Changed AtomGroup methods to properties

Implementation of Issue #372

package/CHANGELOG

@@ -45,8 +45,13 @@ The rules for this file:
     over periodic boundaries.
   * Added triclinic_dimensions to Timestep, returns representation of unit
     cell as triclinic vectors (Issue #276)
+  * Added setter to bfactors property (Issue #372)
+  * Added AtomGroup altLocs and serials properties with setters. (Issue #372)
 
   Changes
+  * Changed many AtomGroup methods to properties.  These are: indices, masses,
+    charges, names, types, radii, resids, resnames, resnums, segids
+    (Issue #372)
   * A ProtoReader class intermediate between IObase and Reader was added so
     specific Readers can be subclassed without __del__ (the ChainReader and
     SingleFrameReader), thus preventing memleaks (Issue #312).

package/MDAnalysis/analysis/align.py

@@ -324,7 +324,7 @@ def alignto(mobile, reference, select="all", mass_weighted=False,
                                                  tol_mass=tol_mass, strict=strict)
 
     if mass_weighted:
-        weights = ref_atoms.masses() / numpy.mean(ref_atoms.masses())
+        weights = ref_atoms.masses / numpy.mean(ref_atoms.masses)
         ref_com = ref_atoms.centerOfMass()
         mobile_com = mobile_atoms.centerOfMass()
     else:
@@ -464,7 +464,7 @@ def rms_fit_trj(traj, reference, select='all', filename=None, rmsdfile=None, pre
     logger.info("RMS-fitting on %d atoms." % len(ref_atoms))
     if mass_weighted:
         # if performing a mass-weighted alignment/rmsd calculation
-        weight = ref_atoms.masses() / ref_atoms.masses().mean()
+        weight = ref_atoms.masses / ref_atoms.masses.mean()
     else:
         weight = None
 
@@ -830,7 +830,7 @@ def get_matching_atoms(ag1, ag2, tol_mass=0.1, strict=False):
                 ag1.numberOfResidues(), ag2.numberOfResidues())
             dbgmsg = "mismatched residue numbers\n" + \
                 "\n".join(["{0} | {1}"  for r1, r2 in
-                           itertools.izip_longest(ag1.resids(), ag2.resids())])
+                           itertools.izip_longest(ag1.resids, ag2.resids)])
             logger.error(errmsg)
             logger.debug(dbgmsg)
             raise SelectionError(errmsg)
@@ -857,8 +857,8 @@ def get_matching_atoms(ag1, ag2, tol_mass=0.1, strict=False):
         # pairwise2 consumes too much memory for thousands of characters in
         # each sequence. Perhaps a solution would be pairwise alignment per residue.
         #
-        # aln_elem = Bio.pairwise2.align.globalms("".join([MDAnalysis.topology.core.guess_atom_element(n) for n in gref.atoms.names()]),
-        #    "".join([MDAnalysis.topology.core.guess_atom_element(n) for n in models[0].atoms.names()]),
+        # aln_elem = Bio.pairwise2.align.globalms("".join([MDAnalysis.topology.core.guess_atom_element(n) for n in gref.atoms.names]),
+        #    "".join([MDAnalysis.topology.core.guess_atom_element(n) for n in models[0].atoms.names]),
         #                               2, -1, -1, -0.1,
         #                               one_alignment_only=True)
 
