UNIFAC PSRK and Joback passing, a lots less bugs

ipqa-research · Oct 18, 2024 · 9bc01d1 · 9bc01d1
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diff --git 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
@@ -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"""
         <div style="border: 1px solid #ccc; padding: 10px; margin-bottom: 20px; border-radius: 5px;">

diff --git 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
+"CCOC(O)=O" multiple solutions
diff --git 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
@@ -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
@@ -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,