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# 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
#
"""\
Topology attribute objects --- :mod:`MDAnalysis.core.topologyattrs`
===================================================================
Common :class:`TopologyAttr` instances that are used by most topology
parsers.
TopologyAttrs are used to contain attributes such as atom names or resids.
These are usually read by the TopologyParser.
"""
from __future__ import division, absolute_import
import six
from six.moves import zip, range
import Bio.Seq
import Bio.SeqRecord
from collections import defaultdict
import copy
import functools
import itertools
import numbers
import numpy as np
import warnings
from ..lib.util import (cached, convert_aa_code, iterable, warn_if_not_unique,
unique_int_1d)
from ..lib import transformations, mdamath
from ..exceptions import NoDataError, SelectionError
from .topologyobjects import TopologyGroup
from . import selection
from .groups import (ComponentBase, GroupBase,
Atom, Residue, Segment,
AtomGroup, ResidueGroup, SegmentGroup,
check_pbc_and_unwrap)
from .. import _TOPOLOGY_ATTRS, _TOPOLOGY_TRANSPLANTS, _TOPOLOGY_ATTRNAMES
def _check_length(func):
"""Wrapper which checks the length of inputs to set_X
Eg:
@_check_length
def set_X(self, group, values):
Will check the length of *values* compared to *group* before proceeding with
anything in the *set_X* method.
Pseudo code for the check:
if group in (Atom, Residue, Segment):
values must be single values, ie int, float or string
else:
values must be single value OR same length as group
"""
_SINGLE_VALUE_ERROR = ("Setting {cls} {attrname} with wrong sized input. "
"Must use single value, length of supplied values: {lenvalues}.")
# Eg "Setting Residue resid with wrong sized input. Must use single value, length of supplied
# values: 2."
_GROUP_VALUE_ERROR = ("Setting {group} {attrname} with wrong sized array. "
"Length {group}: {lengroup}, length of supplied values: {lenvalues}.")
# Eg "Setting AtomGroup masses with wrong sized array. Length AtomGroup: 100, length of
# supplied values: 50."
def _attr_len(values):
# quasi len measurement
# strings, floats, ints are len 0, ie not iterable
# other iterables are just len'd
if iterable(values):
return len(values)
else:
return 0 # special case
@functools.wraps(func)
def wrapper(attr, group, values):
val_len = _attr_len(values)
if isinstance(group, ComponentBase):
if not val_len == 0:
raise ValueError(_SINGLE_VALUE_ERROR.format(
cls=group.__class__.__name__, attrname=attr.singular,
lenvalues=val_len))
else:
if not (val_len == 0 or val_len == len(group)):
raise ValueError(_GROUP_VALUE_ERROR.format(
group=group.__class__.__name__, attrname=attr.attrname,
lengroup=len(group), lenvalues=val_len))
# if everything went OK, continue with the function
return func(attr, group, values)
return wrapper
def _wronglevel_error(attr, group):
"""Generate an error for setting attr at wrong level
attr : TopologyAttr that was accessed
group : Offending Component/Group
Eg:
setting mass of residue, gets called with attr=Masses, group=residue
raises a NotImplementedError with:
'Cannot set masses from Residue. Use 'Residue.atoms.masses'
Mainly used to ensure consistent and helpful error messages
"""
if isinstance(group, (Atom, AtomGroup)):
group_level = 1
elif isinstance(group, (Residue, ResidueGroup)):
group_level = 2
elif isinstance(group, (Segment, SegmentGroup)):
group_level = 3
# What level to go to before trying to set this attr
if isinstance(attr, AtomAttr):
corr_classes = ('atoms', 'atom')
attr_level = 1
elif isinstance(attr, ResidueAttr):
corr_classes = ('residues', 'residue')
attr_level = 2
elif isinstance(attr, SegmentAttr):
corr_classes = ('segments', 'segment')
attr_level = 3
if isinstance(group, ComponentBase) and (attr_level > group_level):
# ie going downards use plurals, going upwards use singulars
# Residue.atom!s!.mass!es! but Atom.segment!!.segid!!
correct = corr_classes[1]
attrname = attr.singular
else:
correct = corr_classes[0]
attrname = attr.attrname
err_msg = "Cannot set {attr} from {cls}. Use '{cls}.{correct}.{attr} = '"
# eg "Cannot set masses from Residue. 'Use Residue.atoms.masses = '"
return NotImplementedError(err_msg.format(
attr=attrname, cls=group.__class__.__name__, correct=correct,
))
class _TopologyAttrMeta(type):
# register TopologyAttrs
def __init__(cls, name, bases, classdict):
type.__init__(type, name, bases, classdict)
attrname = classdict.get('attrname')
singular = classdict.get('singular', attrname)
if attrname is None:
attrname = singular
if singular:
_TOPOLOGY_ATTRS[singular] = _TOPOLOGY_ATTRS[attrname] = cls
_singular = singular.lower().replace('_', '')
_attrname = attrname.lower().replace('_', '')
_TOPOLOGY_ATTRNAMES[_singular] = singular
_TOPOLOGY_ATTRNAMES[_attrname] = attrname
for clstype, transplants in cls.transplants.items():
for name, method in transplants:
_TOPOLOGY_TRANSPLANTS[name] = [attrname, method, clstype]
clean = name.lower().replace('_', '')
_TOPOLOGY_ATTRNAMES[clean] = name
[docs]class TopologyAttr(six.with_metaclass(_TopologyAttrMeta, object)):
"""Base class for Topology attributes.
Note
----
This class is intended to be subclassed, and mostly amounts to
a skeleton. The methods here should be present in all
:class:`TopologyAttr` child classes, but by default they raise
appropriate exceptions.
Attributes
----------
attrname : str
the name used for the attribute when attached to a ``Topology`` object
singular : str
name for the attribute on a singular object (Atom/Residue/Segment)
per_object : str
If there is a strict mapping between Component and Attribute
dtype : int/float/object
Type to coerce this attribute to be. For string use 'object'
top : Topology
handle for the Topology object TopologyAttr is associated with
"""
attrname = 'topologyattrs'
singular = 'topologyattr'
per_object = None # ie Resids per_object = 'residue'
top = None # pointer to Topology object
transplants = defaultdict(list)
target_classes = []
groupdoc = None
singledoc = None
dtype = None
def __init__(self, values, guessed=False):
if self.dtype is None:
self.values = values
else:
self.values = np.asarray(values, dtype=self.dtype)
self._guessed = guessed
@staticmethod
def _gen_initial_values(n_atoms, n_residues, n_segments):
"""Populate an initial empty data structure for this Attribute
The only provided parameters are the "shape" of the Universe
Eg for charges, provide np.zeros(n_atoms)
"""
raise NotImplementedError("No default values")
[docs] @classmethod
def from_blank(cls, n_atoms=None, n_residues=None, n_segments=None,
values=None):
"""Create a blank version of this TopologyAttribute
Parameters
----------
n_atoms : int, optional
Size of the TopologyAttribute atoms
n_residues: int, optional
Size of the TopologyAttribute residues
n_segments : int, optional
Size of the TopologyAttribute segments
values : optional
Initial values for the TopologyAttribute
"""
if values is None:
values = cls._gen_initial_values(n_atoms, n_residues, n_segments)
elif cls.dtype is not None:
# if supplied starting values and statically typed
values = np.asarray(values, dtype=cls.dtype)
return cls(values)
[docs] def copy(self):
"""Return a deepcopy of this attribute"""
return self.__class__(self.values.copy(), guessed=self._guessed)
def __len__(self):
"""Length of the TopologyAttr at its intrinsic level."""
