Struct ferritin_pymol::pymolparsing::parsing::PyObjectMolecule

pub struct PyObjectMolecule {

    pub object: PyObject,
    pub n_cset: i32,
    pub n_bond: i32,
    pub n_atom: i32,
    pub coord_set: Vec<CoordSet>,
    pub cs_tmpl: Option<Vec<CoordSet>>,
    pub bond: Vec<Bond>,
    pub atom: Vec<AtomInfo>,
    pub discrete_flag: i32,
    pub n_discrete: i32,
    pub symmetry: Option<(([f32; 3], [f32; 3]), String)>,
    pub cur_cset: i32,
    pub bond_counter: i32,
    pub atom_counter: i32,
    pub discrete_atm_to_idx: Option<Vec<i32>>,
    pub dcs: Option<Vec<i32>>,
}

PyObjectMolecule: Represents a molecule in PyMOL.

Link

• pymol code
• ObjectMolecule
• Bond
• AtomInfo
• AtomInfo2

Fields

object: PyObject

The base PyObject information

n_cset: i32

Number of coordinate sets

n_bond: i32

Number of bonds

n_atom: i32

Number of atoms

coord_set: Vec<CoordSet>

Vector of coordinate sets

cs_tmpl: Option<Vec<CoordSet>>

Optional template coordinate set

bond: Vec<Bond>

Vector of bonds

atom: Vec<AtomInfo>

Vector of atom information

discrete_flag: i32

Flag for discrete representation

n_discrete: i32

Number of discrete objects

symmetry: Option<(([f32; 3], [f32; 3]), String)>

Optional symmetry information (crystal space group and name)

cur_cset: i32

Current coordinate set index

bond_counter: i32

Counter for bonds

atom_counter: i32

Counter for atoms

discrete_atm_to_idx: Option<Vec<i32>>

Optional mapping of discrete atoms to indices

dcs: Option<Vec<i32>>

Optional discrete coordinate set information

Implementations

impl PyObjectMolecule

pub fn get_name(&self) -> String

pub fn get_atom(&self, atm_idx: i32) -> Atom

Create a PDBTBX::Atom from the pymol object datastructure

pub fn get_chains(&self) -> Vec<String>

Get unique chain names

pub fn get_residues_by_chain(&self, chain: String) -> Vec<i32>

Get each residue by chain.

pub fn get_unit_cell_symmetry(&self) -> (UnitCell, Symmetry)

Unit Cell Symetry.

pub fn create_residue(&self, chain: String, residue_number: i32) -> Residue

Get each residue by chain.

pub fn create_chain(&self, chain: String) -> Chain

pub fn to_pdb(&self) -> PDB

Create a pdbtbx::PDB Note: Only handles the first Model….

Trait Implementations

impl Debug for PyObjectMolecule

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for PyObjectMolecule

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for PyObjectMolecule

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.