# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""Atom selection Hierarchy --- :mod:`MDAnalysis.core.selection`
=============================================================
This module contains objects that represent selections. They are
constructed and then applied to the group.
In general, :meth:`Parser.parse` creates a :class:`Selection` object
from a selection string. This :class:`Selection` object is then passed
an :class:`~MDAnalysis.core.groups.AtomGroup` through its
:meth:`~MDAnalysis.core.groups.AtomGroup.apply` method to apply the
``Selection`` to the ``AtomGroup``.
This is all invisible to the user through the
:meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` method of an
:class:`~MDAnalysis.core.groups.AtomGroup`.
"""
from __future__ import division, absolute_import
import six
from six.moves import zip
import collections
import re
import fnmatch
import functools
import warnings
import numpy as np
from ..lib.util import unique_int_1d
from ..lib import distances
from ..exceptions import SelectionError, NoDataError
[docs]def is_keyword(val):
"""Is val a selection keyword?
Returns False on any of the following strings:
- keys in SELECTIONDICT (tokens from Selection objects)
- keys in OPERATIONS (tokens from LogicOperations)
- (Parentheses)
- The value `None` (used as EOF in selection strings)
"""
return (val in _SELECTIONDICT or
val in _OPERATIONS or
val in ['(', ')'] or
val is None)
[docs]def grab_not_keywords(tokens):
"""Pop tokens from the left until you hit a keyword
Parameters
----------
tokens : collections.deque
deque of strings, some tokens some not
Returns
-------
values : list of strings
All non keywords found until a keyword was hit
Note
----
This function pops the values from the deque
Examples
--------
grab_not_keywords(['H', 'and','resname', 'MET'])
>>> ['H']
grab_not_keywords(['H', 'Ca', 'N', 'and','resname', 'MET'])
>>> ['H', 'Ca' ,'N']
grab_not_keywords(['and','resname', 'MET'])
>>> []
"""
values = []
while not is_keyword(tokens[0]):
val = tokens.popleft()
# Insert escape characters here to use keywords as names?
values.append(val)
return values
_SELECTIONDICT = {}
_OPERATIONS = {}
# These are named args to select_atoms that have a special meaning and must
# not be allowed as names for the 'group' keyword.
_RESERVED_KWARGS=('updating',)
# And and Or are exception and aren't strictly a Selection
# as they work on other Selections rather than doing work themselves.
# So their init is a little strange too....
class _Operationmeta(type):
def __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
try:
_OPERATIONS[classdict['token']] = cls
except KeyError:
pass
class LogicOperation(six.with_metaclass(_Operationmeta, object)):
def __init__(self, lsel, rsel):
self.rsel = rsel
self.lsel = lsel
class AndOperation(LogicOperation):
token = 'and'
precedence = 3
def apply(self, group):
rsel = self.rsel.apply(group)
lsel = self.lsel.apply(group)
# Mask which lsel indices appear in rsel
mask = np.in1d(rsel.indices, lsel.indices)
# and mask rsel according to that
return rsel[mask].unique
class OrOperation(LogicOperation):
token = 'or'
precedence = 3
def apply(self, group):
lsel = self.lsel.apply(group)
rsel = self.rsel.apply(group)
# Find unique indices from both these AtomGroups
# and slice master list using them
idx = np.union1d(lsel.indices, rsel.indices).astype(np.int32)
return group.universe.atoms[idx]
[docs]def return_empty_on_apply(func):
"""
Decorator to return empty AtomGroups from the apply() function
without evaluating it
"""
@functools.wraps(func)
def apply(self, group):
if len(group) == 0:
return group
return func(self, group)
return apply
class _Selectionmeta(type):
def __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
try:
_SELECTIONDICT[classdict['token']] = cls
except KeyError:
pass
class Selection(six.with_metaclass(_Selectionmeta, object)):
pass
class AllSelection(Selection):
token = 'all'
def __init__(self, parser, tokens):
pass
def apply(self, group):
