harmonize output format of subgraph_isomorphism

_proc/.quarto/xref/INDEX

@@ -1,5 +1,5 @@
 {
   "index.ipynb": {
-    "README.md": "6246c3ef"
+    "README.md": "f518931d"
   }
 }

_proc/03_motif.ipynb

@@ -61,7 +61,7 @@
        "\n",
        ">      GlycoDraw (draw_this, vertical=False, compact=False, show_linkage=True,\n",
        ">                 dim=50, highlight_motif=None, highlight_termini_list=[],\n",
-       ">                 filepath=None)\n",
+       ">                 repeat=None, repeat_range=None, filepath=None)\n",
        "\n",
        "Draws a glycan structure based on the provided input.\n",
        "\n",
@@ -74,6 +74,8 @@
        "| dim (int, optional): The dimension (size) of the individual sugar units in the structure. Default: 50.\n",
        "| highlight_motif (string, optional): Glycan motif to highlight within the parent structure.\n",
        "| highlight_termini_list (list): list of monosaccharide positions (from 'terminal', 'internal', and 'flexible')\n",
+       "| repeat (bool | int | str): If specified, indicate repeat unit by brackets (True: n units, int: # of units, str: range of units)\n",
+       "| repeat_range (list of 2 int): List of index integers for the first and last main-chain monosaccharide in repeating unit. Monosaccharides are numbered starting from 0 (invisible placeholder = 0 in case of structure terminating in a linkage) at the reducing end. \n",
        "| filepath (string, optional): The path to the output file to save as SVG or PDF. Default: None."
       ],
       "text/plain": [
@@ -83,7 +85,7 @@
        "\n",
        ">      GlycoDraw (draw_this, vertical=False, compact=False, show_linkage=True,\n",
        ">                 dim=50, highlight_motif=None, highlight_termini_list=[],\n",
-       ">                 filepath=None)\n",
+       ">                 repeat=None, repeat_range=None, filepath=None)\n",
        "\n",
        "Draws a glycan structure based on the provided input.\n",
        "\n",
@@ -96,6 +98,8 @@
        "| dim (int, optional): The dimension (size) of the individual sugar units in the structure. Default: 50.\n",
        "| highlight_motif (string, optional): Glycan motif to highlight within the parent structure.\n",
        "| highlight_termini_list (list): list of monosaccharide positions (from 'terminal', 'internal', and 'flexible')\n",
+       "| repeat (bool | int | str): If specified, indicate repeat unit by brackets (True: n units, int: # of units, str: range of units)\n",
+       "| repeat_range (list of 2 int): List of index integers for the first and last main-chain monosaccharide in repeating unit. Monosaccharides are numbered starting from 0 (invisible placeholder = 0 in case of structure terminating in a linkage) at the reducing end. \n",
        "| filepath (string, optional): The path to the output file to save as SVG or PDF. Default: None."
       ]
      },
@@ -8472,15 +8476,15 @@
        "\n",
        "### get_possible_linkages\n",
        "\n",
-       ">      get_possible_linkages (wildcard, linkage_list={'b1-1', 'a1-6', '?2-?',\n",
-       ">                             '?1-?', 'a1-3', 'a1-4', 'b1-6', 'b2-3', 'a1-7',\n",
-       ">                             'a2-5', 'b2-8', 'a2-8', 'b2-4', 'b2-7', 'a2-6',\n",
-       ">                             '?2-3', 'a2-3', 'a1-8', 'a2-11', '?1-6', 'a1-1',\n",
-       ">                             'b1-8', 'a2-?', '?2-6', 'a2-7', 'b2-6', 'b1-2',\n",
-       ">                             'b1-4', '1-4', '1-6', 'a2-1', 'a2-2', 'b2-1',\n",
-       ">                             'b1-?', 'a1-2', 'b1-7', 'a1-11', '?2-8', 'a1-5',\n",
-       ">                             '?1-3', 'b1-3', 'b1-9', 'b2-2', 'a1-?', 'b1-5',\n",
-       ">                             '?1-2', 'a1-9', 'a2-9', 'b2-5', '?1-4', 'a2-4'},\n",
+       ">      get_possible_linkages (wildcard, linkage_list={'?2-6', 'a1-6', '1-4',\n",
+       ">                             'b1-5', 'a2-8', '1-6', 'a2-5', 'b1-1', 'b2-3',\n",
+       ">                             '?1-3', 'a1-7', 'a1-5', 'b2-6', '?1-?', 'b1-7',\n",
+       ">                             'b2-1', 'a2-?', 'a1-9', '?2-?', 'a1-1', '?2-3',\n",
+       ">                             '?1-6', 'b1-2', '?2-8', 'a2-7', 'a1-?', 'b1-3',\n",
+       ">                             'a2-3', 'a2-2', 'a2-1', 'a1-2', 'a2-4', 'b1-9',\n",
+       ">                             'a1-8', 'a1-11', 'b2-8', '?1-2', 'b1-?', 'a2-11',\n",
+       ">                             'b2-5', 'a2-6', 'b1-4', 'b1-6', 'b2-4', 'a2-9',\n",
+       ">                             '?1-4', 'a1-3', 'b2-2', 'a1-4', 'b1-8', 'b2-7'},\n",
        ">                             libr=None)\n",
        "\n",
        "Retrieves all linkages that match a given wildcard pattern from a list of linkages\n",
@@ -8500,15 +8504,15 @@
        "\n",
        "### get_possible_linkages\n",
        "\n",
-       ">      get_possible_linkages (wildcard, linkage_list={'b1-1', 'a1-6', '?2-?',\n",
-       ">                             '?1-?', 'a1-3', 'a1-4', 'b1-6', 'b2-3', 'a1-7',\n",
-       ">                             'a2-5', 'b2-8', 'a2-8', 'b2-4', 'b2-7', 'a2-6',\n",
-       ">                             '?2-3', 'a2-3', 'a1-8', 'a2-11', '?1-6', 'a1-1',\n",
-       ">                             'b1-8', 'a2-?', '?2-6', 'a2-7', 'b2-6', 'b1-2',\n",
-       ">                             'b1-4', '1-4', '1-6', 'a2-1', 'a2-2', 'b2-1',\n",
-       ">                             'b1-?', 'a1-2', 'b1-7', 'a1-11', '?2-8', 'a1-5',\n",
-       ">                             '?1-3', 'b1-3', 'b1-9', 'b2-2', 'a1-?', 'b1-5',\n",
-       ">                             '?1-2', 'a1-9', 'a2-9', 'b2-5', '?1-4', 'a2-4'},\n",
+       ">      get_possible_linkages (wildcard, linkage_list={'?2-6', 'a1-6', '1-4',\n",
+       ">                             'b1-5', 'a2-8', '1-6', 'a2-5', 'b1-1', 'b2-3',\n",
+       ">                             '?1-3', 'a1-7', 'a1-5', 'b2-6', '?1-?', 'b1-7',\n",
+       ">                             'b2-1', 'a2-?', 'a1-9', '?2-?', 'a1-1', '?2-3',\n",
+       ">                             '?1-6', 'b1-2', '?2-8', 'a2-7', 'a1-?', 'b1-3',\n",
+       ">                             'a2-3', 'a2-2', 'a2-1', 'a1-2', 'a2-4', 'b1-9',\n",
+       ">                             'a1-8', 'a1-11', 'b2-8', '?1-2', 'b1-?', 'a2-11',\n",
+       ">                             'b2-5', 'a2-6', 'b1-4', 'b1-6', 'b2-4', 'a2-9',\n",
+       ">                             '?1-4', 'a1-3', 'b2-2', 'a1-4', 'b1-8', 'b2-7'},\n",
        ">                             libr=None)\n",
        "\n",
        "Retrieves all linkages that match a given wildcard pattern from a list of linkages\n",

