Struct pdbtbx::Atom

pub struct Atom { /* private fields */ }

A struct to represent a single Atom in a protein.

Implementations

impl Atom

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

Create a new Atom. If no or an invalid element is given it tries to find the element by using the full atom name as element. If this is not valid it will use the first character of the name if it is one of “CHNOS”.

pub const fn hetero(&self) -> bool

Determine 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 whether this atom is an hetero atom (true), a non standard atom, or a normal atom (false).

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

Get the position of the atom as a tuple of f64, in the following order: (x, y, z). Given in Å as defined by PDB in the orthogonal coordinate system.

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).

Errors

It fails if one or more of the numbers is not finite (f64.is_finite()).

pub const fn x(&self) -> f64

Get the X position of the atom. Given in Å as defined by PDB in the orthogonal coordinate system. This number has a precision of 8.3 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the X position of the atom in Å.

Errors

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

pub const fn y(&self) -> f64

Get the Y position of the atom. Given in Å as defined by PDB in the orthogonal coordinate system. This number has a precision of 8.3 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the Y position of the atom in Å.

Errors

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

pub const fn z(&self) -> f64

Get the Z position of the atom. Given in Å as defined by PDB in the orthogonal coordinate system. This number has a precision of 8.3 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the Z position of the atom in Å.

Errors

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

pub const fn serial_number(&self) -> usize

Get the serial number of the atom. This number, combined with the alt_loc from the Conformer of this Atom, is defined to be unique in the containing model, which is not enforced. The precision of this number is 5 digits in PDB files. If more than 99,999 atoms are present in the same model, the internal numbering will continue counting up even if the file from which the atoms were read does not. Importantly, this will not affect the saving of the file, only the internal handling of atom serial numbers.

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

Set the serial number of the atom. This number, combined with the alt_loc from the Conformer, of this Atom 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 will be trimmed (whitespace removed) and changed to ASCII uppercase.

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

Set the name of the atom. The name will be trimmed (whitespace removed) and changed to ASCII uppercase as requested by PDB/PDBx standard. For PDB files the name can at most contain 4 characters, enforced when saving the file.

Errors

The name can only contain valid characters, the ASCII graphic characters (char.is_ascii_graphic() || char == ' '). If the name is invalid an error message is provided.

pub const fn occupancy(&self) -> f64

Get the occupancy or Q factor of the atom. This indicates the fraction of unit cells in which this atom is present, in the normal case this will be one (1) and it can range between 1 and 0 (inclusive). This number has a precision of 6.2 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the occupancy or Q factor of the atom.

Errors

It fails if new_occupancy is not finite (f64.is_finite()) or if it is negative.

pub const fn b_factor(&self) -> f64

Get the B factor or temperature factor of the atom. This indicates the uncertainty in the position of the atom as seen over all unit cells in the whole crystal. A low uncertainty is modelled with a low B factor, with zero uncertainty being equal to a B factor of 0. A higher uncertainty is modelled by a high B factor. This number has a precision of 6.2 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the B factor or temperature factor of the atom.

Errors

It fails if new_b_factor is not finite (f64.is_finite()) or if it is negative.

pub fn element(&self) -> Option<&Element>

Get the element of this atom. In PDB files the element can at most contain 2 characters.

pub fn set_element(&mut self, element: Element)

Set the element of this atom.

pub const fn charge(&self) -> isize

Get the charge of the atom. In PDB files the charge is one digit with a sign.

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

Set the charge of this atom. In PDB files the charge is one digit with a sign.

pub fn pdb_charge(&self) -> String

Get the charge in the PDB format [0-9][-+]. If the charge is 0 or outside bounds (below -9 or above 9) it returns an empty string.

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

Get the anisotropic temperature factors, if available. This number has a precision of 8.3 in PDB files and 5 decimal places of precision in mmCIF files.

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

Set the anisotropic temperature factors.

pub fn is_backbone(&self) -> bool

Determine whether this atom is likely to be a part of the backbone of a protein. This is based on this Atom only, for a more precise definition use hierarchy::ContainsAtomConformer::is_backbone.

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

Apply a transformation using a given TransformationMatrix 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. This 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(&self, other: &Atom) -> f64

Gives the distance between the centers of two atoms in Aͦ.

