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Added description of when camelCase deprecations will happen #663

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Jan 26, 2016
Merged

Added description of when camelCase deprecations will happen #663

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168 changes: 117 additions & 51 deletions package/MDAnalysis/core/AtomGroup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -457,6 +457,8 @@
# And the return route
_SINGULAR_PROPERTIES = {v: k for k, v in _PLURAL_PROPERTIES.items()}

_FIFTEEN_DEPRECATION = "This will be removed in version 0.15.0"


@functools.total_ordering
class Atom(object):
Expand Down Expand Up @@ -1175,7 +1177,10 @@ def total_mass(self):
"""Total mass of the selection (masses are taken from the topology or guessed)."""
return np.sum(self.masses, axis=0)

totalMass = deprecate(total_mass, old_name='totalMass', new_name='total_mass')
totalMass = deprecate(total_mass,
old_name='totalMass',
new_name='total_mass',
message=_FIFTEEN_DEPRECATION)

@property
def occupancies(self):
Expand Down Expand Up @@ -1203,6 +1208,7 @@ def occupancies(self, new):
n_atoms = self.universe.coord.n_atoms
self.universe.coord.data['occupancy'] = np.ones(n_atoms)
self.universe.coord.data['occupancy'][self.indices] = new

@property
def charges(self):
"""Array of partial charges of the atoms (as defined in the topology)
Expand All @@ -1220,7 +1226,10 @@ def total_charge(self):
"""Sum of all partial charges (must be defined in topology)."""
return np.sum(self.charges, axis=0)

totalCharge = deprecate(total_charge, old_name='totalCharge', new_name='total_charge')
totalCharge = deprecate(total_charge,
old_name='totalCharge',
new_name='total_charge',
message=_FIFTEEN_DEPRECATION)

@property
def names(self):
Expand Down Expand Up @@ -1712,7 +1721,10 @@ def set_names(self, name):
"""
self.set("name", name, conversion=str)

set_name = deprecate(set_names, old_name='set_name', new_name='set_names')
set_name = deprecate(set_names,
old_name='set_name',
new_name='set_names',
message=_FIFTEEN_DEPRECATION)

def set_resids(self, resid):
"""Set the resids to integer *resid* for **all atoms** in the :class:`AtomGroup`.
Expand Down Expand Up @@ -1756,7 +1768,10 @@ def set_resids(self, resid):
'residues',
ResidueGroup(build_residues(self.universe.atoms)))

set_resid = deprecate(set_resids, old_name='set_resid', new_name='set_resids')
set_resid = deprecate(set_resids,
old_name='set_resid',
new_name='set_resids',
message=_FIFTEEN_DEPRECATION)

def set_resnums(self, resnum):
"""Set the resnums to *resnum* for **all atoms** in the :class:`AtomGroup`.
Expand Down Expand Up @@ -1784,7 +1799,10 @@ def set_resnums(self, resnum):
"""
self.set("resnum", resnum)

set_resnum = deprecate(set_resnums, old_name='set_resnum', new_name='set_resnums')
set_resnum = deprecate(set_resnums,
old_name='set_resnum',
new_name='set_resnums',
message=_FIFTEEN_DEPRECATION)

def set_resnames(self, resname):
"""Set the resnames to string *resname* for **all atoms** in the :class:`AtomGroup`.
Expand All @@ -1805,7 +1823,10 @@ def set_resnames(self, resname):
"""
self.set("resname", resname, conversion=str)

set_resname = deprecate(set_resnames, old_name='set_resname', new_name='set_resnames')
set_resname = deprecate(set_resnames,
old_name='set_resname',
new_name='set_resnames',
message=_FIFTEEN_DEPRECATION)

def set_segids(self, segid):
"""Set the segids to *segid* for all atoms in the :class:`AtomGroup`.
Expand Down Expand Up @@ -1847,7 +1868,10 @@ def set_segids(self, segid):
'segments',
SegmentGroup(segments))

set_segid = deprecate(set_segids, old_name='set_segid', new_name='set_segids')
set_segid = deprecate(set_segids,
old_name='set_segid',
new_name='set_segids',
message=_FIFTEEN_DEPRECATION)

