Struct pdbtbx::Model

pub struct Model { /* private fields */ }

A Model containing multiple Chains.

Implementations

impl<'a> Model

pub const fn new(serial_number: usize) -> Model

Create a new Model.

Arguments

• serial_number - the serial number

pub fn from_iter( serial_number: usize, chains: impl Iterator<Item = Chain> ) -> Model

Create a new Model.

Arguments

• serial_number - the serial number

pub const fn serial_number(&self) -> usize

Get 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 number of Chains making up this Model.

pub fn residue_count(&self) -> usize

Get the number of Residues making up this Model.

pub fn par_residue_count(&self) -> usize

Available on crate feature rayon only.

Get the number of Residues making up this Model in parallel.

pub fn conformer_count(&self) -> usize

Get the number of Conformers making up this Model.

pub fn par_conformer_count(&self) -> usize

Available on crate feature rayon only.

Get the number of Conformers making up this Model in parallel.

pub fn atom_count(&self) -> usize

Get the number of Atoms making up this Model.

pub fn par_atom_count(&self) -> usize

Available on crate feature rayon only.

Get the number of Atoms making up this Model in parallel.

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

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

Arguments

• index - the index of the Chain

Fails

Returns None if the index is out of bounds.

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

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

Arguments

• index - the index of the Chain

Fails

Returns None if the index is out of bounds.

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

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

Arguments

• index - the index of the Residue

Fails

Returns None if the index is out of bounds.

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

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

Arguments

• index - the index of the Residue

Fails

Returns None if the index is out of bounds.

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

Get a reference to a specific Conformer from the Conformers making up this Model.

Arguments

• index - the index of the Conformer

Fails

Returns None if the index is out of bounds.

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

Get a mutable reference to a specific Conformer from the Conformers making up this Model.

Arguments

• index - the index of the Conformer

Fails

Returns None if the index is out of bounds.

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

Get a reference to a specific Atom from the Atoms making up this Model.

Arguments

• index - the index of the Atom

Fails

Returns None if the index is out of bounds.

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

Get a mutable reference to a specific Atom from the Atoms making up this Model.

Arguments

• index - the index of the Atom

Fails

Returns None if the index is out of bounds.

pub fn binary_find_atom( &'a self, serial_number: usize, insertion_code: Option<&str> ) -> Option<AtomConformerResidueChain<'a>>

Get a reference to the specified atom. Its uniqueness is guaranteed by including the insertion_code, with its full hierarchy. The algorithm is based on binary search so it is faster than an exhaustive search, but the full structure is assumed to be sorted. This assumption can be enforced by using pdb.full_sort().

pub fn binary_find_atom_mut( &'a mut self, serial_number: usize, insertion_code: Option<&str> ) -> Option<AtomConformerResidueChainMut<'a>>

Get a mutable reference to the specified atom. Its uniqueness is guaranteed by including the insertion_code, with its full hierarchy. The algorithm is based on binary search so it is faster than an exhaustive search, but the full structure is assumed to be sorted. This assumption can be enforced by using pdb.full_sort().

pub fn find( &'a self, search: Search ) -> impl DoubleEndedIterator<Item = AtomConformerResidueChain<'a>> + '_

Find all hierarchies matching the given search. For more details see Search.

pub fn find_mut( &'a mut self, search: Search ) -> impl DoubleEndedIterator<Item = AtomConformerResidueChainMut<'a>> + '_

Find all hierarchies matching the given search. For more details see Search.

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

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

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

Available on crate feature rayon only.

Get a parallel iterator of references to Chains making up this Model.

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

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

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

Available on crate feature rayon only.

Get a parallel iterator of mutable references to Chains making up this Model.

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

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

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

Available on crate feature rayon only.

Get a parallel iterator of references to Residues making up this Model.

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

Get an iterator of mutable references to Residues making up this Model. Double ended so iterating from the end is just as fast as from the start.

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

Available on crate feature rayon only.

Get a parallel iterator of mutable references to Residues making up this Model.

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

Get an iterator of references to Conformers making up this Model. Double ended so iterating from the end is just as fast as from the start.

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

Available on crate feature rayon only.

Get a parallel iterator of references to Conformers making up this Model.

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

Get an iterator of mutable references to Conformers making up this Model. Double ended so iterating from the end is just as fast as from the start.

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

Available on crate feature rayon only.

Get a parallel iterator of mutable references to Conformers making up this Model.

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

Get an iterator of references to Atoms making up this Model. Double ended so iterating from the end is just as fast as from the start.

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

Available on crate feature rayon only.

Get a parallel iterator of references to Atoms making up this Model.

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

Get an iterator of mutable references to Atoms making up this Model. Double ended so iterating from the end is just as fast as from the start.

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

Available on crate feature rayon only.

Get a parallel iterator of mutable references to Atoms making up this Model.

pub fn atoms_with_hierarchy( &'a self ) -> impl DoubleEndedIterator<Item = AtomConformerResidueChain<'a>> + '_

Get an iterator of references to a struct containing all atoms with their hierarchy making up this Model.

pub fn atoms_with_hierarchy_mut( &'a mut self ) -> impl DoubleEndedIterator<Item = AtomConformerResidueChainMut<'a>> + '_

Get an iterator of mutable references to a struct containing all atoms with their hierarchy making up this Model.

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

Panics if the index is out of bounds.

pub fn remove_chain_by_id(&mut self, id: impl AsRef<str>) -> 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 par_remove_chain_by_id(&mut self, id: impl AsRef<str>) -> bool

Available on crate feature rayon only.

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. Done in parallel.

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 par_remove_empty(&mut self)

Available on crate feature rayon only.

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

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 par_apply_transformation( &mut self, transformation: &TransformationMatrix )

Available on crate feature rayon only.

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

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 sort(&mut self)

Sort the Chains of this Model.

pub fn par_sort(&mut self)

Available on crate feature rayon only.

Sort the Chains of this Model in parallel.

Trait Implementations

impl Clone for Model

fn clone(&self) -> Model

Returns a copy of the value.

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<'de> Deserialize<'de> for Model

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

Deserialize this value from the given Serde deserializer.

impl Display for Model

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

Formats the value using the given formatter.

impl Extend<Chain> for Model

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

Extend the Chains on this Model by the given iterator of Chains.

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 Extend<Model> for PDB

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

Extend the Models on this PDB by the given iterator of Models.

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 FromIterator<Model> for PDB

fn from_iter<T: IntoIterator<Item = Model>>(iter: T) -> Self

Creates a value from an iterator.

impl Ord for Model

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<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: &Rhs) -> bool

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

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.

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 Serialize for Model

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 Model

impl StructuralEq for Model

impl StructuralPartialEq for Model