Once you have the Universe() object, you can select atoms (using a syntax very similar to CHARMM’s atom selection syntax):
>>> kalp = universe.selectAtoms("segid KALP")
MDAnalysis.core.Universe.selectAtoms() returns a MDAnalysis.core.AtomGroup.AtomGroup, so you can use all the methods defined for AtomGroups on them. Selections always return an AtomGroup with atoms sorted according to their index in the topology (this is to ensure that there aren’t any duplicates, which can happen with complicated selections).
One can group subselections using parentheses:
>>> universe.selectAtoms("segid DMPC and not (name H* or name O*)") <AtomGroup with 3420 atoms>
Almost all the basic CHARMM selections work.
It is also possible to export selections for external software packages with the help of Selection exporters.
The following describes all selection keywords currently understood by the selection parser. The following applies to all selections:
- protein, backbone, nucleic, nucleicbackbone
- selects all atoms that belong to a standard set of residues; a protein is identfied by a hard-coded set of residue names so it may not work for esoteric residues.
- 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. A range consists of two numbers separated by a colon (inclusive) such as resid 1:5. A residue number (“resid”) is taken directly from the topology.
- resnum resnum-number-range
- resnum is the canonical residue number; typically it is set to the residue id in the original PDB structure.
- 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 Cα 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). It has non-sensical values when a PDB or GRO file is used as a topology.
- 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
- all atoms not in the selection, e.g. not protein selects all atoms that aren’t part of a protein
- and, or
- combine two selections according to the rules of boolean algebra, 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
- 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
- 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.
- 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.
- 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 -10 protein selects the center of geometry of protein, and creates a cylindrical layer of inner radius 5, external radius 10, maximum z value 10 and minimum z value -10 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, maximum z value 4 and minimum z value -8 around the COG.
- 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.
From version 0.6 onwards, some geometrics selections (around, sphlayer, sphzone, point) can use a k-d tree based, fast search algorithm (about three times faster than the previous version). However, it does not take periodicity into account. The fast algorithm is the default for around. Periodicity is only taken into account with the distance_array() functions via a minimum image convention (and this only works for rectangular simulation cells). If periodic boundary conditions should be taken into account then change the default behaviour of MDAnalysis by setting these two flags:
MDAnalysis.core.flags['use_periodic_selections'] = True MDAnalysis.core.flags['use_KDTree_routines'] = False
- byres selection
- selects all atoms that are in the same segment and residue as selection, e.g. specify the subselection after the byres keyword
- bynum index-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 atoms 5 through 10 inclusive. All atoms in the MDAnalysis.Universe are consecutively numbered, and the index runs from 1 up to the total number of atoms.
- 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 selectAtoms() was called from will be considered. 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 they were defined in an appropriate Universe.
- fullgroup group-name
- just like the group keyword with the difference that all the atoms of group-name are included. The resulting selection may therefore have atoms that were initially absent from the instance selectAtoms() was called from.
For interactive work it becomes rather tedious to type common selection strings repeatedly. MDAnalysis automatically generates a number of instant selectors as attributes of the Universe and number of other levels of the structural hierarchy, namely for AtomGroup, Residue, ResidueGroup, Segment and SegmentGroup.
universe.<segid> or universe.s<segid> (if <segid> starts with a number)
returns a Segment
works for Universe and SegmentGroup
>>> u.s4AKE <Segment '4AKE'>
seg.r<N> selects residue with number <N>
returns a Residue
works for Segment and SegmentGroup
>>> u.s4AKE.r100 <Residue 'GLY', 100>
seg.<resname> selects residues with residue name <resname>
returns a ResidueGroup
works for Segment and SegmentGroup
>>> u.s4AKE.MET <ResidueGroup [<Residue 'MET', 1>, <Residue 'MET', 21>, <Residue 'MET', 34>, <Residue 'MET', 53>, <Residue 'MET', 96>, <Residue 'MET', 174>]> >>> u.s4AKE.CYS <ResidueGroup [<Residue 'CYS', 77>]> >>> u.s4AKE.TRP NoDataError: No atoms defined for AtomGroup
The result is always a ResidueGroup; if no residues can be found then a MDAnalysis.NoDataError is raised.
g.<atomname> selects a single atom or a group of atoms with name <atomname>
works for any group derived from AtomGroup (i.e. all the ones mentioned above)
>>> u.atoms.CG >>> <AtomGroup with 125 atoms> >>> u.s4AKE.CG <AtomGroup with 125 atoms> >>> u.s4AKE.r100.CA < Atom 1516: name 'CA' of type '23' of resname 'GLY', resid 100 and segid '4AKE'> >>> u.s4AKE.r100.CB SelectionError: No atom in residue GLY with name CB
selectAtoms() 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 concatentate two AtomGroups is by using the + operator:
>>> ordered = u.selectAtoms("segid DMPC and resid 3 and name P") + u.selectAtoms("segid DMPC and resid 2 and name P") >>> print list(ordered) [< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>, < Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>]
A shortcut is to provide two or more selections to selectAtoms(), which then does the concatenation automatically:
>>> print list(universe.selectAtoms("segid DMPC and resid 3 and name P", "segid DMPC and resid 2 and name P")) [< Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>, < Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>]
Just for comparison to show that a single selection string does not work as one might expect:
# WRONG! >>> print list(universe.selectAtoms("segid DMPC and ( resid 3 or resid 2 ) and name P")) [< Atom 452: name 'P' of type '180' of resid 'DMPC', 2 and 'DMPC'>, < Atom 570: name 'P' of type '180' of resid 'DMPC', 3 and 'DMPC'>]