building secondary structures of CG

ipqa-research · Apr 22, 2024 · 73f9919 · 73f9919
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diff --git a/reminder.md b/reminder.md
@@ -1 +1,45 @@
+Constantinou Gani secondary test:
 
+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
diff --git a/ugropy/fragmentation_models/models.py b/ugropy/fragmentation_models/models.py
@@ -116,10 +116,10 @@ def _rd(file_path: str, index_col: str = None) -> pd.DataFrame:
 # Primary structures
 _cg = f"{_csvs}/constantinou_gani"
 
-_cg_sg = _rd(f"{_cg}/c_g_prymary_subgroups.csv", "group")
-_cg_problems = _rd(f"{_cg}/cg_problematics.csv", "smarts")
-_cg_hide = _rd(f"{_cg}/hideouts.csv", "group")
-_cg_props = _rd(f"{_cg}/properties_prymary_contrib.csv", "group")
+_cg_sg = _rd(f"{_cg}/primary/c_g_prymary_subgroups.csv", "group")
+_cg_problems = _rd(f"{_cg}/primary/cg_problematics.csv", "smarts")
+_cg_hide = _rd(f"{_cg}/primary/hideouts.csv", "group")
+_cg_props = _rd(f"{_cg}/primary/properties_prymary_contrib.csv", "group")
 
 constantinou_gani_primary = PropertiesEstimator(
     subgroups=_cg_sg,

diff --git a/...nstantinou_gani/c_g_prymary_subgroups.csv → ...ou_gani/primary/c_g_prymary_subgroups.csv b/...nstantinou_gani/c_g_prymary_subgroups.csv → ...ou_gani/primary/c_g_prymary_subgroups.csv
diff --git a/...csv/constantinou_gani/cg_problematics.csv → ...tantinou_gani/primary/cg_problematics.csv b/...csv/constantinou_gani/cg_problematics.csv → ...tantinou_gani/primary/cg_problematics.csv
diff --git a/.../groupscsv/constantinou_gani/hideouts.csv → ...sv/constantinou_gani/primary/hideouts.csv b/.../groupscsv/constantinou_gani/hideouts.csv → ...sv/constantinou_gani/primary/hideouts.csv
diff --git a/...tinou_gani/properties_prymary_contrib.csv → ...ni/primary/properties_prymary_contrib.csv b/...tinou_gani/properties_prymary_contrib.csv → ...ni/primary/properties_prymary_contrib.csv
diff --git a/ugropy/groupscsv/constantinou_gani/secondary/structures.csv b/ugropy/groupscsv/constantinou_gani/secondary/structures.csv
@@ -0,0 +1,16 @@
+group|smarts|contribute
+(CH3)2CH|[CH]([CH3])[CH3]|""{"(CH3)2CH": 1}"
+(CH3)3C|[CH0]([CH3])([CH3])[CH3]|""{"(CH3)3C": 1}"
+CH(CH3)CH(CH3)|[CH]([CH3])[CH]([CH3])|""{"CH(CH3)CH(CH3)": 1}"
+CH(CH3)C(CH3)2|[CH]([CH3])[CH0]([CH3])([CH3])|""{"CH(CH3)C(CH3)2": 1}"
+C(CH3)2C(CH3)2|[CH0]([CH3])([CH3])[CH0]([CH3])([CH3])|""{"C(CH3)2C(CH3)2": 1}"
+3 membered ring|[C;R]1[C;R][C;R]1|""{"3 membered ring": 1}"
+4 membered ring|[C;R]1[C;R][C;R][C;R]1|""{"4 membered ring": 1}"
+5 membered ring|[C;R]1[C;R][C;R][C;R][C;R]1|""{"5 membered ring": 1}"
+6 membered ring|[C;R]1[C;R][C;R][C;R][C;R][C;R]1|""{"6 membered ring": 1}"
+7 membered ring|[C;R]1[C;R][C;R][C;R][C;R][C;R][C;R]1|""{"7 membered ring": 1}"
+CHn=CHm-CHp=CHk|[C]=[C]-[C]=[C]|""{"CHn=CHm-CHp=CHk": 1}""
+CH3-CHm=CHn|[CH3]-[C]=[C]|""{"CH3-CHm=CHn": 1}""
+CH2-CHm=CHn|[CH2]-[C]=[C]|""{"CH2-CHm=CHn": 1}""
+CH-CHm=CHn|[CH1]-[C]=[C]|""{"CH-CHm=CHn": 1}""
+C-CHm=CHn|[CH0]-[C]=[C]|""{"C-CHm=CHn": 1}""