@@ -875,8 +875,8 @@ def log_mismatch(number, ag, rsize, mismatch_resindex=mismatch_resindex):
                     logger.error("Offending residues: group {0}: {1}".format(
                             number,
                             ", ".join(["{0[0]}{0[1]} ({0[2]})".format(r) for r in
-                                       itertools.izip(ag.resnames()[mismatch_resindex],
-                                                      ag.resids()[mismatch_resindex],
+                                       itertools.izip(ag.resnames[mismatch_resindex],
+                                                      ag.resids[mismatch_resindex],
                                                       rsize[mismatch_resindex]
                                                       )])))
                 logger.error("Found {0} residues with non-matching numbers of atoms (#)".format(
@@ -891,7 +891,7 @@ def get_atoms_byres(g, match_mask=numpy.logical_not(mismatch_mask)):
                 # not pretty... but need to do things on a per-atom basis in order
                 # to preserve original selection
                 ag = g.atoms
-                good = ag.resids()[match_mask]
+                good = ag.resids[match_mask]
                 resids = numpy.array([a.resid for a in ag])  # resid for each atom
                 ix_good = numpy.in1d(resids, good)   # boolean array for all matching atoms
                 return ag[numpy.arange(len(ag))[ix_good]]   # workaround for missing boolean indexing
@@ -904,14 +904,14 @@ def get_atoms_byres(g, match_mask=numpy.logical_not(mismatch_mask)):
             mismatch_resindex = numpy.arange(ag1.numberOfResidues())[mismatch_mask]
             logger.warn("Removed {0} residues with non-matching numbers of atoms".format(
                     mismatch_mask.sum()))
-            logger.debug("Removed residue ids: group 1: {0}".format(ag1.resids()[mismatch_resindex]))
-            logger.debug("Removed residue ids: group 2: {0}".format(ag2.resids()[mismatch_resindex]))
+            logger.debug("Removed residue ids: group 1: {0}".format(ag1.resids[mismatch_resindex]))
+            logger.debug("Removed residue ids: group 2: {0}".format(ag2.resids[mismatch_resindex]))
             # replace after logging (still need old ag1 and ag2 for diagnostics)
             ag1 = _ag1
             ag2 = _ag2
             del _ag1, _ag2
 
-    mass_mismatches = (numpy.absolute(ag1.masses() - ag2.masses()) > tol_mass)
+    mass_mismatches = (numpy.absolute(ag1.masses - ag2.masses) > tol_mass)
     if numpy.any(mass_mismatches):
         # Test 2 failed.
         # diagnostic output:

package/MDAnalysis/analysis/contacts.py

@@ -714,7 +714,7 @@ def _plot_qavg_pcolor(self, filename=None, **kwargs):
         """Plot :attr:`ContactAnalysis1.qavg`, the matrix of average native contacts."""
         from pylab import pcolor, gca, meshgrid, xlabel, ylabel, xlim, ylim, colorbar, savefig
 
-        x, y = self.selections[0].resids(), self.selections[1].resids()
+        x, y = self.selections[0].resids, self.selections[1].resids
         X, Y = meshgrid(x, y)
 
         pcolor(X, Y, self.qavg.T, **kwargs)
@@ -742,7 +742,7 @@ def plot_qavg(self, filename=None, **kwargs):
         """
         from pylab import imshow, xlabel, ylabel, xlim, ylim, colorbar, cm, clf, savefig
 
-        x, y = self.selections[0].resids(), self.selections[1].resids()
+        x, y = self.selections[0].resids, self.selections[1].resids
 
         kwargs['origin'] = 'lower'
         kwargs.setdefault('aspect', 'equal')

package/MDAnalysis/analysis/distances.py

@@ -229,8 +229,8 @@ def dist(A, B, offset=0):
         off_A, off_B = offset
     except (TypeError, ValueError):
         off_A = off_B = int(offset)
-    residues_A = numpy.array(A.resids()) + off_A
-    residues_B = numpy.array(B.resids()) + off_B
+    residues_A = numpy.array(A.resids) + off_A
+    residues_B = numpy.array(B.resids) + off_B
     r = A.coordinates() - B.coordinates()
     d = numpy.sqrt(numpy.sum(r * r, axis=1))
     return numpy.array([residues_A, residues_B, d])

package/MDAnalysis/analysis/nuclinfo.py

@@ -127,9 +127,9 @@ def wc_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
 
     .. versionadded:: 0.7.6
     """
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
         a1, a2 = "N3", "N1"
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
         a1, a2 = "N1", "N3"
     wc_dist = universe.selectAtoms(
         " (segid %s and resid %s and name %s)  or (segid %s and resid %s and name %s) " % (seg1, i, a1, seg2, bp, a2))
@@ -159,9 +159,9 @@ def minor_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
 
     .. versionadded:: 0.7.6
     """
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
         a1, a2 = "O2", "C2"
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
         a1, a2 = "C2", "O2"
     c2o2_dist = universe.selectAtoms(
         " (segid %s and resid %s and name %s)  or (segid %s and resid %s and name %s) " % (seg1, i, a1, seg2, bp, a2))
@@ -191,13 +191,13 @@ def major_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
 
