Struct pdbtbx::Atom

pub struct Atom { /* fields omitted */ }

A struct to represent a single Atom in a protein

Implementations

impl Atom

pub fn new(
    hetero: bool,
    serial_number: usize,
    atom_name: &str,
    x: f64,
    y: f64,
    z: f64,
    occupancy: f64,
    b_factor: f64,
    element: &str,
    charge: isize
) -> Option<Atom>

Create a new Atom

pub fn hetero(&self) -> bool

Get if this atom is an hetero atom (true), a non standard atom, or a normal atom (false)

pub fn set_hetero(&mut self, new_hetero: bool)

Set if this atom is an hetero atom (true), a non standard atom, or a normal atom (false)

pub fn pos(&self) -> (f64, f64, f64)

Get the position of the atom as a tuple of f64, in the following order: (x, y, z) Returned in the units of the PDB file, which is defined to be orthogonal coordinate system in Å

pub fn set_pos(&mut self, new_pos: (f64, f64, f64)) -> Result<(), String>

Set the position of the atom as a tuple of f64, in the following order: (x, y, z)

Panics

It panics if one or more of the numbers are not finite (f64.is_finite())

pub fn x(&self) -> f64

Get the X position of the atom Returned in the units of the PDB file, which is defined to be orthogonal coordinate system in Å

pub fn set_x(&mut self, new_pos: f64) -> Result<(), String>

Set the X position of the atom

Panics

It panics if new_pos is not finite (f64.is_finite())

pub fn y(&self) -> f64

Get the Y position of the atom Returned in the units of the PDB file, which is defined to be orthogonal coordinate system in Å

pub fn set_y(&mut self, new_pos: f64) -> Result<(), String>

Set the Y position of the atom

Panics

It panics if new_pos is not finite (f64.is_finite())

pub fn z(&self) -> f64

Get the Z position of the atom Returned in the units of the PDB file, which is defined to be orthogonal coordinate system in Å

pub fn set_z(&mut self, new_pos: f64) -> Result<(), String>

Set the Z position of the atom

Panics

It panics if new_pos is not finite (f64.is_finite())

pub fn serial_number(&self) -> usize

Get the serial number of the atom This number is defined to be unique in the containing model, which is not enforced

pub fn set_serial_number(&mut self, new_serial_number: usize)

Set the serial number of the atom This number is defined to be unique in the containing model, which is not enforced

pub fn name(&self) -> &str

Get the name of the atom The name is max 4 characters and is trimmed

pub fn set_name(&mut self, new_name: &str) -> Result<(), String>

Set the name of the atom. The name will be changed to uppercase as requested by PDB/PDBx standard. If the name is invalid an error message is provided.

Errors

The name can only contain valid characters, the ASCII graphic characters (char.is_ascii_graphic() || char == ’ ’)

pub fn occupancy(&self) -> f64

Get the occupancy of the atom

pub fn set_occupancy(&mut self, new_occupancy: f64) -> Result<(), String>

Set the occupancy of the atom

Panics

It panics if new_occupancy is not finite (f64.is_finite())

pub fn b_factor(&self) -> f64

Get the b-factor or temperature factor of the atom

pub fn set_b_factor(&mut self, new_b_factor: f64) -> Result<(), String>

Set the b-factor of the atom

Panics

It panics if new_b_factor is not finite (f64.is_finite())

pub fn element(&self) -> &str

Get the element of this atom

pub fn atomic_number(&self) -> Option<usize>

Get the atomic number of this atom. If defined it uses self.element(), otherwise it uses self.name() of the atom.

Fails

It fails when the element() or name() is not a valid element name.

pub fn atomic_radius(&self) -> Option<f64>

Get the atomic radius of this Atom in Å. The radius is defined up to ‘Cm’ or 96. Source: Martin Rahm, Roald Hoffmann, and N. W. Ashcroft. Atomic and Ionic Radii of Elements 1-96. Chemistry - A European Journal, 22(41):14625–14632, oct 2016. URL: http://doi.org/10.1002/chem.201602949. Updated to the corrigendum: https://doi.org/10.1002/chem.201700610

Fails

It fails if the element name if this Atom is not defined (see self.atomic_number()). It also fails when the atomic radius is not defined for the given atomic number, so if the atomic number is higher than 96.

pub fn vanderwaals_radius(&self) -> Option<f64>

Gets the van der Waals radius for this Atom in Å.The radius is defined up until ‘Es’ or 99. Source: Alvarez, S. (2013). A cartography of the van der Waals territories. Dalton Transactions, 42(24), 8617. https://doi.org/10.1039/c3dt50599e