return len(self.values)
def __getitem__(self, group):
"""Accepts an AtomGroup, ResidueGroup or SegmentGroup"""
if isinstance(group, (Atom, AtomGroup)):
return self.get_atoms(group)
elif isinstance(group, (Residue, ResidueGroup)):
return self.get_residues(group)
elif isinstance(group, (Segment, SegmentGroup)):
return self.get_segments(group)
def __setitem__(self, group, values):
if isinstance(group, (Atom, AtomGroup)):
return self.set_atoms(group, values)
elif isinstance(group, (Residue, ResidueGroup)):
return self.set_residues(group, values)
elif isinstance(group, (Segment, SegmentGroup)):
return self.set_segments(group, values)
@property
def is_guessed(self):
"""Bool of if the source of this information is a guess"""
return self._guessed
[docs] def get_atoms(self, ag):
"""Get atom attributes for a given AtomGroup"""
raise NoDataError
[docs] def set_atoms(self, ag, values):
"""Set atom attributes for a given AtomGroup"""
raise NotImplementedError
[docs] def get_residues(self, rg):
"""Get residue attributes for a given ResidueGroup"""
raise NoDataError
[docs] def set_residues(self, rg, values):
"""Set residue attributes for a given ResidueGroup"""
raise NotImplementedError
[docs] def get_segments(self, sg):
"""Get segment attributes for a given SegmentGroup"""
raise NoDataError
[docs] def set_segments(self, sg, values):
"""Set segmentattributes for a given SegmentGroup"""
raise NotImplementedError
# core attributes
[docs]class Atomindices(TopologyAttr):
"""Globally unique indices for each atom in the group.
If the group is an AtomGroup, then this gives the index for each atom in
the group. This is the unambiguous identifier for each atom in the
topology, and it is not alterable.
If the group is a ResidueGroup or SegmentGroup, then this gives the indices
of each atom represented in the group in a 1-D array, in the order of the
elements in that group.
"""
attrname = 'indices'
singular = 'index'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom]
def __init__(self):
self._guessed = False
[docs] def set_atoms(self, ag, values):
raise AttributeError("Atom indices are fixed; they cannot be reset")
[docs] def get_atoms(self, ag):
return ag.ix
[docs] def get_residues(self, rg):
return list(self.top.tt.residues2atoms_2d(rg.ix))
[docs] def get_segments(self, sg):
return list(self.top.tt.segments2atoms_2d(sg.ix))
[docs]class Resindices(TopologyAttr):
"""Globally unique resindices for each residue in the group.
If the group is an AtomGroup, then this gives the resindex for each atom in
the group. This unambiguously determines each atom's residue membership.
Resetting these values changes the residue membership of the atoms.
If the group is a ResidueGroup or SegmentGroup, then this gives the
resindices of each residue represented in the group in a 1-D array, in the
order of the elements in that group.
"""
attrname = 'resindices'
singular = 'resindex'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
def __init__(self):
self._guessed = False
[docs] def get_atoms(self, ag):
return self.top.tt.atoms2residues(ag.ix)
[docs] def get_residues(self, rg):
return rg.ix
[docs] def set_residues(self, rg, values):
raise AttributeError("Residue indices are fixed; they cannot be reset")
[docs] def get_segments(self, sg):
return list(self.top.tt.segments2residues_2d(sg.ix))
[docs]class Segindices(TopologyAttr):
"""Globally unique segindices for each segment in the group.
If the group is an AtomGroup, then this gives the segindex for each atom in
the group. This unambiguously determines each atom's segment membership.
It is not possible to set these, since membership in a segment is an
attribute of each atom's residue.
If the group is a ResidueGroup or SegmentGroup, then this gives the
segindices of each segment represented in the group in a 1-D array, in the
order of the elements in that group.
"""
attrname = 'segindices'
singular = 'segindex'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup,
Atom, Residue, Segment]
def __init__(self):
self._guessed = False
[docs] def get_atoms(self, ag):
return self.top.tt.atoms2segments(ag.ix)
[docs] def get_residues(self, rg):
return self.top.tt.residues2segments(rg.ix)
[docs] def get_segments(self, sg):
return sg.ix
[docs] def set_segments(self, sg, values):
raise AttributeError("Segment indices are fixed; they cannot be reset")
# atom attributes
[docs]class AtomAttr(TopologyAttr):
"""Base class for atom attributes.
"""
attrname = 'atomattrs'
singular = 'atomattr'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom]
[docs] def get_atoms(self, ag):
return self.values[ag.ix]
[docs] @_check_length
def set_atoms(self, ag, values):
self.values[ag.ix] = values
[docs] def get_residues(self, rg):
"""By default, the values for each atom present in the set of residues
are returned in a single array. This behavior can be overriden in child
attributes.
"""
aixs = self.top.tt.residues2atoms_2d(rg.ix)
return [self.values[aix] for aix in aixs]
[docs] def set_residues(self, rg, values):
raise _wronglevel_error(self, rg)
[docs] def get_segments(self, sg):
"""By default, the values for each atom present in the set of residues
are returned in a single array. This behavior can be overriden in child
attributes.
"""
aixs = self.top.tt.segments2atoms_2d(sg.ix)
return [self.values[aix] for aix in aixs]
[docs] def set_segments(self, sg, values):
raise _wronglevel_error(self, sg)
# TODO: update docs to property doc
[docs]class Atomids(AtomAttr):
"""ID for each atom.
"""
attrname = 'ids'
singular = 'id'
per_object = 'atom'
dtype = int
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.arange(1, na + 1)
# TODO: update docs to property doc
[docs]class Atomnames(AtomAttr):
"""Name for each atom.
"""
attrname = 'names'
singular = 'name'
per_object = 'atom'
dtype = object
transplants = defaultdict(list)
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(na)], dtype=object)
[docs] def phi_selection(residue, c_name='C', n_name='N', ca_name='CA'):
"""Select AtomGroup corresponding to the phi protein backbone dihedral
C'-N-CA-C.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
AtomGroup
4-atom selection in the correct order. If no C' found in the
previous residue (by resid) then this method returns ``None``.
.. versionchanged:: 1.0.0
Added arguments for flexible atom names and refactored code for
faster atom matching with boolean arrays.
"""
# fnmatch is expensive. try the obv candidate first
prev = residue.universe.residues[residue.ix-1]
sid = residue.segment.segid
rid = residue.resid-1
if not (prev.segment.segid == sid and prev.resid == rid):
sel = 'segid {} and resid {}'.format(sid, rid)
try:
prev = residue.universe.select_atoms(sel).residues[0]
except IndexError:
return None
c_ = prev.atoms[prev.atoms.names == c_name]
if not len(c_) == 1:
return None
atnames = residue.atoms.names
ncac_names = [n_name, ca_name, c_name]
ncac = [residue.atoms[atnames == n] for n in ncac_names]
if not all(len(ag) == 1 for ag in ncac):
return None
sel = c_+sum(ncac)
return sel
transplants[Residue].append(('phi_selection', phi_selection))
[docs] def phi_selections(residues, c_name='C', n_name='N', ca_name='CA'):
"""Select list of AtomGroups corresponding to the phi protein
backbone dihedral C'-N-CA-C.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
list of AtomGroups
4-atom selections in the correct order. If no C' found in the
previous residue (by resid) then corresponding item in the list
is ``None``.