def set_masses(self, mass):
"""Set the atom masses to float *mass* for **all atoms** in the AtomGroup.
Expand All @@ -1865,7 +1889,10 @@ def set_masses(self, mass):
"""
self.set("mass", mass, conversion=float, cache="masses")

set_mass = deprecate(set_masses, old_name='set_mass', new_name='set_masses')
set_mass = deprecate(set_masses,
old_name='set_mass',
new_name='set_masses',
message=_FIFTEEN_DEPRECATION)

def set_types(self, atype):
"""Set the atom types to *atype* for **all atoms** in the AtomGroup.
Expand All @@ -1883,7 +1910,10 @@ def set_types(self, atype):
"""
self.set("type", atype)

set_type = deprecate(set_types, old_name='set_type', new_name='set_types')
set_type = deprecate(set_types,
old_name='set_type',
new_name='set_types',
message=_FIFTEEN_DEPRECATION)

def set_charges(self, charge):
"""Set the partial charges to float *charge* for **all atoms** in the AtomGroup.
Expand All @@ -1901,7 +1931,10 @@ def set_charges(self, charge):
"""
self.set("charge", charge, conversion=float)

set_charge = deprecate(set_charges, old_name='set_charge', new_name='set_charges')
set_charge = deprecate(set_charges,
old_name='set_charge',
new_name='set_charges',
message=_FIFTEEN_DEPRECATION)

def set_radii(self, radius):
"""Set the atom radii to float *radius* for **all atoms** in the AtomGroup.
Expand All @@ -1919,7 +1952,10 @@ def set_radii(self, radius):
"""
self.set("radius", radius, conversion=float)

set_radius = deprecate(set_radii, old_name='set_radius', new_name='set_radii')
set_radius = deprecate(set_radii,
old_name='set_radius',
new_name='set_radii',
message=_FIFTEEN_DEPRECATION)

def set_bfactors(self, bfactor):
"""Set the atom bfactors to float *bfactor* for **all atoms** in the AtomGroup.
Expand All @@ -1937,7 +1973,10 @@ def set_bfactors(self, bfactor):
"""
self.set("bfactor", bfactor, conversion=float)

set_bfactor = deprecate(set_bfactors, old_name='set_bfactor', new_name='set_bfactors')
set_bfactor = deprecate(set_bfactors,
old_name='set_bfactor',
new_name='set_bfactors',
message=_FIFTEEN_DEPRECATION)

def set_altLocs(self, altLoc):
"""Set the altLocs to *altLoc for **all atoms** in the AtomGroup.
Expand All @@ -1951,7 +1990,10 @@ def set_altLocs(self, altLoc):
"""
self.set("altLoc", altLoc, conversion=str)

set_altLoc = deprecate(set_altLocs, old_name='set_altLoc', new_name='set_altLocs')
set_altLoc = deprecate(set_altLocs,
old_name='set_altLoc',
new_name='set_altLocs',
message=_FIFTEEN_DEPRECATION)

def set_serials(self, serial):
"""Set the serials to *serial* for **all atoms** in the AtomGroup.
Expand All @@ -1965,7 +2007,10 @@ def set_serials(self, serial):
"""
self.set("serial", serial, conversion=int)

set_serial = deprecate(set_serials, old_name='set_serial', new_name='set_serials')
set_serial = deprecate(set_serials,
old_name='set_serial',
new_name='set_serials',
message=_FIFTEEN_DEPRECATION)

def center_of_geometry(self, **kwargs):
"""Center of geometry (also known as centroid) of the selection.
Expand All @@ -1986,8 +2031,10 @@ def center_of_geometry(self, **kwargs):
else:
return np.sum(self.positions, axis=0) / self.n_atoms

centerOfGeometry = deprecate(center_of_geometry, old_name='centerOfGeometry',
new_name='center_of_geometry')
centerOfGeometry = deprecate(center_of_geometry,
old_name='centerOfGeometry',
new_name='center_of_geometry',
message=_FIFTEEN_DEPRECATION)

centroid = center_of_geometry

Expand All @@ -2011,7 +2058,10 @@ def center_of_mass(self, **kwargs):
else:
return np.sum(self.positions * self.masses[:, np.newaxis], axis=0) / self.total_mass()

centerOfMass = deprecate(center_of_mass, old_name='centerOfMass', new_name='center_of_mass')
centerOfMass = deprecate(center_of_mass,
old_name='centerOfMass',
new_name='center_of_mass',
message=_FIFTEEN_DEPRECATION)