# Check whether group is identical to the one stored
# in the corresponding universe, in which case this
# is returned directly. This works since the Universe.atoms
# are unique by construction.
if group is group.universe.atoms:
return group
return group[:].unique
class UnarySelection(Selection):
def __init__(self, parser, tokens):
sel = parser.parse_expression(self.precedence)
self.sel = sel
class NotSelection(UnarySelection):
token = 'not'
precedence = 5
def apply(self, group):
notsel = self.sel.apply(group)
return group[~np.in1d(group.indices, notsel.indices)].unique
class GlobalSelection(UnarySelection):
token = 'global'
precedence = 5
def apply(self, group):
return self.sel.apply(group.universe.atoms).unique
[docs]class ByResSelection(UnarySelection):
"""
Selects all atoms that are in the same segment and residue as selection
.. versionchanged:: 1.0.0
Use :code:`"resindices"` instead of :code:`"resids"` (see #2669 and #2672)
"""
token = 'byres'
precedence = 1
def apply(self, group):
res = self.sel.apply(group)
unique_res = unique_int_1d(res.resindices)
mask = np.in1d(group.resindices, unique_res)
return group[mask].unique
[docs]class DistanceSelection(Selection):
"""Base class for distance search based selections"""
[docs] def validate_dimensions(self, dimensions):
r"""Check if the system is periodic in all three-dimensions.
Parameters
----------
dimensions : numpy.ndarray
6-item array denoting system size and angles
Returns
-------
None or numpy.ndarray
Returns argument dimensions if system is periodic in all
three-dimensions, otherwise returns None
"""
if self.periodic and all(dimensions[:3]):
return dimensions
return None
[docs]class AroundSelection(DistanceSelection):
token = 'around'
precedence = 1
def __init__(self, parser, tokens):
self.periodic = parser.periodic
self.cutoff = float(tokens.popleft())
self.sel = parser.parse_expression(self.precedence)
@return_empty_on_apply
def apply(self, group):
indices = []
sel = self.sel.apply(group)
# All atoms in group that aren't in sel
sys = group[~np.in1d(group.indices, sel.indices)]
if not sys or not sel:
return sys[[]]
box = self.validate_dimensions(group.dimensions)
pairs = distances.capped_distance(sel.positions, sys.positions,
self.cutoff, box=box,
return_distances=False)
if pairs.size > 0:
indices = np.sort(pairs[:, 1])
return sys[np.asarray(indices, dtype=np.int64)].unique
[docs]class SphericalLayerSelection(DistanceSelection):
token = 'sphlayer'
precedence = 1
def __init__(self, parser, tokens):
self.periodic = parser.periodic
self.inRadius = float(tokens.popleft())
self.exRadius = float(tokens.popleft())
self.sel = parser.parse_expression(self.precedence)
@return_empty_on_apply
def apply(self, group):
indices = []
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
periodic = box is not None
ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
pairs = distances.capped_distance(ref, group.positions, self.exRadius,
min_cutoff=self.inRadius,
box=box,
return_distances=False)
if pairs.size > 0:
indices = np.sort(pairs[:, 1])
return group[np.asarray(indices, dtype=np.int64)].unique
[docs]class SphericalZoneSelection(DistanceSelection):
token = 'sphzone'
precedence = 1
def __init__(self, parser, tokens):
self.periodic = parser.periodic
self.cutoff = float(tokens.popleft())
self.sel = parser.parse_expression(self.precedence)
@return_empty_on_apply
def apply(self, group):
indices = []
sel = self.sel.apply(group)
box = self.validate_dimensions(group.dimensions)
periodic = box is not None
ref = sel.center_of_geometry().reshape(1, 3).astype(np.float32)
pairs = distances.capped_distance(ref, group.positions, self.cutoff,
box=box,
return_distances=False)
if pairs.size > 0:
indices = np.sort(pairs[:, 1])
return group[np.asarray(indices, dtype=np.int64)].unique
class CylindricalSelection(Selection):
@return_empty_on_apply
def apply(self, group):
sel = self.sel.apply(group)
# Calculate vectors between point of interest and our group
vecs = group.positions - sel.center_of_geometry()
if self.periodic and not np.any(group.dimensions[:3] == 0):
box = group.dimensions[:3]
cyl_z_hheight = self.zmax - self.zmin
if 2 * self.exRadius > box[0]:
raise NotImplementedError(
"The diameter of the cylinder selection ({:.3f}) is larger "
"than the unit cell's x dimension ({:.3f}). Can only do "
"selections where it is smaller or equal."
"".format(2*self.exRadius, box[0]))
if 2 * self.exRadius > box[1]:
raise NotImplementedError(
"The diameter of the cylinder selection ({:.3f}) is larger "
"than the unit cell's y dimension ({:.3f}). Can only do "
"selections where it is smaller or equal."
"".format(2*self.exRadius, box[1]))
if cyl_z_hheight > box[2]:
raise NotImplementedError(
"The total length of the cylinder selection in z ({:.3f}) "
"is larger than the unit cell's z dimension ({:.3f}). Can "
"only do selections where it is smaller or equal."
