migrate leontis-westhof

tests/structure/data/base_pairs/create_bond_orientation_test_data.py

@@ -0,0 +1,77 @@
+import pandas as pd
+import argparse
+import numpy as np
+import json
+
+def process(input, output, chain):
+    data = pd.read_csv(input)
+    # Only retain rows with basepair annotation
+    data = data[data['Leontis-Westhof'].notna()]
+
+    output_list = []
+
+    for _, row in data.iterrows():
+
+        nucleotides = [row['Nucleotide 1'], row['Nucleotide 2']]
+
+        # Extract the Leontis-Westhof annotation
+        lw_string = row['Leontis-Westhof']
+
+        # Some interactions are labelled with `n` for near. These are
+        # ignored
+        if lw_string[0] == 'n':
+            continue
+
+        # Get sugar orientation from string (`c` = cis, `t` = trans)
+        sugar_orientation = lw_string[0]
+
+        # The residue ids of the nucleotides
+        res_ids = [None]*2
+
+        for i, nucleotide in enumerate(nucleotides):
+            nucleotide_list = nucleotide.split('.')
+
+            # if the nucleotide is not part of the specified chain, skip
+            # base pair
+            if nucleotide_list[1] != chain:
+                break
+
+            res_ids[i] = nucleotide_list[3]
+
+        if None in res_ids:
+            continue
+
+        if sugar_orientation == 'c':
+            sugar_orientation = 1
+        elif sugar_orientation == 't':
+            sugar_orientation = 2
+
+        this_output = sorted((int(res_ids[0]), int(res_ids[1])))
+        this_output.append(int(sugar_orientation))
+        output_list.append(this_output)
+    output_list = np.unique(output_list, axis=0).tolist()
+    with open(output, 'w') as f:
+        json.dump(output_list, f, indent=1)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Parse the glycosidic bond orientation annotations in the "
+        "NAKB-database for a specific chain. The annotations can be "
+        "downloaded in the section 'Base Pairs'."
+    )
+    parser.add_argument(
+        "infile",
+        help="The path to the input file."
+    )
+    parser.add_argument(
+        "outfile",
+        help="The path to the output JSON file."
+    )
+    parser.add_argument(
+        "chain",
+        help="The chain ID to be extracted."
+    )
+    args = parser.parse_args()
+
+    process(args.infile, args.outfile, args.chain)
+

tests/structure/data/base_pairs/create_interacting_edge_test_data.py

@@ -0,0 +1,89 @@
+import pandas as pd
+import argparse
+import json
+import numpy as np
+
+def process(input, output, chain):
+    data = pd.read_csv(input)
+    # Only retain rows with basepair annotation
+    data = data[data['Leontis-Westhof'].notna()]
+
+    output_list = []
+
+    for _, row in data.iterrows():
+        nucleotides = [row['Nucleotide 1'], row['Nucleotide 2']]
+
+        # Extract the Leontis-Westhof annotation
+        lw_string = row['Leontis-Westhof']
+
+        # Some interactions are labelled with `n` for near. These are
+        # ignored
+        if lw_string[0] == 'n':
+            continue
+
+        # Get edge annotations from string
+        edges = [lw_string[-2], lw_string[-1]]
+
+        # Dont allow unspecified edges in test data
+        if '.' in edges:
+            continue
+
+        res_ids = [None]*2
+        for i, nucleotide in enumerate(nucleotides):
+            nucleotide_list = nucleotide.split('.')
+
+            # if the nucleotide is not part of the specified chain, skip
+            # base pair
+            if nucleotide_list[1] != chain:
+                break
+
+            res_ids[i] = nucleotide_list[3]
+
+        if None in res_ids:
+            continue
+
+        for i, edge in enumerate(edges):
+            if edge == 'W':
+                edges[i] = 1
+            if edge == 'H':
+                edges[i] = 2
+            if edge == 'S':
+                edges[i] = 3
+
+        # Lower residue id on the left, higher residue id on the right
+        res_ids = np.array(res_ids, dtype=int)
+        edges = np.array(edges, dtype=int)
+        sorter = np.argsort(res_ids)
+        res_ids = res_ids[sorter]
+        edges = edges[sorter]
+
+        output_list.append(
+            (int(res_ids[0]), int(res_ids[1]), int(edges[0]), int(edges[1]))
+        )
+
+    output_list = np.unique(output_list, axis=0).tolist()
+    with open(output, 'w') as f:
+        json.dump(output_list, f, indent=1)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Parse the edge type annotations in the NAKB-database for "
+        "a specific chain. The annotations can be downloaded in the section "
+        "'Base Pairs'."
+    )
+    parser.add_argument(
+        "infile",
+        help="The path to the input file."
+    )
+    parser.add_argument(
+        "outfile",
+        help="The path to the output JSON file."
+    )
+    parser.add_argument(
+        "chain",
+        help="The chain ID to be extracted."
+    )
+    args = parser.parse_args()
+
+    process(args.infile, args.outfile, args.chain)
+