 3, "HCOC": 1}, joback_result={ @@ -68,8 +87,6 @@ identifier="CC1(CO1)C", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result={"CH3": 2, "C": 1, "CH2O": 1}, psrk_result={"CH3": 2, "H2COC": 1}, joback_result={ @@ -83,8 +100,6 @@ identifier="CC1(C(O1)(C)C)C", identifier_type="smiles", cases_module="epoxides", - r=None, - q=None, unifac_result={}, psrk_result={"CH3": 4, "COC": 1}, joback_result={"-CH3": 4, "ring>C<": 2, "-O- (ring)": 1}, diff --git a/tests/cases/esters.py b/tests/cases/esters.py index 11d867a..6d6a60c 100644 --- a/tests/cases/esters.py +++ b/tests/cases/esters.py @@ -10,8 +10,6 @@ identifier_type="smiles", commentary="Methyl acrylate", cases_module="esters", - r=None, - q=None, unifac_result={"CH3": 1, "CH2=CH": 1, "COO": 1}, psrk_result={"CH3": 1, "CH2=CH": 1, "COO": 1}, joback_result={"-CH3": 1, "=CH2": 1, "=CH-": 1, "-COO- (ester)": 1}, @@ -21,8 +19,6 @@ identifier_type="smiles", commentary="", cases_module="esters", - r=None, - q=None, unifac_result={ "CH3": 1, "CH2": 3, @@ -50,8 +46,6 @@ identifier_type="smiles", commentary="Procaine", cases_module="esters", - r=None, - q=None, unifac_result={ "ACNH2": 1, "ACH": 4, @@ -85,8 +79,6 @@ identifier_type="smiles", commentary="Ascorbic acid", cases_module="esters", - r=None, - q=None, unifac_result={"COO": 1, "C=C": 1, "OH": 4, "CH": 2, "CH2": 1}, psrk_result={"COO": 1, "C=C": 1, "OH": 4, "CH": 2, "CH2": 1}, joback_result={ @@ -103,8 +95,6 @@ identifier_type="smiles", commentary="Dilaurin", cases_module="esters", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 20, "CH2COO": 2, "OH": 1, "CH": 1}, psrk_result={"CH3": 2, "CH2": 20, "CH2COO": 2, "OH": 1, "CH": 1}, joback_result={ @@ -120,8 +110,6 @@ identifier_type="smiles", commentary="Aspirin", cases_module="esters", - r=None, - q=None, unifac_result={"CH3COO": 1, "AC": 2, "ACH": 4, "COOH": 1}, psrk_result={"CH3COO": 1, "AC": 2, "ACH": 4, "COOH": 1}, joback_result={ @@ -137,8 +125,6 @@ identifier_type="smiles", commentary="Tert-butyl acetate", cases_module="esters", - r=None, - q=None, unifac_result={"CH3COO": 1, "CH3": 3, "C": 1}, psrk_result={"CH3COO": 1, "CH3": 3, "C": 1}, joback_result={"-CH3": 4, ">C<": 1, "-COO- (ester)": 1}, @@ -148,8 +134,6 @@ identifier_type="smiles", commentary="Triacetin", cases_module="esters", - r=None, - q=None, unifac_result={"CH3COO": 3, "CH2": 2, "CH": 1}, psrk_result={"CH3COO": 3, "CH2": 2, "CH": 1}, joback_result={"-CH3": 3, "-CH2-": 2, ">CH-": 1, "-COO- (ester)": 3}, @@ -159,8 +143,6 @@ identifier_type="smiles", commentary="butyl propanoate", cases_module="esters", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 3, "CH2COO": 1}, psrk_result={"CH3": 2, "CH2": 3, "CH2COO": 1}, joback_result={"-CH3": 2, "-CH2-": 4, "-COO- (ester)": 1}, @@ -170,8 +152,6 @@ identifier_type="smiles", commentary="butyl acetate", cases_module="esters", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 3, "CH3COO": 1}, psrk_result={"CH3": 1, "CH2": 3, "CH3COO": 1}, joback_result={"-CH3": 2, "-CH2-": 3, "-COO- (ester)": 1}, @@ -181,8 +161,6 @@ identifier_type="smiles", commentary="phenyl formate", cases_module="esters", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "HCOO": 1}, psrk_result={"ACH": 5, "AC": 1, "HCOO": 1}, joback_result={}, @@ -192,8 +170,6 @@ identifier_type="smiles", commentary="methyl formate", cases_module="esters", - r=None, - q=None, unifac_result={"HCOO": 1, "CH3": 1}, psrk_result={"HCOO": 1, "CH3": 1}, joback_result={}, @@ -203,8 +179,6 @@ identifier_type="smiles", commentary="ethyl formate", cases_module="esters", - r=None, - q=None, unifac_result={"HCOO": 1, "CH2": 1, "CH3": 1}, psrk_result={"HCOO": 1, "CH2": 1, "CH3": 1}, joback_result={}, diff --git a/tests/cases/ethers.py b/tests/cases/ethers.py index 8ef795b..c7258e3 100644 --- a/tests/cases/ethers.py +++ b/tests/cases/ethers.py @@ -12,8 +12,6 @@ identifier="OC1CC(OC2=CC=CC=C12)C1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={ "ACH": 9, "AC": 2, @@ -43,13 +41,14 @@ identifier="O[C@@H]1CO[C@H](O)[C@@H](O)[C@@H]1O", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH2": 1, "CH": 3, "OH": 4, "CHO": 1}, {"CH": 4, "OH": 4, "CH2O": 1}, ], - psrk_result={"CH2O": 1, "CH": 4, "OH": 4}, + psrk_result=[ + {"CH2": 1, "CH": 3, "OH": 4, "CHO": 1}, + {"CH": 4, "OH": 4, "CH2O": 1}, + ], joback_result={ "ring-CH2-": 1, "ring>CH-": 4, @@ -61,8 +60,6 @@ identifier="C1COCCOCCOCCOC1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH2O": 4, "CH2": 5}, psrk_result={"CH2O": 4, "CH2": 5}, joback_result={"ring-CH2-": 9, "-O- (ring)": 4}, @@ -71,8 +68,6 @@ identifier="C1COCCO1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH2O": 2, "CH2": 2}, psrk_result={"CH2O": 2, "CH2": 2}, joback_result={"ring-CH2-": 4, "-O- (ring)": 2}, @@ -81,8 +76,6 @@ identifier="C1COCO1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH2O": 2, "CH2": 1}, psrk_result={"CH2O": 2, "CH2": 1}, joback_result={"ring-CH2-": 3, "-O- (ring)": 2}, @@ -91,8 +84,6 @@ identifier="C1COCCOCCOCCOCCOCCO1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH2O": 6, "CH2": 6}, psrk_result={"CH2O": 6, "CH2": 6}, joback_result={"ring-CH2-": 12, "-O- (ring)": 6}, @@ -101,8 +92,6 @@ identifier="C1CCOC1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"THF": 1, "CH2": 3}, psrk_result={"THF": 1, "CH2": 3}, joback_result={"ring-CH2-": 4, "-O- (ring)": 1}, @@ -111,8 +100,6 @@ identifier="CC1COCC1C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"THF": 1, "CH2": 1, "CH": 2, "CH3": 2}, psrk_result={"THF": 1, "CH2": 1, "CH": 2, "CH3": 2}, joback_result={ @@ -126,8 +113,6 @@ identifier="CC1COCC1O", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"THF": 1, "CH2": 1, "CH": 2, "CH3": 1, "OH": 1}, psrk_result={"THF": 1, "CH2": 1, "CH": 2, "CH3": 1, "OH": 1}, joback_result={ @@ -142,8 +127,6 @@ identifier="CC(C)OC(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 4, "CH": 1, "CHO": 1}, psrk_result={"CH3": 4, "CH": 1, "CHO": 1}, joback_result={"-CH3": 4, ">CH-": 2, "-O- (non-ring)": 1}, @@ -152,8 +135,6 @@ identifier="CCOCC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH2O": 1}, psrk_result={"CH3": 2, "CH2": 1, "CH2O": 1}, joback_result={"-CH3": 2, "-CH2-": 2, "-O- (non-ring)": 1}, @@ -162,8 +143,6 @@ identifier="COC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 1, "CH3O": 1}, psrk_result={"CH3": 1, "CH3O": 1}, joback_result={"-CH3": 2, "-O- (non-ring)": 1}, @@ -172,13 +151,14 @@ identifier="C1CCC(CC1)OC2CCCCO2", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH2": 8, "CH": 1, "CH2O": 1, "CHO": 1}, {"CH2": 9, "CHO": 2}, ], - psrk_result={"CH2": 8, "CH": 1, "CH2O": 1, "CHO": 1}, + psrk_result=[ + {"CH2": 8, "CH": 1, "CH2O": 1, "CHO": 1}, + {"CH2": 9, "CHO": 2}, + ], joback_result={ "ring-CH2-": 9, "ring>CH-": 2, @@ -190,8 +170,6 @@ identifier="CCOC(=O)OC1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 1, "CH2O": 1, "COO": 1, "AC": 1, "ACH": 5}, psrk_result={"CH3": 1, "CH2O": 1, "COO": 1, "AC": 1, "ACH": 5}, joback_result={ @@ -207,8 +185,6 @@ identifier="CC(C)OC(=O)OC1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 2, "CHO": 1, "COO": 1, "AC": 1, "ACH": 5}, psrk_result={"CH3": 2, "CHO": 1, "COO": 1, "AC": 1, "ACH": 5}, joback_result={ @@ -224,8 +200,6 @@ identifier="CC(C)(C)OC(=O)OC1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -241,8 +215,6 @@ identifier="C1=CC=C(C=C1)COC(=O)OCCO", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"ACCH2": 1, "ACH": 5, "COO": 1, "C2H5O2": 1}, psrk_result={"ACCH2": 1, "ACH": 5, "COO": 1, "C2H5O2": 1}, joback_result={ @@ -258,8 +230,6 @@ identifier="CCOC(=O)OC(C)(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "COO": 1, "CH2O": 1}, psrk_result={"CH3": 4, "C": 1, "COO": 1, "CH2O": 1}, joback_result={ @@ -274,13 +244,14 @@ identifier="CCOC(=O)OC1C(CCC(C1C)C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 4, "CH2": 2, "CH": 4, "CH2O": 1, "COO": 1}, {"CH3": 4, "CH2": 3, "CH": 3, "CHO": 1, "COO": 1}, ], - psrk_result={"CH3": 4, "CH2": 2, "CH": 4, "COO": 1, "CH2O": 1}, + psrk_result=[ + {"CH3": 4, "CH2": 2, "CH": 4, "CH2O": 1, "COO": 1}, + {"CH3": 4, "CH2": 3, "CH": 3, "CHO": 1, "COO": 1}, + ], joback_result={ "-CH3": 4, "-CH2-": 1, @@ -294,8 +265,6 @@ identifier="CCOC(=O)OCC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "COO": 1, "CH2O": 1}, psrk_result={"CH3": 2, "CH2": 1, "COO": 1, "CH2O": 1}, joback_result={ @@ -309,8 +278,6 @@ identifier="COC(=O)OC1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"AC": 1, "ACH": 5, "COO": 1, "CH3O": 1}, psrk_result={"AC": 1, "ACH": 5, "COO": 1, "CH3O": 1}, joback_result={ @@ -325,8 +292,6 @@ identifier="CC(C)(C)OC(=O)OC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "COO": 1, "CH3O": 1}, psrk_result={"CH3": 3, "C": 1, "COO": 1, "CH3O": 1}, joback_result={ @@ -340,13 +305,14 @@ identifier="CC(C)OC(=O)OC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 1, "COO": 1}, {"CH3": 2, "CH": 1, "CH3O": 1, "COO": 1}, ], - psrk_result={"CH3": 2, "CH": 1, "COO": 1, "CH3O": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 1, "COO": 1}, + {"CH3": 2, "CH": 1, "CH3O": 1, "COO": 1}, + ], joback_result={ "-CH3": 3, ">CH-": 1, @@ -358,13 +324,14 @@ identifier="CCOC(=O)OC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "COO": 1}, {"CH3": 1, "CH2": 1, "CH3O": 1, "COO": 1}, ], - psrk_result={"CH3": 1, "CH2": 1, "COO": 1, "CH3O": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "COO": 1}, + {"CH3": 1, "CH2": 1, "CH3O": 1, "COO": 1}, + ], joback_result={ "-CH3": 2, "-CH2-": 1, @@ -376,8 +343,6 @@ identifier="COC(=O)OC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 1, "COO": 1, "CH3O": 1}, psrk_result={"CH3": 1, "COO": 1, "CH3O": 1}, joback_result={"-CH3": 2, "-O- (non-ring)": 1, "-COO- (ester)": 1}, @@ -386,75 +351,80 @@ identifier="COCOC(C)OCOC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH": 1, "CH3O": 2, "CH2O": 2}, {"CH3": 2, "CH3O": 1, "CH2O": 2, "CHO": 1}, {"CH3": 1, "CH2": 1, "CH3O": 2, "CH2O": 1, "CHO": 1}, ], - psrk_result={"CH3O": 2, "CH2O": 2, "CH": 1, "CH3": 1}, + psrk_result=[ + {"CH3": 1, "CH": 1, "CH3O": 2, "CH2O": 2}, + {"CH3": 2, "CH3O": 1, "CH2O": 2, "CHO": 1}, + {"CH3": 1, "CH2": 1, "CH3O": 2, "CH2O": 1, "CHO": 1}, + ], joback_result={"-CH3": 3, "-CH2-": 2, ">CH-": 1, "-O- (non-ring)": 4}, ), Case( identifier="CC(C)OCOC(C)OCOC(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 5, "CH": 1, "CHO": 2, "CH2O": 2}, {"CH3": 5, "CH2": 1, "CH2O": 1, "CHO": 3}, ], - psrk_result={"CH3": 5, "CH": 1, "CHO": 2, "CH2O": 2}, + psrk_result=[ + {"CH3": 5, "CH": 1, "CHO": 2, "CH2O": 2}, + {"CH3": 5, "CH2": 1, "CH2O": 1, "CHO": 3}, + ], joback_result={"-CH3": 5, "-CH2-": 2, ">CH-": 3, "-O- (non-ring)": 4}, ), Case( identifier="CC(C)OCOCC(OCOC(C)C)OCOC(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 6, "CH": 2, "CH2O": 4, "CHO": 2}, {"CH3": 6, "CH2": 1, "CH": 1, "CH2O": 3, "CHO": 3}, {"CH3": 6, "CH2": 2, "CH2O": 2, "CHO": 4}, ], - psrk_result={"CH3": 6, "CH": 2, "CH2O": 4, "CHO": 2}, + psrk_result=[ + {"CH3": 6, "CH": 2, "CH2O": 4, "CHO": 2}, + {"CH3": 6, "CH2": 1, "CH": 1, "CH2O": 3, "CHO": 3}, + {"CH3": 6, "CH2": 2, "CH2O": 2, "CHO": 4}, + ], joback_result={"-CH3": 6, "-CH2-": 4, ">CH-": 4, "-O- (non-ring)": 6}, ), Case( identifier="CC(C)OCOC(OCOC(C)C)OCOC(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 6, "CHO": 3, "CH2O": 3, "CH": 1}, {"CH3": 6, "CH2": 1, "CH2O": 2, "CHO": 4}, ], - psrk_result={"CH3": 6, "CHO": 3, "CH2O": 3, "CH": 1}, + psrk_result=[ + {"CH3": 6, "CHO": 3, "CH2O": 3, "CH": 1}, + {"CH3": 6, "CH2": 1, "CH2O": 2, "CHO": 4}, + ], joback_result={"-CH3": 6, "-CH2-": 3, ">CH-": 4, "-O- (non-ring)": 6}, ), Case( identifier="CC(C)OCOC(C)C", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3": 4, "CHO": 1, "CH2O": 1, "CH": 1}, {"CH3": 4, "CH2": 1, "CHO": 2}, ], - psrk_result={"CH3": 4, "CHO": 1, "CH2O": 1, "CH": 1}, + psrk_result=[ + {"CH3": 4, "CHO": 1, "CH2O": 1, "CH": 1}, + {"CH3": 4, "CH2": 1, "CHO": 2}, + ], joback_result={"-CH3": 4, "-CH2-": 1, ">CH-": 2, "-O- (non-ring)": 2}, ), Case( identifier="CCOCOCC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH3": 2, "CH2O": 2, "CH2": 1}, psrk_result={"CH3": 2, "CH2O": 2, "CH2": 1}, joback_result={"-CH3": 2, "-CH2-": 3, "-O- (non-ring)": 2}, @@ -463,78 +433,76 @@ identifier="COCOC", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result=[ {"CH3O": 2, "CH2": 1}, {"CH3": 1, "CH3O": 1, "CH2O": 1}, ], - psrk_result={"CH3O": 2, "CH2": 1}, + psrk_result=[ + {"CH3O": 2, "CH2": 1}, + {"CH3": 1, "CH3O": 1, "CH2O": 1}, + ], joback_result={"-CH3": 2, "-CH2-": 1, "-O- (non-ring)": 2}, ), Case( identifier="COC(O)=O", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"COOH": 1, "CH3O": 1}, psrk_result={"COOH": 1, "CH3O": 1}, - joback_result={"-CH3": 1, "-O- (non-ring)": 1, "-COOH (acid)": 1}, + joback_result=[ + {"-CH3": 1, "-O- (non-ring)": 1, "-COOH (acid)": 1}, + {"-CH3": 1, "-OH (alcohol)": 1, "-COO- (ester)": 1}, + ], ), Case( identifier="CC(C)OC(O)=O", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"COOH": 1, "CHO": 1, "CH3": 2}, psrk_result={"COOH": 1, "CHO": 1, "CH3": 2}, - joback_result={ - "-CH3": 2, - ">CH-": 1, - "-O- (non-ring)": 1, - "-COOH (acid)": 1, - }, + joback_result=[ + {"-CH3": 2, ">CH-": 1, "-O- (non-ring)": 1, "-COOH (acid)": 1}, + {"-CH3": 2, ">CH-": 1, "-OH (alcohol)": 1, "-COO- (ester)": 1}, + ], ), Case( identifier="CC(C)(C)OC(O)=O", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"OH": 1, "COO": 1, "C": 1, "CH3": 3}, psrk_result={"OH": 1, "COO": 1, "C": 1, "CH3": 3}, - joback_result={ - "-CH3": 3, - ">C<": 1, - "-O- (non-ring)": 1, - "-COOH (acid)": 1, - }, + joback_result=[ + {"-CH3": 3, ">C<": 1, "-O- (non-ring)": 1, "-COOH (acid)": 1}, + {"-CH3": 3, ">C<": 1, "-OH (alcohol)": 1, "-COO- (ester)": 1}, + ], ), Case( identifier="OC(=O)OC1=CC=CC=C1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"OH": 1, "COO": 1, "AC": 1, "ACH": 5}, psrk_result={"OH": 1, "COO": 1, "AC": 1, "ACH": 5}, - joback_result={ - "ring=CH-": 5, - "ring=C<": 1, - "-O- (non-ring)": 1, - "-COOH (acid)": 1, - }, + joback_result=[ + { + "ring=CH-": 5, + "ring=C<": 1, + "-OH (alcohol)": 1, + "-COO- (ester)": 1, + }, + { + "ring=CH-": 5, + "ring=C<": 1, + "-O- (non-ring)": 1, + "-COOH (acid)": 1, + }, + ], ), Case( identifier="C1COCON1", identifier_type="smiles", cases_module="ethers", - r=None, - q=None, unifac_result={"CH2O": 2, "CH2NH": 1}, - psrk_result={}, + psrk_result={"CH2O": 2, "CH2NH": 1}, joback_result={"ring-CH2-": 3, "-O- (ring)": 2, ">NH (ring)": 1}, ), ] diff --git a/tests/cases/halogens.py b/tests/cases/halogens.py index e9cfb7b..3d2a7c3 100644 --- a/tests/cases/halogens.py +++ b/tests/cases/halogens.py @@ -9,8 +9,6 @@ identifier="CCCCCl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 2, "CH2CL": 1}, psrk_result={"CH3": 1, "CH2": 2, "CH2CL": 1}, joback_result={"-CH3": 1, "-CH2-": 3, "-Cl": 1}, @@ -19,8 +17,6 @@ identifier="CC(C)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 2, "CHCL": 1}, psrk_result={"CH3": 2, "CHCL": 1}, joback_result={"-CH3": 2, ">CH-": 1, "-Cl": 1}, @@ -29,8 +25,6 @@ identifier="CC(C)(C)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 3, "CCL": 1}, psrk_result={"CH3": 3, "CCL": 1}, joback_result={"-CH3": 3, ">C<": 1, "-Cl": 1}, @@ -39,8 +33,6 @@ identifier="OC(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"OH": 1, "CHCL2": 1}, psrk_result={"OH": 1, "CHCL2": 1}, joback_result={">CH-": 1, "-Cl": 2, "-OH (alcohol)": 1}, @@ -49,8 +41,6 @@ identifier="C(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH2CL2": 1}, psrk_result={"CH2CL2": 1}, joback_result={"-CH2-": 1, "-Cl": 2}, @@ -59,8 +49,6 @@ identifier="CC(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 1, "CHCL2": 1}, psrk_result={"CH3": 1, "CHCL2": 1}, joback_result={"-CH3": 1, ">CH-": 1, "-Cl": 2}, @@ -69,8 +57,6 @@ identifier="CC(C)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 2, "CCL2": 1}, psrk_result={"CH3": 2, "CCL2": 1}, joback_result={"-CH3": 2, ">C<": 1, "-Cl": 2}, @@ -79,8 +65,6 @@ identifier="C(Cl)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CHCL3": 1}, psrk_result={"CHCL3": 1}, joback_result={">CH-": 1, "-Cl": 3}, @@ -89,8 +73,6 @@ identifier="CC(Cl)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 1, "CCL3": 1}, psrk_result={"CH3": 1, "CCL3": 1}, joback_result={"-CH3": 1, ">C<": 1, "-Cl": 3}, @@ -99,8 +81,6 @@ identifier="C(Cl)(Cl)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCL4": 1}, psrk_result={"CCL4": 1}, joback_result={">C<": 