"".format(cyl_z_hheight, box[2]))
if np.all(group.dimensions[3:] == 90.):
# Orthogonal version
vecs -= box[:3] * np.rint(vecs / box[:3])
else:
# Triclinic version
tribox = group.universe.trajectory.ts.triclinic_dimensions
vecs -= tribox[2] * np.rint(vecs[:, 2] / tribox[2][2])[:, None]
vecs -= tribox[1] * np.rint(vecs[:, 1] / tribox[1][1])[:, None]
vecs -= tribox[0] * np.rint(vecs[:, 0] / tribox[0][0])[:, None]
# First deal with Z dimension criteria
mask = (vecs[:, 2] > self.zmin) & (vecs[:, 2] < self.zmax)
# Mask out based on height to reduce number of radii comparisons
vecs = vecs[mask]
group = group[mask]
# Radial vectors from sel to each in group
radii = vecs[:, 0]**2 + vecs[:, 1]**2
mask = radii < self.exRadius**2
try:
mask &= radii > self.inRadius**2
except AttributeError:
# Only for cylayer, cyzone doesn't have inRadius
pass
return group[mask].unique
class CylindricalZoneSelection(CylindricalSelection):
token = 'cyzone'
precedence = 1
def __init__(self, parser, tokens):
self.periodic = parser.periodic
self.exRadius = float(tokens.popleft())
self.zmax = float(tokens.popleft())
self.zmin = float(tokens.popleft())
self.sel = parser.parse_expression(self.precedence)
class CylindricalLayerSelection(CylindricalSelection):
token = 'cylayer'
precedence = 1
def __init__(self, parser, tokens):
self.periodic = parser.periodic
self.inRadius = float(tokens.popleft())
self.exRadius = float(tokens.popleft())
self.zmax = float(tokens.popleft())
self.zmin = float(tokens.popleft())
self.sel = parser.parse_expression(self.precedence)
[docs]class PointSelection(DistanceSelection):
token = 'point'
def __init__(self, parser, tokens):
self.periodic = parser.periodic
x = float(tokens.popleft())
y = float(tokens.popleft())
z = float(tokens.popleft())
self.ref = np.array([x, y, z], dtype=np.float32)
self.cutoff = float(tokens.popleft())
@return_empty_on_apply
def apply(self, group):
indices = []
box = self.validate_dimensions(group.dimensions)
pairs = distances.capped_distance(self.ref[None, :], group.positions, self.cutoff,
box=box,
return_distances=False)
if pairs.size > 0:
indices = np.sort(pairs[:, 1])
return group[np.asarray(indices, dtype=np.int64)].unique
class AtomSelection(Selection):
token = 'atom'
def __init__(self, parser, tokens):
self.segid = tokens.popleft()
self.resid = int(tokens.popleft())
self.name = tokens.popleft()
def apply(self, group):
sub = group[group.names == self.name]
if sub:
sub = sub[sub.resids == self.resid]
if sub:
sub = sub[sub.segids == self.segid]
return sub.unique
class BondedSelection(Selection):
token = 'bonded'
precedence = 1
def __init__(self, parser, tokens):
self.sel = parser.parse_expression(self.precedence)
def apply(self, group):
grp = self.sel.apply(group)
# Check if we have bonds
if not group.bonds:
warnings.warn("Bonded selection has 0 bonds")
return group[[]]
grpidx = grp.indices
# (n, 2) array of bond indices
bix = np.array(group.bonds.to_indices())
idx = []
# left side
idx.append(bix[:, 0][np.in1d(bix[:, 1], grpidx)])
# right side
idx.append(bix[:, 1][np.in1d(bix[:, 0], grpidx)])
idx = np.union1d(*idx)
return group.universe.atoms[np.unique(idx)]
class SelgroupSelection(Selection):
token = 'group'
def __init__(self, parser, tokens):
grpname = tokens.popleft()
if grpname in _RESERVED_KWARGS:
raise TypeError("The '{}' keyword is reserved and cannot be "
"used as a selection group name."