Fails

It fails if the element name if this Atom is not defined (see self.atomic_number()). It also fails when the atomic radius is not defined for the given atomic number, so if the atomic number is higher than 99.

pub fn covalent_bond_radii(
    &self
) -> Option<(usize, Option<usize>, Option<usize>)>

Gets the covalent bond radii for this Atom. The result is the radius for a single, double and triple bond, where the last two are optional. All values are given in picometers. Sources:

• P. Pyykkö; M. Atsumi (2009). “Molecular Single-Bond Covalent Radii for Elements 1-118”. Chemistry: A European Journal. 15 (1): 186–197. doi:10.1002/chem.200800987
• P. Pyykkö; M. Atsumi (2009). “Molecular Double-Bond Covalent Radii for Elements Li–E112”. Chemistry: A European Journal. 15 (46): 12770–12779. doi:10.1002/chem.200901472
• P. Pyykkö; S. Riedel; M. Patzschke (2005). “Triple-Bond Covalent Radii”. Chemistry: A European Journal. 11 (12): 3511–3520. doi:10.1002/chem.200401299

Fails

It fails if the element name if this Atom is not defined (see self.atomic_number()).

pub fn set_element(&mut self, new_element: &str) -> Result<(), String>

Set the element of this atom. The element will be changed to uppercase as requested by PDB/PDBx standard.

Fails

It fails if the element contains invalid characters (only ASCII graphic and space is allowed). It also fails if the string is too ling, the max length is 2 characters.

pub fn charge(&self) -> isize

Get the charge of the atom

pub fn pdb_charge(&self) -> String

Get the charge in the PDB format [0-9][-+]

pub fn set_charge(&mut self, new_charge: isize)

Set the charge of this atom

pub fn anisotropic_temperature_factors(&self) -> Option<[[f64; 3]; 3]>

Get the anisotropic temperature factors, if available

pub fn set_anisotropic_temperature_factors(&mut self, factors: [[f64; 3]; 3])

Set the anisotropic temperature factors

pub fn backbone(&self) -> bool

Get if this atom is likely to be a part of the backbone of a protein

pub fn apply_transformation(&mut self, transformation: &TransformationMatrix)

Apply a transformation to the position of this atom, the new position is immediately set.

pub fn corresponds(&self, other: &Atom) -> bool

See if the other Atom corresponds with this Atom. Which means that the Atoms are equal except for the position, occupancy, and b_factor. Used to validate that multiple models contain the same atoms, but with different positional data.

pub fn distance_wrapping(&self, other: &Atom, cell: &UnitCell) -> f64

Gives the distance between the centers of two atoms. Wrapping around the unit cell if needed.

pub fn distance(&self, other: &Atom) -> f64

Gives the distance between the centers of two atoms.

pub fn overlaps(&self, other: &Atom) -> Option<bool>

Checks if this Atom overlaps with the given atom. It overlaps if the sphere defined as sitting at the atom position with a radius of the atomic radius (atom.atomic_radius()) intersect with this sphere from the other Atom.

Fails

It fails if for any one of the two atoms the radius (.atomic_radius()) is not defined.

pub fn overlaps_wrapping(&self, other: &Atom, cell: &UnitCell) -> Option<bool>

Checks if this Atom overlaps with the given atom. It overlaps if the sphere defined as sitting at the atom position with a radius of the atomic radius (atom.atomic_radius()) intersect with this sphere from the other Atom. Wrapping around the unit cell if needed.

Fails

It fails if for any one of the two atoms the radius (.atomic_radius()) is not defined.

Trait Implementations

impl Clone for Atom

fn clone(&self) -> Atom

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Atom

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

Formats the value using the given formatter.

impl Display for Atom

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

Formats the value using the given formatter.

impl Eq for Atom

As there are a lot of checks to make sure only ‘normal’ f64 values are used Atom satisfies the properties needed for Eq while having f64 values.

impl Ord for Atom

fn cmp(&self, other: &Self) -> Ordering

This method returns an Ordering between self and other.

#[must_use]pub fn max(self, other: Self) -> Self

Compares and returns the maximum of two values.

#[must_use]pub fn min(self, other: Self) -> Self

Compares and returns the minimum of two values.

#[must_use]pub fn clamp(self, min: Self, max: Self) -> Self

Restrict a value to a certain interval.

impl PartialEq<Atom> for Atom

fn eq(&self, other: &Atom) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Atom) -> bool

This method tests for !=.

impl PartialOrd<Atom> for Atom

fn partial_cmp(&self, other: &Self) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

#[must_use]pub fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

#[must_use]pub fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

#[must_use]pub fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

#[must_use]pub fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl StructuralPartialEq for Atom