.. versionadded:: 1.0.0
"""
u = residues[0].universe
prev = u.residues[residues.ix-1] # obv candidates first
rsid = residues.segids
prid = residues.resids-1
ncac_names = [n_name, ca_name, c_name]
sel = 'segid {} and resid {}'
# replace wrong residues
wix = np.where((prev.segids != rsid) | (prev.resids != prid))[0]
invalid = []
if len(wix):
prevls = list(prev)
for s, r, i in zip(rsid[wix], prid[wix], wix):
try:
prevls[i] = u.select_atoms(sel.format(s, r)).residues[0]
except IndexError:
invalid.append(i)
prev = sum(prevls)
keep_prev = [sum(r.atoms.names == c_name) == 1 for r in prev]
keep_res = [all(sum(r.atoms.names == n) == 1 for n in ncac_names)
for r in residues]
keep = np.array(keep_prev) & np.array(keep_res)
keep[invalid] = False
results = np.zeros_like(residues, dtype=object)
results[~keep] = None
prev = prev[keep]
residues = residues[keep]
keepix = np.where(keep)[0]
c_ = prev.atoms[prev.atoms.names == c_name]
n = residues.atoms[residues.atoms.names == n_name]
ca = residues.atoms[residues.atoms.names == ca_name]
c = residues.atoms[residues.atoms.names == c_name]
results[keepix] = [sum(atoms) for atoms in zip(c_, n, ca, c)]
return list(results)
transplants[ResidueGroup].append(('phi_selections', phi_selections))
[docs] def psi_selection(residue, c_name='C', n_name='N', ca_name='CA'):
"""Select AtomGroup corresponding to the psi protein backbone dihedral
N-CA-C-N'.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
AtomGroup
4-atom selection in the correct order. If no N' found in the
following residue (by resid) then this method returns ``None``.
.. versionchanged:: 1.0.0
Added arguments for flexible atom names and refactored code for
faster atom matching with boolean arrays.
"""
# fnmatch is expensive. try the obv candidate first
_manual_sel = False
sid = residue.segment.segid
rid = residue.resid+1
try:
nxt = residue.universe.residues[residue.ix+1]
except IndexError:
_manual_sel = True
else:
if not (nxt.segment.segid == sid and nxt.resid == rid):
_manual_sel = True
if _manual_sel:
sel = 'segid {} and resid {}'.format(sid, rid)
try:
nxt = residue.universe.select_atoms(sel).residues[0]
except IndexError:
return None
n_ = nxt.atoms[nxt.atoms.names == n_name]
if not len(n_) == 1:
return None
atnames = residue.atoms.names
ncac_names = [n_name, ca_name, c_name]
ncac = [residue.atoms[atnames == n] for n in ncac_names]
if not all(len(ag) == 1 for ag in ncac):
return None
sel = sum(ncac) + n_
return sel
transplants[Residue].append(('psi_selection', psi_selection))
def _get_next_residues_by_resid(residues):
"""Select list of Residues corresponding to the next resid for each
residue in `residues`.
Returns
-------
List of Residues
List of the next residues in the Universe, by resid and segid.
If not found, the corresponding item in the list is ``None``.
.. versionadded:: 1.0.0
"""
u = residues[0].universe
nxres = np.array([None]*len(residues), dtype=object)
ix = np.arange(len(residues))
# no guarantee residues is ordered or unique
last = max(residues.ix)
if last == len(u.residues)-1:
notlast = residues.ix != last
ix = ix[notlast]
residues = residues[notlast]
nxres[ix] = nxt = u.residues[residues.ix+1]
rsid = residues.segids
nrid = residues.resids+1
sel = 'segid {} and resid {}'
# replace wrong residues
wix = np.where((nxt.segids != rsid) | (nxt.resids != nrid))[0]
if len(wix):
for s, r, i in zip(rsid[wix], nrid[wix], wix):
try:
nxres[ix[i]] = u.select_atoms(sel.format(s, r)).residues[0]
except IndexError:
nxres[ix[i]] = None
return nxres
transplants[ResidueGroup].append(('_get_next_residues_by_resid',
_get_next_residues_by_resid))
def _get_prev_residues_by_resid(residues):
"""Select list of Residues corresponding to the previous resid for each
residue in `residues`.
Returns
-------
List of Residues
List of the previous residues in the Universe, by resid and segid.
If not found, the corresponding item in the list is ``None``.
.. versionadded:: 1.0.0
"""
u = residues[0].universe
pvres = np.array([None]*len(residues))
pvres[:] = prev = u.residues[residues.ix-1]
rsid = residues.segids
prid = residues.resids-1
sel = 'segid {} and resid {}'
# replace wrong residues
wix = np.where((prev.segids != rsid) | (prev.resids != prid))[0]
if len(wix):
for s, r, i in zip(rsid[wix], prid[wix], wix):
try:
pvres[i] = u.select_atoms(sel.format(s, r)).residues[0]
except IndexError:
pvres[i] = None
return pvres
transplants[ResidueGroup].append(('_get_prev_residues_by_resid',
_get_prev_residues_by_resid))
[docs] def psi_selections(residues, c_name='C', n_name='N', ca_name='CA'):
"""Select list of AtomGroups corresponding to the psi protein
backbone dihedral N-CA-C-N'.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
List of AtomGroups
4-atom selections in the correct order. If no N' found in the
following residue (by resid) then the corresponding item in the
list is ``None``.
.. versionadded:: 1.0.0
"""
results = np.array([None]*len(residues), dtype=object)
nxtres = residues._get_next_residues_by_resid()
rix = np.where(nxtres)[0]
nxt = sum(nxtres[rix])
residues = residues[rix]
ncac_names = [n_name, ca_name, c_name]
keep_nxt = [sum(r.atoms.names == n_name) == 1 for r in nxt]
keep_res = [all(sum(r.atoms.names == n) == 1 for n in ncac_names)
for r in residues]
keep = np.array(keep_nxt) & np.array(keep_res)
nxt = nxt[keep]
residues = residues[keep]
keepix = np.where(keep)[0]
n = residues.atoms[residues.atoms.names == n_name]
ca = residues.atoms[residues.atoms.names == ca_name]
c = residues.atoms[residues.atoms.names == c_name]
n_ = nxt.atoms[nxt.atoms.names == n_name]
results[rix[keepix]] = [sum(atoms) for atoms in zip(n, ca, c, n_)]
return list(results)
transplants[ResidueGroup].append(('psi_selections', psi_selections))
[docs] def omega_selection(residue, c_name='C', n_name='N', ca_name='CA'):
"""Select AtomGroup corresponding to the omega protein backbone dihedral
CA-C-N'-CA'.
omega describes the -C-N- peptide bond. Typically, it is trans (180
degrees) although cis-bonds (0 degrees) are also occasionally observed
(especially near Proline).
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
AtomGroup
4-atom selection in the correct order. If no C' found in the
previous residue (by resid) then this method returns ``None``.
.. versionchanged:: 1.0.0
Added arguments for flexible atom names and refactored code for
faster atom matching with boolean arrays.
"""
# fnmatch is expensive. try the obv candidate first
_manual_sel = False
sid = residue.segment.segid
rid = residue.resid+1
try:
nxt = residue.universe.residues[residue.ix+1]
except IndexError:
_manual_sel = True
else:
if not (nxt.segment.segid == sid and nxt.resid == rid):
_manual_sel = True
if _manual_sel:
sel = 'segid {} and resid {}'.format(sid, rid)
try:
nxt = residue.universe.select_atoms(sel).residues[0]
except IndexError:
return None
ca = residue.atoms[residue.atoms.names == ca_name]
c = residue.atoms[residue.atoms.names == c_name]
n_ = nxt.atoms[nxt.atoms.names == n_name]
ca_ = nxt.atoms[nxt.atoms.names == ca_name]
if not all(len(ag) == 1 for ag in [ca_, n_, ca, c]):
return None
return ca+c+n_+ca_
transplants[Residue].append(('omega_selection', omega_selection))
[docs] def omega_selections(residues, c_name='C', n_name='N', ca_name='CA'):
"""Select list of AtomGroups corresponding to the omega protein
backbone dihedral CA-C-N'-CA'.
omega describes the -C-N- peptide bond. Typically, it is trans (180
degrees) although cis-bonds (0 degrees) are also occasionally observed
(especially near Proline).