def radius_of_gyration(self, **kwargs):
"""Radius of gyration.
Expand All @@ -2035,7 +2085,10 @@ def radius_of_gyration(self, **kwargs):
rog_sq = np.sum(masses * np.sum(np.power(recenteredpos, 2), axis=1)) / self.total_mass()
return np.sqrt(rog_sq)

radiusOfGyration = deprecate(radius_of_gyration, old_name='radiusOfGyration', new_name='radius_of_gyration')
radiusOfGyration = deprecate(radius_of_gyration,
old_name='radiusOfGyration',
new_name='radius_of_gyration',
message=_FIFTEEN_DEPRECATION)

def shape_parameter(self, **kwargs):
"""Shape parameter.
Expand Down Expand Up @@ -2068,7 +2121,10 @@ def shape_parameter(self, **kwargs):
shape = 27.0 * np.prod(eig_vals - np.mean(eig_vals)) / np.power(np.sum(eig_vals), 3)
return shape

shapeParameter = deprecate(shape_parameter, old_name='shapeParameter', new_name='shape_parameter')
shapeParameter = deprecate(shape_parameter,
old_name='shapeParameter',
new_name='shape_parameter',
message=_FIFTEEN_DEPRECATION)

def asphericity(self, **kwargs):
"""Asphericity.
Expand Down Expand Up @@ -2148,8 +2204,10 @@ def moment_of_inertia(self, **kwargs):

return tens

momentOfInertia = deprecate(moment_of_inertia, old_name='momentOfInertia',
new_name='moment_of_inertia')
momentOfInertia = deprecate(moment_of_inertia,
old_name='momentOfInertia',
new_name='moment_of_inertia',
message=_FIFTEEN_DEPRECATION)

def bbox(self, **kwargs):
"""Return the bounding box of the selection.
Expand Down Expand Up @@ -2304,7 +2362,10 @@ def principal_axes(self, **kwargs):
# Return transposed in more logical form. See Issue 33.
return eigenvec[:, indices].T

principalAxes = deprecate(principal_axes, old_name='principalAxes', new_name='principal_axes')
principalAxes = deprecate(principal_axes,
old_name='principalAxes',
new_name='principal_axes',
message=_FIFTEEN_DEPRECATION)

def get_positions(self, ts=None, copy=False, dtype=np.float32):
"""Get a numpy array of the coordinates.
Expand Down Expand Up @@ -2685,7 +2746,8 @@ def align_principal_axis(self, axis, vector):

align_principalAxis = deprecate(align_principal_axis,
old_name='align_principalAxis',
new_name='align_principal_axis')
new_name='align_principal_axis',
message=_FIFTEEN_DEPRECATION)

def pack_into_box(self, box=None, inplace=True):
r"""Shift all atoms in this group to be within the primary unit cell.
Expand Down Expand Up @@ -2741,7 +2803,10 @@ def pack_into_box(self, box=None, inplace=True):

return self.universe.coord.positions[self.indices]

packIntoBox = deprecate(pack_into_box, old_name='packIntoBox', new_name='pack_into_box')
packIntoBox = deprecate(pack_into_box,
old_name='packIntoBox',
new_name='pack_into_box',
message=_FIFTEEN_DEPRECATION)

def wrap(self, compound="atoms", center="com", box=None):
"""Shift the contents of this AtomGroup back into the unit cell.
Expand Down Expand Up @@ -3027,8 +3092,10 @@ def select_atoms(self, selstr, *othersel, **selgroups):
atomgrp += Selection.Parser.parse(sel, selgroups).apply(self)
return atomgrp

selectAtoms = deprecate(select_atoms, old_name='selectAtoms',
new_name='select_atoms')
selectAtoms = deprecate(select_atoms,
old_name='selectAtoms',
new_name='select_atoms',
message=_FIFTEEN_DEPRECATION)

def split(self, level):
"""Split atomgroup into a list of atomgroups by *level*.
Expand Down Expand Up @@ -3484,7 +3551,10 @@ def set_resids(self, resid):
"""
super(ResidueGroup, self).set_resids(resid)

set_resid = deprecate(set_resids, old_name='set_resid', new_name='set_resids')
set_resid = deprecate(set_resids,
old_name='set_resid',
new_name='set_resids',
message=_FIFTEEN_DEPRECATION)

