In order to aid comprehension, this documentation strives to obey the following formatting/notation conventions.
In text:
- Function/method parameters are set in italics.
- When not used for emphasis, bold text is used to set apart words/phrases with specific contextual meaning.
- Code snippets are set in fixed font, colored red, and boxed:
[v for v in range(6)].- References to Python objects are set in fixed font, colored black (in most cases), and boxed:
~opan.xyz.OpanXYZ. Where practical, they will be linked to the relevant documentation (via~sphinx.ext.intersphinx).Code examples are set in fixed font and boxed the full width of the page:
from opan.utils.vector import proj pvec = proj(vec1, vec2)Interactive usage examples are formatted like a Python console session, as per
~sphinx.ext.doctest:>>> 1 + 2 + 3 6
- Where included, the key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this documentation are to be interpreted as described in
2119.- Mathematical symbols and engineering units are set as in equations, below.
In equations:
- Roman variables are set in serif italics: x + C
- Lowercase Greek variables are set in italics:
$\theta + \pi \over \gamma$ - Uppercase Greek variables are set in upright serif: Φ + Θ
- Vectors are set in bold, upright, serif Roman symbols: r2 − r1
- Matrices are set as bold, uppercase, serif Roman or Greek symbols: M − 1/2FM − 1/2
- Engineering units are set in upright Roman (serif) equation type:
$\left(\mathrm{E_h\over B^2}\right)$
Common symbols:
- N -- the number of atoms in the system of interest
- G -- the number of geometries in an OpenBabel XYZ file
- R, S, ... -- Arbitrary integers