Parameters
----------
c_name: str (optional)
name for the backbone C atom
n_name: str (optional)
name for the backbone N atom
ca_name: str (optional)
name for the alpha-carbon atom
Returns
-------
List of AtomGroups
4-atom selections in the correct order. If no C' found in the
previous residue (by resid) then the corresponding item in the
list is ``None``.
.. versionadded:: 1.0.0
"""
results = np.array([None]*len(residues), dtype=object)
nxtres = residues._get_next_residues_by_resid()
rix = np.where(nxtres)[0]
nxt = sum(nxtres[rix])
residues = residues[rix]
nxtatoms = [ca_name, n_name]
resatoms = [ca_name, c_name]
keep_nxt = [all(sum(r.atoms.names == n) == 1 for n in nxtatoms)
for r in nxt]
keep_res = [all(sum(r.atoms.names == n) == 1 for n in resatoms)
for r in residues]
keep = np.array(keep_nxt) & np.array(keep_res)
nxt = nxt[keep]
residues = residues[keep]
keepix = np.where(keep)[0]
c = residues.atoms[residues.atoms.names == c_name]
ca = residues.atoms[residues.atoms.names == ca_name]
n_ = nxt.atoms[nxt.atoms.names == n_name]
ca_ = nxt.atoms[nxt.atoms.names == ca_name]
results[rix[keepix]] = [sum(atoms) for atoms in zip(ca, c, n_, ca_)]
return list(results)
transplants[ResidueGroup].append(('omega_selections', omega_selections))
[docs] def chi1_selection(residue, n_name='N', ca_name='CA', cb_name='CB',
cg_name='CG'):
"""Select AtomGroup corresponding to the chi1 sidechain dihedral N-CA-CB-CG.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
ca_name: str (optional)
name for the alpha-carbon atom
cb_name: str (optional)
name for the beta-carbon atom
cg_name: str (optional)
name for the gamma-carbon atom
Returns
-------
AtomGroup
4-atom selection in the correct order. If no CB and/or CG is found
then this method returns ``None``.
.. versionchanged:: 1.0.0
Added arguments for flexible atom names and refactored code for
faster atom matching with boolean arrays.
.. versionadded:: 0.7.5
"""
names = [n_name, ca_name, cb_name, cg_name]
ags = [residue.atoms[residue.atoms.names == n] for n in names]
if any(len(ag)!= 1 for ag in ags):
return None
return sum(ags)
transplants[Residue].append(('chi1_selection', chi1_selection))
[docs] def chi1_selections(residues, n_name='N', ca_name='CA', cb_name='CB',
cg_name='CG'):
"""Select list of AtomGroups corresponding to the chi1 sidechain dihedral
N-CA-CB-CG.
Parameters
----------
c_name: str (optional)
name for the backbone C atom
ca_name: str (optional)
name for the alpha-carbon atom
cb_name: str (optional)
name for the beta-carbon atom
cg_name: str (optional)
name for the gamma-carbon atom
Returns
-------
List of AtomGroups
4-atom selections in the correct order. If no CB and/or CG is found
then the corresponding item in the list is ``None``.
.. versionadded:: 1.0.0
"""
results = np.array([None]*len(residues))
names = [n_name, ca_name, cb_name, cg_name]
keep = [all(sum(r.atoms.names == n) == 1 for n in names)
for r in residues]
keepix = np.where(keep)[0]
residues = residues[keep]
atnames = residues.atoms.names
ags = [residues.atoms[atnames == n] for n in names]
results[keepix] = [sum(atoms) for atoms in zip(*ags)]
return list(results)
transplants[ResidueGroup].append(('chi1_selections', chi1_selections))
# TODO: update docs to property doc
[docs]class Atomtypes(AtomAttr):
"""Type for each atom"""
attrname = 'types'
singular = 'type'
per_object = 'atom'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(na)], dtype=object)
# TODO: update docs to property doc
[docs]class Elements(AtomAttr):
"""Element for each atom"""
attrname = 'elements'
singular = 'element'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(na)], dtype=object)
# TODO: update docs to property doc
[docs]class Radii(AtomAttr):
"""Radii for each atom"""
attrname = 'radii'
singular = 'radius'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class RecordTypes(AtomAttr):
"""For PDB-like formats, indicates if ATOM or HETATM
Defaults to 'ATOM'
.. versionchanged:: 0.20.0
Now stores array of dtype object rather than boolean mapping
"""
attrname = 'record_types'
singular = 'record_type'
per_object = 'atom'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['ATOM'] * na, dtype=object)
[docs]class ChainIDs(AtomAttr):
"""ChainID per atom
Note
----
This is an attribute of the Atom, not Residue or Segment
"""
attrname = 'chainIDs'
singular = 'chainID'
per_object = 'atom'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(na)], dtype=object)
[docs]class Tempfactors(AtomAttr):
"""Tempfactor for atoms"""
attrname = 'tempfactors'
singular = 'tempfactor'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class Masses(AtomAttr):
attrname = 'masses'
singular = 'mass'
per_object = 'atom'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup,
Atom, Residue, Segment]
transplants = defaultdict(list)
dtype = np.float64
groupdoc = """Mass of each component in the Group.
If the Group is an AtomGroup, then the masses are for each atom. If the
Group is a ResidueGroup or SegmentGroup, the masses are for each residue or
segment, respectively. These are obtained by summation of the member atoms
for each component.
"""
singledoc = """Mass of the component."""
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs] def get_residues(self, rg):
resatoms = self.top.tt.residues2atoms_2d(rg.ix)
if isinstance(rg._ix, numbers.Integral):
# for a single residue
masses = self.values[resatoms].sum()
else:
# for a residuegroup
masses = np.empty(len(rg))
for i, row in enumerate(resatoms):
masses[i] = self.values[row].sum()
return masses
[docs] def get_segments(self, sg):
segatoms = self.top.tt.segments2atoms_2d(sg.ix)
if isinstance(sg._ix, numbers.Integral):
# for a single segment
masses = self.values[tuple(segatoms)].sum()
else:
# for a segmentgroup
masses = np.array([self.values[row].sum() for row in segatoms])
return masses
[docs] @warn_if_not_unique
@check_pbc_and_unwrap
def center_of_mass(group, pbc=False, compound='group', unwrap=False):
"""Center of mass of (compounds of) the group.
Computes the center of mass of :class:`Atoms<Atom>` in the group.
Centers of mass per :class:`Residue`, :class:`Segment`, molecule, or
fragment can be obtained by setting the `compound` parameter
accordingly. If the masses of a compound sum up to zero, the
center of mass coordinates of that compound will be ``nan`` (not a
number).
Parameters
----------
pbc : bool, optional
If ``True`` and `compound` is ``'group'``, move all atoms to the
primary unit cell before calculation.
If ``True`` and `compound` is ``'segments'`` or ``'residues'``, the
centers of mass of each compound will be calculated without moving
any atoms to keep the compounds intact. Instead, the resulting
center-of-mass position vectors will be moved to the primary unit
cell after calculation.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\
optional
If ``'group'``, the center of mass of all atoms in the group will
be returned as a single position vector. Otherwise, the centers of
mass of each :class:`Segment`, :class:`Residue`, molecule, or
fragment will be returned as an array of position vectors, i.e. a 2d
array.