.format(grpname))
try:
self.grp = parser.selgroups[grpname]
except KeyError:
six.raise_from(
ValueError("Failed to find group: {0}".format(grpname)),
None)
def apply(self, group):
mask = np.in1d(group.indices, self.grp.indices)
return group[mask]
class _ProtoStringSelection(Selection):
"""Selections based on text attributes
.. versionchanged:: 1.0.0
Supports multiple wildcards, based on fnmatch
"""
def __init__(self, parser, tokens):
vals = grab_not_keywords(tokens)
if not vals:
raise ValueError("Unexpected token '{0}'".format(tokens[0]))
self.values = vals
@return_empty_on_apply
def apply(self, group):
# rather than work on group.names, cheat and look at the lookup table
nmattr = getattr(group.universe._topology, self.field)
matches = [] # list of passing indices
# iterate through set of known atom names, check which pass
for nm, ix in nmattr.namedict.items():
if any(fnmatch.fnmatchcase(nm, val) for val in self.values):
matches.append(ix)
# atomname indices for members of this group
nmidx = nmattr.nmidx[getattr(group, self.level)]
return group[np.in1d(nmidx, matches)].unique
[docs]class StringSelection(_ProtoStringSelection):
level = 'ix' # operates on atom level attribute, i.e. '.ix'
[docs]class AtomNameSelection(StringSelection):
"""Select atoms based on 'names' attribute"""
token = 'name'
field = 'names'
[docs]class AtomTypeSelection(StringSelection):
"""Select atoms based on 'types' attribute"""
token = 'type'
field = 'types'
[docs]class RecordTypeSelection(StringSelection):
"""Select atoms based on 'record_type' attribute"""
token = 'record_type'
field = 'record_types'
[docs]class AtomICodeSelection(StringSelection):
"""Select atoms based on icode attribute"""
token = 'icode'
field = 'icodes'
class _ResidueStringSelection(_ProtoStringSelection):
level= 'resindices'
[docs]class ResidueNameSelection(_ResidueStringSelection):
"""Select atoms based on 'resnames' attribute"""
token = 'resname'
field = 'resnames'
[docs]class MoleculeTypeSelection(_ResidueStringSelection):
"""Select atoms based on 'moltypes' attribute"""
token = 'moltype'
field = 'moltypes'
[docs]class SegmentNameSelection(_ProtoStringSelection):
"""Select atoms based on 'segids' attribute"""
token = 'segid'
field = 'segids'
level = 'segindices'
[docs]class AltlocSelection(StringSelection):
"""Select atoms based on 'altLoc' attribute"""
token = 'altloc'
field = 'altLocs'
[docs]class ResidSelection(Selection):
"""Select atoms based on numerical fields
Allows the use of ':' and '-' to specify a range of values
For example
resid 1:10
"""
token = 'resid'
def __init__(self, parser, tokens):
values = grab_not_keywords(tokens)
if not values:
raise ValueError("Unexpected token: '{0}'".format(tokens[0]))
# each value in uppers and lowers is a tuple of (resid, icode)
uppers = []
lowers = []
for val in values:
m1 = re.match("(\d+)(\w?)$", val)
if not m1 is None:
res = m1.groups()
lower = int(res[0]), res[1]
upper = None, None
else:
# check if in appropriate format 'lower:upper' or 'lower-upper'
# each val is one or more digits, maybe a letter
selrange = re.match("(\d+)(\w?)[:-](\d+)(\w?)", val)
if selrange is None: # re.match returns None on failure
raise ValueError("Failed to parse value: {0}".format(val))
res = selrange.groups()
# resid and icode
lower = int(res[0]), res[1]
upper = int(res[2]), res[3]
lowers.append(lower)
uppers.append(upper)
self.lowers = lowers
self.uppers = uppers
def apply(self, group):
# Grab arrays here to reduce number of calls to main topology
vals = group.resids
try: # optional attribute
icodes = group.icodes
except (AttributeError, NoDataError):
icodes = None
# if no icodes and icodes are part of selection, cause a fuss
if (any(v[1] for v in self.uppers) or
any(v[1] for v in self.lowers)):
six.raise_from(ValueError("Selection specified icodes, while the "
"topology doesn't have any."), None)
if not icodes is None:
mask = self._sel_with_icodes(vals, icodes)
else:
mask = self._sel_without_icodes(vals)
return group[mask].unique
def _sel_without_icodes(self, vals):
# Final mask that gets applied to group
mask = np.zeros(len(vals), dtype=bool)
for (u_resid, _), (l_resid, _) in zip(self.uppers, self.lowers):
if u_resid is not None: # range selection
thismask = vals >= l_resid
thismask &= vals <= u_resid
