Struct PrmtopFile 

pub struct PrmtopFile {
    pub version: String,
    pub atoms: Vec<PrmtopAtom>,
    pub bonds: Vec<PrmtopBond>,
    pub angles: Vec<PrmtopAngle>,
    pub extra_sections: HashMap<String, Vec<String>>,
}

AMBER topology file (prmtop / parm7) representation.

Only the most commonly used sections are modelled here; raw section data for every other %FLAG is preserved in extra_sections.

Fields

version: String

Version string from the %VERSION line.

atoms: Vec<PrmtopAtom>

All atoms in topology order.

bonds: Vec<PrmtopBond>

All covalent bonds.

angles: Vec<PrmtopAngle>

All valence angles.

extra_sections: HashMap<String, Vec<String>>

Raw text for unrecognised %FLAG sections.

Implementations

impl PrmtopFile

pub fn new() -> Self

Create an empty PrmtopFile.

pub fn write<W: Write>(&self, writer: &mut W) -> Result<(), AmberIoError>

Write the topology to any Write sink in a simplified prmtop-style text format.

The output is intentionally human-readable rather than byte-perfect AMBER binary prmtop; it is suitable for round-trip testing.

pub fn read<R: Read>(reader: R) -> Result<Self, AmberIoError>

Parse a simplified prmtop-style text produced by PrmtopFile::write.

pub fn natom(&self) -> usize

Return the number of atoms.

Trait Implementations

impl Clone for PrmtopFile

fn clone(&self) -> PrmtopFile

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for PrmtopFile

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for PrmtopFile

fn default() -> PrmtopFile

Returns the “default value” for a type.