Struct pdbtbx::PDB

pub struct PDB {
    pub identifier: Option<String>,
    pub scale: Option<TransformationMatrix>,
    pub origx: Option<TransformationMatrix>,
    pub unit_cell: Option<UnitCell>,
    pub symmetry: Option<Symmetry>,
    // some fields omitted
}

A PDB file containing the 3D coordinates of many atoms making up the 3D structure of a protein, but it can also be used for other molecules.

Fields

identifier: Option<String>

The identifier as posed in the PDB Header or mmCIF entry.id, normally a 4 char string like ‘1UBQ’

scale: Option<TransformationMatrix>

The Scale needed to transform orthogonal coordinates to fractional coordinates, if available

origx: Option<TransformationMatrix>

The OrigX needed to transform orthogonal coordinates to submitted coordinates, if available

unit_cell: Option<UnitCell>

The unit cell of the crystal, containing its size and shape, if available

symmetry: Option<Symmetry>

The Symmetry or space group of the crystal, if available

Implementations

impl PDB

pub fn new() -> PDB

Create an empty PDB struct

pub fn remark_count(&self) -> usize

Get the number of REMARK records in the PDB file

pub fn remarks(&self) -> impl DoubleEndedIterator<Item = &(usize, String)> + '_

Get the remarks, containing the remark-type-number and a line of free text

pub fn remarks_mut(
    &mut self
) -> impl DoubleEndedIterator<Item = &mut (usize, String)> + '_

Get the remarks as mutable references, containing the remark-type-number and a line of free text

pub fn add_remark(&mut self, remark_type: usize, remark_text: String)

Add a remark

Arguments

• remark_type - the remark-type-number
• remark_text - the free line of text, containing the actual remark

Panics

It panics if the text if too long, the text contains invalid characters or the remark-type-number is not valid (wwPDB v3.30).

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

Get the MtriX records for this PDB

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

Get the MtriX records for this PDB, as mutable references

pub fn get_mtrix(&self, index: usize) -> Option<&MtriX>

Get a specific MtriX.

Arguments

• index - the index of the MtriX to return

Fails

It fails when the index is out of bounds.

pub fn get_mtrix_mut(&mut self, index: usize) -> Option<&mut MtriX>

Get a specific MtriX as a mutable reference.

Arguments

• index - the index of the MtriX to return

Fails

It fails when the index is out of bounds.

pub fn add_mtrix(&mut self, mtrix: MtriX)

Add a MtriX to this PDB

pub fn add_model(&mut self, new_model: Model)

Adds a Model to this PDB

pub fn model_count(&self) -> usize

Get the amount of Models making up this PDB

pub fn chain_count(&self) -> usize

Get the amount of Chains making up this PDB.

pub fn residue_count(&self) -> usize

Get the amount of Residues making up this PDB.

pub fn conformer_count(&self) -> usize

Get the amount of Conformers making up this PDB.

pub fn atom_count(&self) -> usize

Get the amount of Atoms making up this PDB.

pub fn total_chain_count(&self) -> usize

Get the amount of Chains making up this PDB. Including all models.

pub fn total_residue_count(&self) -> usize

Get the amount of Residues making up this PDB. Including all models.

pub fn total_conformer_count(&self) -> usize

Get the amount of Conformer making up this PDB. Including all models.

pub fn total_atom_count(&self) -> usize

Get the amount of Atoms making up this PDB. Including all models.

pub fn model(&self, index: usize) -> Option<&Model>

Get a specific Model from list of Models making up this PDB.

Arguments

• index - the index of the Model

Fails

It fails when the index is outside bounds.

pub fn model_mut(&mut self, index: usize) -> Option<&mut Model>

Get a specific Model as a mutable reference from list of Models making up this PDB.

Arguments

• index - the index of the Model

Fails

It fails when the index is outside bounds.

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

Get a specific Chain from the Chains making up this PDB.

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 the Chains making up this PDB.

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 PDB.

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 PDB.

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 PDB.

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 PDB.

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 PDB.

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 PDB.

Arguments

• index - the index of the Atom

Fails

It fails when the index is outside bounds.

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

Get the list of Models making up this PDB.

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

Get the list of Models as mutable references making up this PDB.

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

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

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. As this is done in place this is the fastest way to remove Atoms from this PDB.

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

Remove all Conformers matching the given predicate. The predicate will be run on all Conformers. As this is done in place this is the fastest way to remove Conformers from this PDB.

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. As this is done in place this is the fastest way to remove Residues from this PDB.

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

Remove all Residues matching the given predicate. The predicate will be run on all Residues. As this is done in place this is the fastest way to remove Residues from this PDB.

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

Remove all Chains matching the given predicate. The predicate will be run on all Chains. As this is done in place this is the fastest way to remove Chains from this PDB.

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

Remove the Model specified.

Arguments

• index - the index of the Model to remove

Panics

It panics when the index is outside bounds.

pub fn remove_model_serial_number(&mut self, serial_number: usize) -> bool

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

Arguments

• serial_number - the serial number of the Model to remove

pub fn remove_empty(&mut self)

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

pub fn renumber(&mut self)

This renumbers all numbered structs in the PDB. So it renumbers models, atoms, residues, chains and MtriXs.

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

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

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

Joins two PDBs. If one has multiple models it extends the models of this PDB with the models of the other PDB. If this PDB does not have any models it moves the models of the other PDB to this PDB. If both have one model it moves all chains/residues/atoms form the first model of the other PDB to the first model of this PDB. Effectively the same as calling join on those models.

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

Extend the Models on this PDB by the given iterator.

pub fn sort(&mut self)

Sort the Models of this PDB

pub fn full_sort(&mut self)

Sort all structs in this PDB

Trait Implementations

impl Clone for PDB

fn clone(&self) -> PDB

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for PDB

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

Formats the value using the given formatter.

impl Default for PDB

fn default() -> Self

Returns the “default value” for a type.

impl Display for PDB

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

Formats the value using the given formatter.

impl PartialEq<PDB> for PDB

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

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

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

This method tests for !=.

impl StructuralPartialEq for PDB