.. -*- coding: utf-8 -*- .. _selections: ======================= Atom selection language ======================= AtomGroups can be created by selecting atoms using the MDAnalysis atom selection language: .. ipython:: python :okwarning: import MDAnalysis as mda from MDAnalysis.tests.datafiles import PSF, DCD u = mda.Universe(PSF, DCD) ala = u.select_atoms('resname ALA') ala The :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` method of a :class:`~MDAnalysis.core.groups.AtomGroup` or a :class:`~MDAnalysis.core.universe.Universe` returns an :class:`~MDAnalysis.core.groups.AtomGroup`. These two methods have different behaviour: while :meth:`Universe.select_atoms ` operates on all the atoms in the universe, :meth:`AtomGroup.select_atoms ` only operates on the atoms within the original AtomGroup. A single selection phrase always returns an :class:`~MDAnalysis.core.groups.AtomGroup` with atoms sorted according to their index in the topology. This is to ensure that there are not any duplicates, which can happen with complicated selections. When order matters, :ref:`you can pass in multiple phrases `. This page documents selection keywords and their arguments. :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` also accepts keywords that modify the behaviour of the selection string and the resulting :class:`~MDAnalysis.core.groups.AtomGroup` (documented further down this page). For example, you can: * Pass in :ref:`named AtomGroups as arguments `: .. ipython:: python sph_6 = u.select_atoms("sphzone 6 protein") u.select_atoms("around 3 group sph_6", sph_6=sph_6) * Turn off :ref:`periodic boundary conditions for geometric keywords ` with ``periodic=False``: .. ipython:: python u.select_atoms("around 6 protein", periodic=False) * Create :ref:`dynamic UpdatingAtomGroups ` with ``updating=True``: .. ipython:: python u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True) It is possible to export selections for external software packages with the help of :ref:`selection-exporters`. Selection Keywords ================== The following describes all selection keywords currently understood by the selection parser. The following applies to all selections: * Keywords are case sensitive. * Atoms are automatically sequentially ordered in a resulting selection (see notes below on :ref:`ordered-selections` for how to circumvent this if necessary). * Selections are parsed left to right and parentheses can be used for grouping. For example: .. ipython:: python u.select_atoms("segid DMPC and not (name H* or type OW)") * String selections such as names and residue names can be matched with Unix shell-style wildcards. These rules include: * Using ``*`` in a string matches any number of any characters * ``?`` matches any single character * ``[seq]`` matches any character in *seq*; * ``[!seq]`` matches any character not in *seq* * ``[!?]`` selects empty strings For example, the string ``GL*`` selects all strings that start with "GL", such as "GLU", "GLY", "GLX29", "GLN". ``GL[YN]`` will select all "GLY" and "GLN" strings. Any number of patterns can be included in the search. For more information on pattern matching, see the :mod:`fnmatch` documentation. Simple selections ----------------- protein Selects atoms that belong to a :ref:`hard-coded set of standard protein residue names `. backbone Selects the backbone atoms of a hard-coded set of protein residues. These atoms have the names: CA, C, O, N. nucleic Selects atoms that belong to a :ref:`hard-coded set of standard nucleic residue names `. nucleicbackbone Selects the backbone atoms of a hard-coded set of nucleic residues. These atoms have the names: P, O5', C5', C3', O3' nucleicbase Selects the atoms in :ref:`nucleobases `. nucleicsugar Selects the atoms in nucleic sugars. These have the names: C1', C2', C3', C4', O2', O4', O3' segid *seg-name* select by segid (as given in the topology), e.g. ``segid 4AKE`` or ``segid DMPC`` resid *residue-number-range* ``resid`` can take a single residue number or a range of numbers, followed by insertion codes. A range consists of two selections separated by a colon (inclusive) such as ``resid 1A:1C``. This selects all residues with ``resid==1`` and ``icode in ('A', 'B', 'C')``. A residue number ("resid") and icode is taken directly from the topology. Unlike ``resnum``, ``resid`` is sensitive to insertion codes. resnum *residue-number-range* ``resnum`` can take a single residue number or a range of numbers. A range consists of two numbers separated by a colon (inclusive) such as ``resnum 1:5``. A residue number ("resnum") is taken directly from the topology. Unlike ``resid``, ``resnum`` is insensitive to insertion codes. resname *residue-name* select by residue name, e.g. ``resname LYS`` name *atom-name* select by atom name (as given in the topology). Often, this is force field dependent. Example: ``name CA`` (for C-alpha atoms) or ``name OW`` (for SPC water oxygen) type *atom-type* select by atom type; this is either a string or a number and depends on the force field; it is read from the topology file (e.g. the CHARMM PSF file contains numeric atom types). This uses the ``Atom.type`` :ref:`topology attribute `. atom *seg-name residue-number atom-name* a selector for a single atom consisting of segid resid atomname, e.g. ``DMPC 1 C2`` selects the C2 carbon of the first residue of the DMPC segment altloc *alternative-location* a selection for atoms where alternative locations are available, which is often the case with high-resolution crystal structures e.g. :code:`resid 4 and resname ALA and altloc B` selects only the atoms of ALA-4 that have an altloc B record. icode *icode* a selector for atoms where insertion codes are available. This can be combined with residue numbers using the ``resid`` selector above. e.g. :code:`icode [!?]