`chemparseplot.parse.grammar.xyz`#

XYZ grammar (parsimonious) for multi-atom frames.

Port of the wailord paper thesis: structured grammar parsing for XYZ rather than ad-hoc line splits. Multi-character element symbols and scientific floats are supported.

Added in version 1.9.9.

Module Contents#

Classes#

`XyzAtom`	One atom line: element symbol and Cartesian coordinates (Å).
`XyzFrame`	Parsed single-frame XYZ.

Functions#

`xyz_grammar`	Compiled XYZ grammar (cached).
`_flatten`
`_make_visitor`
`parse_xyz_text`	Parse a single-frame XYZ string with the grammar visitor.
`parse_xyz_file`	Read and parse an XYZ file.
`write_xyz_text`	Serialize a frame back to XYZ text (Å).

Data#

`_XYZ_GRAMMAR_SRC`
`_grammar_cache`

API#

chemparseplot.parse.grammar.xyz._XYZ_GRAMMAR_SRC = <Multiline-String>#

chemparseplot.parse.grammar.xyz._grammar_cache: Any | None#: None

chemparseplot.parse.grammar.xyz.xyz_grammar() → Any[source]#: Compiled XYZ grammar (cached).

class chemparseplot.parse.grammar.xyz.XyzAtom[source]#

One atom line: element symbol and Cartesian coordinates (Å).

symbol: str#: None

x: float#: None

y: float#: None

z: float#: None

class chemparseplot.parse.grammar.xyz.XyzFrame[source]#

Parsed single-frame XYZ.

natoms: int#: None

comment: str#: None

atoms: tuple[chemparseplot.parse.grammar.xyz.XyzAtom, ...]#: None

property symbols: list[str]#

property counts: collections.Counter#

property system: str#: Composition slug as ElementCount joined (e.g. H2, C1O2).

coordinates() → list[tuple[float, float, float]][source]#

chemparseplot.parse.grammar.xyz._flatten(xs: Any) → list[Any][source]#

chemparseplot.parse.grammar.xyz._make_visitor() → Any[source]#

chemparseplot.parse.grammar.xyz.parse_xyz_text(text: str) → chemparseplot.parse.grammar.xyz.XyzFrame[source]#

Parse a single-frame XYZ string with the grammar visitor.

Parameters

text: Full XYZ content including atom count and comment line.

Returns

XyzFrame Structured frame (natoms, comment, atoms).

chemparseplot.parse.grammar.xyz.parse_xyz_file(path: str | pathlib.Path) → chemparseplot.parse.grammar.xyz.XyzFrame[source]#: Read and parse an XYZ file.

chemparseplot.parse.grammar.xyz.write_xyz_text(frame: chemparseplot.parse.grammar.xyz.XyzFrame, *, comment: str | None = None) → str[source]#: Serialize a frame back to XYZ text (Å).

chemparseplot.parse.grammar.xyz#