else: # single residue selection
thismask = vals == l_resid
mask |= thismask
return mask
def _sel_with_icodes(self, vals, icodes):
# Final mask that gets applied to group
mask = np.zeros(len(vals), dtype=bool)
for (u_resid, u_icode), (l_resid, l_icode) in zip(self.uppers, self.lowers):
if u_resid is not None: # Selecting a range
# Special case, if l_resid == u_resid, ie 163A-163C, this simplifies to:
# all 163, and A <= icode <= C
if l_resid == u_resid:
thismask = vals == l_resid
thismask &= icodes >= l_icode
thismask &= icodes <= u_icode
# For 163A to 166B we want:
# [START] all 163 and icode >= 'A'
# [MIDDLE] all of 164 and 165, any icode
# [END] 166 and icode <= 'B'
else:
# start of range
startmask = vals == l_resid
startmask &= icodes >= l_icode
thismask = startmask
# middle of range
mid = np.arange(l_resid + 1, u_resid)
if len(mid): # if there are any resids in the middle
mid_beg, mid_end = mid[0], mid[-1]
midmask = vals >= mid_beg
midmask &= vals <= mid_end
thismask |= midmask
# end of range
endmask = vals == u_resid
endmask &= icodes <= u_icode
thismask |= endmask
else: # Selecting a single residue
thismask = vals == l_resid
thismask &= icodes == l_icode
mask |= thismask
return mask
class RangeSelection(Selection):
value_offset=0
def __init__(self, parser, tokens):
values = grab_not_keywords(tokens)
if not values:
raise ValueError("Unexpected token: '{0}'".format(tokens[0]))
uppers = [] # upper limit on any range
lowers = [] # lower limit on any range
for val in values:
try:
lower = int(val)
upper = None
except ValueError:
# check if in appropriate format 'lower:upper' or 'lower-upper'
selrange = re.match("(\d+)[:-](\d+)", val)
if not selrange:
six.raise_from(ValueError(
"Failed to parse number: {0}".format(val)), None)
lower, upper = np.int64(selrange.groups())
lowers.append(lower)
uppers.append(upper)
self.lowers = lowers
self.uppers = uppers
def apply(self, group):
mask = np.zeros(len(group), dtype=bool)
vals = getattr(group, self.field) + self.value_offset
for upper, lower in zip(self.uppers, self.lowers):
if upper is not None:
thismask = vals >= lower
thismask &= vals <= upper
else:
thismask = vals == lower
mask |= thismask
return group[mask].unique
class ResnumSelection(RangeSelection):
token = 'resnum'
field = 'resnums'
class ByNumSelection(RangeSelection):
token = 'bynum'
field = 'indices'
value_offset = 1 # queries are in 1 based indices
class IndexSelection(RangeSelection):
token = 'index'
field = 'indices'
value_offset = 0 # queries now 0 based indices
class MolidSelection(RangeSelection):
token = 'molnum'
field = 'molnums'
[docs]class ProteinSelection(Selection):
"""Consists of all residues with recognized residue names.
Recognized residue names in :attr:`ProteinSelection.prot_res`.
* from the CHARMM force field::
awk '/RESI/ {printf "'"'"%s"'"',",$2 }' top_all27_prot_lipid.rtf
* manually added special CHARMM, OPLS/AA and Amber residue names.
See Also
--------
:func:`MDAnalysis.lib.util.convert_aa_code`
.. versionchanged:: 1.0.1
prot_res changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'protein'
prot_res = {
# CHARMM top_all27_prot_lipid.rtf
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HSD',
'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR',
'TRP', 'TYR', 'VAL', 'ALAD',
## 'CHO','EAM', # -- special formyl and ethanolamine termini of gramicidin
# PDB
'HIS', 'MSE',
# from Gromacs 4.5.3 oplsaa.ff/aminoacids.rtp
'ARGN', 'ASPH', 'CYS2', 'CYSH', 'QLN', 'PGLU', 'GLUH', 'HIS1', 'HISD',
'HISE', 'HISH', 'LYSH',
# from Gromacs 4.5.3 gromos53a6.ff/aminoacids.rtp
'ASN1', 'CYS1', 'HISA', 'HISB', 'HIS2',
# from Gromacs 4.5.3 amber03.ff/aminoacids.rtp
'HID', 'HIE', 'HIP', 'ORN', 'DAB', 'LYN', 'HYP', 'CYM', 'CYX', 'ASH',
'GLH', 'ACE', 'NME',
# from Gromacs 2016.3 amber99sb-star-ildn.ff/aminoacids.rtp
'NALA', 'NGLY', 'NSER', 'NTHR', 'NLEU', 'NILE', 'NVAL', 'NASN', 'NGLN',
'NARG', 'NHID', 'NHIE', 'NHIP', 'NTRP', 'NPHE', 'NTYR', 'NGLU', 'NASP',
'NLYS', 'NPRO', 'NCYS', 'NCYX', 'NMET', 'CALA', 'CGLY', 'CSER', 'CTHR',
'CLEU', 'CILE', 'CVAL', 'CASF', 'CASN', 'CGLN', 'CARG', 'CHID', 'CHIE',
'CHIP', 'CTRP', 'CPHE', 'CTYR', 'CGLU', 'CASP', 'CLYS', 'CPRO', 'CCYS',
'CCYX', 'CMET', 'CME', 'ASF',
}
def __init__(self, parser, tokens):
pass
def apply(self, group):
