enable prody integration

requirements.txt

@@ -3,3 +3,4 @@ MDAnalysisTests>=2.4.3
 networkx>=3.1
 torch_geometric>=2.0
 torch >= 2.0
+ProDy >= 2.4.1

src/graphpro/model.py

@@ -1,4 +1,6 @@
 import torch
+import prody as pdy
+import MDAnalysis as mda
 
 from functools import reduce
 
@@ -30,14 +32,66 @@ def c_alphas_positions(self, chain: None):
     def c_alphas_residues(self, chain: None):
         pass
 
+    def positions(self):
+        pass
+
+    def names(self):
+        """ Return atoms names
+        """
+        pass
+
+    def resnames(self):
+        """ Returns resnames
+        """
+        pass
+
+    def resnums(self):
+        """ Returns resnumbers
+        """
+        pass
+
+    def chain_ids(self):
+        """ Returns the chainId for each individual atom
+        """
+        pass
+
+    def to_prody(self) -> pdy.AtomGroup:
+        ag = pdy.AtomGroup('name')
+        ag.setCoords(self.positions())
+        ag.setNames(self.names())
+        ag.setResnames(self.resnames())
+        ag.setResnums(self.resnums())
+        ag.setChids(self.chain_ids())
+        return ag
+
 
 class MDAnalisysAtomGroup(AtomGroup):
-    def __init__(self, atom_goup):
-        self.atoms = atom_goup
+    def __init__(self, atom_group):
+        if isinstance(atom_group, mda.Universe):
+            self.atoms = atom_group.atoms
+        else:
+            self.atoms = atom_group
 
     def n_atoms(self):
         return self.n_atoms
 
+
+    def positions(self):
+        return self.atoms.positions
+
+
+    def names(self):
+        return self.atoms.names
+
+    def resnames(self):
+        return self.atoms.resnames
+
+    def resnums(self):
+        return self.atoms.resnums
+
+    def chain_ids(self):
+        return [a.chainID for a in self.atoms]
+
     def _c_alphas(self, chain=None):
         chain_sel = ''
         if chain is not None:

test/graphpro/model_test.py

@@ -14,3 +14,29 @@ def test_model_from_mdanalysis_partial_occupancy():
     ag = MDAnalisysAtomGroup(FIVEHTC)
     assert(len(ag.c_alphas_residues(chain="C")) ==
            len(ag.c_alphas_positions(chain="C")))
+
+
+def test_transform_to_prody_contains_same_atoms():
+    ag = MDAnalisysAtomGroup(FIVEHTC)
+    pdAG = ag.to_prody()
+    assert(len(pdAG) == 3346)
+
+def test_transform_to_prody_cotains_atom_names():
+    ag = MDAnalisysAtomGroup(FIVEHTC)
+    pdAG = ag.to_prody()
+    assert(pdAG.getNames()[0] == 'N')
+
+def test_transform_to_prody_cotains_residue_names():
+    ag = MDAnalisysAtomGroup(FIVEHTC)
+    pdAG = ag.to_prody()
+    assert(pdAG.getResnames()[0] == 'GLY')
+
+def test_transform_to_prody_cotains_residue_number():
+    ag = MDAnalisysAtomGroup(FIVEHTC)
+    pdAG = ag.to_prody()
+    assert(pdAG.getResnums()[0] == 471)
+
+def test_transform_to_prody_contains_chain_id():
+    ag = MDAnalisysAtomGroup(FIVEHTC)
+    pdAG = ag.to_prody()
+    assert(pdAG.getChids()[0] == 'A')