1, "-Cl": 4}, @@ -109,8 +89,6 @@ identifier="C1=CC=C(C=C1)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"ACH": 5, "ACCL": 1}, psrk_result={"ACH": 5, "ACCL": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-Cl": 1}, @@ -119,8 +97,6 @@ identifier="CCI", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "I": 1}, psrk_result={"CH3": 1, "CH2": 1, "I": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "-I": 1}, @@ -129,8 +105,6 @@ identifier="C1=CC=C(C=C1)I", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "I": 1}, psrk_result={"ACH": 5, "AC": 1, "I": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-I": 1}, @@ -139,8 +113,6 @@ identifier="CCBr", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "BR": 1}, psrk_result={"CH3": 1, "CH2": 1, "BR": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "-Br": 1}, @@ -149,8 +121,6 @@ identifier="C1=CC=C(C=C1)Br", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "BR": 1}, psrk_result={"ACH": 5, "AC": 1, "BR": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-Br": 1}, @@ -159,8 +129,6 @@ identifier="ClC(I)=C(Br)C=CC=C", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={ "CH2=CH": 1, "CH=CH": 1, @@ -190,8 +158,6 @@ identifier="C(=C(Cl)Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CH=C": 1, "CL-(C=C)": 3}, psrk_result={"CH=C": 1, "CL-(C=C)": 3}, joback_result={"=CH-": 1, "=C<": 1, "-Cl": 3}, @@ -200,8 +166,6 @@ identifier="C1(=C(C(=C(C(=C1F)F)F)F)F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"ACF": 6}, psrk_result={"ACF": 6}, joback_result={"ring=C<": 6, "-F": 6}, @@ -210,8 +174,6 @@ identifier="FC1=CC=NC=C1", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={"ring=CH-": 4, "ring=C<": 1, "-F": 1, "-N= (ring)": 1}, @@ -220,8 +182,6 @@ identifier="OC(F)(Br)I", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"OH": 1, "I": 1, "BR": 1, "CF": 1}, psrk_result={"OH": 1, "I": 1, "BR": 1, "CF": 1}, joback_result={ @@ -236,8 +196,6 @@ identifier="OC(O)(F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"OH": 2, "CF2": 1}, psrk_result={"OH": 2, "CF2": 1}, joback_result={">C<": 1, "-F": 2, "-OH (alcohol)": 2}, @@ -246,8 +204,6 @@ identifier="OC(F)(F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"OH": 1, "CF3": 1}, psrk_result={"OH": 1, "CF3": 1}, joback_result={">C<": 1, "-F": 3, "-OH (alcohol)": 1}, @@ -256,8 +212,6 @@ identifier="C(C(C(C(F)(F)F)(F)F)(F)F)(C(C(F)(F)F)(F)F)(F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CF3": 2, "CF2": 4}, psrk_result={"CF3": 2, "CF2": 4}, joback_result={">C<": 6, "-F": 14}, @@ -266,8 +220,6 @@ identifier="C1(C(C(C(C(C1(F)F)(F)F)(F)F)(F)F)(F)F)(C(F)(F)F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CF3": 1, "CF2": 5, "CF": 1}, psrk_result={"CF3": 1, "CF2": 5, "CF": 1}, joback_result={">C<": 1, "ring>C<": 6, "-F": 14}, @@ -276,8 +228,6 @@ identifier="FC(F)F", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={">CH-": 1, "-F": 3}, @@ -286,8 +236,6 @@ identifier="FCF", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={"-CH2-": 1, "-F": 2}, @@ -296,8 +244,6 @@ identifier="CF", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={"-CH3": 1, "-F": 1}, @@ -306,8 +252,6 @@ identifier="C(F)(Cl)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCL3F": 1}, psrk_result={"CCL3F": 1}, joback_result={">C<": 1, "-F": 1, "-Cl": 3}, @@ -316,8 +260,6 @@ identifier="C(C(F)(Cl)Cl)(F)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCL2F": 2}, psrk_result={"CCL2F": 2}, joback_result={">C<": 2, "-F": 2, "-Cl": 4}, @@ -326,8 +268,6 @@ identifier="C(F)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"HCCL2F": 1}, psrk_result={"HCCL2F": 1}, joback_result={">CH-": 1, "-F": 1, "-Cl": 2}, @@ -336,8 +276,6 @@ identifier="C(C(F)(F)F)(F)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CF3": 1, "HCCLF": 1}, psrk_result={"CF3": 1, "HCCLF": 1}, joback_result={">CH-": 1, ">C<": 1, "-F": 4, "-Cl": 1}, @@ -346,8 +284,6 @@ identifier="C(C(F)(F)Cl)(F)(F)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCLF2": 2}, psrk_result={"CCLF2": 2}, joback_result={">C<": 2, "-F": 4, "-Cl": 2}, @@ -356,8 +292,6 @@ identifier="C(F)(F)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"HCCLF2": 1}, psrk_result={"HCCLF2": 1}, joback_result={">CH-": 1, "-F": 2, "-Cl": 1}, @@ -366,8 +300,6 @@ identifier="C(F)(F)(F)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCLF3": 1}, psrk_result={"CCLF3": 1}, joback_result={">C<": 1, "-F": 3, "-Cl": 1}, @@ -376,8 +308,6 @@ identifier="C(F)(F)(Cl)Cl", identifier_type="smiles", cases_module="halogens", - r=None, - q=None, unifac_result={"CCL2F2": 1}, psrk_result={"CCL2F2": 1}, joback_result={">C<": 1, "-F": 2, "-Cl": 2}, diff --git a/tests/cases/hydrocarbons.py b/tests/cases/hydrocarbons.py index 2a39b94..d19d5a4 100644 --- a/tests/cases/hydrocarbons.py +++ b/tests/cases/hydrocarbons.py @@ -14,8 +14,6 @@ "CC", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 2}, psrk_result={"CH3": 2}, joback_result={"-CH3": 2}, @@ -24,8 +22,6 @@ "CC(C)(C)C", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1}, psrk_result={"CH3": 4, "C": 1}, joback_result={"-CH3": 4, ">C<": 1}, @@ -34,18 +30,14 @@ "C1CCCCC1", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 6}, psrk_result={"CH2": 6}, - joback_result={"-CH2-": 6}, + joback_result={"ring-CH2-": 6}, ), Case( # 2-methylpropane "CC(C)C", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 3, "CH": 1}, psrk_result={"CH3": 3, "CH": 1}, joback_result={"-CH3": 3, ">CH-": 1}, @@ -54,8 +46,6 @@ "CCCCCC", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 4}, psrk_result={"CH3": 2, "CH2": 4}, joback_result={"-CH3": 2, "-CH2-": 4}, @@ -64,128 +54,102 @@ "C1CC2CCCC3CCCC1C23", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 8, "CH": 4}, psrk_result={"CH2": 8, "CH": 4}, - joback_result={"-CH2-": 8, ">CH-": 4}, + joback_result={"ring-CH2-": 8, "ring>CH-": 4}, ), Case( "C1C2CCCCC2C2CCCCC12", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 9, "CH": 4}, psrk_result={"CH2": 9, "CH": 4}, - joback_result={"-CH2-": 9, ">CH-": 4}, + joback_result={"ring-CH2-": 9, "ring>CH-": 4}, ), Case( "C1C2CC1CCCC2", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 6, "CH": 2}, psrk_result={"CH2": 6, "CH": 2}, - joback_result={"-CH2-": 6, ">CH-": 2}, + joback_result={"ring-CH2-": 6, "ring>CH-": 2}, ), Case( "C1CCCCCCCC1", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 9}, psrk_result={"CH2": 9}, - joback_result={"-CH2-": 9}, + joback_result={"ring-CH2-": 9}, ), Case( "C1C2CC3CC1CC(C2)C3", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 6, "CH": 4}, psrk_result={"CH2": 6, "CH": 4}, - joback_result={"-CH2-": 6, ">CH-": 4}, + joback_result={"ring-CH2-": 6, "ring>CH-": 4}, ), Case( "C12C3C1C1C2C31", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH": 6}, psrk_result={"CH": 6}, - joback_result={">CH-": 6}, + joback_result={"ring>CH-": 6}, ), Case( "C1CC2CC1CCC2", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 6, "CH": 2}, psrk_result={"CH2": 6, "CH": 2}, - joback_result={"-CH2-": 6, ">CH-": 2}, + joback_result={"ring-CH2-": 6, "ring>CH-": 2}, ), Case( "C1CC2CC3CCC2CC13", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 6, "CH": 4}, psrk_result={"CH2": 6, "CH": 4}, - joback_result={"-CH2-": 6, ">CH-": 4}, + joback_result={"ring-CH2-": 6, "ring>CH-": 4}, ), Case( "C12C3C4C1C1C2C3C41", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH": 8}, psrk_result={"CH": 8}, - joback_result={">CH-": 8}, + joback_result={"ring>CH-": 8}, ), Case( "C1CC1", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 3}, psrk_result={"CH2": 3}, - joback_result={"-CH2-": 3}, + joback_result={"ring-CH2-": 3}, ), Case( "C1CCC1", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 4}, psrk_result={"CH2": 4}, - joback_result={"-CH2-": 4}, + joback_result={"ring-CH2-": 4}, ), Case( "CC12C3CCC4CCC1C234", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 4, "CH": 3, "C": 2}, psrk_result={"CH3": 1, "CH2": 4, "CH": 3, "C": 2}, - joback_result={"-CH3": 1, "-CH2-": 4, ">CH-": 3, ">C<": 2}, + joback_result={"-CH3": 1, "ring-CH2-": 4, "ring>CH-": 3, "ring>C<": 2}, ), Case( "CCC(CC)C(C)(C)C", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 5, "CH2": 2, "CH": 1, "C": 1}, psrk_result={"CH3": 5, "CH2": 2, "CH": 1, "C": 1}, joback_result={"-CH3": 5, "-CH2-": 2, ">CH-": 1, ">C<": 1}, @@ -194,20 +158,16 @@ "C1CCC2CCCCC2C1", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 8, "CH": 2}, psrk_result={"CH2": 8, "CH": 2}, - joback_result={"-CH2-": 8, ">CH-": 2}, + joback_result={"ring-CH2-": 8, "ring>CH-": 2}, ), Case( "C1CCC(CC1)CC2CCCCC2", "smiles", "hydrocarbons", - r=None, - q=None, unifac_result={"CH2": 11, "CH": 2}, psrk_result={"CH2": 11, "CH": 2}, - joback_result={"-CH2-": 11, ">CH-": 2}, + joback_result={"-CH2-": 1, "ring-CH2-": 10, "ring>CH-": 2}, ), ] diff --git a/tests/cases/ketones.py b/tests/cases/ketones.py index 98b5401..8491fb3 100644 --- a/tests/cases/ketones.py +++ b/tests/cases/ketones.py @@ -13,8 +13,6 @@ "smiles", "ketones", "2,2-Dimethyl-1,3-propanediol diacetate", - r=None, - q=None, unifac_result={"CH3": 3, "CH": 2, "CH2COO": 1, "CH2CO": 1, "OH": 1}, psrk_result={"CH3": 3, "CH": 2, "CH2COO": 1, "CH2CO": 1, "OH": 1}, joback_result={ @@ -30,8 +28,6 @@ "O=C(CC1=CC=CC=C1)CC1=CC=CC=C1", "smiles", "ketones", - r=None, - q=None, unifac_result={"ACH": 10, "AC": 1, "ACCH2": 1, "CH2CO": 1}, psrk_result={"ACH": 10, "AC": 1, "ACCH2": 1, "CH2CO": 1}, joback_result={ @@ -45,8 +41,6 @@ "CC(=O)CC1=CC=CC=C1", "smiles", "ketones", - r=None, - q=None, unifac_result={"CH3CO": 1, "ACH": 5, "ACCH2": 1}, psrk_result={"CH3CO": 1, "ACH": 5, "ACCH2": 1}, joback_result={ @@ -61,8 +55,6 @@ "CC(C)(C)C(=O)CC1=CC=CC=C1", "smiles", "ketones", - r=None, - q=None, unifac_result={"CH3": 3, "ACH": 5, "AC": 1, "CH2CO": 1, "C": 1}, psrk_result={"CH3": 3, "ACH": 5, "AC": 1, "CH2CO": 1, "C": 1}, joback_result={ @@ -79,8 +71,6 @@ "smiles", "ketones", commentary="Cyclopropanone", - r=None, - q=None, unifac_result={"CH2": 1, "CH2CO": 1}, psrk_result={"CH2": 1, "CH2CO": 1}, joback_result={"ring-CH2-": 2, ">C=O (ring)": 1}, @@ -90,8 +80,6 @@ "smiles", "ketones", commentary="(9Z)-Cycloheptadec-9-en-1-one", - r=None, - q=None, unifac_result={"CH2": 13, "CH=CH": 1, "CH2CO": 1}, psrk_result={"CH2": 13, "CH=CH": 1, "CH2CO": 1}, joback_result={"ring-CH2-": 14, "ring=CH-": 2, ">C=O (ring)": 1}, @@ -101,8 +89,6 @@ "smiles", "ketones", commentary="1-(4-tert-butyl-2,6-dimethylphenyl)ethanone", - r=None, - q=None, unifac_result={ "ACH": 2, "AC": 2, @@ -132,8 +118,6 @@ "smiles", "ketones", commentary="Acetophenone", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "CH3CO": 1}, psrk_result={"ACH": 5, "AC": 1, "CH3CO": 1}, joback_result={ @@ -148,8 +132,6 @@ "smiles", "ketones", commentary="acetone", - r=None, - q=None, unifac_result={"CH3CO": 1, "CH3": 1}, psrk_result={"CH3CO": 1, "CH3": 1}, joback_result={"-CH3": 2, ">C=O (non-ring)": 1}, @@ -159,8 +141,6 @@ "smiles", "ketones", commentary="3-pentanone", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH2CO": 1}, psrk_result={"CH3": 2, "CH2": 1, "CH2CO": 1}, joback_result={"-CH3": 2, "-CH2-": 2, ">C=O (non-ring)": 1}, @@ -170,13 +150,14 @@ "smiles", "ketones", commentary="2-butanone", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH2": 1, "CH3CO": 1}, {"CH3": 2, "CH2CO": 1}, ], - psrk_result={"CH3": 1, "CH2": 1, "CH3CO": 1}, + psrk_result=[ + {"CH3": 1, "CH2": 1, "CH3CO": 1}, + {"CH3": 2, "CH2CO": 1}, + ], joback_result={"-CH3": 2, "-CH2-": 1, ">C=O (non-ring)": 1}, ), ] diff --git a/tests/cases/nitrogen.py b/tests/cases/nitrogen.py index ec5b9d8..ced7c73 100644 --- a/tests/cases/nitrogen.py +++ b/tests/cases/nitrogen.py @@ -12,8 +12,6 @@ identifier="CC1(CC(CC(C1)(C)CN=C=O)N=C=O)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CH2": 4, "CH": 1, "C": 2, "NCO": 2}, psrk_result={}, joback_result={ @@ -31,8 +29,6 @@ identifier="CC(=O)N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "AMH2": 1}, psrk_result={"CH3": 1, "AMH2": 1}, joback_result={"-CH3": 1, ">C=O (non-ring)": 1, "-NH2": 1}, @@ -41,8 +37,6 @@ identifier="CC(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "AMHCH3": 1}, psrk_result={"CH3": 1, "AMHCH3": 1}, joback_result={"-CH3": 2, ">C=O (non-ring)": 1, ">NH (non-ring)": 1}, @@ -51,8 +45,6 @@ identifier="CCNC(=O)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "AMHCH2": 1}, psrk_result={"CH3": 2, "AMHCH2": 1}, joback_result={ @@ -66,8 +58,6 @@ identifier="CC(=O)N(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "AM(CH3)2": 1}, psrk_result={"CH3": 1, "AM(CH3)2": 1}, joback_result={"-CH3": 3, ">C=O (non-ring)": 1, ">N- (non-ring)": 1}, @@ -76,8 +66,6 @@ identifier="CCN(C)C(=O)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "AMCH3CH2": 1}, psrk_result={"CH3": 2, "AMCH3CH2": 1}, joback_result={ @@ -91,8 +79,6 @@ identifier="CCN(CC)C(=O)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "AM(CH2)2": 1}, psrk_result={"CH3": 3, "AM(CH2)2": 1}, joback_result={ @@ -106,8 +92,6 @@ identifier="CCN(C(C)C)C(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -123,8 +107,6 @@ identifier="CC(C)NC(=O)N(C)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -139,8 +121,6 @@ identifier="CCN(CC)C(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 4, "CHNH": 1, "AM(CH2)2": 1}, psrk_result={"CH3": 4, "CHNH": 1, "AM(CH2)2": 1}, joback_result={ @@ -156,8 +136,6 @@ identifier="CCN(C)C(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CHNH": 1, "AMCH3CH2": 1}, psrk_result={"CH3": 3, "CHNH": 1, "AMCH3CH2": 1}, joback_result={ @@ -173,8 +151,6 @@ identifier="CC(C)NC(=O)N(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CHNH": 1, "AM(CH3)2": 1}, psrk_result={"CH3": 2, "CHNH": 1, "AM(CH3)2": 1}, joback_result={ @@ -189,8 +165,6 @@ identifier="CCNC(=O)N(CC)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 4, "CH": 1, "CH2N": 1, "AMHCH2": 1}, psrk_result={"CH3": 4, "CH": 1, "CH2N": 1, "AMHCH2": 1}, joback_result={ @@ -206,8 +180,6 @@ identifier="CCNC(=O)N(C)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CH": 1, "CH3N": 1, "AMHCH2": 1}, psrk_result={"CH3": 3, "CH": 1, "CH3N": 1, "AMHCH2": 1}, joback_result={ @@ -223,8 +195,6 @@ identifier="CCNC(=O)N(CC)CC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CH2NH": 1, "AM(CH2)2": 1}, psrk_result={"CH3": 3, "CH2NH": 1, "AM(CH2)2": 1}, joback_result={ @@ -239,8 +209,6 @@ identifier="CCNC(=O)N(C)CC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH2NH": 1, "AMCH3CH2": 1}, psrk_result={"CH3": 2, "CH2NH": 1, "AMCH3CH2": 1}, joback_result={ @@ -255,8 +223,6 @@ identifier="CCNC(=O)N(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH2NH": 1, "AM(CH3)2": 1, "CH3": 1}, psrk_result={"CH2NH": 1, "AM(CH3)2": 1, "CH3": 1}, joback_result={ @@ -271,8 +237,6 @@ identifier="CCN(C(C)C)C(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CH": 1, "CH2N": 1, "AMHCH3": 1}, psrk_result={"CH3": 3, "CH": 1, "CH2N": 1, "AMHCH3": 1}, joback_result={ @@ -288,8 +252,6 @@ identifier="CNC(=O)N(C)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH": 1, "CH3N": 1, "AMHCH3": 1}, psrk_result={"CH3": 2, "CH": 1, "CH3N": 1, "AMHCH3": 1}, joback_result={ @@ -304,8 +266,6 @@ identifier="CCN(CC)C(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH3NH": 1, "AM(CH2)2": 1}, psrk_result={"CH3": 2, "CH3NH": 1, "AM(CH2)2": 1}, joback_result={ @@ -320,8 +280,6 @@ identifier="CCN(C)C(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH3NH": 1, "AMCH3CH2": 1}, psrk_result={"CH3": 1, "CH3NH": 1, "AMCH3CH2": 1}, joback_result={ @@ -336,8 +294,6 @@ identifier="CNC(=O)N(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3NH": 1, "AM(CH3)2": 1}, psrk_result={"CH3NH": 1, "AM(CH3)2": 1}, joback_result={ @@ -351,8 +307,6 @@ identifier="CC(C)NC(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -366,8 +320,6 @@ identifier="CCNC(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CHNH": 1, "AMHCH2": 1}, psrk_result={"CH3": 3, "CHNH": 1, "AMHCH2": 1}, joback_result={ @@ -382,8 +334,6 @@ identifier="CCNC(=O)NCC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH2NH": 1, "AMHCH2": 1}, psrk_result={"CH3": 2, "CH2NH": 1, "AMHCH2": 1}, joback_result={ @@ -397,8 +347,6 @@ identifier="CNC(=O)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CHNH": 1, "AMHCH3": 1}, psrk_result={"CH3": 2, "CHNH": 1, "AMHCH3": 1}, joback_result={ @@ -412,13 +360,14 @@ identifier="CCNC(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH2NH": 1, "AMHCH3": 1, "CH3": 