basic guesser features

package/MDAnalysis/__init__.py

@@ -179,7 +179,7 @@
 _TOPOLOGY_ATTRS = {}  # {attrname: cls}
 _TOPOLOGY_TRANSPLANTS = {}   # {name: [attrname, method, transplant class]}
 _TOPOLOGY_ATTRNAMES = {}  # {lower case name w/o _ : name}
-
+_GUESSERS = {}
 
 # custom exceptions and warnings
 from .exceptions import (

package/MDAnalysis/converters/OpenMMParser.py

@@ -60,7 +60,6 @@
 
 from ..topology.base import TopologyReaderBase
 from ..topology.tables import SYMB2Z
-from ..topology.guessers import guess_types, guess_masses
 from ..core.topology import Topology
 from ..core.topologyattrs import (
     Atomids,
@@ -108,11 +107,6 @@ def _mda_topology_from_omm_topology(self, omm_topology):
         -------
         top : MDAnalysis.core.topology.Topology
 
-        Note
-        ----
-        When none of the elements are present in the openmm topolgy, their
-        atomtypes are guessed using their names and their masses are
-        then guessed using their atomtypes.
 
         When partial elements are present, values from available elements
         are used whereas the absent elements are assigned an empty string
@@ -192,8 +186,6 @@ def _mda_topology_from_omm_topology(self, omm_topology):
                                                dtype=object)))
 
             else:
-                atomtypes = guess_types(atomnames)
-                masses = guess_masses(atomtypes)
                 wmsg = ("Element information is missing for all the atoms. "
                         "Elements attribute will not be populated. "
                         "Atomtype attribute will be guessed using atom "

package/MDAnalysis/converters/RDKitParser.py

@@ -47,7 +47,6 @@
 import numpy as np
 
 from ..topology.base import TopologyReaderBase, change_squash
-from ..topology import guessers
 from ..core.topologyattrs import (
     Atomids,
     Atomnames,
@@ -97,9 +96,6 @@ class RDKitParser(TopologyReaderBase):
      - RSChirality
      - Segids
 
-    Guesses the following:
-     - Atomtypes
-
     Depending on RDKit's input, the following Attributes might be present:
      - Charges
      - Resnames
@@ -303,8 +299,8 @@ def parse(self, **kwargs):
         if atomtypes:
             attrs.append(Atomtypes(np.array(atomtypes, dtype=object)))
         else:
-            atomtypes = guessers.guess_types(names)
-            attrs.append(Atomtypes(atomtypes, guessed=True))
+            atomtypes = elements
+            attrs.append(Atomtypes(atomtypes))
 
         # Partial charges
         if charges:

package/MDAnalysis/coordinates/PDB.py

@@ -154,7 +154,6 @@
 from ..lib.util import store_init_arguments
 from . import base
 from .timestep import Timestep
-from ..topology.core import guess_atom_element
 from ..exceptions import NoDataError
 
 

package/MDAnalysis/core/groups.py

@@ -3262,16 +3262,16 @@ def split(self, level):
         return [self[levelindices == index] for index in
                 unique_int_1d(levelindices)]
 
-    def guess_bonds(self, vdwradii=None):
+    def guess_bonds(self, vdwradii=None, context='default'):
         """Guess bonds that exist within this :class:`AtomGroup` and add them to
         the underlying :attr:`~AtomGroup.universe`.
 
         Parameters
         ----------
         vdwradii : dict, optional
-            Dict relating atom types: vdw radii
-
-
+        Dict relating atom types: vdw radii
+        context : string
+        context of the universe
         See Also
         --------
         :func:`MDAnalysis.topology.guessers.guess_bonds`
@@ -3281,9 +3281,8 @@ def guess_bonds(self, vdwradii=None):
         .. versionchanged:: 0.20.2
            Now applies periodic boundary conditions when guessing bonds.
         """
-        from ..topology.core import guess_bonds, guess_angles, guess_dihedrals
         from .topologyattrs import Bonds, Angles, Dihedrals
-
+        from ..guesser.base import get_guesser
         def get_TopAttr(u, name, cls):
             """either get *name* or create one from *cls*"""
             try:
@@ -3292,18 +3291,19 @@ def get_TopAttr(u, name, cls):
                 attr = cls([])
                 u.add_TopologyAttr(attr)
                 return attr
-
+        guesser = get_guesser(context, atoms=self.atoms,
+                              positions=self.atoms.positions,
+                              vdwradii=vdwradii, box=self.dimensions)
         # indices of bonds
-        b = guess_bonds(self.atoms, self.atoms.positions,
-                        vdwradii=vdwradii, box=self.dimensions)
+        b = guesser.guess_Attr('bonds')
         bondattr = get_TopAttr(self.universe, 'bonds', Bonds)
         bondattr._add_bonds(b, guessed=True)
 
-        a = guess_angles(self.bonds)
+        a = guesser.guess_Attr('angles', bonds=self.bonds)
         angleattr = get_TopAttr(self.universe, 'angles', Angles)
         angleattr._add_bonds(a, guessed=True)
 
-        d = guess_dihedrals(self.angles)
+        d = guesser.guess_Attr('dihedrals', angles=self.angles)
         diheattr = get_TopAttr(self.universe, 'dihedrals', Dihedrals)
         diheattr._add_bonds(d)