     .. versionadded:: 0.7.6
     """
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DC", "DG", "C", "G", "CYT", "GUA"]:
-        if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DC", "C", "CYT"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DC", "DG", "C", "G", "CYT", "GUA"]:
+        if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DC", "C", "CYT"]:
             a1, a2 = "N4", "O6"
         else:
             a1, a2 = "O6", "N4"
-    if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DT", "DA", "A", "T", "U", "ADE", "THY", "URA"]:
-        if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DT", "T", "THY", "U", "URA"]:
+    if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DT", "DA", "A", "T", "U", "ADE", "THY", "URA"]:
+        if universe.selectAtoms(" resid %s " % (i,)).resnames[0] in ["DT", "T", "THY", "U", "URA"]:
             a1, a2 = "O4", "N6"
         else:
             a1, a2 = "N6", "O4"

package/MDAnalysis/analysis/rms.py

@@ -323,7 +323,7 @@ def __init__(self, traj, reference=None, select='all', groupselections=None, fil
                                  "the same number of atoms: N_ref=%d, N_traj=%d" %
                                  (len(self.ref_atoms), len(self.traj_atoms)))
         logger.info("RMS calculation for %d atoms." % len(self.ref_atoms))
-        mass_mismatches = (numpy.absolute(self.ref_atoms.masses() - self.traj_atoms.masses()) > self.tol_mass)
+        mass_mismatches = (numpy.absolute(self.ref_atoms.masses - self.traj_atoms.masses) > self.tol_mass)
         if numpy.any(mass_mismatches):
             # diagnostic output:
             logger.error("Atoms: reference | trajectory")
@@ -392,7 +392,7 @@ def run(self, **kwargs):
 
         if mass_weighted:
             # if performing a mass-weighted alignment/rmsd calculation
-            weight = self.ref_atoms.masses() / self.ref_atoms.masses().mean()
+            weight = self.ref_atoms.masses / self.ref_atoms.masses.mean()
         else:
             weight = None
 

package/MDAnalysis/coordinates/DCD.py

@@ -517,7 +517,7 @@ def timeseries(self, asel, start=0, stop=-1, skip=1, format='afc'):
             raise NoDataError("Timeseries requires at least one atom to analyze")
         if len(format) != 3 and format not in ['afc', 'acf', 'caf', 'cfa', 'fac', 'fca']:
             raise ValueError("Invalid timeseries format")
-        atom_numbers = list(asel.indices())
+        atom_numbers = list(asel.indices)
         # Check if the atom numbers can be grouped for efficiency, then we can read partial buffers
         # from trajectory file instead of an entire timestep
         # XXX needs to be implemented

package/MDAnalysis/coordinates/PDB.py

@@ -1078,7 +1078,7 @@ def _write_timestep(self, ts, multiframe=False):
             coor = ts._pos
 
         if hasattr(self.obj, "indices"):
-            coor = coor[self.obj.indices()]
+            coor = coor[self.obj.indices]
 
         if len(atoms) != len(coor):
             raise ValueError(

package/MDAnalysis/coordinates/XYZ.py

@@ -136,12 +136,12 @@ def _get_atomnames(self, atoms):
         """Return a list of atom names"""
         # AtomGroup
         try:
-            return atoms.names()
+            return atoms.names
         except AttributeError:
             pass
         # universe?
         try:
-            return atoms.atoms.names()
+            return atoms.atoms.names
         except AttributeError:
             pass
         # list or string (can be a single atom name... deal with this in write_next_timestep() once we know numatoms)
@@ -185,12 +185,12 @@ def write(self, obj):
                     ts = ts_full
                 else:
                     # Only populate a time step with the selected atoms.
-                    ts = ts_full.copy_slice(atoms.indices())
+                    ts = ts_full.copy_slice(atoms.indices)
             elif hasattr(obj, 'trajectory'):
                 # For Universe only --- get everything
                 ts = obj.trajectory.ts
             # update atom names
-            self.atomnames = atoms.names()
+            self.atomnames = atoms.names
         else:
             ts = obj