Struct AtomInfo

pub struct AtomInfo {

    pub resv: i32,
    pub chain: String,
    pub alt: String,
    pub resi: String,
    pub segi: String,
    pub resn: String,
    pub name: String,
    pub elem: Element,
    pub text_type: String,
    pub label: String,
    pub ss_type: String,
    pub is_hydrogen: bool,
    pub custom_type: i32,
    pub priority: i32,
    pub b: f64,
    pub q: f64,
    pub vdw: f64,
    pub partial_charge: f64,
    pub formal_charge: i32,
    pub is_hetatm: bool,
    pub vis_rep: RepBitmask,
    pub color: i32,
    pub id: i32,
    pub cartoon: i32,
    pub flags: i64,
    pub is_bonded: bool,
    pub chem_flag: i32,
    pub geom: i32,
    pub valence: i32,
    pub is_masked: bool,
    pub is_protected: bool,
    pub protons: i32,
    pub unique_id: i64,
    pub stereo: i8,
    pub discrete_state: i32,
    pub elec_radius: f64,
    pub rank: i32,
    pub hb_donor: bool,
    pub hb_acceptor: bool,
    pub atomic_color: i32,
    pub has_setting: bool,
    pub anisou_1: f32,
    pub anisou_2: f32,
    pub anisou_3: f32,
    pub anisou_4: f32,
    pub anisou_5: f32,
    pub anisou_6: f32,
    pub custom: String,
}

AtomInfo

This struct contains various properties of an atom, including its position, chemical properties, and visualization settings.

Pymol Source

• AtomInfo.h
  • Lots of goodies in here including constants defined for Atom type; Atom Geometry; VDW Radius; Chirality.
• AtomInfo.cpp
• AtomInforAsPyList
• VDW Radius of Elements w

Fields

resv: i32

Residue sequence number

chain: String

Chain identifier

alt: String

Alternate location indicator

resi: String

Residue identifier

segi: String

Segment identifier

resn: String

Residue name

name: String

Atom name

elem: Element

Element symbol

text_type: String

Text type

label: String

Label text

ss_type: String

Secondary structure type

is_hydrogen: bool

Flag indicating if the atom is hydrogen

custom_type: i32

Custom type identifier

priority: i32

Priority value

b: f64

B-factor (temperature factor)

q: f64

Occupancy

vdw: f64

Van der Waals radius

partial_charge: f64

Partial charge

formal_charge: i32

Formal charge

is_hetatm: bool

Flag indicating if the atom is a heteroatom

vis_rep: RepBitmask

Visualization representation

color: i32

Color index (color is an index into the color vec)

id: i32

Atom ID

cartoon: i32

Cartoon representation type (0 = default which is auto (use ssType))

flags: i64

Various flags

is_bonded: bool

Flag indicating if the atom is bonded

chem_flag: i32

Chemical flag (not sure what this is)

geom: i32

Geometry type (cAtomInfo*)

valence: i32

Valence (number of explicit and implicit neighbors, independent of bond order)

is_masked: bool

Flag indicating if the atom is masked

is_protected: bool

Flag indicating if the atom is protected

protons: i32

Number of protons (atomic number)

unique_id: i64

Unique identifier

stereo: i8

Stereochemistry indicator

discrete_state: i32

Discrete state

elec_radius: f64

Electronic radius

rank: i32

Rank

hb_donor: bool

Hydrogen bond donor flag

hb_acceptor: bool

Hydrogen bond acceptor flag

atomic_color: i32

Atomic color

has_setting: bool

Flag indicating if the atom has custom settings

anisou_1: f32

Anisotropic temperature factor 1

anisou_2: f32

Anisotropic temperature factor 2

anisou_3: f32

Anisotropic temperature factor 3

anisou_4: f32

Anisotropic temperature factor 4

anisou_5: f32

Anisotropic temperature factor 5

anisou_6: f32

Anisotropic temperature factor 6

custom: String

Custom data string

Implementations

impl AtomInfo

pub fn is_metal()

is the atom a metal?

pub fn is_visible()

pub fn atom_info_brack_residue()

pub fn to_pdbtbx_atom(&self) -> Atom

Conversion to PDBTBX

Trait Implementations

impl Debug for AtomInfo

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for AtomInfo

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

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for AtomInfo

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

where __S: Serializer,

Serialize this value into the given Serde serializer.