SelectionsΒΆ

class chemfiles::Selection

This class allow to select some atoms in a Frame, using a specific selection language.

The selection language is built by combining basic operations. Each basic operation follows the <selector> <operator> <value> structure, where <operator> can be a comparison operator in == != < <= > >=.

Implemented <selector> and associated <value> types are given below:

  • name: select atoms on their name. <value> must be a string, and only the == and != operators are allowed. Examples: name == C; name != Hw.
  • index: select atoms on their index in the frame. <value> must be an integer. Examples: index == 4; index > 304.
  • mass: select atoms on their mass. <value> must be a number. Examples: mass 4; mass < 2.0.
  • x|y|z: select atoms on their position.

must be a number. Examples:x <= 7.3;z != 4.2;y > 2. -vx|vy|vz: select atoms on their velocity. <value> must be a number. Examples: vx <= 7.3; vz != 4.2; vy > 2.

These basic operations can be combined by three logical operators: and, or and not. Parentheses can be used to remove ambiguity when using multiple operators. 

`name == H and (x < 45.9 or vz >= 67) and (not index == 67)`

Some selections also accept a short form, where the comparison operator is elided and implicitly ==. These selections are name, index and mass. So name O or index 234 is equivalent to name == O or index == 234.

Two other special operation are the all and none selection, matching respectively all and none of the atoms in the frame.

Public Functions

Selection(const std::string & selection)

Create a selection using the given string.

Exceptions
  • ParserError -

    if there is a semantic error in the selection

  • LexerError -

    if there is a syntaxic error in the selection

std::vector< Bool > evaluate(const Frame & frame) const

Evaluate the selection on a given frame. This function returns a vector of size Frame::natoms(), containing true at the index i if the atom at index i matches the selection, and false otherwise.

class chemfiles::Bool

Because the standard spacialization std::vector<bool> is optimized for space requirements and hard to work with, chemfiles uses a small wrapper around the bool type, the Bool class.

Public Functions

Bool(bool value)

Construct a Bool from a given bool value.

bool operator!() const

Negate this boolean.

operator bool() const

Convert this boolean to the bool standard type.