1}, {"CH3": 1, "CH3NH": 1, "AMHCH2": 1}, ], - psrk_result={"CH2NH": 1, "AMHCH3": 1, "CH3": 1}, + psrk_result=[ + {"CH2NH": 1, "AMHCH3": 1, "CH3": 1}, + {"CH3": 1, "CH3NH": 1, "AMHCH2": 1}, + ], joback_result={ "-CH3": 2, "-CH2-": 1, @@ -430,8 +379,6 @@ identifier="CNC(=O)NC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3NH": 1, "AMHCH3": 1}, psrk_result={"CH3NH": 1, "AMHCH3": 1}, joback_result={"-CH3": 2, ">C=O (non-ring)": 1, ">NH (non-ring)": 2}, @@ -440,8 +387,6 @@ identifier="CN", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3NH2": 1}, psrk_result={"CH3NH2": 1}, joback_result={"-CH3": 1, "-NH2": 1}, @@ -450,8 +395,6 @@ identifier="CC(C)N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CHNH2": 1}, psrk_result={"CH3": 2, "CHNH2": 1}, joback_result={"-CH3": 2, ">CH-": 1, "-NH2": 1}, @@ -460,8 +403,6 @@ identifier="CCCN", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "CH2NH2": 1}, psrk_result={"CH3": 1, "CH2": 1, "CH2NH2": 1}, joback_result={"-CH3": 1, "-CH2-": 2, "-NH2": 1}, @@ -470,8 +411,6 @@ identifier="COC1=C(OC)C2=C3C(CC22CCC(=O)C=C2)NCCC3=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={ "CH2": 2, "C": 1, @@ -512,8 +451,6 @@ identifier="C1C2=C(C=CN1)C3=CC=CC=C3N2", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -527,8 +464,6 @@ identifier="CC(C)N(CN)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -543,8 +478,6 @@ identifier="CC(C)N(C)CN", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH": 1, "CH2NH2": 1, "CH3N": 1}, psrk_result={"CH3": 2, "CH": 1, "CH2NH2": 1, "CH3N": 1}, joback_result={ @@ -559,8 +492,6 @@ identifier="CC(C)NC(C)NC(C)(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 6, "C": 1, "CHNH": 2}, psrk_result={"CH3": 6, "C": 1, "CHNH": 2}, joback_result={"-CH3": 6, ">CH-": 2, ">C<": 1, ">NH (non-ring)": 2}, @@ -569,8 +500,6 @@ identifier="CC(C)NC(C)N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CHNH2": 1, "CHNH": 1}, psrk_result={"CH3": 3, "CHNH2": 1, "CHNH": 1}, joback_result={"-CH3": 3, ">CH-": 2, "-NH2": 1, ">NH (non-ring)": 1}, @@ -579,8 +508,6 @@ identifier="CCC(C)(C)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 5, "CH2": 1, "C": 1, "CHNH": 1}, psrk_result={"CH3": 5, "CH2": 1, "C": 1, "CHNH": 1}, joback_result={ @@ -595,48 +522,50 @@ identifier="CCNC(C)CC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH2": 2, "CHNH": 1}, {"CH3": 3, "CH2": 1, "CH": 1, "CH2NH": 1}, ], - psrk_result={"CH3": 3, "CH2": 1, "CH": 1, "CH2NH": 1}, + psrk_result=[ + {"CH3": 3, "CH2": 2, "CHNH": 1}, + {"CH3": 3, "CH2": 1, "CH": 1, "CH2NH": 1}, + ], joback_result={"-CH3": 3, "-CH2-": 2, ">CH-": 1, ">NH (non-ring)": 1}, ), Case( identifier="CCCNC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2": 1, "CH2NH": 1}, {"CH3": 1, "CH2": 2, "CH3NH": 1}, ], - psrk_result={"CH3": 1, "CH2": 2, "CH3NH": 1}, + psrk_result=[ + {"CH3": 2, "CH2": 1, "CH2NH": 1}, + {"CH3": 1, "CH2": 2, "CH3NH": 1}, + ], joback_result={"-CH3": 2, "-CH2-": 2, ">NH (non-ring)": 1}, ), Case( identifier="CN1CCCC1CC(=O)CC1CCCN1C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH2": 6, "CH": 2, "CH2CO": 1, "CH3N": 1, "CH2N": 1}, {"CH2": 7, "CH": 2, "CH2CO": 1, "CH3N": 2}, {"CH3": 2, "CH2": 5, "CH": 2, "CH2CO": 1, "CH2N": 2}, ], - psrk_result={"CH2": 7, "CH": 2, "CH2CO": 1, "CH3N": 2}, + psrk_result=[ + {"CH3": 1, "CH2": 6, "CH": 2, "CH2CO": 1, "CH3N": 1, "CH2N": 1}, + {"CH2": 7, "CH": 2, "CH2CO": 1, "CH3N": 2}, + {"CH3": 2, "CH2": 5, "CH": 2, "CH2CO": 1, "CH2N": 2}, + ], joback_result={}, ), Case( identifier="CNC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH3NH": 1}, psrk_result={"CH3": 1, "CH3NH": 1}, joback_result={"-CH3": 2, ">NH (non-ring)": 1}, @@ -645,8 +574,6 @@ identifier="CCNCC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH2NH": 1}, psrk_result={"CH3": 2, "CH2": 1, "CH2NH": 1}, joback_result={"-CH3": 2, "-CH2-": 2, ">NH (non-ring)": 1}, @@ -655,8 +582,6 @@ identifier="CC(C)NC(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 4, "CH": 1, "CHNH": 1}, psrk_result={"CH3": 4, "CH": 1, "CHNH": 1}, joback_result={"-CH3": 4, ">CH-": 2, ">NH (non-ring)": 1}, @@ -665,8 +590,6 @@ identifier="CC(C)NCN", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH2NH2": 1, "CHNH": 1}, psrk_result={"CH3": 2, "CH2NH2": 1, "CHNH": 1}, joback_result={ @@ -681,8 +604,6 @@ identifier="C1CN2CCC1CC2", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH2": 5, "CH": 1, "CH2N": 1}, psrk_result={"CH2": 5, "CH": 1, "CH2N": 1}, joback_result={}, @@ -691,8 +612,6 @@ identifier="CCN(CC(=O)CC)C1=CC=CC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={ "CH3": 2, "CH2": 1, @@ -722,8 +641,6 @@ identifier="CCN(C(C)C)C(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 5, "CH": 2, "CH2N": 1}, psrk_result={"CH3": 5, "CH": 2, "CH2N": 1}, joback_result={"-CH3": 5, "-CH2-": 1, ">CH-": 2, ">N- (non-ring)": 1}, @@ -732,21 +649,20 @@ identifier="CCN(C)CC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2": 2, "CH3N": 1}, {"CH3": 3, "CH2": 1, "CH2N": 1}, ], - psrk_result={"CH3": 2, "CH2": 2, "CH3N": 1}, + psrk_result=[ + {"CH3": 2, "CH2": 2, "CH3N": 1}, + {"CH3": 3, "CH2": 1, "CH2N": 1}, + ], joback_result={"-CH3": 3, "-CH2-": 2, ">N- (non-ring)": 1}, ), Case( identifier="CN(C)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CH3N": 1}, psrk_result={"CH3": 2, "CH3N": 1}, joback_result={"-CH3": 3, ">N- (non-ring)": 1}, @@ -755,8 +671,6 @@ identifier="CCN(CC)CC", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 3, "CH2": 2, "CH2N": 1}, psrk_result={"CH3": 3, "CH2": 2, "CH2N": 1}, joback_result={"-CH3": 3, "-CH2-": 3, ">N- (non-ring)": 1}, @@ -765,8 +679,6 @@ identifier="C1=CC=C(C=C1)N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"ACH": 5, "ACNH2": 1}, psrk_result={"ACH": 5, "ACNH2": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-NH2": 1}, @@ -775,8 +687,6 @@ identifier="C1=CC2=C(C=C1)C1=C(C=NC=C1)C1=C2C=CC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"ACH": 8, "AC": 4, "C5H3N": 1}, psrk_result={"ACH": 8, "AC": 4, "C5H3N": 1}, joback_result={"ring=CH-": 11, "ring=C<": 6, "-N= (ring)": 1}, @@ -785,8 +695,6 @@ identifier="CC1=CC(C)=CN=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "C5H3N": 1}, psrk_result={"CH3": 2, "C5H3N": 1}, joback_result={ @@ -800,8 +708,6 @@ identifier="O=C1CCC2=C(O1)C=CN=C2", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH2COO": 1, "C5H3N": 1, "CH2": 1}, psrk_result={"CH2COO": 1, "C5H3N": 1, "CH2": 1}, joback_result={ @@ -816,8 +722,6 @@ identifier="CCCC1=CC=C(CC2=CC=NC=C2)C=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "ACH": 4, "ACCH2": 2, "C5H4N": 1, "CH2": 1}, psrk_result={"CH3": 1, "ACH": 4, "ACCH2": 2, "C5H4N": 1, "CH2": 1}, joback_result={ @@ -832,21 +736,20 @@ identifier="CN1CCCC1C2=CN=CC=C2", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result=[ {"CH2": 3, "CH3N": 1, "C5H4N": 1, "CH": 1}, {"CH3": 1, "CH2": 2, "CH": 1, "CH2N": 1, "C5H4N": 1}, ], - psrk_result={"CH2": 3, "CH3N": 1, "C5H4N": 1, "CH": 1}, + psrk_result=[ + {"CH2": 3, "CH3N": 1, "C5H4N": 1, "CH": 1}, + {"CH3": 1, "CH2": 2, "CH": 1, "CH2N": 1, "C5H4N": 1}, + ], joback_result={}, ), Case( identifier="CC1=CC(C)=C(C)C=N1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -860,8 +763,6 @@ identifier="C1=CC=C(C=C1)C1=CC=NC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"ACH": 5, "AC": 1, "C5H4N": 1}, psrk_result={"ACH": 5, "AC": 1, "C5H4N": 1}, joback_result={"ring=CH-": 9, "ring=C<": 2, "-N= (ring)": 1}, @@ -870,8 +771,6 @@ identifier="CC(=C)C1=CC=NC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH2=C": 1, "C5H4N": 1}, psrk_result={"CH3": 1, "CH2=C": 1, "C5H4N": 1}, joback_result={ @@ -887,8 +786,6 @@ identifier="CC1=NC=CC(O)=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"C5H3N": 1, "CH3": 1, "OH": 1}, psrk_result={"C5H3N": 1, "CH3": 1, "OH": 1}, joback_result={ @@ -903,8 +800,6 @@ identifier="C1=CC=NC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"C5H5N": 1}, psrk_result={"C5H5N": 1}, joback_result={"ring=CH-": 5, "-N= (ring)": 1}, @@ -913,8 +808,6 @@ identifier="CC1=CN=CC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"C5H4N": 1, "CH3": 1}, psrk_result={"C5H4N": 1, "CH3": 1}, joback_result={ @@ -928,8 +821,6 @@ identifier="CC1=C(N=CC=C1)C", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"C5H3N": 1, "CH3": 2}, psrk_result={"C5H3N": 1, "CH3": 2}, joback_result={ @@ -943,8 +834,6 @@ identifier="CC#N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3CN": 1}, psrk_result={"CH3CN": 1}, joback_result={"-CH3": 1, "-CN": 1}, @@ -953,8 +842,6 @@ identifier="CCC#N", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH2CN": 1}, psrk_result={"CH3": 1, "CH2CN": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "-CN": 1}, @@ -963,8 +850,6 @@ identifier="CCCC1=CC=C(C[N+]([O-])=O)C=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={ "CH3": 1, "ACH": 4, @@ -993,8 +878,6 @@ identifier="[O-][N+](=O)CC1=CC=CC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"ACH": 5, "CH2NO2": 1, "AC": 1}, psrk_result={"ACH": 5, "CH2NO2": 1, "AC": 1}, joback_result={"-CH2-": 1, "ring=CH-": 5, "ring=C<": 1, "-NO2": 1}, @@ -1003,8 +886,6 @@ identifier="C[N+](=O)[O-]", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3NO2": 1}, psrk_result={"CH3NO2": 1}, joback_result={"-CH3": 1, "-NO2": 1}, @@ -1013,8 +894,6 @@ identifier="CCC[N+](=O)[O-]", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 1, "CH2NO2": 1}, psrk_result={"CH3": 1, "CH2": 1, "CH2NO2": 1}, joback_result={"-CH3": 1, "-CH2-": 2, "-NO2": 1}, @@ -1023,8 +902,6 @@ identifier="CC(C)[N+](=O)[O-]", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"CH3": 2, "CHNO2": 1}, psrk_result={"CH3": 2, "CHNO2": 1}, joback_result={"-CH3": 2, ">CH-": 1, "-NO2": 1}, @@ -1033,8 +910,6 @@ identifier="C1=CC=C(C=C1)[N+](=O)[O-]", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={"ACH": 5, "ACNO2": 1}, psrk_result={"ACH": 5, "ACNO2": 1}, joback_result={"ring=CH-": 5, "ring=C<": 1, "-NO2": 1}, @@ -1043,8 +918,6 @@ identifier="[O-][N+](=O)C1=CC=NC=C1", identifier_type="smiles", cases_module="nitrogen", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ diff --git a/tests/cases/particulars.py b/tests/cases/particulars.py index e9e8076..5a14fe7 100644 --- a/tests/cases/particulars.py +++ b/tests/cases/particulars.py @@ -13,8 +13,6 @@ "smiles", "particulars", "Water", - r=None, - q=None, unifac_result={"H2O": 1}, psrk_result={"H2O": 1}, joback_result={}, @@ -23,8 +21,6 @@ identifier="C1=COC(=C1)C=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"FURFURAL": 1}, psrk_result={"FURFURAL": 1}, joback_result={ @@ -38,8 +34,6 @@ identifier="CS(=O)C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"DMSO": 1}, psrk_result={"DMSO": 1}, joback_result={}, @@ -48,8 +42,6 @@ identifier="C=CC#N", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"ACRY": 1}, psrk_result={"ACRY": 1}, joback_result={"=CH2": 1, "=CH-": 1, "-CN": 1}, @@ -58,48 +50,58 @@ identifier="BrCN(CC1=CC=NC=C1)C=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C5H4N": 1, "BR": 1, "HCON(CH2)2": 1}, psrk_result={"C5H4N": 1, "BR": 1, "HCON(CH2)2": 1}, - joback_result={}, + joback_result={ + "-CH2-": 2, + "ring=CH-": 4, + "ring=C<": 1, + "-Br": 1, + "O=CH- (aldehyde)": 1, + ">N- (non-ring)": 1, + "-N= (ring)": 1, + }, ), Case( identifier="BrCN(CC1=CC=CC=C1)C=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"ACH": 5, "BR": 1, "HCON(CH2)2": 1, "AC": 1}, psrk_result={"ACH": 5, "BR": 1, "HCON(CH2)2": 1, "AC": 1}, - joback_result={}, + joback_result={ + "-CH2-": 2, + "ring=CH-": 5, + "ring=C<": 1, + "-Br": 1, + "O=CH- (aldehyde)": 1, + ">N- (non-ring)": 1, + }, ), Case( identifier="CN(C)C=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"DMF": 1}, psrk_result={"DMF": 1}, - joback_result={}, + joback_result={"-CH3": 2, "O=CH- (aldehyde)": 1, ">N- (non-ring)": 1}, ), Case( identifier="CCN(CC)C=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"CH3": 2, "HCON(CH2)2": 1}, psrk_result={"CH3": 2, "HCON(CH2)2": 1}, - joback_result={}, + joback_result={ + "-CH3": 2, + "-CH2-": 2, + "O=CH- (aldehyde)": 1, + ">N- (non-ring)": 1, + }, ), Case( identifier="CN1CCCC1=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"NMP": 1}, psrk_result={"NMP": 1}, joback_result={}, @@ -108,8 +110,6 @@ identifier="C1COCCN1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"MORPH": 1}, psrk_result={"MORPH": 1}, joback_result={"ring-CH2-": 4, "-O- (ring)": 1, ">NH (ring)": 1}, @@ -118,8 +118,6 @@ identifier="OC1=CSC=C1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H3S": 1, "OH": 1}, psrk_result={"C4H3S": 1, "OH": 1}, joback_result={ @@ -133,8 +131,6 @@ identifier="CC1=C(SC=C1)C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H2S": 1, "CH3": 2}, psrk_result={"C4H2S": 1, "CH3": 2}, joback_result={ @@ -148,8 +144,6 @@ identifier="C1=CSC=C1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H4S": 1}, psrk_result={"C4H4S": 1}, joback_result={"ring=CH-": 4, "-S- (ring)": 1}, @@ -158,8 +152,6 @@ identifier="CC1=CC=CS1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H3S": 1, "CH3": 1}, psrk_result={"C4H3S": 1, "CH3": 1}, joback_result={ @@ -173,8 +165,6 @@ identifier="OC1=CC=CS1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H3S": 1, "OH": 1}, psrk_result={"C4H3S": 1, "OH": 1}, joback_result={ @@ -188,8 +178,6 @@ identifier="OC1=CSC=C1O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H2S": 1, "OH": 2}, psrk_result={"C4H2S": 1, "OH": 2}, joback_result={ @@ -203,8 +191,6 @@ identifier="OC1=CC(O)=CS1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H2S": 1, "OH": 2}, psrk_result={"C4H2S": 1, "OH": 2}, joback_result={ @@ -218,8 +204,6 @@ identifier="OC1=CC=C(O)S1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"C4H2S": 1, "OH": 2}, psrk_result={"C4H2S": 1, "OH": 2}, joback_result={ @@ -233,8 +217,6 @@ identifier="N1C=CN=C1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"IMIDAZOL": 1}, psrk_result={}, joback_result={"ring=CH-": 3, ">NH (ring)": 1, "-N= (ring)": 1}, @@ -243,8 +225,6 @@ identifier="FC(F)(F)S(=O)(=O)[N-]S(=O)(=O)C(F)(F)F", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"BTI": 1}, psrk_result={}, joback_result={}, @@ -253,8 +233,6 @@ identifier="hydrogen peroxide", identifier_type="name", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={}, @@ -263,8 +241,6 @@ identifier="methane", identifier_type="name", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CH4": 1}, joback_result={}, @@ -273,8 +249,6 @@ identifier="C1(=CC=CC=C1)OC(C)(C)C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -289,8 +263,6 @@ identifier="[O-][O+]=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"O3": 1}, joback_result={"-O- (non-ring)": 1, "=O (other than above)": 2}, @@ -299,28 +271,22 @@ identifier="C=C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"H2C=CH2": 1}, - joback_result={}, + joback_result={"=CH2": 2}, ), Case( identifier="C#C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CH=-CH": 1}, - joback_result={}, + joback_result={"CH": 2}, ), Case( identifier="N", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"NH3": 1}, joback_result={}, @@ -329,8 +295,6 @@ identifier="[C-]#[O+]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CO": 1}, joback_result={}, @@ -339,8 +303,6 @@ identifier="S", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"H2S": 1}, joback_result={}, @@ -349,8 +311,6 @@ identifier="N#N", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"N2": 1}, joback_result={}, @@ -359,8 +319,6 @@ identifier="[Ar]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"AR": 1}, joback_result={}, @@ -369,8 +327,6 @@ identifier="C(=O)=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CO2": 1}, joback_result={"=C=": 1, "=O (other than above)": 2}, @@ -379,8 +335,6 @@ identifier="C", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CH4": 1}, joback_result={}, @@ -389,8 +343,6 @@ identifier="O=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"O2": 1}, joback_result={"=O (other than above)": 2}, @@ -399,8 +351,6 @@ identifier="O=S=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"SO2": 1}, joback_result={"=O (other than above)": 2, "-S- (non-ring)": 1}, @@ -409,8 +359,6 @@ identifier="[N]=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"NO": 1}, joback_result={}, @@ -419,8 +367,6 @@ identifier="[N-]=[N+]=O", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"N2O": 1}, joback_result={}, @@ -429,8 +375,6 @@ identifier="FS(F)(F)(F)(F)F", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"SF6": 