Struct pdbtbx::Model

pub struct Model { /* fields omitted */ }

A Model containing multiple Chains

Implementations

impl Model

pub fn new(serial_number: usize) -> Model

Create a new Model

Arguments

• serial_number - the serial number

pub fn serial_number(&self) -> usize

The serial number of this Model

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

Set the serial number of this Model

pub fn chain_count(&self) -> usize

Get the amount of Chains making up this Model.

pub fn residue_count(&self) -> usize

Get the amount of Residues making up this Model.

pub fn conformer_count(&self) -> usize

Get the amount of Conformers making up this Model.

pub fn atom_count(&self) -> usize

Get the amount of Atoms making up this Model.

pub fn chain(&self, index: usize) -> Option<&Chain>

Get a specific Chain from list of Chains making up this Model.

Arguments

• index - the index of the Chain

Fails

It fails when the index is outside bounds.

pub fn chain_mut(&mut self, index: usize) -> Option<&mut Chain>

Get a specific Chain as a mutable reference from list of Chains making up this Model.

Arguments

• index - the index of the Chain

Fails

It fails when the index is outside bounds.

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

Get a specific Residue from the Residues making up this Model.

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 the Residues making up this Model.

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 the Conformers making up this Model.

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 the Conformers making up this Model.

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 Model.

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 Model.

Arguments

• index - the index of the Atom

Fails

It fails when the index is outside bounds.

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

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

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

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

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

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

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

Add a new Atom to this Model. It finds if there already is a Chain with the given chain_id if there is it will add this atom to that Chain, otherwise it will create a new Chain and add that to the list of Chains making up this Model. It does the same for the Residue, so it will create a new one if there does not yet exist a Residue with the given serial number.

Arguments

• new_atom - the new Atom to add
• chain_id - the id of the Chain to add the Atom to
• 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 Chain id or Residue name contains any invalid characters.

pub fn add_chain(&mut self, chain: Chain)

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

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 Model.

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 Model.

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 Model.

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

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

pub fn remove_chain(&mut self, index: usize) -> Chain

Remove the Chain specified.

Arguments

• index - the index of the Chain to remove

Panics

It panics when the index is outside bounds.

pub fn remove_chain_by_id(&mut self, id: String) -> bool

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

Arguments

• id - the id of the Chain to remove

pub fn remove_empty(&mut self)

Remove all empty Chain from this Model, and all empty Residues from the Chains.

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

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

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

Join this Model with another Model, this moves all atoms from the other Model to this Model. All other (meta) data of this Model will stay the same. It will add new Chains and Residues as defined in the other model.

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

Extend the Chains on this Model by the given iterator.

pub fn sort(&mut self)

Sort the Chains of this Model

Trait Implementations

impl Clone for Model

fn clone(&self) -> Model

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Model

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

Formats the value using the given formatter.

impl Display for Model

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

Formats the value using the given formatter.

impl Eq for Model

impl Ord for Model

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<Model> for Model

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

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

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

This method tests for !=.

impl PartialOrd<Model> for Model

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 Model

impl StructuralPartialEq for Model