Merge pull request #28 from alexandrefassio/master

Latest version

Author: alexandrefassio

luna/analysis/residues.py

@@ -1,4 +1,6 @@
 from collections import Counter, defaultdict
+import pandas as pd
+from luna.mol.entry import MolEntry
 
 
 class InteractingResidues:
@@ -78,3 +80,73 @@ def calculate_residues_frequency(interaction_tuples):
             global_freq[k].add(entry, interacting_res_mapping[k])
 
     return global_freq
+
+
+def generate_residue_matrix(interactions_mngrs, by_interaction=True):
+
+    data_by_entry = defaultdict(lambda: defaultdict(int))
+    residues = set()
+
+    for inter_mngr in interactions_mngrs:
+        entry = inter_mngr.entry
+
+        for inter in inter_mngr:
+            # Continue if no target is in the interaction.
+            if not inter.src_grp.has_target() and not inter.trgt_grp.has_target():
+                continue
+            # Ignore interactions involving the same compounds.
+            if inter.src_grp.compounds == inter.trgt_grp.compounds:
+                continue
+
+            if inter.src_grp.has_hetatm():
+                comp1 = sorted(inter.src_grp.compounds)
+                comp2 = sorted(inter.trgt_grp.compounds)
+            elif inter.trgt_grp.has_hetatm():
+                comp1 = sorted(inter.trgt_grp.compounds)
+                comp2 = sorted(inter.src_grp.compounds)
+            else:
+                comp1 = sorted(inter.src_grp.compounds)
+                comp2 = sorted(inter.trgt_grp.compounds)
+                comp1, comp2 = sorted([comp1, comp2])
+
+            comp1 = ";".join(["%s/%s/%d%s" % (r.parent.id, r.resname, r.id[1], r.id[2].strip()) for r in comp1])
+            comp2 = ";".join(["%s/%s/%d%s" % (r.parent.id, r.resname, r.id[1], r.id[2].strip()) for r in comp2])
+
+            entry_id = entry.mol_id if isinstance(entry, MolEntry) else entry.to_string()
+            if by_interaction:
+                key = (entry_id, inter.type)
+            else:
+                key = entry_id
+
+            data_by_entry[key][comp2] += 1
+
+            residues.add(comp2)
+
+    heatmap_data = defaultdict(list)
+
+    if by_interaction:
+        entries = set([k[0] for k in data_by_entry.keys()])
+        interactions = set([k[1] for k in data_by_entry.keys()])
+
+        for e in entries:
+            for i in interactions:
+                for res in residues:
+                    heatmap_data["entry"].append(e)
+                    heatmap_data["interaction"].append(i)
+                    heatmap_data["residues"].append(res)
+                    heatmap_data["frequency"].append(data_by_entry[(e, i)][res])
+
+    else:
+        for key in data_by_entry:
+            for res in data_by_entry[key]:
+                heatmap_data["entry"].append(key)
+
+                heatmap_data["residues"].append(res)
+                heatmap_data["frequency"].append(data_by_entry[key][res])
+
+    df = pd.DataFrame.from_dict(heatmap_data)
+
+    if by_interaction:
+        return pd.pivot_table(df, index=['entry', 'interaction'], columns='residues', values='frequency', fill_value=0)
+    else:
+        return pd.pivot_table(df, index='entry', columns='residues', values='frequency', fill_value=0)

luna/version.py

@@ -5,7 +5,7 @@
             and interaction fingerprints;
        - PATCH stands for backward compatible bug fixes.
 """
-version_info = (0, 9, 0)
+version_info = (0, 10, 0)
 version = '.'.join(str(c) for c in version_info)
 __version__ = version