Return iterative resisue ids from tpr files.

Since Gromacs doesn't care about the residue number in gro files, they are
not stored in the tpr files and thus have to be reproduced by hand.
This solution increases the residue index with each new molecule.

pygmx/tpxio.pyx

@@ -49,38 +49,32 @@ cdef atoms_from_topology(gmx_mtop_t *topology):
         int moltype, resind
 
     atoms = []
-    masses = []
-    charges = []
     residues = []
+    res_id = 0
     for i_molblock in range(topology.nmolblock):
         moltype = topology.molblock[i_molblock].type
-
         c_atoms = topology.moltype[moltype].atoms
-        mol_atoms = []
+        for n in range(topology.molblock[i_molblock].nmol):
-        mol_q = []
+            mol_atoms = []
-        mol_m = []
+            res_id += 1
-        for i_atom in range(c_atoms.nr):
+            for i_atom in range(c_atoms.nr):
-            resind = c_atoms.atom[i_atom].resind
+                resind = c_atoms.atom[i_atom].resind
-            resname = c_atoms.resinfo[resind].name[0]
+                resname = c_atoms.resinfo[resind].name[0]
-            if resname not in residues:
+                if resname not in residues:
-                residues.append(resname)
+                    residues.append(resname)
-            resid = residues.index(resname) + 1
+                resid = residues.index(resname) + 1
-            mol_atoms.append((
+                mol_atoms.append((
-                resid,
+                    res_id,
-                resname,
+                    resname,
-                c_atoms.atomname[i_atom][0],
+                    c_atoms.atomname[i_atom][0],
-            ))
+                ))
-            mol_q.append(c_atoms.atom[i_atom].q)
+            atoms += mol_atoms
-            mol_m.append(c_atoms.atom[i_atom].m)
-        n_mol = topology.molblock[i_molblock].nmol
-        atoms += mol_atoms * n_mol
-        charges += mol_q * n_mol
-        masses += mol_m * n_mol
-
     return np.array(atoms)
 
+
 ctypedef object (*atom_func)(t_atom)
 
+
 cdef atom_charge(t_atom atom):
     return atom.q