1}, joback_result={}, @@ -439,8 +383,6 @@ identifier="[He]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HE": 1}, joback_result={}, @@ -449,8 +391,6 @@ identifier="[Ne]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"NE": 1}, joback_result={}, @@ -459,8 +399,6 @@ identifier="[Kr]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"KR": 1}, joback_result={}, @@ -469,8 +407,6 @@ identifier="[Xe]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"XE": 1}, joback_result={}, @@ -479,8 +415,6 @@ identifier="F", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HF": 1}, joback_result={}, @@ -489,8 +423,6 @@ identifier="Cl", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HCL": 1}, joback_result={}, @@ -499,8 +431,6 @@ identifier="Br", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HBR": 1}, joback_result={}, @@ -509,8 +439,6 @@ identifier="I", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HI": 1}, joback_result={}, @@ -519,8 +447,6 @@ identifier="C(=O)=S", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"COS": 1}, joback_result={}, @@ -529,8 +455,6 @@ identifier="C1CO1", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={"CH2": 1, "CH2O": 1}, psrk_result={"H2COCH2": 1}, joback_result={"ring-CH2-": 2, "-O- (ring)": 1}, @@ -539,8 +463,6 @@ identifier="FF", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"F2": 1}, joback_result={"-F": 2}, @@ -549,8 +471,6 @@ identifier="ClCl", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CL2": 1}, joback_result={"-Cl": 2}, @@ -559,8 +479,6 @@ identifier="BrBr", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"BR2": 1}, joback_result={"-Br": 2}, @@ -569,8 +487,6 @@ identifier="C#N", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"HCN": 1}, joback_result={}, @@ -579,18 +495,14 @@ identifier="N(=O)[O]", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"NO2": 1}, - joback_result={}, + joback_result={"=O (other than above)": 2, "-N= (non-ring)": 1}, ), Case( identifier="C(F)(F)(F)F", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CF4": 1}, joback_result={">C<": 1, "-F": 4}, @@ -599,8 +511,6 @@ identifier="N(=O)Cl", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CLNO": 1}, joback_result={ @@ -613,8 +523,6 @@ identifier="CC(C)(C)N", identifier_type="smiles", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={"CH3": 3, "CNH2": 1}, joback_result={"-CH3": 3, ">C<": 1, "-NH2": 1}, @@ -623,8 +531,6 @@ identifier="hydrogen", identifier_type="name", cases_module="particulars", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={}, diff --git a/tests/cases/silicon.py b/tests/cases/silicon.py index 0a2c730..b1bd5fd 100644 --- a/tests/cases/silicon.py +++ b/tests/cases/silicon.py @@ -9,8 +9,6 @@ identifier="C[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "SIH3": 1}, psrk_result={"CH3": 1, "SIH3": 1}, joback_result={}, @@ -19,8 +17,6 @@ identifier="CC[Si](CC)([H])[H]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 2, "SIH2": 1}, psrk_result={"CH3": 2, "CH2": 2, "SIH2": 1}, joback_result={}, @@ -29,21 +25,20 @@ identifier="C[Si](O[Si](C)(C)C)(O[Si](C)(C)C)[H]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, {"CH3": 7, "SIH": 1, "SIO": 2}, ], - psrk_result={"CH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, + psrk_result=[ + {"CH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, + {"CH3": 7, "SIH": 1, "SIO": 2}, + ], joback_result={}, ), Case( identifier="C[Si](C)(C)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 6, "SI": 1, "SIO": 1}, psrk_result={"CH3": 6, "SI": 1, "SIO": 1}, joback_result={}, @@ -52,47 +47,48 @@ identifier="C[SiH2]O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "SIH2": 1, "SIHO": 1}, {"CH3": 3, "SIH": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 3, "SIH": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 3, "SIH2": 1, "SIHO": 1}, + {"CH3": 3, "SIH": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="C[SiH2]O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 4, "SIH2": 1, "SIO": 1}, {"CH3": 4, "SI": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 4, "SI": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 4, "SIH2": 1, "SIO": 1}, + {"CH3": 4, "SI": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="C[SiH](C)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 5, "SIH": 1, "SIO": 1}, {"CH3": 5, "SI": 1, "SIHO": 1}, ], - psrk_result={"CH3": 5, "SI": 1, "SIHO": 1}, + psrk_result=[ + {"CH3": 5, "SIH": 1, "SIO": 1}, + {"CH3": 5, "SI": 1, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CC(C)(C)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 6, "C": 1, "SIO": 1}, psrk_result={"CH3": 6, "C": 1, "SIO": 1}, joback_result={}, @@ -101,73 +97,76 @@ identifier="CC(C)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 5, "CH": 1, "SIO": 1}, {"CH3": 5, "CHO": 1, "SI": 1}, ], - psrk_result={"CH3": 5, "CHO": 1, "SI": 1}, + psrk_result=[ + {"CH3": 5, "CH": 1, "SIO": 1}, + {"CH3": 5, "CHO": 1, "SI": 1}, + ], joback_result={}, ), Case( identifier="CC(C)O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 4, "CH": 1, "SIHO": 1}, {"CH3": 4, "CHO": 1, "SIH": 1}, ], - psrk_result={"CH3": 4, "CHO": 1, "SIH": 1}, + psrk_result=[ + {"CH3": 4, "CH": 1, "SIHO": 1}, + {"CH3": 4, "CHO": 1, "SIH": 1}, + ], joback_result={}, ), Case( identifier="C[SiH2]OC(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH": 1, "SIH2O": 1}, {"CH3": 3, "CHO": 1, "SIH2": 1}, ], - psrk_result={"CH3": 3, "CHO": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 3, "CH": 1, "SIH2O": 1}, + {"CH3": 3, "CHO": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="CCO[SiH2]C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2": 1, "SIH2O": 1}, {"CH3": 2, "CH2O": 1, "SIH2": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 2, "CH2": 1, "SIH2O": 1}, + {"CH3": 2, "CH2O": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="CO[SiH2]C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "SIH2O": 1}, {"CH3": 1, "CH3O": 1, "SIH2": 1}, ], - psrk_result={"CH3": 1, "CH3O": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 2, "SIH2O": 1}, + {"CH3": 1, "CH3O": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="C[Si](O[Si](C)([H])[H])([H])[H]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 2, "SIH2": 1, "SIH2O": 1}, psrk_result={"CH3": 2, "SIH2": 1, "SIH2O": 1}, joback_result={}, @@ -176,8 +175,6 @@ identifier="C[Si](C)(O[Si](C)(C)[H])[H]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 4, "SIH": 1, "SIHO": 1}, psrk_result={"CH3": 4, "SIH": 1, "SIHO": 1}, joback_result={}, @@ -186,8 +183,6 @@ identifier="C[Si]1(O[Si](O[Si](O[Si](O1)(C)C)(C)C)(C)C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 8, "SIO": 4}, psrk_result={"CH3": 8, "SIO": 4}, joback_result={}, @@ -196,8 +191,6 @@ identifier="CC(=O)O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3COO": 1, "SIH3": 1}, psrk_result={"CH3COO": 1, "SIH3": 1}, joback_result={}, @@ -206,8 +199,6 @@ identifier="CC(=O)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3COO": 1, "SIH3": 1, "SIH2": 1}, psrk_result={"CH3COO": 1, "SIH3": 1, "SIH2": 1}, joback_result={}, @@ -216,8 +207,6 @@ identifier="CC(=O)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3COO": 1, "SIH3": 2, "SIH": 1}, psrk_result={"CH3COO": 1, "SIH3": 2, "SIH": 1}, joback_result={}, @@ -226,8 +215,6 @@ identifier="CC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3COO": 1, "SIH3": 3, "SI": 1}, psrk_result={"CH3COO": 1, "SIH3": 3, "SI": 1}, joback_result={}, @@ -236,8 +223,6 @@ identifier="CCC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "CH2COO": 1, "SIH3": 3, "SI": 1}, psrk_result={"CH3": 1, "CH2COO": 1, "SIH3": 3, "SI": 1}, joback_result={}, @@ -246,8 +231,6 @@ identifier="CC(C)C(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 2, "CH": 1, "COO": 1, "SIH3": 3, "SI": 1}, psrk_result={"CH3": 2, "CH": 1, "COO": 1, "SIH3": 3, "SI": 1}, joback_result={}, @@ -256,8 +239,6 @@ identifier="[SiH3]OC(=O)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 2, "SIH2O": 1}, psrk_result={"COO": 1, "SIH3": 2, "SIH2O": 1}, joback_result={}, @@ -266,8 +247,6 @@ identifier="[SiH3][SiH2]OC(=O)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 2, "SIH2O": 1, "SIH2": 1}, psrk_result={"COO": 1, "SIH3": 2, "SIH2O": 1, "SIH2": 1}, joback_result={}, @@ -276,34 +255,34 @@ identifier="[SiH3][SiH2]OC(=O)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"COO": 1, "SIH3": 3, "SIH2": 1, "SIHO": 1}, {"COO": 1, "SIH3": 3, "SIH": 1, "SIH2O": 1}, ], - psrk_result={"COO": 1, "SIH3": 3, "SIH2O": 1, "SIH": 1}, + psrk_result=[ + {"COO": 1, "SIH3": 3, "SIH2": 1, "SIHO": 1}, + {"COO": 1, "SIH3": 3, "SIH": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH2]OC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"COO": 1, "SIH3": 4, "SIH2": 1, "SIO": 1}, {"COO": 1, "SIH3": 4, "SI": 1, "SIH2O": 1}, ], - psrk_result={"COO": 1, "SIH3": 4, "SIH2O": 1, "SI": 1}, + psrk_result=[ + {"COO": 1, "SIH3": 4, "SIH2": 1, "SIO": 1}, + {"COO": 1, "SIH3": 4, "SI": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="[SiH3]OC(=O)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 3, "SIHO": 1}, psrk_result={"COO": 1, "SIH3": 3, "SIHO": 1}, joback_result={}, @@ -312,8 +291,6 @@ identifier="[SiH3][SiH]([SiH3])OC(=O)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 4, "SIHO": 1, "SIH": 1}, psrk_result={"COO": 1, "SIH3": 4, "SIHO": 1, "SIH": 1}, joback_result={}, @@ -322,21 +299,20 @@ identifier="[SiH3][SiH]([SiH3])OC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"COO": 1, "SIH3": 5, "SIH": 1, "SIO": 1}, {"COO": 1, "SIH3": 5, "SI": 1, "SIHO": 1}, ], - psrk_result={"COO": 1, "SIH3": 5, "SIHO": 1, "SI": 1}, + psrk_result=[ + {"COO": 1, "SIH3": 5, "SIH": 1, "SIO": 1}, + {"COO": 1, "SIH3": 5, "SI": 1, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="[SiH3]OC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 4, "SIO": 1}, psrk_result={"COO": 1, "SIH3": 4, "SIO": 1}, joback_result={}, @@ -345,8 +321,6 @@ identifier="[SiH3][Si]([SiH3])([SiH3])OC(=O)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"COO": 1, "SIH3": 6, "SIO": 1, "SI": 1}, psrk_result={"COO": 1, "SIH3": 6, "SIO": 1, "SI": 1}, joback_result={}, @@ -355,8 +329,6 @@ identifier="[SiH3]OC=O", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"HCOO": 1, "SIH3": 1}, psrk_result={"HCOO": 1, "SIH3": 1}, joback_result={}, @@ -365,8 +337,6 @@ identifier="[SiH3][SiH2]OC=O", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"HCOO": 1, "SIH3": 1, "SIH2": 1}, psrk_result={"HCOO": 1, "SIH3": 1, "SIH2": 1}, joback_result={}, @@ -375,8 +345,6 @@ identifier="[SiH3][SiH]([SiH3])OC=O", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"HCOO": 1, "SIH3": 2, "SIH": 1}, psrk_result={"HCOO": 1, "SIH3": 2, "SIH": 1}, joback_result={}, @@ -385,8 +353,6 @@ identifier="[SiH3][Si]([SiH3])([SiH3])OC=O", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"HCOO": 1, "SIH3": 3, "SI": 1}, psrk_result={"HCOO": 1, "SIH3": 3, "SI": 1}, joback_result={}, @@ -395,8 +361,6 @@ identifier="COC(=O)O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3O": 1, "COO": 1, "SIH3": 1}, psrk_result={"CH3O": 1, "COO": 1, "SIH3": 1}, joback_result={}, @@ -405,47 +369,48 @@ identifier="COC(=O)O[SiH2]C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "COO": 1, "SIH2O": 1}, {"CH3": 1, "CH3O": 1, "COO": 1, "SIH2": 1}, ], - psrk_result={"CH3": 1, "CH3O": 1, "COO": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 2, "COO": 1, "SIH2O": 1}, + {"CH3": 1, "CH3O": 1, "COO": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="COC(=O)O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "COO": 1, "SIHO": 1}, {"CH3": 2, "CH3O": 1, "COO": 1, "SIH": 1}, ], - psrk_result={"CH3": 2, "CH3O": 1, "COO": 1, "SIH": 1}, + psrk_result=[ + {"CH3": 3, "COO": 1, "SIHO": 1}, + {"CH3": 2, "CH3O": 1, "COO": 1, "SIH": 1}, + ], joback_result={}, ), Case( identifier="COC(=O)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 4, "COO": 1, "SIO": 1}, {"CH3": 3, "CH3O": 1, "COO": 1, "SI": 1}, ], - psrk_result={"CH3": 3, "CH3O": 1, "COO": 1, "SI": 1}, + psrk_result=[ + {"CH3": 4, "COO": 1, "SIO": 1}, + {"CH3": 3, "CH3O": 1, "COO": 1, "SI": 1}, + ], joback_result={}, ), Case( identifier="CCOC(=O)O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "CH2O": 1, "COO": 1, "SIH3": 1}, psrk_result={"CH3": 1, "CH2O": 1, "COO": 1, "SIH3": 1}, joback_result={}, @@ -454,47 +419,48 @@ identifier="CCOC(=O)O[SiH2]C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2": 1, "COO": 1, "SIH2O": 1}, {"CH3": 2, "CH2O": 1, "COO": 1, "SIH2": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "COO": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 2, "CH2": 1, "COO": 1, "SIH2O": 1}, + {"CH3": 2, "CH2O": 1, "COO": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="CCOC(=O)O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH2": 1, "COO": 1, "SIHO": 1}, {"CH3": 3, "CH2O": 1, "COO": 1, "SIH": 1}, ], - psrk_result={"CH3": 3, "CH2O": 1, "COO": 1, "SIH": 1}, + psrk_result=[ + {"CH3": 3, "CH2": 1, "COO": 1, "SIHO": 1}, + {"CH3": 3, "CH2O": 1, "COO": 1, "SIH": 1}, + ], joback_result={}, ), Case( identifier="CCOC(=O)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 4, "CH2": 1, "COO": 1, "SIO": 1}, {"CH3": 4, "CH2O": 1, "COO": 1, "SI": 1}, ], - psrk_result={"CH3": 4, "CH2O": 1, "COO": 1, "SI": 1}, + psrk_result=[ + {"CH3": 4, "CH2": 1, "COO": 1, "SIO": 1}, + {"CH3": 4, "CH2O": 1, "COO": 1, "SI": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OC(=O)O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 2, "CHO": 1, "COO": 1, "SIH3": 1}, psrk_result={"CH3": 2, "CHO": 1, "COO": 1, "SIH3": 1}, joback_result={}, @@ -503,47 +469,48 @@ identifier="C[SiH2]OC(=O)OC(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH": 1, "COO": 1, "SIH2O": 1}, {"CH3": 3, "CHO": 1, "COO": 1, "SIH2": 1}, ], - psrk_result={"CH3": 3, "CHO": 1, "COO": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 3, "CH": 1, "COO": 1, "SIH2O": 1}, + {"CH3": 3, "CHO": 1, "COO": 1, "SIH2": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OC(=O)O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 4, "CH": 1, "COO": 1, "SIHO": 1}, {"CH3": 4, "CHO": 1, "COO": 1, "SIH": 1}, ], - psrk_result={"CH3": 4, "CHO": 1, "COO": 1, "SIH": 1}, + psrk_result=[ + {"CH3": 4, "CH": 1, "COO": 1, "SIHO": 1}, + {"CH3": 4, "CHO": 1, "COO": 1, "SIH": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OC(=O)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 5, "CH": 1, "COO": 1, "SIO": 1}, {"CH3": 5, "CHO": 1, "COO": 1, "SI": 1}, ], - psrk_result={"CH3": 5, "CHO": 1, "COO": 1, "SI": 1}, + psrk_result=[ + {"CH3": 5, "CH": 1, "COO": 1, "SIO": 1}, + {"CH3": 5, "CHO": 1, "COO": 1, "SI": 1}, + ], joback_result={}, ), Case( identifier="C[SiH2]OC(=O)OC(C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "COO": 1, "SIH2O": 1}, psrk_result={"CH3": 4, "C": 1, "COO": 1, "SIH2O": 1}, joback_result={}, @@ -552,8 +519,6 @@ identifier="C[SiH](C)OC(=O)OC(C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 5, "C": 1, "COO": 1, "SIHO": 1}, psrk_result={"CH3": 5, "C": 1, "COO": 1, "SIHO": 1}, joback_result={}, @@ -562,8 +527,6 @@ identifier="CC(C)(C)OC(=O)O[Si](C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 6, "C": 1, "COO": 1, "SIO": 1}, psrk_result={"CH3": 6, "C": 1, "COO": 1, "SIO": 1}, joback_result={}, @@ -572,8 +535,6 @@ identifier="CC(C)(C)OC(=O)O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={}, @@ -582,61 +543,64 @@ identifier="[SiH3][SiH]([SiH3])O[SiH2]O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 4, "SIH": 1, "SIH2O": 1, "SIHO": 1}, {"SIH3": 4, "SIH2": 1, "SIHO": 2}, ], - psrk_result={"SIH3": 4, "SIH": 1, "SIH2O": 1, "SIHO": 1}, + psrk_result=[ + {"SIH3": 4, "SIH": 1, "SIH2O": 1, "SIHO": 1}, + {"SIH3": 4, "SIH2": 1, "SIHO": 2}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH]([SiH3])O[SiH2]O[SiH](O[SiH2]O[SiH]([SiH3])[SiH3])O[SiH2]O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 6, "SIH": 1, "SIH2O": 3, "SIHO": 3}, {"SIH3": 6, "SIH2": 1, "SIH2O": 2, "SIHO": 4}, ], - psrk_result={"SIH3": 6, "SIH": 1, "SIH2O": 3, "SIHO": 3}, + psrk_result=[ + {"SIH3": 6, "SIH": 1, "SIH2O": 3, "SIHO": 3}, + {"SIH3": 6, "SIH2": 1, "SIH2O": 2, "SIHO": 4}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH]([SiH3])O[SiH2]O[SiH2][SiH](O[SiH2]O[SiH]([SiH3])[SiH3])O[SiH2]O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 6, "SIH": 2, "SIH2O": 4, "SIHO": 