MDTaj’s trajectory analysis functions use 0-based arrays of “atom indices” to refer to subsets or groups of atoms in trajectories. To generate these index arrays, MDTraj includes a powerful text-based atom selection domain-specific language operating on the Topology. The following are all valid selection queries:
top.select("water") top.select("resSeq 35") top.select("water and name O") top.select("mass 5.5 to 20") top.select("resname =~ 'C.*'") top.select("protein and (backbone or resname ALA)")
These queries return a numpy array of integers containing the indices of the matching atoms. Equivalent python code for every selection expression can be generated using Topology.select_expression.
>>> top.select_expression("water and name O") "[atom.index for atom in topology.atoms if (atom.residue.is_water and (atom.name == 'O'))]"
MDTraj recognizes the following keywords. Each keyword maps directly to a property on the MDTraj topology object’s Atom/Residue/Chain tree.
|backbone||is_backbone||bool||Whether atom is in the backbone of a protein residue|
|sidechain||is_sidechain||bool||Whether atom is in the sidechain of a protein residue|
|protein||is_protein||bool||Whether atom is part of a protein residue|
|water||is_water, waters||bool||Whether atom is part of a water residue|
|index||int||Atom index (0-based)|
|n_bonds||int||Number of bonds this atom participates in|
|type||element, symbol||str||1 or 2-letter chemical symbols from the periodic table|
|mass||float||Element atomic mass (daltons)|
|residue||resSeq||int||Residue Sequence record (generally 1-based, but depends on topology)|
|resid||resi||int||Residue index (0-based)|
|rescode||code, resc`||str||1-letter residue code|
|chainid||int||Chain index (0-based)|
Integer, floating point, and string literals are also parsed. Both single-quoted, strings, double-quoted strings, and bare words are also parsed as string literals.
# The following queries are equivalent top.select("symbol == O") top.select("symbol == 'O'") top.select('symbol == "O"')
Standard boolean operations (and, or, and not) as well as their C-style aliases (&&, ||, !) are supported. The expected logical operators (<, <=, ==, !=, >=, >) are also available, as along with their FORTRAN-style synonyms (lt, le, eq, ne, ge, gt).
A regular-expression matching operator, =~, is available. For example, to match any of the names 'C1', 'C2', 'C3', 'C4', you can use the following query. The regular expression syntax is just the native python Regex syntax
top.select("name =~ 'C[1-4]'")
An implicit equality relation is implied between adjacent expressions
# The following queries are equivalent top.select("resid 35") top.select("resid == 35")
Range queries are also supported. The range condition is an expression of the form <expression> <low> to <high>, which resolves to <low> <= <expression> <= <high>. For example
# The following queries are equivalent top.select("resid 10 to 30") top.select("(10 <= resid) and (resid <= 30)")
MDTraj atom selection DSL lets users specify an expression which operates on a single Atom and return a bool, which is used subsequently as the predicate for a filter expression. The expressions compile to Python bytecode, and are then executed directly against the topology object in the python VM.
This is done in two steps: first, query strings are parsed according to a grammar defined using PyParsing. The parse tree is traversed, and used to construct an abstract syntax tree corresponding to the equivalent Python atom selection expression (e.g. Topology.select_expression).