MDTaj's :ref:`trajectory analysis <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.
| Keyword | Synonyms | Type | Description |
all |
everything |
bool |
Matches everything |
none |
nothing |
bool |
Matches nothing |
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 |
name |
str |
Atom name | |
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) |
resname |
resn |
str |
Residue name |
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).