Struct pdbtbx::Residue

pub struct Residue { /* private fields */ }

A Residue containing multiple Conformers

Implementations

impl<'a> Residue

pub fn new( number: isize, insertion_code: Option<&str>, conformer: Option<Conformer> ) -> Option<Self>

Create a new Residue

Arguments

• number - the serial number
• insertion_code - the insertion code
• conformer - if available it can already add an conformer

Fails

It fails and returns None if any of the characters making up the insertion_code are invalid.

pub const fn serial_number(&self) -> isize

Get the serial number of the Residue.

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

Set the serial number of the Residue.

pub fn insertion_code(&self) -> Option<&str>

Get the insertion code of the Residue.

pub fn set_insertion_code(&mut self, new_code: impl AsRef<str>) -> bool

Set the insertion code of the Residue. Fails and returns false if the new_code contains invalid characters

pub fn remove_insertion_code(&mut self)

Set the insertion code of the Residue to None.

pub fn id(&self) -> (isize, Option<&str>)

Returns the uniquely identifying construct for this Residue, consisting of the serial number and the insertion code.

pub fn name(&self) -> Option<&str>

The ID or name of the Residue, it will only give a value if there is only one conformer or if all conformers have the same name

pub fn conformer_count(&self) -> usize

The number of Conformers making up this Residue.

pub fn atom_count(&self) -> usize

Get the number of Atoms making up this Residue.

pub fn par_atom_count(&self) -> usize

Available on crate feature rayon only.

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

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

Get a reference to a specific Conformer from the list of Conformers making up this Residue.

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 list of Conformers making up this Residue.

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 list of Conformers making up this Residue.

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 list of Conformers making up this Residue.

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, alternative_location: Option<&str> ) -> Option<AtomConformer<'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, alternative_location: Option<&str> ) -> Option<AtomConformerMut<'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 = AtomConformer<'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 = AtomConformerMut<'a>> + '_

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

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 = AtomConformer<'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 = AtomConformerMut<'a>> + '_

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

pub fn add_conformer(&mut self, new_conformer: Conformer)

Add a new conformer to the list of conformers making up this Residue.

Arguments

• new_conformer - the new conformer to add

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

Add a new Atom to this Residue. If a Residue with the given serial number already exists, the Atom will be added to it, otherwise a new Residue is created to hold the created atom and added to the list of Residues in its chain.

Arguments

• new_atom - the new Atom to add
• 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 Residue name contains any invalid characters.

pub fn remove_empty(&mut self)

Remove all empty Conformers from this Residue.

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 Residue.

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 Residue.

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

Remove the specified conformer.

Arguments

• index - the index of the Conformer to remove

Panics

Panics when the index is outside bounds.

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

Remove the specified conformer. Returns true if a matching Conformer was found and removed. Removes the first matching Conformer from the list.

Arguments

• id - the identifying construct of the Conformer to remove

Panics

Panics when the index is outside bounds.

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

Available on crate feature rayon only.

Remove the specified Conformer. Returns true if a matching Conformer was found and removed. It removes the first matching Conformer from the list. Searching is done in parallel.

Arguments

• id - the identifying construct of the Conformer to remove

Panics

Panics when the index is outside bounds.

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

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

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

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

pub fn sort(&mut self)

Sort the Conformers of this Residue

pub fn par_sort(&mut self)

Available on crate feature rayon only.

Sort the Conformers of this Residue in parallel

Trait Implementations

impl Clone for Residue

fn clone(&self) -> Residue

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Residue

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Residue

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

Deserialize this value from the given Serde deserializer.

impl Display for Residue

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

Formats the value using the given formatter.

impl Extend<Conformer> for Residue

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

Extend the Conformers on this Residue by the given iterator.

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<Residue> for Chain

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

Extend the Residues on this Chain by the given iterator of Residues.

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 Residue

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<Residue> for Residue

fn eq(&self, other: &Residue) -> 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<Residue> for Residue

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 Residue

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 Residue

impl StructuralEq for Residue

impl StructuralPartialEq for Residue