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

Gives the distance between the centers of two atoms in Aͦ, wrapping around the unit cell if needed. This will give the shortest distance between the two atoms or any of their copies given a crystal of the size of the given unit cell stretching out to all sides.

pub fn angle(&self, atom2: &Atom, atom3: &Atom) -> f64

Gives the angle between the centers of three atoms in degrees. The angle is calculated as the angle between the two lines that include atoms [1, 2] and [2, 3]

pub fn dihedral(&self, atom2: &Atom, atom3: &Atom, atom4: &Atom) -> f64

Gives the dihedral between the centers of four atoms in degrees. The angle is calculated as the angle between the two planes spanned by atoms [1, 2, 3] and [2, 3, 4].

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

Checks if this Atom overlaps with the given atom. It overlaps if the distance between the atoms is less then the sum of the radius from this atom and the other atom. The used radius is AtomicRadius.unbound.

Note: the atomic radius used is the unbound radius, this is in most cases bigger than the bound radius and as such can result in false positives.

It fails if for any one of the two atoms the element or unbound radius is not known.

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

Checks if this Atom overlaps with the given atom. It overlaps if the distance between the atoms is less then the sum of the radius from this atom and the other atom. The used radius is AtomicRadius.unbound. Wrapping around the unit cell if needed. Meaning it will give the shortest distance between the two atoms or any of their copies given a crystal of the size of the given unit cell stretching out to all sides.

Note: the atomic radius used is the unbound radius, this is in most cases bigger than the bound radius and as such can result in false positives.

It fails if for any one of the two atoms the element or unbound radius is not known.

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

Checks if this Atom overlaps with the given atom. It overlaps if the distance between the atoms is less then the sum of the radius from this atom and the other atom. The used radius is AtomicRadius.covalent_single.

Note: the atomic radius used in the bound radius to a single atom, this is similar to the bound radius for double or triple bonds but could result in incorrect results.

It fails if for any one of the two atoms the element is not known.

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

Checks if this Atom overlaps with the given atom. It overlaps if the distance between the atoms is less then the sum of the radius from this atom and the other atom. The used radius is AtomicRadius.covalent_single. Wrapping around the unit cell if needed. Meaning it will give the shortest distance between the two atoms or any of their copies given a crystal of the size of the given unit cell stretching out to all sides.

Note: the atomic radius used is the bound radius to a single atom, this is similar to the bound radius for double or triple bonds but could result in incorrect results.

It fails if for any one of the two atoms the element is not known.

Trait Implementations

impl Clone for Atom

fn clone(&self) -> Self

The clone implementation needs to use the constructor to guarantee the uniqueness of the counter

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<'de> Deserialize<'de> for Atom

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Display for Atom

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

Formats the value using the given formatter.

impl Extend<Atom> for Conformer

fn extend<T: IntoIterator<Item = Atom>>(&mut self, iter: T)

Extend the Atoms on this Conformer by the given iterator over Atoms.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl Ord for Atom

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

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Selfwhere Self: Sized + PartialOrd<Self>,

Restrict a value to a certain interval.

impl PartialEq<Atom> for Atom

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

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

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

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

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.

fn lt(&self, other: &Rhs) -> bool

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

fn le(&self, other: &Rhs) -> bool

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

fn gt(&self, other: &Rhs) -> bool

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

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 PointDistance for &Atom

fn distance_2(&self, other: &(f64, f64, f64)) -> f64

Returns the squared euclidean distance between an object to a point.

fn contains_point(&self, point: &<Self::Envelope as Envelope>::Point) -> bool

Returns true if a point is contained within this object.

fn distance_2_if_less_or_equal( &self, point: &<Self::Envelope as Envelope>::Point, max_distance_2: <<Self::Envelope as Envelope>::Point as Point>::Scalar ) -> Option<<<Self::Envelope as Envelope>::Point as Point>::Scalar>

Returns the squared distance to this object, or None if the distance is larger than a given maximum value.

impl RTreeObject for &Atom

type Envelope = AABB<(f64, f64, f64)>

The object’s envelope type. Usually, AABB will be the right choice. This type also defines the object’s dimensionality.

fn envelope(&self) -> Self::Envelope

Returns the object’s envelope.

impl Serialize for Atom

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

Serialize this value into the given Serde serializer.

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.