2}, {"SIH3": 6, "SIH2": 1, "SIH": 1, "SIH2O": 3, "SIHO": 3}, {"SIH3": 6, "SIH2": 2, "SIH2O": 2, "SIHO": 4}, ], - psrk_result={"SIH3": 6, "SIH": 2, "SIH2O": 4, "SIHO": 2}, + psrk_result=[ + {"SIH3": 6, "SIH": 2, "SIH2O": 4, "SIHO": 2}, + {"SIH3": 6, "SIH2": 1, "SIH": 1, "SIH2O": 3, "SIHO": 3}, + {"SIH3": 6, "SIH2": 2, "SIH2O": 2, "SIHO": 4}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH]([SiH3])O[SiH2]O[SiH]([SiH3])O[SiH2]O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 5, "SIH": 1, "SIH2O": 2, "SIHO": 2}, {"SIH3": 5, "SIH2": 1, "SIH2O": 1, "SIHO": 3}, ], - psrk_result={"SIH3": 5, "SIH": 1, "SIH2O": 2, "SIHO": 2}, + psrk_result=[ + {"SIH3": 5, "SIH": 1, "SIH2O": 2, "SIHO": 2}, + {"SIH3": 5, "SIH2": 1, "SIH2O": 1, "SIHO": 3}, + ], joback_result={}, ), Case( identifier="[SiH3]O[SiH2]O[SiH]([SiH3])O[SiH2]O[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={}, @@ -645,34 +609,34 @@ identifier="[SiH3][SiH](O[Si]([SiH3])([SiH3])[SiH3])O[Si]([SiH3])([SiH3])[SiH3]", # noqa identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, {"SIH3": 7, "SIH": 1, "SIO": 2}, ], - psrk_result={"SIH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, + psrk_result=[ + {"SIH3": 7, "SI": 1, "SIHO": 1, "SIO": 1}, + {"SIH3": 7, "SIH": 1, "SIO": 2}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH](O[Si]([SiH3])([SiH3])[SiH3])O[Si]([SiH3])(O[SiH]([SiH3])O[Si]([SiH3])([SiH3])[SiH3])O[SiH]([SiH3])O[Si]([SiH3])([SiH3])[SiH3]", # noqa identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 13, "SI": 1, "SIHO": 3, "SIO": 3}, {"SIH3": 13, "SIH": 1, "SIHO": 2, "SIO": 4}, ], - psrk_result={"SIH3": 13, "SI": 1, "SIHO": 3, "SIO": 3}, + psrk_result=[ + {"SIH3": 13, "SI": 1, "SIHO": 3, "SIO": 3}, + {"SIH3": 13, "SIH": 1, "SIHO": 2, "SIO": 4}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH](O[SiH2][Si]([SiH3])(O[SiH]([SiH3])O[Si]([SiH3])([SiH3])[SiH3])O[SiH]([SiH3])O[Si]([SiH3])([SiH3])[SiH3])O[Si]([SiH3])([SiH3])[SiH3]", # noqa identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 13, "SI": 2, "SIH2O": 1, "SIHO": 3, "SIO": 2}, {"SIH3": 13, "SIH2": 1, "SI": 1, "SIHO": 3, "SIO": 3}, @@ -680,28 +644,33 @@ {"SIH3": 13, "SIH2": 1, "SIH": 1, "SIHO": 2, "SIO": 4}, {"SIH3": 13, "SIH": 2, "SIH2O": 1, "SIHO": 1, "SIO": 4}, ], - psrk_result={"SIH3": 13, "SI": 2, "SIH2O": 1, "SIHO": 3, "SIO": 2}, + psrk_result=[ + {"SIH3": 13, "SI": 2, "SIH2O": 1, "SIHO": 3, "SIO": 2}, + {"SIH3": 13, "SIH2": 1, "SI": 1, "SIHO": 3, "SIO": 3}, + {"SIH3": 13, "SIH": 1, "SI": 1, "SIH2O": 1, "SIHO": 2, "SIO": 3}, + {"SIH3": 13, "SIH2": 1, "SIH": 1, "SIHO": 2, "SIO": 4}, + {"SIH3": 13, "SIH": 2, "SIH2O": 1, "SIHO": 1, "SIO": 4}, + ], joback_result={}, ), Case( identifier="[SiH3][SiH](O[Si]([SiH3])([SiH3])[SiH3])O[Si]([SiH3])([SiH3])O[SiH]([SiH3])O[Si]([SiH3])([SiH3])[SiH3]", # noqa identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"SIH3": 10, "SI": 1, "SIHO": 2, "SIO": 2}, {"SIH3": 10, "SIH": 1, "SIHO": 1, "SIO": 3}, ], - psrk_result={"SIH3": 10, "SI": 1, "SIHO": 2, "SIO": 2}, + psrk_result=[ + {"SIH3": 10, "SI": 1, "SIHO": 2, "SIO": 2}, + {"SIH3": 10, "SIH": 1, "SIHO": 1, "SIO": 3}, + ], joback_result={}, ), Case( identifier="[SiH3]OCO[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={}, @@ -710,22 +679,22 @@ identifier="COCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3O": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1}, {"CH3": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, {"CH2": 1, "CH3O": 1, "SIH3": 1, "SIH2O": 1}, ], - psrk_result={"CH3O": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1}, + psrk_result=[ + {"CH3O": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1}, + {"CH3": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, + {"CH2": 1, "CH3O": 1, "SIH3": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="[SiH3]OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH2O": 1, "SIH3": 2, "SIH2O": 1}, psrk_result={"CH2O": 1, "SIH3": 2, "SIH2O": 1}, joback_result={}, @@ -734,49 +703,52 @@ identifier="C[SiH2]OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIH2O": 1}, {"CH3": 1, "CH2": 1, "SIH3": 1, "SIH2O": 2}, ], - psrk_result={"CH3": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 1, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIH2O": 1}, + {"CH3": 1, "CH2": 1, "SIH3": 1, "SIH2O": 2}, + ], joback_result={}, ), Case( identifier="C[SiH](C)OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIHO": 1}, {"CH3": 2, "CH2": 1, "SIH3": 1, "SIH2O": 1, "SIHO": 1}, {"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIHO": 1}, + {"CH3": 2, "CH2": 1, "SIH3": 1, "SIH2O": 1, "SIHO": 1}, + {"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="C[Si](C)(C)OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIO": 1}, {"CH3": 3, "CH2": 1, "SIH3": 1, "SIH2O": 1, "SIO": 1}, {"CH3": 3, "CH2O": 1, "SIH3": 1, "SI": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 3, "CH2O": 1, "SIH3": 1, "SI": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 3, "CH2O": 1, "SIH3": 1, "SIH2": 1, "SIO": 1}, + {"CH3": 3, "CH2": 1, "SIH3": 1, "SIH2O": 1, "SIO": 1}, + {"CH3": 3, "CH2O": 1, "SIH3": 1, "SI": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="CC(C)(C)OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, psrk_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, joback_result={}, @@ -785,22 +757,22 @@ identifier="CC(C)OCO[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH3": 1, "SIH2": 1, "CHO": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, + {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, + {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="[SiH3]OCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH2O": 1, "SIH3": 3, "SIHO": 1}, psrk_result={"CH2O": 1, "SIH3": 3, "SIHO": 1}, joback_result={}, @@ -809,35 +781,36 @@ identifier="C[SiH](C)OCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, {"CH3": 2, "CH2": 1, "SIH3": 2, "SIHO": 2}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, + {"CH3": 2, "CH2": 1, "SIH3": 2, "SIHO": 2}, + ], joback_result={}, ), Case( identifier="C[Si](C)(C)OCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH2O": 1, "SIH3": 2, "SIH": 1, "SIO": 1}, {"CH3": 3, "CH2": 1, "SIH3": 2, "SIHO": 1, "SIO": 1}, {"CH3": 3, "CH2O": 1, "SIH3": 2, "SI": 1, "SIHO": 1}, ], - psrk_result={"CH3": 3, "CH2O": 1, "SIH3": 2, "SI": 1, "SIHO": 1}, + psrk_result=[ + {"CH3": 3, "CH2O": 1, "SIH3": 2, "SIH": 1, "SIO": 1}, + {"CH3": 3, "CH2": 1, "SIH3": 2, "SIHO": 1, "SIO": 1}, + {"CH3": 3, "CH2O": 1, "SIH3": 2, "SI": 1, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CC(C)(C)OCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, psrk_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, joback_result={}, @@ -846,49 +819,52 @@ identifier="COCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3O": 1, "CH2O": 1, "SIH3": 2, "SIH": 1}, {"CH3": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, {"CH2": 1, "CH3O": 1, "SIH3": 2, "SIHO": 1}, ], - psrk_result={"CH3O": 1, "CH2O": 1, "SIH3": 2, "SIH": 1}, + psrk_result=[ + {"CH3O": 1, "CH2O": 1, "SIH3": 2, "SIH": 1}, + {"CH3": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, + {"CH2": 1, "CH3O": 1, "SIH3": 2, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 2, "SIH": 1}, {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH3": 2, "SIH": 1, "CHO": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 2, "SIH": 1}, + {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, + {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CCOCO[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH2O": 2, "SIH3": 2, "SIH": 1}, {"CH3": 1, "CH2": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, ], - psrk_result={"CH3": 1, "CH2O": 2, "SIH3": 2, "SIH": 1}, + psrk_result=[ + {"CH3": 1, "CH2O": 2, "SIH3": 2, "SIH": 1}, + {"CH3": 1, "CH2": 1, "CH2O": 1, "SIH3": 2, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="[SiH3]OCO[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH2O": 1, "SIH3": 4, "SIO": 1}, psrk_result={"CH2O": 1, "SIH3": 4, "SIO": 1}, joback_result={}, @@ -897,21 +873,20 @@ identifier="C[Si](C)(C)OCO[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CH2O": 1, "SIH3": 3, "SI": 1, "SIO": 1}, {"CH3": 3, "CH2": 1, "SIH3": 3, "SIO": 2}, ], - psrk_result={"CH3": 3, "CH2O": 1, "SIH3": 3, "SI": 1, "SIO": 1}, + psrk_result=[ + {"CH3": 3, "CH2O": 1, "SIH3": 3, "SI": 1, "SIO": 1}, + {"CH3": 3, "CH2": 1, "SIH3": 3, "SIO": 2}, + ], joback_result={}, ), Case( identifier="CC(C)(C)OCO[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, psrk_result={"CH3": 3, "C": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, joback_result={}, @@ -920,36 +895,38 @@ identifier="COCO[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3O": 1, "CH2O": 1, "SIH3": 3, "SI": 1}, {"CH3": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, {"CH2": 1, "CH3O": 1, "SIH3": 3, "SIO": 1}, ], - psrk_result={"CH3O": 1, "CH2O": 1, "SIH3": 3, "SI": 1}, + psrk_result=[ + {"CH3O": 1, "CH2O": 1, "SIH3": 3, "SI": 1}, + {"CH3": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, + {"CH2": 1, "CH3O": 1, "SIH3": 3, "SIO": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OCO[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 3, "SI": 1}, {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "SIH3": 3, "SI": 1, "CHO": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 3, "SI": 1}, + {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, + {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 3, "SIO": 1}, + ], joback_result={}, ), Case( identifier="CC(O[SiH3])O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "CHO": 1, "SIH3": 2, "SIH2O": 1}, psrk_result={"CH3": 1, "CHO": 1, "SIH3": 2, "SIH2O": 1}, joback_result={}, @@ -958,22 +935,22 @@ identifier="CC(O[SiH2][SiH3])O[SiH](C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, {"CH3": 3, "CH": 1, "SIH3": 1, "SIH2O": 1, "SIHO": 1}, {"CH3": 3, "CHO": 1, "SIH3": 1, "SIH2": 1, "SIHO": 1}, ], - psrk_result={"CH3": 3, "CHO": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 1, "SIH3": 1, "SIH": 1, "SIH2O": 1}, + {"CH3": 3, "CH": 1, "SIH3": 1, "SIH2O": 1, "SIHO": 1}, + {"CH3": 3, "CHO": 1, "SIH3": 1, "SIH2": 1, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CC(O[SiH2][SiH3])OC(C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, psrk_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, joback_result={}, @@ -982,62 +959,66 @@ identifier="COC(C)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, {"CH3": 2, "CHO": 1, "SIH3": 1, "SIH2O": 1}, {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, + {"CH3": 2, "CHO": 1, "SIH3": 1, "SIH2O": 1}, + {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="CC(C)OC(C)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 2, "SIH3": 1, "SIH2": 1}, {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 3, "CHO": 2, "SIH3": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 2, "SIH3": 1, "SIH2": 1}, + {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="CCOC(C)O[SiH2][SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, ], - psrk_result={"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, + psrk_result=[ + {"CH3": 2, "CH2O": 1, "CHO": 1, "SIH3": 1, "SIH2": 1}, + {"CH3": 2, "CH2": 1, "CHO": 1, "SIH3": 1, "SIH2O": 1}, + {"CH3": 2, "CH": 1, "CH2O": 1, "SIH3": 1, "SIH2O": 1}, + ], joback_result={}, ), Case( identifier="CC(O[SiH](C)C)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, {"CH3": 3, "CH": 1, "SIH3": 2, "SIHO": 2}, ], - psrk_result={"CH3": 3, "CHO": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 1, "SIH3": 2, "SIH": 1, "SIHO": 1}, + {"CH3": 3, "CH": 1, "SIH3": 2, "SIHO": 2}, + ], joback_result={}, ), Case( identifier="CC(O[SiH3])O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "CHO": 1, "SIH3": 3, "SIHO": 1}, psrk_result={"CH3": 1, "CHO": 1, "SIH3": 3, "SIHO": 1}, joback_result={}, @@ -1046,8 +1027,6 @@ identifier="CC(O[SiH]([SiH3])[SiH3])OC(C)(C)C", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, psrk_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, joback_result={}, @@ -1056,35 +1035,36 @@ identifier="CC(C)OC(C)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 2, "SIH3": 2, "SIH": 1}, {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, ], - psrk_result={"CH3": 3, "CHO": 2, "SIH3": 2, "SIH": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 2, "SIH3": 2, "SIH": 1}, + {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 2, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="COC(C)O[SiH]([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 2, "SIH": 1}, {"CH3": 2, "CHO": 1, "SIH3": 2, "SIHO": 1}, {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 2, "SIHO": 1}, ], - psrk_result={"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 2, "SIH": 1}, + psrk_result=[ + {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 2, "SIH": 1}, + {"CH3": 2, "CHO": 1, "SIH3": 2, "SIHO": 1}, + {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 2, "SIHO": 1}, + ], joback_result={}, ), Case( identifier="CC(O[SiH3])O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 1, "CHO": 1, "SIH3": 4, "SIO": 1}, psrk_result={"CH3": 1, "CHO": 1, "SIH3": 4, "SIO": 1}, joback_result={}, @@ -1093,8 +1073,6 @@ identifier="CC(OC(C)(C)C)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, psrk_result={"CH3": 4, "C": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, joback_result={}, @@ -1103,27 +1081,30 @@ identifier="CC(C)OC(C)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 3, "CHO": 2, "SIH3": 3, "SI": 1}, {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, ], - psrk_result={"CH3": 3, "CHO": 2, "SIH3": 3, "SI": 1}, + psrk_result=[ + {"CH3": 3, "CHO": 2, "SIH3": 3, "SI": 1}, + {"CH3": 3, "CH": 1, "CHO": 1, "SIH3": 3, "SIO": 1}, + ], joback_result={}, ), Case( identifier="COC(C)O[Si]([SiH3])([SiH3])[SiH3]", identifier_type="smiles", cases_module="silicon", - r=None, - q=None, unifac_result=[ {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 3, "SI": 1}, {"CH3": 2, "CHO": 1, "SIH3": 3, "SIO": 1}, {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 3, "SIO": 1}, ], - psrk_result={"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 3, "SI": 1}, + psrk_result=[ + {"CH3": 1, "CH3O": 1, "CHO": 1, "SIH3": 3, "SI": 1}, + {"CH3": 2, "CHO": 1, "SIH3": 3, "SIO": 1}, + {"CH3": 1, "CH": 1, "CH3O": 1, "SIH3": 3, "SIO": 1}, + ], joback_result={}, ), ] diff --git a/tests/cases/sulfur.py b/tests/cases/sulfur.py index f4634f9..d487aa2 100644 --- a/tests/cases/sulfur.py +++ b/tests/cases/sulfur.py @@ -9,8 +9,6 @@ identifier="C(=S)=S", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CS2": 1}, psrk_result={"CS2": 1}, joback_result={}, @@ -19,8 +17,6 @@ identifier="CCCC1=CC=C(C=C1)C(C)S", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={}, psrk_result={ "CH3": 2, @@ -43,8 +39,6 @@ identifier="CCCC1=CC=C(CS)C=C1", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={ "CH3": 1, "ACH": 4, @@ -73,8 +67,6 @@ identifier="CC1=CC=C(CS)C=C1", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"ACH": 4, "ACCH3": 1, "CH2SH": 1, "AC": 1}, psrk_result={"ACH": 4, "ACCH3": 1, "CH2SH": 1, "AC": 1}, joback_result={ @@ -89,8 +81,6 @@ identifier="SCC1=CC=NC=C1", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"C5H4N": 1, "CH2SH": 1}, psrk_result={"C5H4N": 1, "CH2SH": 1}, joback_result={ @@ -105,8 +95,6 @@ identifier="CS", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3SH": 1}, psrk_result={"CH3SH": 1}, joback_result={"-CH3": 1, "-SH": 1}, @@ -115,8 +103,6 @@ identifier="CCS", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3": 1, "CH2SH": 1}, psrk_result={"CH3": 1, "CH2SH": 1}, joback_result={"-CH3": 1, "-CH2-": 1, "-SH": 1}, @@ -125,8 +111,6 @@ identifier="CSC", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3": 1, "CH3S": 1}, psrk_result={"CH3": 1, "CH3S": 1}, joback_result={"-CH3": 2, "-S- (non-ring)": 1}, @@ -135,8 +119,6 @@ identifier="CCSCC", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH2S": 1}, psrk_result={"CH3": 2, "CH2": 1, "CH2S": 1}, joback_result={"-CH3": 2, "-CH2-": 2, "-S- (non-ring)": 1}, @@ -145,8 +127,6 @@ identifier="CC(C)SC(C)C", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3": 4, "CH": 1, "CHS": 1}, psrk_result={"CH3": 4, "CH": 1, "CHS": 1}, joback_result={"-CH3": 4, ">CH-": 2, "-S- (non-ring)": 1}, @@ -155,8 +135,6 @@ identifier="C1CCS(=O)(=O)C1", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH2": 