resname_attr = group.universe._topology.resnames
# which values in resname attr are in prot_res?
matches = [ix for (nm, ix) in resname_attr.namedict.items()
if nm in self.prot_res]
# index of each atom's resname
nmidx = resname_attr.nmidx[group.resindices]
# intersect atom's resname index and matches to prot_res
return group[np.in1d(nmidx, matches)].unique
[docs]class NucleicSelection(Selection):
"""All atoms in nucleic acid residues with recognized residue names.
Recognized residue names:
* from the CHARMM force field ::
awk '/RESI/ {printf "'"'"%s"'"',",$2 }' top_all27_prot_na.rtf
* recognized: 'ADE', 'URA', 'CYT', 'GUA', 'THY'
* recognized (CHARMM in Gromacs): 'DA', 'DU', 'DC', 'DG', 'DT'
.. versionchanged:: 0.8
additional Gromacs selections
.. versionchanged:: 1.0.1
nucl_res changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'nucleic'
nucl_res = {
'ADE', 'URA', 'CYT', 'GUA', 'THY', 'DA', 'DC', 'DG', 'DT', 'RA',
'RU', 'RG', 'RC', 'A', 'T', 'U', 'C', 'G',
'DA5', 'DC5', 'DG5', 'DT5',
'DA3', 'DC3', 'DG3', 'DT3',
'RA5', 'RU5', 'RG5', 'RC5',
'RA3', 'RU3', 'RG3', 'RC3'
}
def __init__(self, parser, tokens):
pass
def apply(self, group):
resnames = group.universe._topology.resnames
nmidx = resnames.nmidx[group.resindices]
matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.nucl_res]
mask = np.in1d(nmidx, matches)
return group[mask].unique
[docs]class BackboneSelection(ProteinSelection):
"""A BackboneSelection contains all atoms with name 'N', 'CA', 'C', 'O'.
This excludes OT* on C-termini
(which are included by, eg VMD's backbone selection).
.. versionchanged:: 1.0.1
bb_atoms changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'backbone'
bb_atoms = {'N', 'CA', 'C', 'O'}
def apply(self, group):
atomnames = group.universe._topology.names
resnames = group.universe._topology.resnames
# filter by atom names
name_matches = [ix for (nm, ix) in atomnames.namedict.items()
if nm in self.bb_atoms]
nmidx = atomnames.nmidx[group.ix]
group = group[np.in1d(nmidx, name_matches)]
# filter by resnames
resname_matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.prot_res]
nmidx = resnames.nmidx[group.resindices]
group = group[np.in1d(nmidx, resname_matches)]
return group.unique
[docs]class NucleicBackboneSelection(NucleicSelection):
"""Contains all atoms with name "P", "C5'", C3'", "O3'", "O5'".
These atoms are only recognized if they are in a residue matched
by the :class:`NucleicSelection`.
.. versionchanged:: 1.0.1
bb_atoms changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'nucleicbackbone'
bb_atoms = {"P", "C5'", "C3'", "O3'", "O5'"}
def apply(self, group):
atomnames = group.universe._topology.names
resnames = group.universe._topology.resnames
# filter by atom names
name_matches = [ix for (nm, ix) in atomnames.namedict.items()
if nm in self.bb_atoms]
nmidx = atomnames.nmidx[group.ix]
group = group[np.in1d(nmidx, name_matches)]
# filter by resnames
resname_matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.nucl_res]
nmidx = resnames.nmidx[group.resindices]
group = group[np.in1d(nmidx, resname_matches)]
return group.unique
[docs]class BaseSelection(NucleicSelection):
"""Selection of atoms in nucleobases.