Note that, in any case, *only* the positions of :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their centers.
Returns
-------
center : numpy.ndarray
Position vector(s) of the center(s) of mass of the group.
If `compound` was set to ``'group'``, the output will be a single
position vector.
If `compound` was set to ``'segments'`` or ``'residues'``, the
output will be a 2d coordinate array of shape ``(n, 3)`` where ``n``
is the number of compounds.
Note
----
* This method can only be accessed if the underlying topology has
information about atomic masses.
.. versionchanged:: 0.8 Added `pbc` parameter
.. versionchanged:: 0.19.0 Added `compound` parameter
.. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'``
compounds
.. versionchanged:: 0.20.0 Added `unwrap` parameter
"""
atoms = group.atoms
return atoms.center(weights=atoms.masses, pbc=pbc, compound=compound, unwrap=unwrap)
transplants[GroupBase].append(
('center_of_mass', center_of_mass))
[docs] @warn_if_not_unique
def total_mass(group, compound='group'):
"""Total mass of (compounds of) the group.
Computes the total mass of :class:`Atoms<Atom>` in the group.
Total masses per :class:`Residue`, :class:`Segment`, molecule, or
fragment can be obtained by setting the `compound` parameter
accordingly.
Parameters
----------
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\
optional
If ``'group'``, the total mass of all atoms in the group will be
returned as a single value. Otherwise, the total masses per
:class:`Segment`, :class:`Residue`, molecule, or fragment will be
returned as a 1d array.
Note that, in any case, *only* the masses of :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
Returns
-------
float or numpy.ndarray
Total mass of (compounds of) the group.
If `compound` was set to ``'group'``, the output will be a single
value. Otherwise, the output will be a 1d array of shape ``(n,)``
where ``n`` is the number of compounds.
.. versionchanged:: 0.20.0 Added `compound` parameter
"""
return group.accumulate("masses", compound=compound)
transplants[GroupBase].append(
('total_mass', total_mass))
[docs] @warn_if_not_unique
@check_pbc_and_unwrap
def moment_of_inertia(group, pbc=False, **kwargs):
"""Tensor moment of inertia relative to center of mass as 3x3 numpy
array.
Parameters
----------
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
.. versionchanged:: 0.8 Added *pbc* keyword
.. versionchanged:: 0.20.0 Added `unwrap` parameter
"""
atomgroup = group.atoms
unwrap = kwargs.pop('unwrap', False)
compound = kwargs.pop('compound', 'group')
com = atomgroup.center_of_mass(
pbc=pbc, unwrap=unwrap, compound=compound)
if compound != 'group':
com = (com * group.masses[:, None]
).sum(axis=0) / group.masses.sum()
if pbc:
pos = atomgroup.pack_into_box(inplace=False) - com
elif unwrap:
pos = atomgroup.unwrap(compound=compound, inplace=False) - com
else:
pos = atomgroup.positions - com
masses = atomgroup.masses
# Create the inertia tensor
# m_i = mass of atom i
# (x_i, y_i, z_i) = pos of atom i
# Ixx = sum(m_i*(y_i^2+z_i^2));
# Iyy = sum(m_i*(x_i^2+z_i^2));
# Izz = sum(m_i*(x_i^2+y_i^2))
# Ixy = Iyx = -1*sum(m_i*x_i*y_i)
# Ixz = Izx = -1*sum(m_i*x_i*z_i)
# Iyz = Izy = -1*sum(m_i*y_i*z_i)
tens = np.zeros((3, 3), dtype=np.float64)
# xx
tens[0][0] = (masses * (pos[:, 1] ** 2 + pos[:, 2] ** 2)).sum()
# xy & yx
tens[0][1] = tens[1][0] = - (masses * pos[:, 0] * pos[:, 1]).sum()
# xz & zx
tens[0][2] = tens[2][0] = - (masses * pos[:, 0] * pos[:, 2]).sum()
# yy
tens[1][1] = (masses * (pos[:, 0] ** 2 + pos[:, 2] ** 2)).sum()
# yz + zy
tens[1][2] = tens[2][1] = - (masses * pos[:, 1] * pos[:, 2]).sum()
# zz
tens[2][2] = (masses * (pos[:, 0] ** 2 + pos[:, 1] ** 2)).sum()
return tens
transplants[GroupBase].append(
('moment_of_inertia', moment_of_inertia))
[docs] @warn_if_not_unique
def radius_of_gyration(group, pbc=False, **kwargs):
"""Radius of gyration.
Parameters
----------
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
.. versionchanged:: 0.8 Added *pbc* keyword
"""
atomgroup = group.atoms
masses = atomgroup.masses
com = atomgroup.center_of_mass(pbc=pbc)
if pbc:
recenteredpos = atomgroup.pack_into_box(inplace=False) - com
else:
recenteredpos = atomgroup.positions - com
rog_sq = np.sum(masses * np.sum(recenteredpos**2,
axis=1)) / atomgroup.total_mass()
return np.sqrt(rog_sq)
transplants[GroupBase].append(
('radius_of_gyration', radius_of_gyration))
[docs] @warn_if_not_unique
def shape_parameter(group, pbc=False, **kwargs):
"""Shape parameter.
See [Dima2004a]_ for background information.
Parameters
----------
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
References
----------
.. [Dima2004a] Dima, R. I., & Thirumalai, D. (2004). Asymmetry
in the shapes of folded and denatured states of
proteins. *J Phys Chem B*, 108(21),
6564-6570. doi:`10.1021/jp037128y
<https://doi.org/10.1021/jp037128y>`_
.. versionadded:: 0.7.7
.. versionchanged:: 0.8 Added *pbc* keyword
"""
atomgroup = group.atoms
masses = atomgroup.masses
com = atomgroup.center_of_mass(pbc=pbc)
if pbc:
recenteredpos = atomgroup.pack_into_box(inplace=False) - com
else:
recenteredpos = atomgroup.positions - com
tensor = np.zeros((3, 3))
for x in range(recenteredpos.shape[0]):
tensor += masses[x] * np.outer(recenteredpos[x, :],
recenteredpos[x, :])
tensor /= atomgroup.total_mass()
eig_vals = np.linalg.eigvalsh(tensor)
shape = 27.0 * np.prod(eig_vals - np.mean(eig_vals)
) / np.power(np.sum(eig_vals), 3)
return shape
transplants[GroupBase].append(
('shape_parameter', shape_parameter))
[docs] @warn_if_not_unique
@check_pbc_and_unwrap
def asphericity(group, pbc=False, unwrap=None, compound='group'):
"""Asphericity.
See [Dima2004b]_ for background information.
Parameters
----------
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their centers.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional
Which type of component to keep together during unwrapping.
References
----------
.. [Dima2004b] Dima, R. I., & Thirumalai, D. (2004). Asymmetry
in the shapes of folded and denatured states of
proteins. *J Phys Chem B*, 108(21),
6564-6570. doi:`10.1021/jp037128y
<https://doi.org/10.1021/jp037128y>`_
.. versionadded:: 0.7.7
.. versionchanged:: 0.8 Added *pbc* keyword
.. versionchanged:: 0.20.0 Added *unwrap* and *compound* parameter
"""
atomgroup = group.atoms
masses = atomgroup.masses
com = atomgroup.center_of_mass(
pbc=pbc, unwrap=unwrap, compound=compound)
if compound != 'group':
com = (com * group.masses[:, None]
).sum(axis=0) / group.masses.sum()
if pbc:
recenteredpos = (atomgroup.pack_into_box(inplace=False) - com)
elif unwrap:
recenteredpos = (atomgroup.unwrap(inplace=False) - com)
else:
recenteredpos = (atomgroup.positions - com)
tensor = np.zeros((3, 3))
for x in range(recenteredpos.shape[0]):
tensor += masses[x] * np.outer(recenteredpos[x],
recenteredpos[x])
tensor /= atomgroup.total_mass()
eig_vals = np.linalg.eigvalsh(tensor)
shape = (3.0 / 2.0) * (np.sum((eig_vals - np.mean(eig_vals))**2) /
np.sum(eig_vals)**2)
return shape
transplants[GroupBase].append(
('asphericity', asphericity))
[docs] @warn_if_not_unique
def principal_axes(group, pbc=False):
"""Calculate the principal axes from the moment of inertia.
e1,e2,e3 = AtomGroup.principal_axes()
The eigenvectors are sorted by eigenvalue, i.e. the first one
corresponds to the highest eigenvalue and is thus the first principal
axes.