` selects atoms *without* insertion codes. moltype *molecule-type* select by the ``moltype`` :ref:`topology attribute `, e.g. ``moltype Protein_A``. At the moment, only the TPR format defines the ``moltype``. Boolean ------- not all atoms not in the selection, e.g. ``not protein`` selects all atoms that aren't part of a protein and the intersection of two selections, i.e. the boolean and. e.g. ``protein and not resname ALA`` selects all atoms that belong to a protein but are not in an alanine residue or the union of two selections, i.e. the boolean or. e.g. ``protein and not (resname ALA or resname LYS)`` selects all atoms that belong to a protein, but are not in a lysine or alanine residue .. _geometric: Geometric --------- The geometric keywords below all implement periodic boundary conditions by default when valid cell dimensions are accessible from the Universe. This can be turned off by passing in the keyword ``periodic=False``: .. ipython:: python u.select_atoms("around 6 protein", periodic=False) around *distance selection* selects all atoms a certain cutoff away from another selection, e.g. ``around 3.5 protein`` selects all atoms not belonging to protein that are within 3.5 Angstroms from the protein sphzone *externalRadius selection* selects all atoms within a spherical zone centered in the center of geometry (COG) of a given selection, e.g. ``sphzone 6.0 ( protein and ( resid 130 or resid 80 ) )`` selects the center of geometry of protein, resid 130, resid 80 and creates a sphere of radius 6.0 around the COG. sphlayer *innerRadius externalRadius selection* selects all atoms within a spherical layer centered in the center of geometry (COG) of a given selection, e.g., ``sphlayer 2.4 6.0 ( protein and ( resid 130 or resid 80 ) )`` selects the center of geometry of protein, resid 130, resid 80 and creates a spherical layer of inner radius 2.4 and external radius 6.0 around the COG. cyzone *externalRadius zMax zMin selection* selects all atoms within a cylindric zone centered in the center of geometry (COG) of a given selection, e.g. ``cyzone 15 4 -8 protein and resid 42`` selects the center of geometry of protein and resid 42, and creates a cylinder of external radius 15 centered on the COG. In z, the cylinder extends from 4 above the COG to 8 below. Positive values for *zMin*, or negative ones for *zMax*, are allowed. cylayer *innerRadius externalRadius zMax zMin selection* selects all atoms within a cylindric layer centered in the center of geometry (COG) of a given selection, e.g. ``cylayer 5 10 10 -8 protein`` selects the center of geometry of protein, and creates a cylindrical layer of inner radius 5, external radius 10 centered on the COG. In z, the cylinder extends from 10 above the COG to 8 below. Positive values for *zMin*, or negative ones for *zMax*, are allowed. point *x y z distance* selects all atoms within a cutoff of a point in space, make sure coordinate is separated by spaces, e.g. ``point 5.0 5.0 5.0 3.5`` selects all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0) prop *[abs] property operator value* selects atoms based on position, using *property* **x**, **y**, or **z** coordinate. Supports the **abs** keyword (for absolute value) and the following *operators*: **<, >, <=, >=, ==, !=**. For example, ``prop z >= 5.0`` selects all atoms with z coordinate greater than 5.0; ``prop abs z <= 5.0`` selects all atoms within -5.0 <= z <= 5.0. Similarity and connectivity --------------------------- same *subkeyword* as *selection* selects all atoms that have the same *subkeyword* value as any atom in *selection*. Allowed *subkeyword* values are the atom properties: ``name, type, resname, resid, resnum, segid, mass, charge, radius, bfactor``, the groups an atom belong to: ``residue, segment, fragment``, and the atom coordinates ``x, y, z``. (Note that ``bfactor`` currently only works for MMTF formats.) e.g. ``same charge as protein`` selects all atoms that have the same charge as any atom in protein. byres *selection* selects all atoms that are in the same segment and residue as selection, e.g. specify the subselection after the byres keyword. ``byres`` is a shortcut to ``same residue as`` bonded *selection* selects all atoms that are bonded to selection e.g.: ``name H and bonded name N`` selects only hydrogens bonded to nitrogens Index ----- index *index-range* selects all atoms within a range of (0-based) inclusive indices, e.g. ``index 0`` selects the first atom in the universe; ``index 5:10`` selects the 6th through 11th atoms, inclusive. This uses the ``Atom.index`` :ref:`topology