Atom selection language

AtomGroups can be created by selecting atoms using the MDAnalysis atom selection language:

In [1]: import MDAnalysis as mda

In [2]: from MDAnalysis.tests.datafiles import PSF, DCD

In [3]: u = mda.Universe(PSF, DCD)

In [4]: ala = u.select_atoms('resname ALA')

In [5]: ala
Out[5]: <AtomGroup with 190 atoms>

The select_atoms() method of a AtomGroup or a Universe returns an AtomGroup. These two methods have different behaviour: while Universe.select_atoms operates on all the atoms in the universe, AtomGroup.select_atoms only operates on the atoms within the original AtomGroup. A single selection phrase always returns an 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, you can pass in multiple phrases.

This page documents selection keywords and their arguments. select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). For example, you can:

In [6]: sph_6 = u.select_atoms("sphzone 6 protein")

In [7]: u.select_atoms("around 3 group sph_6", sph_6=sph_6)
Out[7]: <AtomGroup with 81 atoms>

In [8]: u.select_atoms("around 6 protein", periodic=False)
Out[8]: <AtomGroup with 0 atoms>

In [9]: u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True)
Out[9]: <AtomGroup with 917 atoms, with selection 'prop x < 5 and prop y < 5 and prop z < 5' on the entire Universe.>

It is possible to export selections for external software packages with the help of 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 Ordered selections for how to circumvent this if necessary).

  • Selections are parsed left to right and parentheses can be used for grouping. For example:

In [10]: u.select_atoms("segid DMPC and not (name H* or type OW)")
Out[10]: <AtomGroup with 0 atoms>

  • String selections such as names and residue names can be matched with Unix shell-style wildcards. Using * in a string matches any number of any characters; ? matches any single character; [seq] matches any character in seq; and [!seq] matches any character not in seq. 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 fnmatch documentation.

Simple selections

protein

Selects atoms that belong to a 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 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 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 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. resid 4 and resname ALA and altloc B selects only the atoms of ALA-4 that have an altloc B record.

moltype molecule-type

select by the moltype 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

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:

In [11]: u.select_atoms("around 6 protein", periodic=False)
Out[11]: <AtomGroup with 0 atoms>
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 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 topology attribute. bynum simply adds 1 to the 0-indexed Atom.index.

Preexisting selections and modifiers

group group-name

selects the atoms in the AtomGroup passed to the function as an argument named group-name. Only the atoms common to group-name and the instance 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 Universe.

global selection

by default, when issuing select_atoms() from an 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 select_atoms() from a Universe, global is ignored.

Dynamic selections

By default select_atoms() returns an AtomGroup, in which the list of atoms is constant across trajectory frame changes. If select_atoms() is invoked with named argument updating set to True, an UpdatingAtomGroup instance will be returned instead.

# A dynamic selection of corner atoms:
In [12]: ag_updating = u.select_atoms("prop x < 5 and prop y < 5 and prop z < 5", updating=True)

In [13]: ag_updating
Out[13]: <AtomGroup with 917 atoms, with selection 'prop x < 5 and prop y < 5 and prop z < 5' on the entire Universe.>

It behaves just like an AtomGroup object, with the difference that the selection expressions are re-evaluated every time the trajectory frame changes (this happens lazily, only when the UpdatingAtomGroup object is accessed so that there is no redundant updating going on):

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]: <AtomGroup with 923 atoms, with selection 'prop x < 5 and prop y < 5 and prop z < 5' on the entire Universe.>

Using the group selection keyword for Preexisting selections and modifiers, one can make updating selections depend on AtomGroup, or even other 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:

In [16]: chained_ag_updating = ag_updating.select_atoms("resid 1:1000", updating=True)

In [17]: chained_ag_updating
Out[17]: <AtomGroup with 923 atoms, with selection 'resid 1:1000' on another AtomGroup.>

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]: <AtomGroup with 921 atoms, with selection 'resid 1:1000' on another AtomGroup.>

Finally, a non-updating selection or a slicing/addition operation made on an UpdatingAtomGroup will return a static AtomGroup, which will no longer update across frames:

In [20]: static_ag = ag_updating.select_atoms("resid 1:1000")

In [21]: static_ag
Out[21]: <AtomGroup with 921 atoms>

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]: <AtomGroup with 921 atoms>

Ordered selections

select_atoms() sorts the atoms in the 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:

In [14]: ordered = u.select_atoms("resid 3 and name CA") + u.select_atoms("resid 2 and name CA")

In [15]: list(ordered)
Out[15]: 
[<Atom 46: CA of type 22 of resname ILE, resid 3 and segid 4AKE>,
 <Atom 22: CA of type 22 of resname ARG, resid 2 and segid 4AKE>]

A shortcut is to provide two or more selections to select_atoms(), which then does the concatenation automatically:

In [16]: list(u.select_atoms("resid 3 and name CA", "resid 2 and name CA"))
Out[16]: 
[<Atom 46: CA of type 22 of resname ILE, resid 3 and segid 4AKE>,
 <Atom 22: CA of type 22 of resname ARG, resid 2 and segid 4AKE>]

Just for comparison to show that a single selection string does not work as one might expect:

In [17]: list(u.select_atoms("(resid 3 or resid 2) and name CA"))
Out[17]: 
[<Atom 22: CA of type 22 of resname ARG, resid 2 and segid 4AKE>,
 <Atom 46: CA of type 22 of resname ILE, resid 3 and segid 4AKE>]