The eigenvectors form a right-handed coordinate system.
Parameters
----------
pbc : bool, optional
If ``True``, move all atoms within the primary unit cell before
calculation. [``False``]
Returns
-------
axis_vectors : array
3 x 3 array with ``v[0]`` as first, ``v[1]`` as second, and
``v[2]`` as third eigenvector.
.. versionchanged:: 0.8 Added *pbc* keyword
.. versionchanged:: 1.0.0
Always return principal axes in right-hand convention.
"""
atomgroup = group.atoms
e_val, e_vec = np.linalg.eig(atomgroup.moment_of_inertia(pbc=pbc))
# Sort
indices = np.argsort(e_val)[::-1]
# Make transposed in more logical form. See Issue 33.
e_vec = e_vec[:, indices].T
# Make sure the right hand convention is followed
if np.dot(np.cross(e_vec[0], e_vec[1]), e_vec[2]) < 0:
e_vec *= -1
return e_vec
transplants[GroupBase].append(
('principal_axes', principal_axes))
[docs] def align_principal_axis(group, axis, vector):
"""Align principal axis with index `axis` with `vector`.
Parameters
----------
axis : {0, 1, 2}
Index of the principal axis (0, 1, or 2), as produced by
:meth:`~principal_axes`.
vector : array_like
Vector to align principal axis with.
Notes
-----
To align the long axis of a channel (the first principal axis, i.e.
*axis* = 0) with the z-axis::
u.atoms.align_principal_axis(0, [0,0,1])
u.atoms.write("aligned.pdb")
"""
p = group.principal_axes()[axis]
angle = np.degrees(mdamath.angle(p, vector))
ax = transformations.rotaxis(p, vector)
# print "principal[%d] = %r" % (axis, p)
# print "axis = %r, angle = %f deg" % (ax, angle)
return group.rotateby(angle, ax)
transplants[GroupBase].append(
('align_principal_axis', align_principal_axis))
# TODO: update docs to property doc
[docs]class Charges(AtomAttr):
attrname = 'charges'
singular = 'charge'
per_object = 'atom'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup,
Atom, Residue, Segment]
transplants = defaultdict(list)
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs] def get_residues(self, rg):
resatoms = self.top.tt.residues2atoms_2d(rg.ix)
if isinstance(rg._ix, numbers.Integral):
charges = self.values[resatoms].sum()
else:
charges = np.empty(len(rg))
for i, row in enumerate(resatoms):
charges[i] = self.values[row].sum()
return charges
[docs] def get_segments(self, sg):
segatoms = self.top.tt.segments2atoms_2d(sg.ix)
if isinstance(sg._ix, numbers.Integral):
# for a single segment
charges = self.values[tuple(segatoms)].sum()
else:
# for a segmentgroup
charges = np.array([self.values[row].sum() for row in segatoms])
return charges
[docs] @warn_if_not_unique
def total_charge(group, compound='group'):
"""Total charge of (compounds of) the group.
Computes the total charge of :class:`Atoms<Atom>` in the group.
Total charges per :class:`Residue`, :class:`Segment`, molecule, or
fragment can be obtained by setting the `compound` parameter
accordingly.
Parameters
----------
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\
optional
If 'group', the total charge of all atoms in the group will
be returned as a single value. Otherwise, the total charges per
:class:`Segment`, :class:`Residue`, molecule, or fragment
will be returned as a 1d array.
Note that, in any case, *only* the charges of :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
Returns
-------
float or numpy.ndarray
Total charge of (compounds of) the group.
If `compound` was set to ``'group'``, the output will be a single
value. Otherwise, the output will be a 1d array of shape ``(n,)``
where ``n`` is the number of compounds.
.. versionchanged:: 0.20.0 Added `compound` parameter
"""
return group.accumulate("charges", compound=compound)
transplants[GroupBase].append(
('total_charge', total_charge))
# TODO: update docs to property doc
[docs]class Bfactors(AtomAttr):
"""Crystallographic B-factors in A**2 for each atom"""
attrname = 'bfactors'
singular = 'bfactor'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
# TODO: update docs to property doc
[docs]class Occupancies(AtomAttr):
attrname = 'occupancies'
singular = 'occupancy'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
# TODO: update docs to property doc
[docs]class AltLocs(AtomAttr):
"""AltLocs for each atom"""
attrname = 'altLocs'
singular = 'altLoc'
per_object = 'atom'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(na)], dtype=object)
[docs]class GBScreens(AtomAttr):
"""Generalized Born screening factor"""
attrname = 'gbscreens'
singular = 'gbscreen'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class SolventRadii(AtomAttr):
"""Intrinsic solvation radius"""
attrname = 'solventradii'
singular = 'solventradius'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class NonbondedIndices(AtomAttr):
"""Nonbonded index (AMBER)"""
attrname = 'nbindices'
singular = 'nbindex'
per_object = 'atom'
dtype = int
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na, dtype=np.int32)
[docs]class RMins(AtomAttr):
"""The Rmin/2 LJ parameter"""
attrname = 'rmins'
singular = 'rmin'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class Epsilons(AtomAttr):
"""The epsilon LJ parameter"""
attrname = 'epsilons'
singular = 'epsilon'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class RMin14s(AtomAttr):
"""The Rmin/2 LJ parameter for 1-4 interactions"""
attrname = 'rmin14s'
singular = 'rmin14'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class Epsilon14s(AtomAttr):
"""The epsilon LJ parameter for 1-4 interactions"""
attrname = 'epsilon14s'
singular = 'epsilon14'
per_object = 'atom'
dtype = float
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.zeros(na)
[docs]class ResidueAttr(TopologyAttr):
attrname = 'residueattrs'
singular = 'residueattr'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Residue]
per_object = 'residue'
[docs] def get_atoms(self, ag):
rix = self.top.tt.atoms2residues(ag.ix)
return self.values[rix]
[docs] def set_atoms(self, ag, values):
raise _wronglevel_error(self, ag)
[docs] def get_residues(self, rg):
return self.values[rg.ix]
[docs] @_check_length
def set_residues(self, rg, values):
self.values[rg.ix] = values
[docs] def get_segments(self, sg):
"""By default, the values for each residue present in the set of
segments are returned in a single array. This behavior can be overriden
in child attributes.
"""
rixs = self.top.tt.segments2residues_2d(sg.ix)
return [self.values[rix] for rix in rixs]
[docs] def set_segments(self, sg, values):
raise _wronglevel_error(self, sg)
# TODO: update docs to property doc
[docs]class Resids(ResidueAttr):
"""Residue ID"""
attrname = 'resids'
singular = 'resid'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
dtype = int
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.arange(1, nr + 1)
# TODO: update docs to property doc
[docs]class Resnames(ResidueAttr):
attrname = 'resnames'
singular = 'resname'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
transplants = defaultdict(list)
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(nr)], dtype=object)
[docs] def sequence(self, **kwargs):
"""Returns the amino acid sequence.