2, "(CH2)2SU": 1}, psrk_result={}, joback_result={}, @@ -165,8 +143,6 @@ identifier="CC1CC(S(=O)(=O)C1)C", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 1, "CH": 1, "CH2CHSU": 1}, psrk_result={}, joback_result={}, @@ -175,8 +151,6 @@ identifier="CC(C)S", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={}, psrk_result={"CH3": 2, "CHSH": 1}, joback_result={"-CH3": 2, ">CH-": 1, "-SH": 1}, @@ -185,8 +159,6 @@ identifier="CC(S)C1=CC=CC=C1", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={}, psrk_result={"CH3": 1, "ACH": 5, "CHSH": 1, "AC": 1}, joback_result={ @@ -201,8 +173,6 @@ identifier="CC(C)(C)S", identifier_type="smiles", cases_module="sulfur", - r=None, - q=None, unifac_result={}, psrk_result={"CH3": 3, "CSH": 1}, joback_result={"-CH3": 3, ">C<": 1, "-SH": 1}, diff --git a/tests/cases/unsaturated_hydrocarbons.py b/tests/cases/unsaturated_hydrocarbons.py index cbba8b3..0f32f3a 100644 --- a/tests/cases/unsaturated_hydrocarbons.py +++ b/tests/cases/unsaturated_hydrocarbons.py @@ -12,8 +12,6 @@ "CC=C(C)C1=C(C=CC=C1C=C)C(C)=C(C)C", "smiles", "insaturated hydrocarbons", - r=None, - q=None, unifac_result={ "CH3": 5, "CH2=CH": 1, @@ -43,8 +41,6 @@ "CC=CC(C)=C(C)C=C", "smiles", "insaturated hydrocarbons", - r=None, - q=None, unifac_result={"CH2=CH": 1, "CH=CH": 1, "C=C": 1, "CH3": 3}, psrk_result={"CH2=CH": 1, "CH=CH": 1, "C=C": 1, "CH3": 3}, joback_result={"-CH3": 3, "=CH2": 1, "=CH-": 3, "=C<": 2}, @@ -54,8 +50,6 @@ "smiles", "insaturated hydrocarbons", commentary="alpha-pinene", - r=None, - q=None, unifac_result={"CH3": 3, "CH2": 2, "CH": 2, "C": 1, "CH=C": 1}, psrk_result={"CH3": 3, "CH2": 2, "CH": 2, "C": 1, "CH=C": 1}, joback_result={ @@ -72,8 +66,6 @@ "smiles", "insaturated hydrocarbons", commentary="d-limonene", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 3, "CH": 1, "CH2=C": 1, "CH=C": 1}, psrk_result={"CH3": 2, "CH2": 3, "CH": 1, "CH2=C": 1, "CH=C": 1}, joback_result={ @@ -91,8 +83,6 @@ "smiles", "insaturated hydrocarbons", commentary="2,3-Dimethyl-1,3-cyclohexadiene", - r=None, - q=None, unifac_result={"CH2": 2, "CH=C": 2, "CH3": 2}, psrk_result={"CH2": 2, "CH=C": 2, "CH3": 2}, joback_result={"-CH3": 2, "ring-CH2-": 2, "ring=CH-": 2, "ring=C<": 2}, @@ -102,8 +92,6 @@ "smiles", "insaturated hydrocarbons", commentary="3,3'-(Pentane-1,3-diyl)dicyclohexene", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 9, "CH": 3, "CH=CH": 2}, psrk_result={"CH3": 1, "CH2": 9, "CH": 3, "CH=CH": 2}, joback_result={ @@ -120,8 +108,6 @@ "smiles", "insaturated hydrocarbons", commentary="cyclohexene", - r=None, - q=None, unifac_result={"CH2": 4, "CH=CH": 1}, psrk_result={"CH2": 4, "CH=CH": 1}, joback_result={"ring-CH2-": 4, "ring=CH-": 2}, @@ -131,8 +117,6 @@ "smiles", "insaturated hydrocarbons", commentary="2,3-dimethylbutene-2", - r=None, - q=None, unifac_result={"C=C": 1, "CH3": 4}, psrk_result={"C=C": 1, "CH3": 4}, joback_result={"-CH3": 4, "=C<": 2}, @@ -142,8 +126,6 @@ "smiles", "insaturated hydrocarbons", commentary="2-methyl-2-butene", - r=None, - q=None, unifac_result={"CH=C": 1, "CH3": 3}, psrk_result={"CH=C": 1, "CH3": 3}, joback_result={"-CH3": 3, "=CH-": 1, "=C<": 1}, @@ -153,8 +135,6 @@ "smiles", "insaturated hydrocarbons", commentary="2-methyl-1-butene", - r=None, - q=None, unifac_result={"CH2": 1, "CH2=C": 1, "CH3": 2}, psrk_result={"CH2": 1, "CH2=C": 1, "CH3": 2}, joback_result={"-CH3": 2, "-CH2-": 1, "=CH2": 1, "=C<": 1}, @@ -164,8 +144,6 @@ "smiles", "insaturated hydrocarbons", commentary="2-hexene", - r=None, - q=None, unifac_result={"CH2": 2, "CH=CH": 1, "CH3": 2}, psrk_result={"CH2": 2, "CH=CH": 1, "CH3": 2}, joback_result={"-CH3": 2, "-CH2-": 2, "=CH-": 2}, @@ -175,8 +153,6 @@ "smiles", "insaturated hydrocarbons", commentary="1-hexene", - r=None, - q=None, unifac_result={"CH2": 3, "CH2=CH": 1, "CH3": 1}, psrk_result={"CH2": 3, "CH2=CH": 1, "CH3": 1}, joback_result={"-CH3": 1, "-CH2-": 3, "=CH2": 1, "=CH-": 1}, @@ -185,8 +161,6 @@ "C=C=C", "smiles", "insaturated hydrocarbons", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={"=CH2": 2, "=C=": 1}, @@ -195,8 +169,6 @@ "CC=CC(C)C(C)=C=C", "smiles", "insaturated hydrocarbons", - r=None, - q=None, unifac_result={}, psrk_result={}, joback_result={ @@ -212,8 +184,6 @@ identifier="CC#CC1=CC=CC=C1", identifier_type="smiles", cases_module="insaturated hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 1, "ACH": 5, "AC": 1, "C=-C": 1}, psrk_result={"CH3": 1, "ACH": 5, "AC": 1, "C=-C": 1}, joback_result={"-CH3": 1, "C": 2, "ring=CH-": 5, "ring=C<": 1}, @@ -222,8 +192,6 @@ identifier="CCCCC#C", identifier_type="smiles", cases_module="insaturated hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 1, "CH2": 3, "CH=-C": 1}, psrk_result={"CH3": 1, "CH2": 3, "CH=-C": 1}, joback_result={"-CH3": 1, "-CH2-": 3, "CH": 1, "C": 1}, @@ -232,8 +200,6 @@ identifier="CCCC#CC", identifier_type="smiles", cases_module="insaturated hydrocarbons", - r=None, - q=None, unifac_result={"CH3": 2, "CH2": 2, "C=-C": 1}, psrk_result={"CH3": 2, "CH2": 2, "C=-C": 1}, joback_result={"-CH3": 2, "-CH2-": 2, "C": 2}, diff --git a/tests/test_hideouts.py b/tests/test_hideouts.py deleted file mode 100644 index 73616ce..0000000 --- a/tests/test_hideouts.py +++ /dev/null @@ -1,110 +0,0 @@ -import json - -from ugropy import psrk, unifac - - -# test if i'm not missing any potential hideout -# ============================================================================= -# UNIFAC -# ============================================================================= -def test_unifac_ch2_hideouts(): - for group in unifac.subgroups.index: - # exceptions (full molecules gropus and well ch2...) - if group in ["CH2CL2", "CH2", "THF", "DOH", "NMP", "MORPH"]: - continue - - string_contribution = unifac.subgroups.loc[group, "contribute"] - contribution = json.loads(string_contribution) - - # Check if CH2 is being substracted in the contribution of the group - if "CH2" in contribution.keys(): - assert group in unifac.hideouts.loc["CH2"].values - continue - else: - # Check if CH2 is being substracted in the contribution of the - # groups in the contribution of "group" - for grp in list(contribution.keys())[1:]: - str_contribution = unifac.subgroups.loc[grp, "contribute"] - contrib = json.loads(str_contribution) - - if "CH2" in contrib.keys(): - assert group in unifac.hideouts.loc["CH2"].values - break - - -def test_unifac_ch_hideouts(): - for group in unifac.subgroups.index: - # exceptions (full molecules gropus and well ch...) - if group in ["HCCL2F", "CHCL3", "CH", "FURFURAL"]: - continue - - string_contribution = unifac.subgroups.loc[group, "contribute"] - contribution = json.loads(string_contribution) - - # Check if CH is being substracted in the contribution of the group - if "CH" in contribution.keys(): - assert group in unifac.hideouts.loc["CH"].values - continue - else: - # Check if CH is being substracted in the contribution of the - # groups in the contribution of "group" - for grp in list(contribution.keys())[1:]: - str_contribution = unifac.subgroups.loc[grp, "contribute"] - contrib = json.loads(str_contribution) - - if "CH" in contrib.keys(): - assert group in unifac.hideouts.loc["CH"].values - break - - -# ============================================================================= -# PSRK -# ============================================================================= -def test_psrk_ch2_hideouts(): - for group in psrk.subgroups.index: - # exceptions (full molecules gropus and well ch2...) - if group in ["CH2CL2", "CH2", "THF", "DOH", "NMP", "MORPH", "H2COCH2"]: - continue - - string_contribution = psrk.subgroups.loc[group, "contribute"] - contribution = json.loads(string_contribution) - - # Check if CH2 is being substracted in the contribution of the group - if "CH2" in contribution.keys(): - assert group in psrk.hideouts.loc["CH2"].values - continue - else: - # Check if CH2 is being substracted in the contribution of the - # groups in the contribution of "group" - for grp in list(contribution.keys())[1:]: - str_contribution = psrk.subgroups.loc[grp, "contribute"] - contrib = json.loads(str_contribution) - - if "CH2" in contrib.keys(): - assert group in psrk.hideouts.loc["CH2"].values - break - - -def test_psrk_ch_hideouts(): - for group in psrk.subgroups.index: - # exceptions (full molecules gropus and well ch...) - if group in ["HCCL2F", "CHCL3", "CH", "FURFURAL"]: - continue - - string_contribution = psrk.subgroups.loc[group, "contribute"] - contribution = json.loads(string_contribution) - - # Check if CH is being substracted in the contribution of the group - if "CH" in contribution.keys(): - assert group in psrk.hideouts.loc["CH"].values - continue - else: - # Check if CH is being substracted in the contribution of the - # groups in the contribution of "group" - for grp in list(contribution.keys())[1:]: - str_contribution = psrk.subgroups.loc[grp, "contribute"] - contrib = json.loads(str_contribution) - - if "CH" in contrib.keys(): - assert group in psrk.hideouts.loc["CH"].values - break diff --git a/tests/test_joback.py b/tests/test_joback.py new file mode 100644 index 0000000..3be5dee --- /dev/null +++ b/tests/test_joback.py @@ -0,0 +1,66 @@ +from cases import TCase + +import pytest + +from ugropy import joback + + +@pytest.mark.dependency(name="joback") +@pytest.mark.joback +class TestJoback(TCase): + # Store al the groups detected in all the cases here: + tested_groups = set() + + def asserts(self, case, solver): + if case.joback_result is None: + pytest.skip( + f"No Joback result defined for {case.identifier}, " + f"{case.cases_module}" + ) + + result = joback.get_groups( + identifier=case.identifier, + identifier_type=case.identifier_type, + solver=solver, + search_multiple_solutions=True, + ) + + if len(result) > 1: + for r in result: + comp = r.subgroups in case.joback_result + + if not comp: + message = ( + "\n" + f"Case: {case.identifier}\n" + f"Test module: {case.cases_module}\n" + f"Expected: {case.joback_result}\n" + f"Obtained: {[r.subgroups for r in result]}" + ) + + assert False, message + + self.tested_groups.update(r.subgroups.keys()) + else: + comp = result[0].subgroups == case.joback_result + + self.tested_groups.update(result[0].subgroups.keys()) + + if not comp: + message = ( + "\n" + f"Case: {case.identifier}\n" + f"Test module: {case.cases_module}\n" + f"Expected: {case.joback_result}\n" + f"Obtained: {result[0].subgroups}" + ) + + assert False, message + + +@pytest.mark.dependency(depends=["joback"]) +@pytest.mark.joback +def test_psrk_groups_coverage(): + # Check if all the groups were detected on at least one case + for group in TestJoback.tested_groups: + assert group in joback.subgroups.index, f"Group {group} not tested" diff --git a/ugropy/__init__.py b/ugropy/__init__.py index a62d2d9..0b76db9 100644 --- a/ugropy/__init__.py +++ b/ugropy/__init__.py @@ -7,6 +7,7 @@ ) from .core.ilp_solvers.ilp_solver import ILPSolver from .core.ilp_solvers.default_solver import DefaultSolver +from .models.joback import joback from .models.unifac import unifac from .models.psrk import psrk @@ -18,6 +19,7 @@ "writers", "instantiate_mol_object", "FragmentationModel", + "joback", "unifac", "psrk", "ILPSolver", diff --git a/ugropy/core/frag_classes/base/fragmentation_model.py b/ugropy/core/frag_classes/base/fragmentation_model.py index 8cf687e..d486037 100644 --- a/ugropy/core/frag_classes/base/fragmentation_model.py +++ b/ugropy/core/frag_classes/base/fragmentation_model.py @@ -71,6 +71,7 @@ def get_groups( identifier_type: str = "name", solver: ILPSolver = DefaultSolver, search_multiple_solutions: bool = False, + **kwargs, ) -> Union[FragmentationResult, List[FragmentationResult]]: # ===================================================================== # Direct fragments detection @@ -81,7 +82,7 @@ def get_groups( # No groups detected if detections == {}: - return self.set_fragmentation_result(mol, [{}]) + return self.set_fragmentation_result(mol, [{}], **kwargs) # ===================================================================== # Search for overlapping atoms and free atoms @@ -92,11 +93,11 @@ def get_groups( # If there is free atoms in the molecule can't fragment with the model if np.size(free_atoms) > 0: - return self.set_fragmentation_result(mol, [{}]) + return self.set_fragmentation_result(mol, [{}], **kwargs) # If no overlapping or the model allows overlapping we are done if np.size(overlapping_atoms) == 0 or self.allow_overlapping: - return self.set_fragmentation_result(mol, [detections]) + return self.set_fragmentation_result(mol, [detections], **kwargs) # ===================================================================== # Solve overlapping atoms @@ -110,7 +111,7 @@ def get_groups( if not problem.selected_fragments: # This could happend, no solution found. Example: # "CC(C)(C)OC(=O)OC1=CC=CC=C1" on UNIFAC. - return self.set_fragmentation_result(mol, [{}]) + return self.set_fragmentation_result(mol, [{}], **kwargs) solutions = [] @@ -123,7 +124,7 @@ def get_groups( solutions.append(solution) - return self.set_fragmentation_result(mol, solutions) + return self.set_fragmentation_result(mol, solutions, **kwargs) def set_fragmentation_result( self, diff --git a/ugropy/core/frag_classes/gibss_model/gibbs_model.py b/ugropy/core/frag_classes/gibss_model/gibbs_model.py index b596e59..b5af7b4 100644 --- a/ugropy/core/frag_classes/gibss_model/gibbs_model.py +++ b/ugropy/core/frag_classes/gibss_model/gibbs_model.py @@ -1,12 +1,19 @@ """GibbsModel fragmentation module.""" -from typing import Union +from collections import defaultdict + +from rdkit import Chem + +from typing import Union, List import pandas as pd from ugropy.core.frag_classes.base.fragmentation_model import ( FragmentationModel, ) +from ugropy.core.frag_classes.gibss_model.gibbs_result import ( + GibbsFragmentationResult, +) class GibbsModel(FragmentationModel): @@ -56,15 +63,33 @@ def __init__( else: self.subgroups_info = subgroups_info - # def set_fragmentation_result( - # self, - # molecule: Chem.rdchem.Mol, - # subgroups: dict, - # subgroups_atoms_indexes: dict, - # ) -> "GibbsFragmentationResult": + def set_fragmentation_result( + self, + molecule: Chem.rdchem.Mol, + solutions_fragments: List[dict], + ) -> List[GibbsFragmentationResult]: + + sols = [] + occurs = [] + + for solution in solutions_fragments: + occurrences = defaultdict(int) + groups_atoms = defaultdict(list) + + for frag, atoms in solution.items(): + name = frag.split("_")[0] + occurrences[name] += 1 + groups_atoms[name].append(atoms) - # result = GibbsFragmentationResult( - # self, molecule, subgroups, subgroups_atoms_indexes - # ) + if occurrences not in occurs: + sols.append( + GibbsFragmentationResult( + molecule, + dict(occurrences), + dict(groups_atoms), + self.subgroups_info, + ) + ) + occurs.append(occurrences) - # return result + return sols diff --git a/ugropy/core/frag_classes/gibss_model/gibbs_result.py b/ugropy/core/frag_classes/gibss_model/gibbs_result.py index ff55695..3bedb44 100644 --- a/ugropy/core/frag_classes/gibss_model/gibbs_result.py +++ b/ugropy/core/frag_classes/gibss_model/gibbs_result.py @@ -1,6 +1,7 @@ +import pandas as pd + from rdkit import Chem -from ugropy.core.frag_classes.gibss_model.gibbs_model import GibbsModel from ugropy.core.frag_classes.base.fragmentation_result import ( FragmentationResult, ) @@ -9,26 +10,20 @@ class GibbsFragmentationResult(FragmentationResult): def __init__( self, - model: GibbsModel, - molecule: Chem.Mol, + molecule: Chem.rdchem.Mol, subgroups: dict, subgroups_atoms_indexes: dict, + subgroups_info: pd.DataFrame, ): super().