attribute `. bynum *number-range* selects all atoms within a range of (1-based) inclusive indices, e.g. ``bynum 1`` selects the first atom in the universe; ``bynum 5:10`` selects 5th through 10th atoms, inclusive. .. note:: These are **not** the same as the 1-indexed ``Atom.id`` :ref:`topology attribute `. ``bynum`` simply adds 1 to the 0-indexed ``Atom.index``. .. _preexisting-selections: Preexisting selections and modifiers ------------------------------------ group `group-name` selects the atoms in the :class:`AtomGroup` passed to the function as an argument named `group-name`. Only the atoms common to `group-name` and the instance :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` was called from will be considered, unless ``group`` is preceded by the ``global`` keyword. `group-name` will be included in the parsing just by comparison of atom indices. This means that it is up to the user to make sure the `group-name` group was defined in an appropriate :class:`Universe`. global *selection* by default, when issuing :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` from an :class:`~MDAnalysis.core.groups.AtomGroup`, selections and subselections are returned intersected with the atoms of that instance. Prefixing a selection term with ``global`` causes its selection to be returned in its entirety. As an example, the ``global`` keyword allows for ``lipids.select_atoms("around 10 global protein")`` --- where ``lipids`` is a group that does not contain any proteins. Were ``global`` absent, the result would be an empty selection since the ``protein`` subselection would itself be empty. When calling :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` from a :class:`~MDAnalysis.core.universe.Universe`, ``global`` is ignored. .. _dynamic-selections: Dynamic selections ================== By default :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` returns an :class:`~MDAnalysis.core.groups.AtomGroup`, in which the list of atoms is constant across trajectory frame changes. If :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` is invoked with named argument ``updating`` set to ``True``, an :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` instance will be returned instead. .. ipython:: python # A dynamic selection of corner atoms: ag_updating = u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True) ag_updating It behaves just like an :class:`~MDAnalysis.core.groups.AtomGroup` object, with the difference that the selection expressions are re-evaluated every time the trajectory frame changes (this happens lazily, only when the :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` object is accessed so that there is no redundant updating going on): .. code-block:: ipython In [14]: u.trajectory.next() Out[14]: < Timestep 1 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] > In [15]: ag_updating Out[15]: Using the ``group`` selection keyword for :ref:`preexisting-selections`, one can make updating selections depend on :class:`~MDAnalysis.core.groups.AtomGroup`, or even other :class:`~MDAnalysis.core.groups.UpdatingAtomGroup`, instances. Likewise, making an updating selection from an already updating group will cause later updates to also reflect the updating of the base group: .. code-block:: ipython In [16]: chained_ag_updating = ag_updating.select_atoms("resid 1:1000", updating=True) In [17]: chained_ag_updating Out[17]: In [18]: u.trajectory.next() Out[18]: < Timestep 2 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] > In [19]: chained_ag_updating Out[19]: Finally, a non-updating selection or a slicing/addition operation made on an :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` will return a static :class:`~MDAnalysis.core.groups.AtomGroup`, which will no longer update across frames: .. code-block:: ipython In [20]: static_ag = ag_updating.select_atoms("resid 1:1000") In [21]: static_ag Out[21]: In [22]: u.trajectory.next() Out[22]: < Timestep 3 with unit cell dimensions [ 0. 0. 0. 90. 90. 90.] > In [23]: static_ag Out[23]: .. _ordered-selections: Ordered selections ================== :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` sorts the atoms in the :class:`~MDAnalysis.core.groups.AtomGroup` by atom index before returning them (this is to eliminate possible duplicates in the selection). If the ordering of atoms is crucial (for instance when describing angles or dihedrals) or if duplicate atoms are required then one has to concatenate multiple AtomGroups, which does not sort them. The most straightforward way to concatenate two AtomGroups is by using the ``+`` operator: .. ipython:: python :okwarning: ordered = u.select_atoms("resid 3 and name CA") + u.select_atoms("resid 2 and name CA") list(ordered) A shortcut is to provide *two or more* selections to :meth:`~MDAnalysis.core.universe.Universe.select_atoms`, which then does the concatenation automatically: .. ipython:: python :okwarning: list(u.select_atoms("resid 3 and name CA", "resid 2 and name CA")) Just for comparison to show that a single selection string does not work as one might expect: .. ipython:: python :okwarning: list(u.select_atoms("(resid 3 or resid 2) and name CA"))