Struct pdbtbx::Chain

pub struct Chain { /* fields omitted */ }

A Chain containing multiple Residues

Implementations

impl Chain

pub fn new(id: &str) -> Option<Chain>

Create a new Chain

Arguments

• id - the identifier

Fails

It fails if the identifier is an invalid character.

pub fn id(&self) -> &str

The ID of the Chain

pub fn set_id(&mut self, new_id: &str) -> bool

Set the ID of the Chain, returns false if the new id is an invalid character. The ID will be changed to uppercase as requested by PDB/PDBx standard.

pub fn database_reference(&self) -> Option<&DatabaseReference>

Get the database reference, if any, for this chain.

pub fn database_reference_mut(&mut self) -> Option<&mut DatabaseReference>

Get the database reference mutably, if any, for this chain.

pub fn set_database_reference(&mut self, reference: DatabaseReference)

Set the database reference for this chain.

pub fn residue_count(&self) -> usize

Get the amount of Residues making up this Chain

pub fn conformer_count(&self) -> usize

Get the amount of Conformers making up this Chain

pub fn atom_count(&self) -> usize

Get the amount of Atoms making up this Chain

pub fn residue(&self, index: usize) -> Option<&Residue>

Get a specific Residue from list of Residues making up this Chain.

Arguments

• index - the index of the Residue

Fails

It fails when the index is outside bounds.

pub fn residue_mut(&mut self, index: usize) -> Option<&mut Residue>

Get a specific Residue as a mutable reference from list of Residues making up this Chain.

Arguments

• index - the index of the Residue

Fails

It fails when the index is outside bounds.

pub fn conformer(&self, index: usize) -> Option<&Conformer>

Get a specific Conformer from list of Conformers making up this Chain.

Arguments

• index - the index of the Conformer

Fails

It fails when the index is outside bounds.

pub fn conformer_mut(&mut self, index: usize) -> Option<&mut Conformer>

Get a specific Conformer as a mutable reference from list of Conformers making up this Chain.

Arguments

• index - the index of the Conformer

Fails

It fails when the index is outside bounds.

pub fn atom(&self, index: usize) -> Option<&Atom>

Get a specific Atom from the Atoms making up this Chain.

Arguments

• index - the index of the Atom

Fails

It fails when the index is outside bounds.

pub fn atom_mut(&mut self, index: usize) -> Option<&mut Atom>

Get a specific Atom as a mutable reference from the Atoms making up this Chain.

Arguments

• index - the index of the Atom

Fails

It fails when the index is outside bounds.

pub fn residues(&self) -> impl DoubleEndedIterator<Item = &Residue> + '_

Get the list of Residues making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn residues_mut(
    &mut self
) -> impl DoubleEndedIterator<Item = &mut Residue> + '_

Get the list of Residues as mutable references making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn conformers(&self) -> impl DoubleEndedIterator<Item = &Conformer> + '_

Get the list of Conformers making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn conformers_mut(
    &mut self
) -> impl DoubleEndedIterator<Item = &mut Conformer> + '_

Get the list of Conformers as mutable references making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn atoms(&self) -> impl DoubleEndedIterator<Item = &Atom> + '_

Get the list of Atoms making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn atoms_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Atom> + '_

Get the list of Atoms as mutable references making up this Chain. Double ended so iterating from the end is just as fast as from the start.

pub fn add_atom(
    &mut self,
    new_atom: Atom,
    residue_id: (isize, Option<&str>),
    conformer_id: (&str, Option<&str>)
)

Add a new Atom to this Chain. It finds if there already is a Residue with the given serial number if there is it will add this atom to that Residue, otherwise it will create a new Residue and add that to the list of Residues making up this Chain.

Arguments

• new_atom - the new Atom to add
• residue_id - the id construct of the Residue to add the Atom to
• conformer_id - the id construct of the Conformer to add the Atom to

Panics

It panics if the Residue name contains any invalid characters.

pub fn add_residue(&mut self, residue: Residue)

Add a Residue end of to the list of Residues making up this Chain. This does not detect any duplicates of names or serial numbers in the list of Residues.

pub fn insert_residue(&mut self, index: usize, residue: Residue)

Inserts a Residue to the index in the list of Residues making up this Chain. This does not detect any duplicates of names or serial numbers in the list of Residues. This panics if index > len.

pub fn remove_atoms_by<F>(&mut self, predicate: F) where
    F: Fn(&Atom) -> bool, 

Remove all Atoms matching the given predicate. As this is done in place this is the fastest way to remove Atoms from this Chain.

pub fn remove_conformers_by<F>(&mut self, predicate: F) where
    F: Fn(&Conformer) -> bool, 

Remove all Conformers matching the given predicate. As this is done in place this is the fastest way to remove Conformers from this Chain.

pub fn remove_residues_by<F>(&mut self, predicate: F) where
    F: Fn(&Residue) -> bool, 

Remove all residues matching the given predicate. As this is done in place this is the fastest way to remove Residues from this Chain.

pub fn remove_residue(&mut self, index: usize)

Remove the Residue specified.

Arguments

• index - the index of the Residue to remove

Panics

It panics when the index is outside bounds.

pub fn remove_residue_by_id(&mut self, id: (isize, Option<&str>)) -> bool

Remove the Residue specified. It returns true if it found a matching Residue and removed it. It removes the first matching Residue from the list.

Arguments

• id - the id construct of the Residue to remove (see Residue.id())

pub fn remove_empty(&mut self)

Remove all empty Residues from this Chain, and all empty Conformers from the Residues.

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

Apply a transformation to the position of all atoms making up this Chain, the new position is immediately set.

pub fn join(&mut self, other: Chain)

Join this Chain with another Chain, this moves all atoms from the other Chain to this Chain. All other (meta) data of this Chain will stay the same.

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

Extend the Residues on this Chain by the given iterator.

pub fn sort(&mut self)

Sort the residues of this chain

Trait Implementations

impl Clone for Chain

fn clone(&self) -> Chain

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Chain

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

Formats the value using the given formatter.

impl Display for Chain

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

Formats the value using the given formatter.

impl Eq for Chain

impl Ord for Chain

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<Chain> for Chain

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

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

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

This method tests for !=.

impl PartialOrd<Chain> for Chain

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 StructuralEq for Chain

impl StructuralPartialEq for Chain