def set_resnums(self, resnum):
"""Set the resnums to *resnum* for **all residues** in the :class:`ResidueGroup`.
Expand Down Expand Up @@ -3512,7 +3582,10 @@ def set_resnums(self, resnum):
"""
super(ResidueGroup, self).set_resnums(resnum)

set_resnum = deprecate(set_resnums, old_name='set_resnum', new_name='set_resnums')
set_resnum = deprecate(set_resnums,
old_name='set_resnum',
new_name='set_resnums',
message=_FIFTEEN_DEPRECATION)

def set_resnames(self, resname):
"""Set the resnames to string *resname* for **all residues** in the
Expand All @@ -3534,7 +3607,10 @@ def set_resnames(self, resname):
"""
super(ResidueGroup, self).set_resnames(resname)

set_resname = deprecate(set_resnames, old_name='set_resname', new_name='set_resnames')
set_resname = deprecate(set_resnames,
old_name='set_resname',
new_name='set_resnames',
message=_FIFTEEN_DEPRECATION)

# All other AtomGroup.set_xxx() methods should just work as
# ResidueGroup.set_xxx() because we overrode self.set(); the ones above
Expand Down Expand Up @@ -3704,7 +3780,10 @@ def set_segids(self, segid):
"""
super(SegmentGroup, self).set_segids(segid)

set_segid = deprecate(set_segids, old_name='set_segid', new_name='set_segids')
set_segid = deprecate(set_segids,
old_name='set_segid',
new_name='set_segids',
message=_FIFTEEN_DEPRECATION)

def __getattr__(self, attr):
if attr.startswith('s') and attr[1].isdigit():
Expand Down Expand Up @@ -3814,16 +3893,6 @@ def __init__(self, *args, **kwargs):
charges, atom masses, ... then these data will be available to
MDAnalysis. A "structure" file (PSF, PDB or GRO, in the sense of a
topology) is always required.
*coordinatefile*
A trajectory (such as CHARMM DCD, Gromacs XTC/TRR/GRO, XYZ, XYZ.bz2) or a PDB that
will provide coordinates, possibly multiple frames.
If a **list of filenames** is provided then they are sequentially read and appear
as one single trajectory to the Universe. The list can contain different file
formats.

.. deprecated:: 0.8
Do not use the *coordinatefile* keyword argument, just provide trajectories as
positional arguments.

*permissive*
currently only relevant for PDB files: Set to ``True`` in order to ignore most errors
Expand Down Expand Up @@ -3974,14 +4043,6 @@ def __init__(self, *args, **kwargs):
# Load coordinates
self.load_new(coordinatefile, **kwargs)

# Deprecated bonds mode handling here, remove eventually.
if 'bonds' in kwargs:
warnings.warn("The 'bonds' keyword has been deprecated"
" and will be removed in 0.11.0."
" Please use 'guess_bonds' instead.")
if kwargs.get('bonds') in ['all', True]:
kwargs['guess_bonds'] = True

if kwargs.get('guess_bonds', False):
self.atoms.guess_bonds(vdwradii=kwargs.get('vdwradii',None))

Expand Down Expand Up @@ -4547,8 +4608,10 @@ def select_atoms(self, sel, *othersel, **selgroups):
"""
return self.atoms.select_atoms(sel, *othersel, **selgroups)

selectAtoms = deprecate(select_atoms, old_name='selectAtoms',
new_name='select_atoms')
selectAtoms = deprecate(select_atoms,
old_name='selectAtoms',
new_name='select_atoms',
message=_FIFTEEN_DEPRECATION)

def __repr__(self):
return "<Universe with {n_atoms} atoms{bonds}>".format(
Expand Down Expand Up @@ -4675,7 +4738,10 @@ def as_Universe(*args, **kwargs):
return args[0]
return Universe(*args, **kwargs)

asUniverse = deprecate(as_Universe, old_name='asUniverse', new_name='as_Universe')
asUniverse = deprecate(as_Universe,
old_name='asUniverse',
new_name='as_Universe',
message=_FIFTEEN_DEPRECATION)

def Merge(*args):
"""Return a :class:`Universe` from two or more :class:`AtomGroup` instances.
Expand Down
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