Crate pdbtbx

pdbtbx (PDB Toolbox)

A library to work with crystallographic Protein DataBank files. It can parse the main part of the PDB and mmCIF format (it is actively in development so more will follow). The resulting structure can be used to edit and interrogate the 3D structure of the protein. The changed structures can be saved in a PDB or mmCIF file for use in other software.

Goals

This library is designed to be a dependable, safe, stable and fast way of handling PDB files in idiomatic Rust. It is the goal to be very community driven, to make it into a project that is as useful to everyone while keeping true to its core principles.

Why

As Rust is a recent language so there is not a lot of support for scientific work in Rust compared to languages that are used much longer (like the ubiquitous Python). I think that using Rust would have huge benefits over other languages in bigger scientific projects. It is not just me, more scientists are turning to Rust [Perkel, J. M.]. I want to make it easier for scientists to start using Rust by writing this library.

How to use it

The following example opens a pdb file (1ubq.pdb). Removes all H atoms. Calculates the average B factor (or temperature factor) and prints that. It also saves the resulting PDB to a file.

use pdbtbx::*;
let (mut pdb, _errors) = pdbtbx::open("example-pdbs/1ubq.pdb").unwrap();

pdb.remove_atoms_by(|atom| atom.element() == Some(&Element::H)); // Remove all H atoms

let mut avg_b_factor = 0.0;
for atom in pdb.atoms() { // Iterate over all atoms in the structure
    avg_b_factor += atom.b_factor();
}
avg_b_factor /= pdb.atom_count() as f64;

println!("The average B factor of the protein is: {}", avg_b_factor);
pdbtbx::save(&pdb, "dump/1ubq_no_hydrogens.pdb", pdbtbx::StrictnessLevel::Loose);

High level documentation

general_docs

Parallelization

Rayon is used to create parallel iterators for all logical candidates. Use the parallel version of an iterator by prefixing the name with par_. Among other the looping iterators, like atoms(), residues() and atoms_with_hierarchy() are implemented as parallel iterators. The Rayon implementations are gated behind the rayon feature which is enabled by default.

Serialization

Enable the serde feature for Serde support.

Spatial lookup of atoms

Enable the rstar feature for rstar support. This enables you to generate R*trees making it possible to do very fast lookup for atoms with spatial queries. So for example finding close atoms is very fast. See the documentation of this crate for more information on how to make use of all of its features.

use pdbtbx::*;
let (mut pdb, _errors) = pdbtbx::open("example-pdbs/1ubq.pdb").unwrap();
// You can loop over all atoms within 3.5 Aͦ of a specific atom
// Note: The `locate_within_distance` method takes a squared distance
let tree = pdb.create_atom_rtree();
for atom in tree.locate_within_distance(pdb.atom(42).unwrap().pos(), 3.5 * 3.5) {
    println!("{}", atom);
}

// You can even get information about the hierarchy of these atoms
// (the chain, residue and conformer that contain this atom)
let tree = pdb.create_hierarchy_rtree();
let mut total = 0;
for hierarchy in tree.locate_within_distance(pdb.atom(42).unwrap().pos(), 3.5 * 3.5) {
    if hierarchy.is_backbone() {
        total += 1;
    }
}
println!("There are {} backbone atoms within 3.5Aͦ of the atom at index 42", total);

References

1. [Perkel, J. M.] Perkel, J. M. (2020). Why scientists are turning to Rust. Nature, 588(7836), 185–186. https://doi.org/10.1038/d41586-020-03382-2

Modules

• general_docs
  Here you can find high level documentation for this crate.

Structs

• Atom
  A struct to represent a single Atom in a protein.
• AtomConformer
  A struct to hold references to an Atom and its containing Conformer.
• AtomConformerMut
  A struct to hold mutable references to an Atom and its containing Conformer.
• AtomConformerResidue
  A struct to hold references to an Atom and its containing Conformer and Residue.
• AtomConformerResidueChain
  A struct to hold references to an Atom and its containing Conformer, Residue, and Chain.
• AtomConformerResidueChainModel
  A struct to hold references to an Atom and its containing Conformer, Residue, Chain, and Model.
• AtomConformerResidueChainModelMut
  A struct to hold mutable references to an Atom and its containing Conformer, Residue, Chain, and Model.
• AtomConformerResidueChainMut
  A struct to hold mutable references to an Atom and its containing Conformer, Residue, and Chain.
• AtomConformerResidueMut
  A struct to hold mutable references to an Atom and its containing Conformer and Residue.
• AtomicRadius
  Hold all atomic radii for a single element. So that in the code it is obvious which radius you use. All values are in Å (10e-10 m or 0.1 nm).
• Chain
  A Chain containing multiple Residues
• Conformer
  A Conformer containing multiple atoms, analogous to atom_group in cctbx
• Database
  The information about the database see DBREF documentation wwPDB v3.30 https://www.wwpdb.org/documentation/file-format-content/format33/sect3.html#DBREF
• DatabaseReference
  A DatabaseReference containing the cross-reference to a corresponding database sequence for a Chain.
• Model
  A Model containing multiple Chains.
• MtriX
  A transformation expressing non-crystallographic symmetry, used when transformations are required to generate the whole asymmetric subunit
• PDB
  A PDB struct is generated by opening a PDB or mmCIF file. It contains all information present in this file, like its atoms, bonds, hierarchy , and metadata. The struct can be used to access, interact with, and edit this data.
• PDBError
  An error surfacing while handling a PDB
• Position
  A position in a file for use in parsing/lexing
• ReadOptions
  Options and flags which can be used to configure how a structure file is opened.
• Residue
  A Residue containing multiple Conformers
• SequenceDifference
  A difference between the sequence of the database and the pdb file
• SequencePosition
  The position of the sequence for a cross-reference of sequences.
• Symmetry
  A Space group of a crystal
• TransformationMatrix
  A 3D affine transformation matrix
• UnitCell
  A unit cell of a crystal, containing its dimensions and angles