The format of the sequence is selected with the keyword *format*:
============== ============================================
*format* description
============== ============================================
'SeqRecord' :class:`Bio.SeqRecord.SeqRecord` (default)
'Seq' :class:`Bio.Seq.Seq`
'string' string
============== ============================================
The sequence is returned by default (keyword ``format = 'SeqRecord'``)
as a :class:`Bio.SeqRecord.SeqRecord` instance, which can then be
further processed. In this case, all keyword arguments (such as the
*id* string or the *name* or the *description*) are directly passed to
:class:`Bio.SeqRecord.SeqRecord`.
If the keyword *format* is set to ``'Seq'``, all *kwargs* are ignored
and a :class:`Bio.Seq.Seq` instance is returned. The difference to the
record is that the record also contains metadata and can be directly
used as an input for other functions in :mod:`Bio`.
If the keyword *format* is set to ``'string'``, all *kwargs* are
ignored and a Python string is returned.
.. rubric:: Example: Write FASTA file
Use :func:`Bio.SeqIO.write`, which takes sequence records::
import Bio.SeqIO
# get the sequence record of a protein component of a Universe
protein = u.select_atoms("protein")
record = protein.sequence(id="myseq1", name="myprotein")
Bio.SeqIO.write(record, "single.fasta", "fasta")
A FASTA file with multiple entries can be written with ::
Bio.SeqIO.write([record1, record2, ...], "multi.fasta", "fasta")
Parameters
----------
format : string, optional
- ``"string"``: return sequence as a string of 1-letter codes
- ``"Seq"``: return a :class:`Bio.Seq.Seq` instance
- ``"SeqRecord"``: return a :class:`Bio.SeqRecord.SeqRecord`
instance
Default is ``"SeqRecord"``
id : optional
Sequence ID for SeqRecord (should be different for different
sequences)
name : optional
Name of the protein.
description : optional
Short description of the sequence.
kwargs : optional
Any other keyword arguments that are understood by
class:`Bio.SeqRecord.SeqRecord`.
Raises
------
:exc:`ValueError` if a residue name cannot be converted to a
1-letter IUPAC protein amino acid code; make sure to only
select protein residues.
:exc:`TypeError` if an unknown *format* is selected.
.. versionadded:: 0.9.0
"""
formats = ('string', 'Seq', 'SeqRecord')
format = kwargs.pop("format", "SeqRecord")
if format not in formats:
raise TypeError("Unknown format='{0}': must be one of: {1}".format(
format, ", ".join(formats)))
try:
sequence = "".join([convert_aa_code(r)
for r in self.residues.resnames])
except KeyError as err:
six.raise_from(ValueError("AtomGroup contains a residue name '{0}' that "
"does not have a IUPAC protein 1-letter "
"character".format(err.message)), None)
if format == "string":
return sequence
seq = Bio.Seq.Seq(sequence)
if format == "Seq":
return seq
return Bio.SeqRecord.SeqRecord(seq, **kwargs)
transplants[ResidueGroup].append(
('sequence', sequence))
# TODO: update docs to property doc
[docs]class Resnums(ResidueAttr):
attrname = 'resnums'
singular = 'resnum'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
dtype = int
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.arange(1, nr + 1)
[docs]class ICodes(ResidueAttr):
"""Insertion code for Atoms"""
attrname = 'icodes'
singular = 'icode'
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(nr)], dtype=object)
[docs]class Moltypes(ResidueAttr):
"""Name of the molecule type
Two molecules that share a molecule type share a common template topology.
"""
attrname = 'moltypes'
singular = 'moltype'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Atom, Residue]
dtype = object
[docs]class Molnums(ResidueAttr):
"""Name of the molecule type
Two molecules that share a molecule type share a common template topology.
"""
attrname = 'molnums'
singular = 'molnum'
target_classes = [AtomGroup, ResidueGroup, Atom, Residue]
dtype = np.intp
# segment attributes
[docs]class SegmentAttr(TopologyAttr):
"""Base class for segment attributes.
"""
attrname = 'segmentattrs'
singular = 'segmentattr'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup, Segment]
per_object = 'segment'
[docs] def get_atoms(self, ag):
six = self.top.tt.atoms2segments(ag.ix)
return self.values[six]
[docs] def set_atoms(self, ag, values):
raise _wronglevel_error(self, ag)
[docs] def get_residues(self, rg):
six = self.top.tt.residues2segments(rg.ix)
return self.values[six]
[docs] def set_residues(self, rg, values):
raise _wronglevel_error(self, rg)
[docs] def get_segments(self, sg):
return self.values[sg.ix]
[docs] @_check_length
def set_segments(self, sg, values):
self.values[sg.ix] = values
# TODO: update docs to property doc
[docs]class Segids(SegmentAttr):
attrname = 'segids'
singular = 'segid'
target_classes = [AtomGroup, ResidueGroup, SegmentGroup,
Atom, Residue, Segment]
transplants = defaultdict(list)
dtype = object
@staticmethod
def _gen_initial_values(na, nr, ns):
return np.array(['' for _ in range(ns)], dtype=object)
def _check_connection_values(func):
"""
Checks values passed to _Connection methods for:
- appropriate number of atom indices
- coerces them to tuples of ints (for hashing)
- ensures that first value is less than last (reversibility & hashing)
.. versionadded:: 1.0.0
"""
@functools.wraps(func)
def wrapper(self, values, *args, **kwargs):
if not all(len(x) == self._n_atoms
and all(isinstance(y, (int, np.integer)) for y in x)
for x in values):
raise ValueError(("{} must be an iterable of tuples with {}"
" atom indices").format(self.attrname,
self._n_atoms))
clean = []
for v in values:
if v[0] > v[-1]:
v = v[::-1]
clean.append(tuple(v))
return func(self, clean, *args, **kwargs)
return wrapper
class _Connection(AtomAttr):
"""Base class for connectivity between atoms
.. versionchanged:: 1.0.0
Added type checking to atom index values.
"""
@_check_connection_values
def __init__(self, values, types=None, guessed=False, order=None):
self.values = values
if types is None:
types = [None] * len(values)
self.types = types
if guessed in (True, False):
# if single value passed, multiply this across
# all bonds
guessed = [guessed] * len(values)
self._guessed = guessed
if order is None:
order = [None] * len(values)
self.order = order
self._cache = dict()
def copy(self):
"""Return a deepcopy of this attribute"""
return self.__class__(copy.copy(self.values),
copy.copy(self.types),
copy.copy(self._guessed),
copy.copy(self.order))
def __len__(self):
return len(self._bondDict)
@property
@cached('bd')
def _bondDict(self):
"""Lazily built mapping of atoms:bonds"""
bd = defaultdict(list)
for b, t, g, o in zip(self.values, self.types,
self._guessed, self.order):
for a in b:
bd[a].append((b, t, g, o))
return bd
def set_atoms(self, ag):
return NotImplementedError("Cannot set bond information")
def get_atoms(self, ag):
try:
unique_bonds = set(itertools.chain(
*[self._bondDict[a] for a in ag.ix]))
except TypeError:
# maybe we got passed an Atom
unique_bonds = self._bondDict[ag.ix]
bond_idx, types, guessed, order = np.hsplit(
np.array(sorted(unique_bonds)), 4)
bond_idx = np.array(bond_idx.ravel().tolist(), dtype=np.int32)
types = types.ravel()
guessed = guessed.ravel()
order = order.ravel()
return TopologyGroup(bond_idx, ag.universe,
self.singular[:-1],
types,
guessed,
order)
@_check_connection_values
def _add_bonds(self, values, types=None, guessed=True, order=None):
if types is None:
types = itertools.cycle((None,))
if guessed in (True, False):
guessed = itertools.cycle((guessed,))
if order is None:
order = itertools.cycle((None,))
existing = set(self.values)
for v, t, g, o in zip(values, types, guessed, order):
if v not in existing:
self.values.append(v)
self.types.append(t)
self._guessed.append(g)
self.order.append(o)
# kill the old cache of bond Dict
try:
del self._cache['bd']
except KeyError:
pass
@_check_connection_values
def _delete_bonds(self, values):
"""
.. versionadded:: 1.0.0
"""
to_check = set(values)
self_values = set(self.values)
if not to_check.issubset(self_values):
missing = to_check-self_values
indices = ', '.join(map(str, missing))
raise ValueError(('Cannot delete nonexistent '
'{attrname} with atom indices:'
'{indices}').format(attrname=self.attrname,
indices=indices))
idx = [self.values.index(v) for v in to_check]
for i in sorted(idx, reverse=True):
del self.values[i]
for attr in ('types', '_guessed', 'order'):
arr = np.array(getattr(self, attr), dtype='object')
new = np.delete(arr, idx)
setattr(self, attr, list(new))
# kill the old cache of bond Dict
try:
del self._cache['bd']
except KeyError:
pass
[docs]class Bonds(_Connection):
"""Bonds between two atoms
Must be initialised by a list of zero based tuples.