__init__(molecule, subgroups, subgroups_atoms_indexes) - self.r = 0.0 - self.q = 0.0 - - self._set_r_and_q(model) - - def _set_r_and_q(self, model: GibbsModel) -> None: - """Set R and Q values to the subgroups.""" r = 0.0 q = 0.0 - for group, n in self.subgroups.items(): - r += n * model.subgroups_info.loc[group, "R"] - q += n * model.subgroups_info.loc[group, "Q"] + if self.subgroups != {}: + for group, n in self.subgroups.items(): + r += n * subgroups_info.loc[group, "R"] + q += n * subgroups_info.loc[group, "Q"] - self.r = r - self.q = q + self.r = r + self.q = q diff --git a/ugropy/core/frag_classes/joback/__init__.py b/ugropy/core/frag_classes/joback/__init__.py new file mode 100644 index 0000000..927149e --- /dev/null +++ b/ugropy/core/frag_classes/joback/__init__.py @@ -0,0 +1,5 @@ +from .joback_model import JobackModel +from .joback_result import JobackFragmentationResult + + +__all__ = ["JobackModel", "JobackFragmentationResult"] diff --git a/ugropy/core/frag_classes/joback/joback.py b/ugropy/core/frag_classes/joback/joback.py deleted file mode 100644 index 9628c56..0000000 --- a/ugropy/core/frag_classes/joback/joback.py +++ /dev/null @@ -1,13 +0,0 @@ -from ugropy.constants import _csvs -from ugropy.models.joback import Joback -from ugropy.models.read_csv import _rd - -# ============================================================================= -# Joback -# ============================================================================= -# _jo = _csvs / "joback" - -# _jo_sg = _rd(_jo / "joback_subgroups.csv", "group") -# _jo_props = _rd(_jo / "properties_contrib.csv", "group") - -# joback = Joback(subgroups=_jo_sg, properties_contributions=_jo_props) diff --git a/ugropy/core/frag_classes/joback/joback_model.py b/ugropy/core/frag_classes/joback/joback_model.py new file mode 100644 index 0000000..893690d --- /dev/null +++ b/ugropy/core/frag_classes/joback/joback_model.py @@ -0,0 +1,109 @@ +"""GibbsModel fragmentation module.""" + +from collections import defaultdict + +from typing import List, Union + +import pandas as pd + +from rdkit import Chem + +from ugropy.core.frag_classes.base.fragmentation_model import ( + FragmentationModel, +) +from ugropy.core.frag_classes.joback.joback_result import ( + JobackFragmentationResult, +) +from ugropy.core.ilp_solvers.ilp_solver import ILPSolver +from ugropy.core.ilp_solvers.default_solver import DefaultSolver + + +class JobackModel(FragmentationModel): + """Joback Fragmentation model dedicated to properties estimation models. + + Parameters + ---------- + subgroups : pd.DataFrame + Model's subgroups. Index: 'group' (subgroups names). Mandatory columns: + 'smarts' (SMARTS representations of the group to detect its precense in + the molecule), 'molecular_weight' (molecular weight of the subgroups + used to check that the result is correct). + properties_contributions : pd.DataFrame, optional + Group's properties contributions, by default None + + Attributes + ---------- + subgroups : pd.DataFrame + Model's subgroups. Index: 'group' (subgroups names). Mandatory columns: + 'smarts' (SMARTS representations of the group to detect its precense in + the molecule), 'molecular_weight' (molecular weight of the subgroups + used to check that the result is correct). + detection_mols : dict + Dictionary cotaining all the rdkit Mol object from the detection_smarts + subgroups column + properties_contributions : pd.DataFrame + Group's properties contributions. + """ + + def __init__( + self, + subgroups: pd.DataFrame, + properties_contributions: Union[pd.DataFrame, None], + ) -> None: + + super().__init__(subgroups) + + # Properties + self.properties_contributions = properties_contributions + + def get_groups( + self, + identifier: Union[str, Chem.rdchem.Mol], + identifier_type: str = "name", + solver: ILPSolver = DefaultSolver, + search_multiple_solutions: bool = False, + normal_boiling_point: float = None, + ) -> Union[JobackFragmentationResult, List[JobackFragmentationResult]]: + + sol = super().get_groups( + identifier=identifier, + identifier_type=identifier_type, + solver=solver, + search_multiple_solutions=search_multiple_solutions, + normal_boiling_point=normal_boiling_point, + ) + + return sol + + def set_fragmentation_result( + self, + molecule: Chem.rdchem.Mol, + solutions_fragments: List[dict], + normal_boiling_point: float, + ) -> List[JobackFragmentationResult]: + + sols = [] + occurs = [] + + for solution in solutions_fragments: + occurrences = defaultdict(int) + groups_atoms = defaultdict(list) + + for frag, atoms in solution.items(): + name = frag.split("_")[0] + occurrences[name] += 1 + groups_atoms[name].append(atoms) + + if occurrences not in occurs: + sols.append( + JobackFragmentationResult( + molecule, + dict(occurrences), + dict(groups_atoms), + self.properties_contributions, + normal_boiling_point=normal_boiling_point, + ) + ) + occurs.append(occurrences) + + return sols diff --git a/ugropy/core/frag_classes/joback/joback_result.py b/ugropy/core/frag_classes/joback/joback_result.py new file mode 100644 index 0000000..e0eaf15 --- /dev/null +++ b/ugropy/core/frag_classes/joback/joback_result.py @@ -0,0 +1,343 @@ +from typing import Union + +import pandas as pd + +from rdkit import Chem +from rdkit.Chem import Descriptors + +from ugropy.core.frag_classes.base.fragmentation_result import ( + FragmentationResult, +) + + +import numpy as np + + +class JobackFragmentationResult(FragmentationResult): + """Joback group contribution properties estimator. + + The class recieves either the Joback and Reid model's :cite:p:`joback1, + joback2` groups, name or smiles of a molecule and estimates the its + properties. + + Parameters + ---------- + identifier : str or rdkit.Chem.rdchem.Mol + Identifier of a molecule (name, SMILES, groups, or Chem.rdchem.Mol). + Example: you can use hexane, CCCCCC, {"-CH3": 2, "-CH2-": 4} for name, + SMILES and groups respectively. + identifier_type : str, optional + Use 'name' to search a molecule by name, 'smiles' to provide the + molecule SMILES representation, 'groups' to provide Joback groups or + 'mol' to provide a rdkit.Chem.rdchem.Mol object, by default "name". + normal_boiling_point : float, optional + If provided, will be used to estimate critical temperature, acentric + factor, and vapor pressure instead of the estimated normal boiling + point, by default None. + + Attributes + ---------- + subgroups : dict + Joback functional groups of the molecule. + experimental_boiling_temperature : float + User provided experimental normal boiling point [K]. + critical_temperature : float + Joback estimated critical temperature [K]. + critical_pressure : float + Joback estimated critical pressure [bar]. + critical_volume : float + Joback estimated critical volume [cm³/mol]. + normal_boiling_point : float + Joback estimated normal boiling point [K]. + fusion_temperature : float + Joback estimated fusion temperature [K]. + h_formation : float + Joback estimated enthalpy of formation ideal gas at 298 K [kJ/mol]. + g_formation : float + Joback estimated Gibbs energy of formation ideal gas at 298 K [K]. + heat_capacity_ideal_gas_params : dict + Joback estimated Reid's ideal gas heat capacity equation parameters + [J/mol/K]. + h_fusion : float + Joback estimated fusion enthalpy [kJ/mol]. + h_vaporization : float + Joback estimated vaporization enthalpy at the normal boiling point + [kJ/mol]. + sum_na : float + Joback n_A contribution to liquid viscosity [N/s/m²]. + sum_nb : float + Joback n_B contribution to liquid viscosity [N/s/m²]. + molecular_weight : float + Molecular weight from Joback's subgroups [g/mol]. + acentric_factor : float + Acentric factor from Lee and Kesler's equation :cite:p:`joback1`. + vapor_pressure_params : dict + Vapor pressure G and k parameters for the Riedel-Plank-Miller + :cite:p:`joback1` equation [bar]. + """ + + def __init__( + self, + molecule: Chem.rdchem.Mol, + subgroups: dict, + subgroups_atoms_indexes: dict, + properties_contributions: pd.DataFrame, + normal_boiling_point: float = None, + ) -> None: + # Initialize the FragmentationResult attributes + super().__init__(molecule, subgroups, subgroups_atoms_indexes) + + # experimental boiling temperature + self.experimental_boiling_temperature = normal_boiling_point + + # Original Joback properties + self.critical_temperature = None + self.critical_pressure = None + self.critical_volume = None + self.normal_boiling_point = None + self.fusion_temperature = None + self.h_formation = None + self.g_formation = None + self.heat_capacity_ideal_gas_params = np.array([]) + self.h_fusion = None + self.h_vaporization = None + self.sum_na = None + self.sum_nb = None + self.molecular_weight = None + + # Extra properties + self.acentric_factor = None + self.vapor_pressure_params = {} + + # Fill the properties' values + if self.subgroups != {}: + self._calculate_properties(properties_contributions) + + def heat_capacity_ideal_gas( + self, temperature: Union[float, np.ndarray] + ) -> Union[float, np.ndarray]: + """Calculate the ideal gas heat capacity [J/mol/K]. + + Uses the Joback estimated Reid's ideal gas heat capacity equation + parameters [J/mol/K]. + + Parameters + ---------- + temperature : Union[float, np.ndarray] + Temperature [K] + + Returns + ------- + Union[float, np.ndarray] + Ideal gas heat capacity [J/mol/K]. + """ + a, b, c, d = self.heat_capacity_ideal_gas_params + + t = temperature + + return a + b * t + c * t**2 + d * t**3 + + def heat_capacity_liquid( + self, temperature: Union[float, np.ndarray] + ) -> Union[float, np.ndarray]: + """Calculate the liquid heat capacity [J/mol/K]. + + Uses the Rowlinson-Bondi :cite:p:`joback1` equation with the Joback + estimated properties. + + Parameters + ---------- + temperature : Union[float, np.ndarray] + Temperature [K] + + Returns + ------- + Union[float, np.ndarray] + Ideal gas heat capacity [J/mol/K]. + """ + tr = temperature / self.critical_temperature + w = self.acentric_factor + + c_p0 = self.heat_capacity_ideal_gas(temperature) + + c_pl = c_p0 + R * ( + 2.56 + + 0.436 * (1 - tr) ** (-1) + + w + * ( + 2.91 + + 4.28 * (1 - tr) ** (-1 / 3) * tr ** (-1) + + 0.296 * (1 - tr) ** (-1) + ) + ) + + return c_pl + + def viscosity_liquid( + self, temperature: Union[float, np.ndarray] + ) -> Union[float, np.ndarray]: + """Calculate the Joback estimated liquid viscosity [N/s/m²]. + + Parameters + ---------- + temperature : Union[float, np.ndarray] + Temperature [K] + + Returns + ------- + Union[float, np.ndarray] + Liquid viscosity [N/s/m²]. + """ + t = temperature + + n_l = self.molecular_weight * np.exp( + (self.sum_na - 597.82) / t + self.sum_nb - 11.202 + ) + return n_l + + def vapor_pressure( + self, temperature: Union[float, np.ndarray] + ) -> Union[float, np.ndarray]: + """Calculate the vapor pressure [bar]. + + Uses the Riedel-Plank-Miller :cite:p:`joback1` equation with the Joback + estimated properties. + + Parameters + ---------- + temperature : Union[float, np.ndarray] + Temperature [K] + + Returns + ------- + Union[float, np.ndarray] + Vapor pressure [bar] + """ + tr = temperature / self.critical_temperature + + g = self.vapor_pressure_params["G"] + k = self.vapor_pressure_params["k"] + + vp_r = np.exp(-g / tr * (1 - tr**2 + k * (3 + tr) * (1 - tr) ** 3)) + + vp = vp_r * self.critical_pressure + + return vp + + def _calculate_properties(self, contribs: pd.DataFrame) -> None: + """Obtain the molecule properties from Joback's groups.""" + groups = list(self.subgroups.keys()) + ocurr = list(self.subgroups.values()) + + df = contribs.loc[groups] + + # ===================================================================== + # Calculate complete contribution properties (no contribution missing) + # ===================================================================== + tc_c = df["Tc"].to_numpy() + pc_c = df["Pc"].to_numpy() + vc_c = df["Vc"].to_numpy() + tb_c = df["Tb"].to_numpy() + tf_c = df["Tf"].to_numpy() + hform_c = df["Hform"].to_numpy() + gform_c = df["Gform"].to_numpy() + hvap_c = df["Hvap"].to_numpy() + numa_c = df["num_of_atoms"].to_numpy() + mw_c = Descriptors.MolWt(self.molecule) + + # Molecular weight + self.molecular_weight = mw_c + + # Joback normal boiling point (Tb) + self.normal_boiling_point = 198.2 + np.dot(ocurr, tb_c) + + # Fusion temperature (Tf) + self.fusion_temperature = 122.5 + np.dot(ocurr, tf_c) + + # Used normal boiling point for calculations + if self.experimental_boiling_temperature is not None: + tb = self.experimental_boiling_temperature + else: + tb = self.normal_boiling_point + + # Critical temperature (Tc) normal boiling temperature for calculations + self.critical_temperature = tb * ( + 0.584 + 0.965 * np.dot(ocurr, tc_c) - (np.dot(ocurr, tc_c)) ** 2 + ) ** (-1) + + # Critical pressure (Pc) + self.critical_pressure = ( + 0.113 + 0.0032 * np.dot(ocurr, numa_c) - np.dot(ocurr, pc_c) + ) ** (-2) + + # Critical volume (Vc) + self.critical_volume = 17.5 + np.dot(ocurr, vc_c) + + # Standard enthalpy of formation (298 K) + self.h_formation = 68.29 + np.dot(ocurr, hform_c) + + # Standard Gibbs energy of formation (298 K) + self.g_formation = 53.88 + np.dot(ocurr, gform_c) + + # Enthalpy of vaporization + self.h_vaporization = 15.30 + np.dot(ocurr, hvap_c) + + # ===================================================================== + # Incomplete contribution properties (some contribution missing) + # ===================================================================== + # Heat capacity + if "-N= (ring)" not in groups: + a_c = df["a"].to_numpy() + b_c = df["b"].to_numpy() + c_c = df["c"].to_numpy() + d_c = df["d"].to_numpy() + + a = np.dot(ocurr, a_c) - 37.93 + b = np.dot(ocurr, b_c) + 0.21 + c = np.dot(ocurr, c_c) - 3.91e-4 + d = np.dot(ocurr, d_c) + 2.06e-7 + + self.heat_capacity_ideal_gas_params = np.array([a, b, c, d]) + + # Enthalpy of fusion + if all(df["Hfusion"].notnull()): + hfusion_c = df["Hfusion"].to_numpy() + self.h_fusion = -0.88 + np.dot(ocurr, hfusion_c) + + # Liquid viscosity + if all(df["na"].notnull()): + na_c = df["na"].to_numpy() + nb_c = df["nb"].to_numpy() + + self.sum_na = np.dot(ocurr, na_c) + self.sum_nb = np.dot(ocurr, nb_c) + + # ===================================================================== + # Extra properties + # ===================================================================== + # Reduced normal boiling point temperature + t_br = tb / self.critical_temperature + + # Lee and Kesler's equation (acentric factor) + pc = self.critical_pressure + self.acentric_factor = ( + -np.log(pc) + - 5.92714 + + 6.09648 / t_br + + 1.28862 * np.log(t_br) + - 0.169347 * t_br**6 + ) / ( + 15.2518 + - 15.6875 / t_br + - 13.4721 * np.log(t_br) + + 0.43577 * t_br**6 + ) + + # Riedel-Plank-Miller equation (vapor pressure [bar]) + h = t_br * np.log(self.critical_pressure / 1.01325) / (1 - t_br) + + g = 0.4835 + 0.4605 * h + + k = (h / g - (1 + t_br)) / ((3 + t_br) * (1 - t_br) ** 2) + + self.vapor_pressure_params = {"G": g, "k": k} diff --git a/ugropy/groupscsv/joback/joback_problematics.csv b/ugropy/groupscsv/joback/joback_problematics.csv deleted file mode 100644 index 4aa6def..0000000 --- a/ugropy/groupscsv/joback/joback_problematics.csv +++ /dev/null @@ -1,8 +0,0 @@ -smarts|contribute -? ester -[CH0;R]([*;!O])(=O)[OH0]|"{"">C=O (ring)"": -1, ""-O- (ring)"": -1}" -[CH0;!R]([*;!O])(=O)[OH0]|"{"">C=O (non-ring)"": -1, ""-O- (non-ring)"": -1}" -[CH0;!R]([OH0;!R])(=O)[OH0;!R]|"{""-COO- (ester)"": -1, "">C=O (non-ring)"": -1, ""-O- (non-ring)"": -1}" -[CH0;R]([OH0;R])(=O)[OH0;R]|"{""-COO- (ester)"": -1, "">C=O (ring)"": -1, ""-O- (ring)"": -1}" -? ester with acid -[CH0]([OH0])(=O)(-[OH])|"{""-COO- (ester)"": -1}" \ No newline at end of file diff --git a/ugropy/groupscsv/joback/joback_subgroups.csv b/ugropy/groupscsv/joback/joback_subgroups.csv index c2d38ad..c12525b 100644 --- a/ugropy/groupscsv/joback/joback_subgroups.csv +++ b/ugropy/groupscsv/joback/joback_subgroups.csv @@ -1,42 +1,42 @@ -group|detection_smarts|smarts|contribute|composed|molecular_weight --CH3|[CX4H3]||"{""-CH3"": 1}"|n|15.035 --CH2-|[CX4H2;!R]||"{""-CH2-"": 1}"|n|14.027 ->CH-|[CX4H;!R]||"{"">CH-"": 1}"|n|13.019 ->C<|[CX4H0;!R]||"{"">C<"": 1}"|n|12.011 -=CH2|[CH2]=[*]|[CH2D1]|"{""=CH2"": 1}"|n|14.0266 -=CH-|[CHX3;!R]||"{""=CH-"": 1}"|n|13.0188 -=C<|[CX3H0;!R](=[!O])(*)[*]|[CX3H0;!R]|"{""=C<"": 1}"|n|12.011 -=C=|[CX2H0;!R](=*)(=*)|[CX2H0]|"{""=C="": 1}"|n|12.011 -CH|[CH]#[!N]|[CHD1]|"{""CH"": 1}"|n|13.019 -C|[CH0X2;!$([CH0](=*)=*)]|[CH0D2]|"{""C"": 1}"|n|12.011 -ring-CH2-|[#6X4H2;R]||"{""ring-CH2-"": 1}"|n|14.027 -ring>CH-|[#6X4H;R]||"{""ring>CH-"": 1}"|n|13.019 -ring>C<|[#6X4H0;R]||"{""ring>C<"": 1}"|n|12.011 -ring=CH-|[#6X3H;R]||"{""ring=CH-"": 1}"|n|13.019 -ring=C<|[$([CH0;R](=[!O])(-*)-*),$([cH0])]|[#6H0X3;R]|"{""ring=C<"": 1}"|n|12.011 --F|[F]||"{""-F"": 1}"|n|18.998 --Cl|[Cl]||"{""-Cl"": 1}"|n|35.453 --Br|[Br]||"{""-Br"": 1}"|n|79.904 --I|[I]||"{""-I"": 1}"|n|126.9 --OH (alcohol)|[OH][#6;!c]|[OH]|"{""-OH (alcohol)"": 1}"|n|17.007 --OH (phenol)|[OH][c]|[OH]|"{""-OH (phenol)"": 1}"|n|17.007 --O- (non-ring)|[OX2H0;!R]||"{""-O- (non-ring)"": 1}"|n|15.999 --O- (ring)|[#8X2H0;R]||"{""-O- (ring)"": 1}"|n|15.999 ->C=O (non-ring)|[CX3H0;!R](=[O])(*)[*]|[CX3H0;!R](=[O])|"{"">C=O (non-ring)"": 1}"|n|28.01 ->C=O (ring)|[#6X3H0;R](=[O])(*)[*]|[#6X3H0;R](=[O])|"{"">C=O (ring)"": 1}"|n|28.01 -O=CH- (aldehyde)|[CH](=O)([#6])|[CH](=O)|"{""O=CH- (aldehyde)"": 1, ""=CH-"": -1}"|n|29.018 --COOH (acid)|[CH0](*)(=O)(-[OH])|[CH0](=O)(-[OH])|"{""-COOH (acid)"": 1, ""-OH (alcohol)"": -1, "">C=O (non-ring)"": -1}"|n|45.017 --COO- (ester)|[CH0](*)(=O)[OH0][#6]|[CH0](=O)[OH0]|"{""-COO- (ester)"": 1}"|n|44.009 -=O (other than above)|[$([OH0]=[*]);!