Recognized atom names (from CHARMM):
'N9', 'N7', 'C8', 'C5', 'C4', 'N3', 'C2', 'N1', 'C6',
'O6','N2','N6', 'O2','N4','O4','C5M'
.. versionchanged:: 1.0.1
base_atoms changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'nucleicbase'
base_atoms = {
'N9', 'N7', 'C8', 'C5', 'C4', 'N3', 'C2', 'N1', 'C6',
'O6', 'N2', 'N6',
'O2', 'N4', 'O4', 'C5M'}
def apply(self, group):
atomnames = group.universe._topology.names
resnames = group.universe._topology.resnames
# filter by atom names
name_matches = [ix for (nm, ix) in atomnames.namedict.items()
if nm in self.base_atoms]
nmidx = atomnames.nmidx[group.ix]
group = group[np.in1d(nmidx, name_matches)]
# filter by resnames
resname_matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.nucl_res]
nmidx = resnames.nmidx[group.resindices]
group = group[np.in1d(nmidx, resname_matches)]
return group.unique
[docs]class NucleicSugarSelection(NucleicSelection):
"""Contains all atoms with name C1', C2', C3', C4', O2', O4', O3'.
.. versionchanged:: 1.0.1
sug_atoms changed to set (from numpy array)
performance improved by ~100x on larger systems
"""
token = 'nucleicsugar'
sug_atoms = {"C1'", "C2'", "C3'", "C4'", "O4'"}
def apply(self, group):
atomnames = group.universe._topology.names
resnames = group.universe._topology.resnames
# filter by atom names
name_matches = [ix for (nm, ix) in atomnames.namedict.items()
if nm in self.sug_atoms]
nmidx = atomnames.nmidx[group.ix]
group = group[np.in1d(nmidx, name_matches)]
# filter by resnames
resname_matches = [ix for (nm, ix) in resnames.namedict.items()
if nm in self.nucl_res]
nmidx = resnames.nmidx[group.resindices]
group = group[np.in1d(nmidx, resname_matches)]
return group.unique
[docs]class PropertySelection(Selection):
"""Some of the possible properties:
x, y, z, radius, mass,
"""
token = 'prop'
ops = dict([
('>', np.greater),
('<', np.less),
('>=', np.greater_equal),
('<=', np.less_equal),
('==', np.equal),
('!=', np.not_equal),
])
# order here is important, need to check <= before < so the
# larger (in terms of string length) symbol is considered first
_op_symbols = ('<=', '>=', '==', '!=', '<', '>')
# symbols to replace with when flipping
# eg 6 > x -> x <= 6, 5 == x -> x == 5
opposite_ops = {
'==': '==', '!=': '!=',
'<': '>=', '>=': '<',
'>': '<=', '<=': '>',
}
props = {'mass', 'charge', 'x', 'y', 'z'}
def __init__(self, parser, tokens):
"""
Possible splitting around operator:
prop x < 5
prop x< 5
prop x <5
prop x<5
"""
prop = tokens.popleft()
oper = None
value = None
if prop == "abs":
self.absolute = True
prop = tokens.popleft()
else:
self.absolute = False
# check if prop has any extra information atm
for possible in self._op_symbols:
try:
x, y = prop.split(possible)
except ValueError:
# won't unpack into 2 args unless *possible* is present
pass
else:
prop = x
oper = possible + y # add back after splitting
break
if oper is None:
oper = tokens.popleft()
# check if oper has the value appended
for possible in self._op_symbols:
if possible in oper:
x, y = oper.split(possible)
if y: # '<='.split('<=') == ['', ''], therefore y won't exist
oper = possible
value = y
break
if value is None:
value = tokens.popleft()
# check if we flip prop and value
# eg 5 > x -> x <= 5
if value in self.props:
prop, value = value, prop
oper = self.opposite_ops[oper]
self.prop = prop
try:
self.operator = self.ops[oper]
except KeyError:
six.raise_from(ValueError(
"Invalid operator : '{0}' Use one of : '{1}'"
"".format(oper, self.ops.keys())),
None)
self.value = float(value)
def apply(self, group):
try:
col = {'x': 0, 'y': 1, 'z': 2}[self.prop]
except KeyError:
if self.prop == 'mass':
values = group.masses
elif self.prop == 'charge':
values = group.charges
else:
six.raise_from(SelectionError(
"Expected one of : {0}"
"".format(['x', 'y', 'z', 'mass', 'charge'])), None)
else:
values = group.positions[:, col]
if self.absolute:
values = np.abs(values)
mask = self.operator(values, self.value)
return group[mask].unique
[docs]class SameSelection(Selection):
"""
Selects all atoms that have the same subkeyword value as any atom in selection
.. versionchanged:: 1.0.0
Map :code:`"residue"` to :code:`"resindices"` and :code:`"segment"` to
:code:`"segindices"` (see #2669 and #2672)
"""
token = 'same'
precedence = 1
prop_trans = {
'fragment': None,
'x': None,
'y': None,
'z': None,
'residue': 'resindices',
'segment': 'segindices',
'name': 'names',
'type': 'types',
'resname': 'resnames',
'resid': 'resids',
'segid': 'segids',
'mass': 'masses',
'charge': 'charges',
'radius': 'radii',
'bfactor': 'bfactors',
'resnum': 'resnums',
}
def __init__(self, parser, tokens):
prop = tokens.popleft()
if prop not in self.prop_trans:
raise ValueError("Unknown same property : {0}"
"Choose one of : {1}"
"".format(prop, self.prop_trans.keys()))
self.prop = prop
parser.expect("as")
self.sel = parser.parse_expression(self.precedence)
self.prop = prop
def apply(self, group):
res = self.sel.apply(group)
if not res:
return group[[]] # empty selection
# Fragment must come before self.prop_trans lookups!
if self.prop == 'fragment':
# Combine all fragments together, then check where group
# indices are same as fragment(s) indices
allfrags = functools.reduce(lambda x, y: x + y, res.fragments)
mask = np.in1d(group.indices, allfrags.indices)
return group[mask].unique
# [xyz] must come before self.prop_trans lookups too!
try:
pos_idx = {'x': 0, 'y': 1, 'z': 2}[self.prop]
except KeyError:
# The self.prop string was already checked,
# so don't need error checking here.
# KeyError at this point is impossible!
attrname = self.prop_trans[self.prop]
vals = getattr(res, attrname)
mask = np.in1d(getattr(group, attrname), vals)
return group[mask].unique
else:
vals = res.positions[:, pos_idx]
pos = group.positions[:, pos_idx]
# isclose only does one value at a time
mask = np.vstack([np.isclose(pos, v)
for v in vals]).any(axis=0)
return group[mask].unique
[docs]class SelectionParser(object):
"""A small parser for selection expressions. Demonstration of
recursive descent parsing using Precedence climbing (see
http://www.engr.mun.ca/~theo/Misc/exp_parsing.htm). Transforms
expressions into nested Selection tree.
For reference, the grammar that we parse is ::
E(xpression)--> Exp(0)
Exp(p) --> P {B Exp(q)}
P --> U Exp(q) | "(" E ")" | v
B(inary) --> "and" | "or"
U(nary) --> "not"
T(erms) --> segid [value]
| resname [value]
| resid [value]
| name [value]
| type [value]
"""
# Borg pattern: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/66531
_shared_state = {}
def __new__(cls, *p, **k):
self = object.__new__(cls, *p, **k)
self.__dict__ = cls._shared_state
return self
[docs] def expect(self, token):
"""Anticipate and remove a given token"""
if self.tokens[0] == token:
self.tokens.popleft()
else:
raise SelectionError(
"Unexpected token: '{0}' Expected: '{1}'"
"".format(self.tokens[0], token))
[docs] def parse(self, selectstr, selgroups, periodic=None):
"""Create a Selection object from a string.
Parameters
----------
selectstr : str
The string that describes the selection
selgroups : AtomGroups
AtomGroups to be used in `group` selections
periodic : bool, optional
for distance based selections, whether to consider
periodic boundary conditions
Returns
-------
The appropriate Selection object. Use the .apply method on
this to perform the selection.
Raises
------
SelectionError
If anything goes wrong in creating the Selection object.
"""
self.periodic = periodic
self.selectstr = selectstr
self.selgroups = selgroups
tokens = selectstr.replace('(', ' ( ').replace(')', ' ) ')
self.tokens = collections.deque(tokens.split() + [None])
parsetree = self.parse_expression(0)
if self.tokens[0] is not None:
raise SelectionError(
"Unexpected token at end of selection string: '{0}'"
"".format(self.tokens[0]))
return parsetree
def parse_expression(self, p):
exp1 = self._parse_subexp()
while (self.tokens[0] in _OPERATIONS and
_OPERATIONS[self.tokens[0]].precedence >= p):
op = _OPERATIONS[self.tokens.popleft()]
q = 1 + op.precedence
exp2 = self.parse_expression(q)
exp1 = op(exp1, exp2)
return exp1
def _parse_subexp(self):
op = self.tokens.popleft()
if op == '(':
exp = self.parse_expression(0)
self.expect(')')
return exp
try:
return _SELECTIONDICT[op](self, self.tokens)
except KeyError:
six.raise_from(
SelectionError("Unknown selection token: '{0}'".format(op)),
None)
except ValueError as e:
six.raise_from(
SelectionError("Selection failed: '{0}'".format(e)),
None)
# The module level instance
Parser = SelectionParser()