These indices refer to the atom indices.
E.g., ` [(0, 1), (1, 2), (2, 3)]`
Also adds the `bonded_atoms`, `fragment` and `fragments`
attributes.
"""
attrname = 'bonds'
# Singular is the same because one Atom might have
# many bonds, so still asks for "bonds" in the plural
singular = 'bonds'
transplants = defaultdict(list)
_n_atoms = 2
[docs] def bonded_atoms(self):
"""An :class:`~MDAnalysis.core.groups.AtomGroup` of all
:class:`Atoms<MDAnalysis.core.groups.Atom>` bonded to this
:class:`~MDAnalysis.core.groups.Atom`."""
idx = [b.partner(self).index for b in self.bonds]
return self.universe.atoms[idx]
transplants[Atom].append(
('bonded_atoms', property(bonded_atoms, None, None,
bonded_atoms.__doc__)))
[docs] def fragindex(self):
"""The index (ID) of the
:class:`~MDAnalysis.core.topologyattrs.Bonds.fragment` this
:class:`~MDAnalysis.core.groups.Atom` is part of.
Note
----
This property is only accessible if the underlying topology contains
bond information.
.. versionadded:: 0.20.0
"""
return self.universe._fragdict[self.ix].ix
[docs] def fragindices(self):
"""The
:class:`fragment indices<MDAnalysis.core.topologyattrs.Bonds.fragindex>`
of all :class:`Atoms<MDAnalysis.core.groups.Atom>` in this
:class:`~MDAnalysis.core.groups.AtomGroup`.
A :class:`numpy.ndarray` with
:attr:`~numpy.ndarray.shape`\ ``=(``\ :attr:`~AtomGroup.n_atoms`\ ``,)``
and :attr:`~numpy.ndarray.dtype`\ ``=numpy.int64``.
Note
----
This property is only accessible if the underlying topology contains
bond information.
.. versionadded:: 0.20.0
"""
fragdict = self.universe._fragdict
return np.array([fragdict[aix].ix for aix in self.ix], dtype=np.intp)
[docs] def fragment(self):
"""An :class:`~MDAnalysis.core.groups.AtomGroup` representing the
fragment this :class:`~MDAnalysis.core.groups.Atom` is part of.
A fragment is a
:class:`group of atoms<MDAnalysis.core.groups.AtomGroup>` which are
interconnected by :class:`~MDAnalysis.core.topologyattrs.Bonds`, i.e.,
there exists a path along one
or more :class:`~MDAnalysis.core.topologyattrs.Bonds` between any pair
of :class:`Atoms<MDAnalysis.core.groups.Atom>`
within a fragment. Thus, a fragment typically corresponds to a molecule.
Note
----
This property is only accessible if the underlying topology contains
bond information.
.. versionadded:: 0.9.0
"""
return self.universe._fragdict[self.ix].fragment
[docs] def fragments(self):
"""Read-only :class:`tuple` of
:class:`fragments<MDAnalysis.core.topologyattrs.Bonds.fragment>`.
Contains all fragments that
any :class:`~MDAnalysis.core.groups.Atom` in this
:class:`~MDAnalysis.core.groups.AtomGroup` is part of.
A fragment is a
:class:`group of atoms<MDAnalysis.core.groups.AtomGroup>` which are
interconnected by :class:`~MDAnalysis.core.topologyattrs.Bonds`, i.e.,
there exists a path along one
or more :class:`~MDAnalysis.core.topologyattrs.Bonds` between any pair
of :class:`Atoms<MDAnalysis.core.groups.Atom>`
within a fragment. Thus, a fragment typically corresponds to a molecule.
Note
----
* This property is only accessible if the underlying topology contains
bond information.
* The contents of the fragments may extend beyond the contents of this
:class:`~MDAnalysis.core.groups.AtomGroup`.
.. versionadded:: 0.9.0
"""
fragdict = self.universe._fragdict
return tuple(sorted(set(fragdict[aix].fragment for aix in self.ix),
key=lambda x: x[0].ix))
[docs] def n_fragments(self):
"""The number of unique
:class:`~MDAnalysis.core.topologyattrs.Bonds.fragments` the
:class:`Atoms<MDAnalysis.core.groups.Atom>` of this
:class:`~MDAnalysis.core.groups.AtomGroup` are part of.
Note
----
This property is only accessible if the underlying topology contains
bond information.
.. versionadded:: 0.20.0
"""
return len(unique_int_1d(self.fragindices))
transplants[Atom].append(
('fragment', property(fragment, None, None,
fragment.__doc__)))
transplants[Atom].append(
('fragindex', property(fragindex, None, None,
fragindex.__doc__)))
transplants[AtomGroup].append(
('fragments', property(fragments, None, None,
fragments.__doc__)))
transplants[AtomGroup].append(
('fragindices', property(fragindices, None, None,
fragindices.__doc__)))
transplants[AtomGroup].append(
('n_fragments', property(n_fragments, None, None,
n_fragments.__doc__)))
[docs]class UreyBradleys(_Connection):
"""Angles between two atoms
Initialise with a list of 2 long tuples
These indices refer to the atom indices.
.. versionadded:: 1.0.0
"""
attrname = 'ureybradleys'
singular = 'ureybradleys'
transplants = defaultdict(list)
_n_atoms = 2
[docs]class Angles(_Connection):
"""Angles between three atoms
Initialise with a list of 3 long tuples
E.g., `[(0, 1, 2), (1, 2, 3), (2, 3, 4)]`
These indices refer to the atom indices.
"""
attrname = 'angles'
singular = 'angles'
transplants = defaultdict(list)
_n_atoms = 3
[docs]class Dihedrals(_Connection):
"""A connection between four sequential atoms"""
attrname = 'dihedrals'
singular = 'dihedrals'
transplants = defaultdict(list)
_n_atoms = 4
[docs]class Impropers(_Connection):
"""An imaginary dihedral between four atoms"""
attrname = 'impropers'
singular = 'impropers'
transplants = defaultdict(list)
_n_atoms = 4
[docs]class CMaps(_Connection):
"""
A connection between five atoms
.. versionadded:: 1.0.0
"""
attrname = 'cmaps'
singular = 'cmaps'
transplants = defaultdict(list)
_n_atoms = 5