_proc/04_network.ipynb

@@ -54,8 +54,8 @@
        "\n",
        "### construct_network\n",
        "\n",
-       ">      construct_network (glycans, libr=None, allowed_ptms={'3S', 'OAc', '6S',\n",
-       ">                         '6P', '1P', 'OP', '4Ac', '3P', 'OS', '9Ac'},\n",
+       ">      construct_network (glycans, libr=None, allowed_ptms={'3P', '3S', 'OS',\n",
+       ">                         '1P', '9Ac', '6P', '6S', 'OP', 'OAc', '4Ac'},\n",
        ">                         edge_type='monolink', permitted_roots=None)\n",
        "\n",
        "construct a glycan biosynthetic network\n",
@@ -77,8 +77,8 @@
        "\n",
        "### construct_network\n",
        "\n",
-       ">      construct_network (glycans, libr=None, allowed_ptms={'3S', 'OAc', '6S',\n",
-       ">                         '6P', '1P', 'OP', '4Ac', '3P', 'OS', '9Ac'},\n",
+       ">      construct_network (glycans, libr=None, allowed_ptms={'3P', '3S', 'OS',\n",
+       ">                         '1P', '9Ac', '6P', '6S', 'OP', 'OAc', '4Ac'},\n",
        ">                         edge_type='monolink', permitted_roots=None)\n",
        "\n",
        "construct a glycan biosynthetic network\n",