biotite.structure

A subpackage for handling molecular structures.

In this context an atom is described by two kinds of attributes: the coordinates and the annotations. The annotations include information about polypetide chain id, residue id, residue name, hetero atom information, atom name and optionally more. The coordinates are a NumPy float ndarray of length 3, containing the x, y and z coordinates.

An Atom contains data for a single atom, it stores the annotations as scalar values and the coordinates as length 3 ndarray.

An AtomArray stores data for an entire structure model containing n atoms. Therefore the annotations are represented as ndarray objects of length n, the so called annotation arrays. The coordinates are a (n x 3) ndarray.

An AtomArrayStack stores data for m models, where each model contains the same atoms at different positions. Hence, the annotation arrays are represented as ndarray objects of length n like the AtomArray, while the coordinates are a (m x n x 3) ndarray.

Like an AtomArray can be iterated to obtain Atom objects, an AtomArrayStack yields AtomArray objects. All three types must not be subclassed.

The following annotation categories are mandatory:

Category	Type	Examples	Description
chain_id	string (U4)	‘A’,’S’,’AB’, …	Polypeptide chain
res_id	int	1,2,3, …	Sequence position of residue
ins_code	string (U1)	‘’, ‘A’,’B’,..	PDB insertion code (iCode)
res_name	string (U5)	‘GLY’,’ALA’, …	Residue name
hetero	bool	True, False	False for ATOM, true for HETATM
atom_name	string (U6)	‘CA’,’N’, …	Atom name
element	string (U2)	‘C’,’O’,’SE’, …	Chemical Element

For all Atom, AtomArray and AtomArrayStack objects these annotations are initially set with default values. Additionally to these annotations, an arbitrary amount of annotation categories can be added via add_annotation() or set_annotation(). The annotation arrays can be accessed either via the method get_annotation() or directly (e.g. array.res_id).

The following annotation categories are optionally used by some functions:

Category	Type	Examples	Description
atom_id	int	1,2,3, …	Atom serial number
b_factor	float	0.9, 12.3, …	Temperature factor
occupancy	float	.1, .3, .9, …	Occupancy
charge	int	-2,-1,0,1,2, …	Electric charge of the atom
sym_id	string	‘1’,’2’,’3’, …	Symmetry ID for assemblies/symmetry mates

For each type, the attributes can be accessed directly. Both AtomArray and AtomArrayStack support NumPy style indexing. The index is propagated to each attribute. If a single integer is used as index, an object with one dimension less is returned (AtomArrayStack -> AtomArray, AtomArray -> Atom). If a slice, index array or a boolean mask is given, a substructure is returned (AtomArrayStack -> AtomArrayStack, AtomArray -> AtomArray) As in NumPy, these are not necessarily deep copies of the originals: The attributes of the sliced object may still point to the original ndarray. Use the copy() method if a deep copy is required.

Bond information can be associated to an AtomArray or AtomArrayStack by setting the bonds attribute with a BondList. A BondList specifies the indices of atoms that form chemical bonds. Some functionalities require that the input structure has an associated BondList. If no BondList is associated, the bonds attribute is None.

Based on the implementation in NumPy arrays, this package furthermore contains a comprehensive set of functions for structure analysis, manipulation and visualization.

The universal length unit in this package is Å.

Structure types

Atom	A representation of a single atom.
AtomArray	An array representation of a model consisting of multiple atoms.
AtomArrayStack	A collection of multiple AtomArray instances, where each atom array has equal annotation arrays.
concatenate	Concatenate multiple AtomArray or AtomArrayStack objects into a single AtomArray or AtomArrayStack, respectively.
array	Create an AtomArray from a list of Atom.
stack	Create an AtomArrayStack from a list of AtomArray.
repeat	Repeat atoms (AtomArray or AtomArrayStack) multiple times in the same model with different coordinates.
from_template	Create an AtomArrayStack using template atoms and given coordinates.

Boxes and unit cells

vectors_from_unitcell	Calculate the three vectors spanning a box from the unit cell lengths and angles.
unitcell_from_vectors	Get the unit cell lengths and angles from box vectors.
box_volume	Get the volume of one ore multiple boxes.
repeat_box	Repeat the atoms in a box by duplicating and placing them in adjacent boxes.
repeat_box_coord	Similar to repeat_box(), repeat the coordinates in a box by duplicating and placing them in adjacent boxes.
move_inside_box	Move all coordinates into the given box, with the box vectors originating at (0,0,0).
remove_pbc	Remove segmentation caused by periodic boundary conditions from each molecule in the given structure.
remove_pbc_from_coord	Remove segmentation caused by periodic boundary conditions from given coordinates.
coord_to_fraction	Transform coordinates to fractions of box vectors.
fraction_to_coord	Transform fractions of box vectors to coordinates.
is_orthogonal	Check, whether a box or multiple boxes is/are orthogonal.

