proper bonds for old topology

molecularnodes/entities/trajectory/oxdna/OXDNAParser.py

@@ -21,10 +21,26 @@ def _parseatoms(self):
         with open(self.filename) as f:
             first_line = f.readline()
 
-        dimensions = np.array(first_line.split(), dtype=int)
-        n_atoms = dimensions[0]
-
-        array = np.loadtxt(self.filename, skiprows=1, max_rows=n_atoms, dtype=str)
+        is_new_topology = "5->3" in first_line
+
+        if not is_new_topology:
+            dimensions = np.array(first_line.split(), dtype=int)
+            n_atoms = dimensions[0]
+            array = np.loadtxt(self.filename, skiprows=1, max_rows=n_atoms, dtype=str)
+
+            # each topology item has two bond columns, which say what the base is bonded
+            # from and what it is bonded to. -1 means it is not bonded
+            # we need to turn that into an array of bond pairs
+            bond_idx = np.zeros((n_atoms * 2, 2), int)
+            row_numbers = np.arange(n_atoms, dtype=int)
+            for i in range(2):
+                rows = row_numbers + (i * n_atoms)
+                bond_idx[rows, 0] = array[:, (i + 2)]
+                bond_idx[rows, 1] = row_numbers
+
+            # drop any that have -1 as they aren't bonded to anything
+            mask = np.logical_and(bond_idx[:, 0] != -1, bond_idx[:, 1] != -1)
+            bond_idx = bond_idx[mask, :]
 
         attrs = []
         idx = np.arange(1, n_atoms + 1, dtype=int)
@@ -35,10 +51,6 @@ def _parseatoms(self):
 
         topo = Topology(n_atoms, n_atoms, 1, attrs=attrs)
 
-        bond_idx = array[:, 2:].astype(int)
-        mask = np.logical_and(bond_idx[:, 0] != -1, bond_idx[:, 1] != -1)
-        bond_idx = bond_idx[mask, :]
-
         bonds = Bonds(bond_idx)
         topo.add_TopologyAttr(bonds)
 

tests/test_dna.py

@@ -1,5 +1,3 @@
-import numpy as np
-import molecularnodes as mn
 import pytest
 import MDAnalysis as mda
 from molecularnodes.entities.trajectory import dna