Enums

• Bond
  Bond types between two atoms
• Context
  A struct to define the context of an error message
• Element
  All elements from the periodic system.
• ErrorLevel
  This indicates the level of the error, to handle it differently based on the level of the raised error.
• Format
  Used to set which format to read the file in.
• Ops
  All operators that can be used in a search
• Search
  A collection of multiple search Terms in the search for (an) atom(s) in a PDB. You can use bitwise and (&), or (|), and xor (^) to chain a search. In the same way you can use not ! to negate a search term.
• StrictnessLevel
  The strictness to operate in, this defines at which ErrorLevel the program should stop execution upon finding an error.
• Term
  Any parameter to use in a Search for atom(s) in a PDB. For position related searches look into the rstar crate which can be combined with this crate using the rstar feature, see PDB::create_atom_rtree and PDB::create_hierarchy_rtree. The rstar crate makes spatial lookup and queries way faster and feasible to use in high performance environments.

Traits

• ContainsAtomConformer
  A trait which defines all functions on a hierarchy which contains Atoms and Conformers.
• ContainsAtomConformerMut
  A trait which defines all functions on a mutable hierarchy which contains Atoms and Conformers.
• ContainsAtomConformerResidue
  A trait which defines all functions on a hierarchy which contains Atoms, Conformers, and Residues.
• ContainsAtomConformerResidueChain
  A trait which defines all functions on a hierarchy which contains Atoms, Conformers, Residues, and Chains.
• ContainsAtomConformerResidueChainModel
  A trait which defines all functions on a hierarchy which contains Atoms, Conformers, Residues, Chains, and Models.
• ContainsAtomConformerResidueChainModelMut
  A trait which defines all functions on a mutable hierarchy which contains Atoms, Conformers, Residues, Chains, and Models.
• ContainsAtomConformerResidueChainMut
  A trait which defines all functions on a mutable hierarchy which contains Atoms, Conformers, Residues, and Chains.
• ContainsAtomConformerResidueMut
  A trait which defines all functions on a mutable hierarchy which contains Atoms, Conformers, and Residues.

Functions

• check_char
  Checks if a char is allowed in a PDB file. The char has to be ASCII graphic or a space. Returns true if the char is valid.
• number_to_base26
  Converts a number into a base26 with only the alphabet as possible chars
• open
  Open an atomic data file, either PDB or mmCIF/PDBx.
• open_gzDeprecated
  Open a compressed atomic data file, either PDB or mmCIF/PDBx. The correct type will be determined based on the file extension (.pdb.gz or .cif.gz).
• open_mmcifDeprecated
  Parse the given mmCIF file into a PDB struct. Returns a PDBError if a BreakingError is found. Otherwise it returns the PDB with all errors/warnings found while parsing it.
• open_mmcif_bufreadDeprecated
  Open’s mmCIF file from a BufRead. This allows opening mmCIF files directly from memory.
• open_mmcif_rawDeprecated
  Parse the given mmCIF &str into a PDB struct. This allows opening mmCIF files directly from memory. Returns a PDBError if a BreakingError is found. Otherwise it returns the PDB with all errors/warnings found while parsing it.
• open_pdbDeprecated
  Parse the given file into a PDB struct. Returns a PDBError if a BreakingError is found. Otherwise it returns the PDB with all errors/warnings found while parsing it.
• open_pdb_rawDeprecated
  Parse the input stream into a PDB struct. To allow for direct streaming from sources, like from RCSB.org. Returns a PDBError if a BreakingError is found. Otherwise it returns the PDB with all errors/warnings found while parsing it.
• prepare_identifier
  Creates a valid identifier from the given string slice. Does not change the case.
• prepare_identifier_uppercase
  Creates a valid identifier from the given string slice. Also turns the identifier to uppercase.
• save
  Save the given PDB struct to the given file, validating it beforehand. If validation gives rise to problems, use the save_raw function. The correct file type (pdb or mmCIF/PDBx) will be determined based on the given file extension.
• save_gz
  Save the given PDB struct to the given file and compressing to gz, validating it beforehand. If validation gives rise to problems, use the save_raw function. The correct file type (pdb or mmCIF/PDBx) will be determined based on the given file extension.
• save_mmcif
  Save the given PDB struct to the given file as mmCIF or PDBx.
• save_mmcif_gz
  Save the given PDB struct to the given file as mmCIF or PDBx and compresses to .gz
• save_mmcif_raw
  Save the given PDB struct to the given BufWriter. It does not validate or renumber the PDB, so if that is needed that needs to be done in preparation. It does change the output format based on the StrictnessLevel given.
• save_pdb
  Save the given PDB struct to the given file, validating it beforehand.
• save_pdb_gz
  Save the given PDB struct to the given file, validating it beforehand, and use gzip compression.
• save_pdb_raw
  Save the given PDB struct to the given BufWriter. It does not validate or renumber the PDB, so if that is needed, that needs to be done in preparation. It does change the output format based on the StrictnessLevel given.
• valid_identifier
  Checks a string using check_char. Returns true if the text is valid.
• valid_text
  Checks a string using check_char. Returns true if the text is valid.
• validate
  Validate a given PDB file in terms of invariants that should be held up. It returns PDBErrors with the warning messages.
• validate_pdb
  Validates this models specifically for the PDB format. It returns PDBErrors with the warning messages. It extends the validation specified in the validate function with PDB specific validations.