$([OH0]=[#6X3]);!$([O]=[NX3,NX3+]~[O-])]|[OH0X1]|"{""=O (other than above)"": 1}"|n|15.999 --NH2|[NH2]||"{""-NH2"": 1}"|n|16.0226 ->NH (non-ring)|[$([#7X3H1](-*)-*);!R]|[#7X3H1]|"{"">NH (non-ring)"": 1}"|n|15.0148 ->NH (ring)|[#7X3H1;R]||"{"">NH (ring)"": 1}"|n|15.0148 ->N- (non-ring)|[$([#7X3H0](-*)(-*)-*);!R]|[#7X3H0]|"{"">N- (non-ring)"": 1}"|n|14.007 --N= (non-ring)|[#7X2H0;!R]||"{""-N= (non-ring)"": 1}"|n|14.007 --N= (ring)|[#7X2H0;R]||"{""-N= (ring)"": 1}"|n|14.007 -=NH|[#7X2H1]||"{""=NH"": 1}"|n|15.0148 --CN|[#6X2]#[#7X1H0]||"{""-CN"": 1, ""C"": -1}"|n|26.018 --NO2|[NX3,NX3+](=[O])~[O-]||"{""-NO2"": 1}"|n|46.005 --SH|[SH]||"{""-SH"": 1}"|n|33.0728 --S- (non-ring)|[SH0X2;!R]||"{""-S- (non-ring)"": 1}"|n|32.065 --S- (ring)|[#16H0X2;R]||"{""-S- (ring)"": 1}"|n|32.065 \ No newline at end of file +group|smarts|molecular_weight +-CH3|[CX4H3]|15.035 +-CH2-|[CX4H2;!R]|14.027 +>CH-|[CX4H;!R]|13.019 +>C<|[CX4H0;!R]|12.011 +=CH2|[CX3H2]|14.0266 +=CH-|[CHX3;!R]|13.0188 +=C<|[CX3H0;!R]|12.011 +=C=|[CX2H0;!R;!$([CH0](-*)#*)]|12.011 +CH|[CX2H;!$([CH]#[N])]|13.019 +C|[CH0X2;!$([CH0](=*)=*)]|12.011 +ring-CH2-|[#6X4H2;R]|14.027 +ring>CH-|[#6X4H;R]|13.019 +ring>C<|[#6X4H0;R]|12.011 +ring=CH-|[#6X3H;R]|13.019 +ring=C<|[#6H0X3;R;!$([CH0](=O)(-*)(-*))]|12.011 +-F|[FX1H0]|18.998 +-Cl|[ClX1H0]|35.453 +-Br|[BrX1H0]|79.904 +-I|[IX1H0]|126.9 +-OH (alcohol)|[OH;$([OH][C])]|17.007 +-OH (phenol)|[OH;$([OH][c])]|17.007 +-O- (non-ring)|[OX2H0;!R]|15.999 +-O- (ring)|[#8X2H0;R]|15.999 +>C=O (non-ring)|[CX3H0;!R;!$([CX3H0](=O)-O)](=[O])|28.01 +>C=O (ring)|[CX3H0;R;!$([CX3H0](=O)-O)](=[O])|28.01 +O=CH- (aldehyde)|[CH;!$([CH]-O)]=O|29.018 +-COOH (acid)|[CH0](=O)(-[OH])|45.017 +-COO- (ester)|[CH0](=O)[OH0]|44.009 +=O (other than above)|[OH0X1;!$([OH0]=[#6X3]);!$([O]=[NX3,NX3+]~[O-])]|15.999 +-NH2|[NH2]|16.0226 +>NH (non-ring)|[#7X3H1;!R]|15.0148 +>NH (ring)|[#7X3H1;R]|15.0148 +>N- (non-ring)|[#7X3H0;!R]|14.007 +-N= (non-ring)|[#7X2H0;!R]|14.007 +-N= (ring)|[#7X2H0;R]|14.007 +=NH|[#7X2H1]|15.0148 +-CN|[#6H0X2]#[#7X1H0]|26.018 +-NO2|[NX3,NX3+](=[O])~[O-]|46.005 +-SH|[SH]|33.0728 +-S- (non-ring)|[SH0X2;!R]|32.065 +-S- (ring)|[#16H0X2;R]|32.065 \ No newline at end of file diff --git a/ugropy/groupscsv/psrk/psrk_subgroups.csv b/ugropy/groupscsv/psrk/psrk_subgroups.csv index de9747d..f812bbf 100644 --- a/ugropy/groupscsv/psrk/psrk_subgroups.csv +++ b/ugropy/groupscsv/psrk/psrk_subgroups.csv @@ -110,18 +110,18 @@ C4H2S|[s;$([s](:[cH]:[cH]1):[cH0]:[cH0]:1),$([s](:[cH]:[cH0]1):[cH0]:[cH]:1),$([ H2C=CH2|[CH2]=[CH2]|28.0532 CH=-CH|[CH]#[CH]|26.0376 NH3|[NH3]|17.0304 -CO|[CH0]#[O]|28.01 +CO|[CH0X1]#[OH0X1]|28.01 H2|[#1][#1]|2.0156 -H2S|[SH2]|34.0806 -N2|N#N|28.014 +H2S|[SH2X2]|34.0806 +N2|[NH0X1]#[NH0X1]|28.014 AR|[Ar]|39.948 CO2|[CH0](=O)=O|44.009 CH4|[CH4]|16.0422 O2|[OX1]=[OX1]|31.998 ? D2|[2H][2H]|4.02820356 -SO2|[S](=O)=O|64.063 +SO2|[SX2](=O)=O|64.063 NO|[NX1]=[OX1]|30.006 -N2O|[N]=[N]=[O]|44.013 +N2O|[NX1]=[NX2]=[OX1]|44.013 SF6|[S]([F])([F])([F])([F])([F])[F]|146.053 HE|[He]|4.0026 NE|[Ne]|20.18 @@ -131,9 +131,9 @@ HF|[FH]|20.0058 HCL|[ClH]|36.4608 HBR|[BrH]|80.9118 HI|[IH]|127.9078 -COS|O=C=S|60.075 -CHSH|[CH][SH]|46.0916 -CSH|[CH0][SH]|45.0838 +COS|[OX1]=[CX2]=[SX1]|60.075 +CHSH|[CH][SX2H]|46.0916 +CSH|[CH0][SX2H]|45.0838 H2COCH|[CH2]([O]1)[CH]1|43.0444 HCOCH|[CH]([O]1)[CH]1|42.0366 HCOC|[CH0]([O]1)[CH]1|41.0288 diff --git a/ugropy/models/joback.py b/ugropy/models/joback.py index e891102..8460559 100644 --- a/ugropy/models/joback.py +++ b/ugropy/models/joback.py @@ -1,402 +1,13 @@ -"""PropertiesEstimator module.""" +from ugropy.constants import _csvs +from ugropy.core.frag_classes.joback.joback_model import JobackModel +from ugropy.models.read_csv import _rd -from typing import Union +# ============================================================================= +# Joback +# ============================================================================= +_jb = _csvs / "joback" -import pandas as pd +_jb_sg = _rd(_jb / "joback_subgroups.csv", "group") +_jb_props = _rd(_jb / "properties_contrib.csv", "group") -from ugropy.core.frag_classes.base_class.fragmentation_model import ( - FragmentationModel, -) -from ugropy.core.frag_classes.base_class.fragmentation_model import ( - FragmentationResult, -) - -from rdkit import Chem - -import numpy as np - - -class Joback(FragmentationModel): - """Joback Fragmentation model dedicated to properties estimation models. - - Parameters - ---------- - subgroups : pd.DataFrame - Model's subgroups. Index: 'group' (subgroups names). Mandatory columns: - 'smarts' (SMARTS representations of the group to detect its precense in - the molecule), 'molecular_weight' (molecular weight of the subgroups - used to check that the result is correct). - properties_contributions : pd.DataFrame, optional - Group's properties contributions, by default None - - Attributes - ---------- - subgroups : pd.DataFrame - Model's subgroups. Index: 'group' (subgroups names). Mandatory columns: - 'smarts' (SMARTS representations of the group to detect its precense in - the molecule), 'molecular_weight' (molecular weight of the subgroups - used to check that the result is correct). - detection_mols : dict - Dictionary cotaining all the rdkit Mol object from the detection_smarts - subgroups column - properties_contributions : pd.DataFrame - Group's properties contributions. - """ - - def __init__( - self, - subgroups: pd.DataFrame, - properties_contributions: Union[pd.DataFrame, None] = None, - ): - super().__init__(subgroups) - - # Properties contributions - self.properties_contributions = properties_contributions - - def set_fragmentation_result( - self, - molecule: Chem.rdchem.Mol, - subgroups_occurrences: dict, - subgroups_atoms_indexes: dict, - **kwargs, - ) -> "JobackFragmentationResult": - - result = JobackFragmentationResult( - self, - molecule, - subgroups_occurrences, - subgroups_atoms_indexes, - **kwargs, - ) - - return result - - -class JobackFragmentationResult(FragmentationResult): - """Joback group contribution properties estimator. - - The class recieves either the Joback and Reid model's :cite:p:`joback1, - joback2` groups, name or smiles of a molecule and estimates the its - properties. - - Parameters - ---------- - identifier : str or rdkit.Chem.rdchem.Mol - Identifier of a molecule (name, SMILES, groups, or Chem.rdchem.Mol). - Example: you can use hexane, CCCCCC, {"-CH3": 2, "-CH2-": 4} for name, - SMILES and groups respectively. - identifier_type : str, optional - Use 'name' to search a molecule by name, 'smiles' to provide the - molecule SMILES representation, 'groups' to provide Joback groups or - 'mol' to provide a rdkit.Chem.rdchem.Mol object, by default "name". - normal_boiling_point : float, optional - If provided, will be used to estimate critical temperature, acentric - factor, and vapor pressure instead of the estimated normal boiling - point, by default None. - - Attributes - ---------- - subgroups : dict - Joback functional groups of the molecule. - experimental_boiling_temperature : float - User provided experimental normal boiling point [K]. - critical_temperature : float - Joback estimated critical temperature [K]. - critical_pressure : float - Joback estimated critical pressure [bar]. - critical_volume : float - Joback estimated critical volume [cm³/mol]. - normal_boiling_point : float - Joback estimated normal boiling point [K]. - fusion_temperature : float - Joback estimated fusion temperature [K]. - h_formation : float - Joback estimated enthalpy of formation ideal gas at 298 K [kJ/mol]. - g_formation : float - Joback estimated Gibbs energy of formation ideal gas at 298 K [K]. - heat_capacity_ideal_gas_params : dict - Joback estimated Reid's ideal gas heat capacity equation parameters - [J/mol/K]. - h_fusion : float - Joback estimated fusion enthalpy [kJ/mol]. - h_vaporization : float - Joback estimated vaporization enthalpy at the normal boiling point - [kJ/mol]. - sum_na : float - Joback n_A contribution to liquid viscosity [N/s/m²]. - sum_nb : float - Joback n_B contribution to liquid viscosity [N/s/m²]. - molecular_weight : float - Molecular weight from Joback's subgroups [g/mol]. - acentric_factor : float - Acentric factor from Lee and Kesler's equation :cite:p:`joback1`. - vapor_pressure_params : dict - Vapor pressure G and k parameters for the Riedel-Plank-Miller - :cite:p:`joback1` equation [bar]. - """ - - def __init__( - self, - model: Joback, - molecule: Chem.rdchem.Mol, - subgroups: dict, - subgroups_atoms_indexes: dict, - normal_boiling_point: float = None, - ) -> None: - # Initialize the FragmentationResult attributes - super().__init__(molecule, subgroups, subgroups_atoms_indexes) - - # experimental boiling temperature - self.experimental_boiling_temperature = normal_boiling_point - - # Original Joback properties - self.critical_temperature = None - self.critical_pressure = None - self.critical_volume = None - self.normal_boiling_point = None - self.fusion_temperature = None - self.h_formation = None - self.g_formation = None - self.heat_capacity_ideal_gas_params = np.array([]) - self.h_fusion = None - self.h_vaporization = None - self.sum_na = None - self.sum_nb = None - self.molecular_weight = None - - # Extra properties - self.acentric_factor = None - self.vapor_pressure_params = {} - - # Fill the properties' values - if self.subgroups != {}: - self._calculate_properties(model) - - def heat_capacity_ideal_gas( - self, temperature: Union[float, np.ndarray] - ) -> Union[float, np.ndarray]: - """Calculate the ideal gas heat capacity [J/mol/K]. - - Uses the Joback estimated Reid's ideal gas heat capacity equation - parameters [J/mol/K]. - - Parameters - ---------- - temperature : Union[float, np.ndarray] - Temperature [K] - - Returns - ------- - Union[float, np.ndarray] - Ideal gas heat capacity [J/mol/K]. - """ - a, b, c, d = self.heat_capacity_ideal_gas_params - - t = temperature - - return a + b * t + c * t**2 + d * t**3 - - def heat_capacity_liquid( - self, temperature: Union[float, np.ndarray] - ) -> Union[float, np.ndarray]: - """Calculate the liquid heat capacity [J/mol/K]. - - Uses the Rowlinson-Bondi :cite:p:`joback1` equation with the Joback - estimated properties. - - Parameters - ---------- - temperature : Union[float, np.ndarray] - Temperature [K] - - Returns - ------- - Union[float, np.ndarray] - Ideal gas heat capacity [J/mol/K]. - """ - tr = temperature / self.critical_temperature - w = self.acentric_factor - - c_p0 = self.heat_capacity_ideal_gas(temperature) - - c_pl = c_p0 + R * ( - 2.56 - + 0.436 * (1 - tr) ** (-1) - + w - * ( - 2.91 - + 4.28 * (1 - tr) ** (-1 / 3) * tr ** (-1) - + 0.296 * (1 - tr) ** (-1) - ) - ) - - return c_pl - - def viscosity_liquid( - self, temperature: Union[float, np.ndarray] - ) -> Union[float, np.ndarray]: - """Calculate the Joback estimated liquid viscosity [N/s/m²]. - - Parameters - ---------- - temperature : Union[float, np.ndarray] - Temperature [K] - - Returns - ------- - Union[float, np.ndarray] - Liquid viscosity [N/s/m²]. - """ - t = temperature - - n_l = self.molecular_weight * np.exp( - (self.sum_na - 597.82) / t + self.sum_nb - 11.202 - ) - return n_l - - def vapor_pressure( - self, temperature: Union[float, np.ndarray] - ) -> Union[float, np.ndarray]: - """Calculate the vapor pressure [bar]. - - Uses the Riedel-Plank-Miller :cite:p:`joback1` equation with the Joback - estimated properties. - - Parameters - ---------- - temperature : Union[float, np.ndarray] - Temperature [K] - - Returns - ------- - Union[float, np.ndarray] - Vapor pressure [bar] - """ - tr = temperature / self.critical_temperature - - g = self.vapor_pressure_params["G"] - k = self.vapor_pressure_params["k"] - - vp_r = np.exp(-g / tr * (1 - tr**2 + k * (3 + tr) * (1 - tr) ** 3)) - - vp = vp_r * self.critical_pressure - - return vp - - def _calculate_properties(self, model: Joback) -> None: - """Obtain the molecule properties from Joback's groups.""" - groups = list(self.subgroups.keys()) - ocurr = list(self.subgroups.values()) - - df = model.properties_contributions.loc[groups] - - # ===================================================================== - # Calculate complete contribution properties (no contribution missing) - # ===================================================================== - tc_c = df["Tc"].to_numpy() - pc_c = df["Pc"].to_numpy() - vc_c = df["Vc"].to_numpy() - tb_c = df["Tb"].to_numpy() - tf_c = df["Tf"].to_numpy() - hform_c = df["Hform"].to_numpy() - gform_c = df["Gform"].to_numpy() - hvap_c = df["Hvap"].to_numpy() - numa_c = df["num_of_atoms"].to_numpy() - mw_c = model.subgroups.loc[groups, "molecular_weight"].to_numpy() - - # Molecular weight - self.molecular_weight = np.dot(ocurr, mw_c) - - # Joback normal boiling point (Tb) - self.normal_boiling_point = 198.2 + np.dot(ocurr, tb_c) - - # Fusion temperature (Tf) - self.fusion_temperature = 122.5 + np.dot(ocurr, tf_c) - - # Used normal boiling point for calculations - if self.experimental_boiling_temperature is not None: - tb = self.experimental_boiling_temperature - else: - tb = self.normal_boiling_point - - # Critical temperature (Tc) normal boiling temperature for calculations - self.critical_temperature = tb * ( - 0.584 + 0.965 * np.dot(ocurr, tc_c) - (np.dot(ocurr, tc_c)) ** 2 - ) ** (-1) - - # Critical pressure (Pc) - self.critical_pressure = ( - 0.113 + 0.0032 * np.dot(ocurr, numa_c) - np.dot(ocurr, pc_c) - ) ** (-2) - - # Critical volume (Vc) - self.critical_volume = 17.5 + np.dot(ocurr, vc_c) - - # Standard enthalpy of formation (298 K) - self.h_formation = 68.29 + np.dot(ocurr, hform_c) - - # Standard Gibbs energy of formation (298 K) - self.g_formation = 53.88 + np.dot(ocurr, gform_c) - - # Enthalpy of vaporization - self.h_vaporization = 15.30 + np.dot(ocurr, hvap_c) - - # ===================================================================== - # Incomplete contribution properties (some contribution missing) - # ===================================================================== - # Heat capacity - if "-N= (ring)" not in groups: - a_c = df["a"].to_numpy() - b_c = df["b"].to_numpy() - c_c = df["c"].to_numpy() - d_c = df["d"].to_numpy() - - a = np.dot(ocurr, a_c) - 37.93 - b = np.dot(ocurr, b_c) + 0.21 - c = np.dot(ocurr, c_c) - 3.91e-4 - d = np.dot(ocurr, d_c) + 2.06e-7 - - self.heat_capacity_ideal_gas_params = np.array([a, b, c, d]) - - # Enthalpy of fusion - if all(df["Hfusion"].notnull()): - hfusion_c = df["Hfusion"].to_numpy() - self.h_fusion = -0.88 + np.dot(ocurr, hfusion_c) - - # Liquid viscosity - if all(df["na"].notnull()): - na_c = df["na"].to_numpy() - nb_c = df["nb"].to_numpy() - - self.sum_na = np.dot(ocurr, na_c) - self.sum_nb = np.dot(ocurr, nb_c) - - # ===================================================================== - # Extra properties - # ===================================================================== - # Reduced normal boiling point temperature - t_br = tb / self.critical_temperature - - # Lee and Kesler's equation (acentric factor) - pc = self.critical_pressure - self.acentric_factor = ( - -np.log(pc) - - 5.92714 - + 6.09648 / t_br - + 1.28862 * np.log(t_br) - - 0.169347 * t_br**6 - ) / ( - 15.2518 - - 15.6875 / t_br - - 13.4721 * np.log(t_br) - + 0.43577 * t_br**6 - ) - - # Riedel-Plank-Miller equation (vapor pressure [bar]) - h = t_br * np.log(self.critical_pressure / 1.01325) / (1 - t_br) - - g = 0.4835 + 0.4605 * h - - k = (h / g - (1 + t_br)) / ((3 + t_br) * (1 - t_br) ** 2) - - self.vapor_pressure_params = {"G": g, "k": k} +joback = JobackModel(_jb_sg, _jb_props) diff --git a/ugropy/models/psrk.py b/ugropy/models/psrk.py index d204614..be9f6d3 100644 --- a/ugropy/models/psrk.py +++ b/ugropy/models/psrk.py @@ -4,7 +4,7 @@ # ============================================================================= -# LV-UNIFAC +# PSRK # ============================================================================= _psrk = _csvs / "psrk"