new functional groups and old one revisited

Auto-Mech · Oct 11, 2024 · d89f041 · d89f041
1 parent 9438691
commit d89f041
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Showing 4 changed files with 865 additions and 301 deletions.
diff --git a/automol/graph/__init__.py b/automol/graph/__init__.py
@@ -46,6 +46,11 @@
     ts_geometry_from_reactants,
 )
 
+# # super species groups
+from ._3super_func_group import (
+    SuperFunctionalGroup,
+    classify_species,
+)
 # submodules:
 from .base import ts, vmat
 
@@ -363,9 +368,13 @@
 from .base._func_group import (
     FunctionalGroup,
     alcohol_groups,
+    alkoxy_OC_groups,
     aldehyde_groups,
+    alkane_sites,
     alkene_sites,
     alkyne_sites,
+    propyne_sites,
+    allene_sites,
     amide_groups,
     bonds_of_order,
     bonds_of_type,
@@ -382,9 +391,19 @@
     ketone_groups,
     methyl_groups,
     aromatic_groups,
+    benzene_groups,
     phenyl_groups,
     benzyl_groups,
     cyclopentadienyl_groups,
+    cyclopentadiene_groups,
+    cyclopentadienone_groups,
+    fulvene_groups,
+    phenoxy_groups,
+    allyl_groups,
+    allyl_groups_lowestspin,
+    cyclopentenyl_groups,
+    c5h5o_groups,
+    furan_groups,
     neighbors_of_type,
     nitro_groups,
     peroxy_groups,
@@ -690,9 +709,13 @@
     "is_hydrocarbon_species",
     "is_radical_species",
     # # finders for reactive sites and groups
+    "alkane_sites",
     "alkene_sites",
     "alkyne_sites",
+    "propyne_sites",
+    "allene_sites",
     "alcohol_groups",
+    "alkoxy_OC_groups",
     "peroxy_groups",
     "hydroperoxy_groups",
     "ether_groups",
@@ -707,9 +730,19 @@
     "thiol_groups",
     "methyl_groups",
     "aromatic_groups",
+    "benzene_groups",
     "phenyl_groups",
     "benzyl_groups",
     "cyclopentadienyl_groups",
+    "cyclopentadiene_groups",
+    "cyclopentadienone_groups",
+    "fulvene_groups",
+    "phenoxy_groups",
+    "allyl_groups",
+    "allyl_groups_lowestspin",
+    "cyclopentenyl_groups",
+    "c5h5o_groups",
+    "furan_groups",
     "radical_dissociation_products",
     # # helper functions
     "bonds_of_type",
@@ -743,4 +776,7 @@
     "svg_string",
     "ipywidget",
     "perturb_geometry_planar_dihedrals",
+    # # species classification
+    "SuperFunctionalGroup",
+    "classify_species",
 ]
diff --git a/automol/graph/base/__init__.py b/automol/graph/base/__init__.py
@@ -346,10 +346,14 @@
 from ._func_group import is_radical_species
 
 # # finders for reactive sites and groups
+from ._func_group import alkane_sites
 from ._func_group import alkene_sites
 from ._func_group import alkyne_sites
+from ._func_group import propyne_sites
+from ._func_group import allene_sites
 from ._func_group import alcohol_groups
 from ._func_group import peroxy_groups
+from ._func_group import alkoxy_OC_groups
 from ._func_group import hydroperoxy_groups
 from ._func_group import ether_groups
 from ._func_group import cyclic_ether_groups
@@ -363,9 +367,19 @@
 from ._func_group import thiol_groups
 from ._func_group import methyl_groups
 from ._func_group import aromatic_groups
+from ._func_group import benzene_groups
 from ._func_group import phenyl_groups
 from ._func_group import benzyl_groups
 from ._func_group import cyclopentadienyl_groups
+from ._func_group import cyclopentadiene_groups
+from ._func_group import cyclopentadienone_groups
+from ._func_group import fulvene_groups
+from ._func_group import phenoxy_groups
+from ._func_group import allyl_groups
+from ._func_group import allyl_groups_lowestspin
+from ._func_group import cyclopentenyl_groups
+from ._func_group import c5h5o_groups
+from ._func_group import furan_groups
 from ._func_group import radical_dissociation_products
 
 # # helper functions
@@ -675,9 +689,13 @@
     "is_hydrocarbon_species",
     "is_radical_species",
     # # finders for reactive sites and groups
+    "alkane_sites",
     "alkene_sites",
     "alkyne_sites",
+    "propyne_sites",
+    "allene_sites",
     "alcohol_groups",
+    "alkoxy_OC_groups",
     "peroxy_groups",
     "hydroperoxy_groups",
     "ether_groups",
@@ -692,9 +710,19 @@
     "thiol_groups",
     "methyl_groups",
     "aromatic_groups",
+    "benzene_groups",
     "phenyl_groups",
     "benzyl_groups",
     "cyclopentadienyl_groups",
+    "cyclopentadiene_groups",
+    "cyclopentadienone_groups",
+    "fulvene_groups",
+    "phenoxy_groups",
+    "allyl_groups",
+    "allyl_groups_lowestspin",
+    "cyclopentenyl_groups",
+    "c5h5o_groups",
+    "furan_groups",
     "radical_dissociation_products",
     # # helper functions
     "bonds_of_type",