Chemfiles selection language is based on the similar selection language provided by VMD. A selection is a string, and evaluating a selection consist to take this string and a Frame, and get the indexes of atoms in the frame matching the selection.
The selection string can contain names, numbers and operators. Name are sequences of
letter, numbers and _ (underscore) in any order, starting by a letter. Numbers
can be integers, floating-point numbers using a dot (.) as decimal separator, or
numbers in scientific notation (456.745e-45). Operators can be any of == != < <= > >=.
These operators means respectivly equal; not equal; less; less or equal; more and
more or equal.
Simple selections consist of a selector and a condition. Supported selectors are:
all and none: Select respectively all and none of the atoms.name: select atoms based on their name. This selector support three forms:
name == <value>, name != <value> and a short form name <value>
which is equivalent to name == <value>;index: select atoms based on their index in the frame. Any operator can be used,
and the atom index is compared to a positive integer value. The short form
index <value> is equivalent to index == <value>. Examples: index < 6,
index >= 42;mass: select atoms based on their mass. Any operator can be used. The short form
mass <value> is equivalent to mass == <value>. Examples: mass < 2.0,
mass == 4.2;x, y and z: select atoms based on their position components. Any
operator can be used, and their is no short form with this selection. == and
!= can be used, but comparing floating point values will procude strange
results most of the time. Examples: x > 5.3; z <= 5.3;vx, vy and vz: select atoms based on their velocity components. These
selectors works the same way as x, y and z.Simple selections can be combined together using booleans operations:
<selection_1> and <selection_2>: an atom will match this selction if and only
if it matches selection_1 and selection_2;<selection_1> or <selection_2>: an atom will match this selction if it matches
any of selection_1 or selection_2;not <selection>: an atom will match this selction if and only if it DO NOT
matches selection.In order to remove ambiguity when using multiple boolean operations, selections should use parentheses. If no parentheses are present, all operators will be considered left-associatives.
Some more complex selections:
name H and not x < 5.0
(z < 45 and name O) or name C
vx > 3 or vy > 3 or vz > 3