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. This disregards all Hetero Chains.

pub fn residue_count(&self) -> usize

Get the amount of Residues making up this Model. This disregards all Hetero Residues.

pub fn atom_count(&self) -> usize

Get the amount of Atoms making up this Model. This disregards all Hetero Atoms.

pub fn total_chain_count(&self) -> usize

Get the amount of Chains making up this Model. This includes all Hetero Chains.

pub fn total_residue_count(&self) -> usize

Get the amount of Residues making up this Model. This includes all Hetero Residues.

pub fn total_atom_count(&self) -> usize

Get the amount of Atoms making up this Model. This includes all Hetero Atoms.

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 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. This disregards all Hetero Chains. 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. This disregards all Hetero Chains. 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. This disregards all Hetero Residues. 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. This disregards all Hetero Residues. 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. This disregards all Hetero Atoms. 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. This disregards all Hetero Atoms. Double ended so iterating from the end is just as fast as from the start.

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

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

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

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

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

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

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

Get the list of Residues as mutable references making up this Model. This disregards all Normal Residues Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Atoms making up this Model. This disregards all Normal Atoms. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Atoms as mutable references making up this Model. This disregards all Normal Atoms. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Chains making up this Model. This includes all Normal and Hetero Chains. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Chains as mutable references making up this Model. This includes all Normal and Hetero Chains. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Residues making up this Model. This includes all Normal and Hetero Residues. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Residues as mutable references making up this Model. This includes all Normal and Hetero Residues Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Atoms making up this Model. This includes all Normal and Hetero Atoms. Double ended so iterating from the end is just as fast as from the start.

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

Get the list of Atoms as mutable references making up this Model. This includes all Normal and Hetero Atoms. 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: char,
    residue_serial_number: usize,
    residue_name: [char; 3]
)

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_serial_number - the serial number of the Residue to add the Atom to
• residue_name - the name of the Residue to add the Atom to, only used to create a new Residue if needed

Panics

It panics if the Chain id or Residue name contains any invalid characters.

pub fn add_hetero_atom(
    &mut self,
    new_atom: Atom,
    chain_id: char,
    residue_serial_number: usize,
    residue_name: [char; 3]
)

Add a new Atom to the hetero Atoms of 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_serial_number - the serial number of the Residue to add the Atom to
• residue_name - the name of the Residue to add the Atom to, only used to create a new Residue if needed

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 add_hetero_chain(&mut self, chain: Chain)

Add a Chain to the list of Hetero 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. The predicate will be run on all Atoms (Normal and Hetero). As this is done in place this is the fastest way to remove Atoms 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. The predicate will be run on all Residues (Normal and Hetero). 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. The predicate will be run on all Chains (Normal and Hetero). 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)

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_id(&mut self, id: char) -> 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 apply_transformation(&mut self, transformation: &TransformationMatrix)

Apply a transformation to the position of all atoms (Normal and Hetero) 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.

Trait Implementations

impl Clone for Model

pub fn clone(&self) -> Self

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Model

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

Formats the value using the given formatter.

impl Display for Model

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

Formats the value using the given formatter.

impl PartialEq<Model> for Model

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

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

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

This method tests for !=.