Bonds

BondList	A bond list stores indices of atoms (usually of an AtomArray or AtomArrayStack) that form chemical bonds together with the type (or order) of the bond.
BondType	This enum type represents the type of a chemical bond.
connect_via_residue_names	Create a BondList for a given atom array (stack), based on the deposited bonds for each residue in the RCSB components.cif dataset.
connect_via_distances	Create a BondList for a given atom array, based on pairwise atom distances.
find_connected	Get indices to all atoms that are directly or inderectly connected to the root atom indicated by the given index.
find_rotatable_bonds	Find all rotatable bonds in a given BondList.

Geometry

displacement	Measure the displacement vector, i.e. the vector difference, from one array of atom coordinates to another array of coordinates.
index_displacement	Measure the displacement, i.e. the vector difference, between pairs of atoms.
distance	Measure the euclidian distance between atoms.
index_distance	Measure the euclidian distance between pairs of atoms.
angle	Measure the angle between 3 atoms.
index_angle	Measure the angle between triples of atoms.
dihedral	Measure the dihedral angle between 4 atoms.
index_dihedral	Measure the dihedral angle between quadruples of atoms.
centroid	Measure the centroid of a structure.
mass_center	Calculate the center(s) of mass of an atom array or stack.
gyration_radius	Compute the radius/radii of gyration of an atom array or stack.
rdf	Compute the radial distribution function g(r) (RDF) for one or multiple given central positions based on a given system of particles.

Transformations

translate	Translate the given atoms or coordinates by a given vector.
rotate	Rotate the given atoms or coordinates about the x, y and z axes by given angles.
rotate_centered	Rotate the given atoms or coordinates about the x, y and z axes by given angles.
rotate_about_axis	Rotate the given atoms or coordinates about a given axis by a given angle.
align_vectors	Apply a transformation to atoms or coordinates, that would transfer a origin vector to a target vector.
orient_principal_components	Translate and rotate the atoms to be centered at the origin with the principal axes aligned to the Cartesian axes, as specified by the order parameter.

Superimpositions

superimpose	Superimpose structures onto each other, minimizing the RMSD between them.
superimpose_homologs	Superimpose one protein or nucleotide chain onto another one, considering sequence differences and conformational outliers.
superimpose_without_outliers	Superimpose structures onto a fixed structure, ignoring conformational outliers.
AffineTransformation	An affine transformation, consisting of translations and a rotation.

Filters

filter_canonical_nucleotides	Filter all atoms of one array that belong to canonical nucleotides.
filter_nucleotides	Filter all atoms of one array that belong to nucleotides.
filter_canonical_amino_acids	Filter all atoms of one array that belong to canonical amino acid residues.
filter_amino_acids	Filter all atoms of one array that belong to amino acid residues.
filter_carbohydrates	Filter all atoms of one array that belong to carbohydrates.
filter_peptide_backbone	Filter all peptide backbone atoms of one array.
filter_phosphate_backbone	Filter all phosphate backbone atoms of one array.
filter_linear_bond_continuity	Filter for atoms such that their bond length with the next atom lies within the provided boundaries.
filter_polymer	Filter for atoms that are a part of a consecutive standard macromolecular polymer entity.
filter_solvent	Filter all atoms of one array that are part of the solvent.
filter_monoatomic_ions	Filter all atoms of an atom array, that are monoatomic ions (e.g. sodium or chloride ions).
filter_intersection	Filter all atoms of one array that exist also in another array.
filter_first_altloc	Filter all atoms, that have the first altloc ID appearing in a residue.
filter_highest_occupancy_altloc	For each residue, filter all atoms, that have the altloc ID with the highest occupancy for this residue.

Checks

check_atom_id_continuity	Check if the atom IDs are incremented by more than 1 or decremented, from one atom to the next one.
check_res_id_continuity	Check if the residue IDs are incremented by more than 1 or decremented, from one atom to the next one.
check_backbone_continuity	Check if the (peptide or phosphate) backbone atoms have non-reasonable distance to the next atom.
check_duplicate_atoms	Check if a structure contains duplicate atoms, i.e. two atoms in a structure have the same annotations (coordinates may be different).
check_linear_continuity	Check linear (consecutive) bond continuity of atoms in atom array.

Repair

create_continuous_res_ids	Create an array of continuous residue IDs for a given structure.
infer_elements	Infer the elements of atoms based on their atom name.
create_atom_names	Create atom names for a single residue based on elements.

Residue level utility

get_residue_starts	Get indices for an atom array, each indicating the beginning of a residue.
get_residues	Get the residue IDs and names of an atom array (stack).
apply_residue_wise	Apply a function to intervals of data, where each interval corresponds to one residue.
spread_residue_wise	Expand residue-wise data to atom-wise data.
get_residue_masks	Get boolean masks indicating the residues to which the given atom indices belong.
get_residue_starts_for	For each given atom index, get the index that points to the start of the residue that atom belongs to.
get_residue_positions	For each given atom index, obtain the position of the residue corresponding to this index in the input array.
get_residue_count	Get the amount of residues in an atom array (stack).
residue_iter	Iterate over all residues in an atom array (stack).

Chain level utility

get_chain_starts	Get the indices in an atom array, which indicates the beginning of a new chain.
apply_chain_wise	Apply a function to intervals of data, where each interval corresponds to one chain.
spread_chain_wise	Expand chain-wise data to atom-wise data.
get_chain_masks	Get boolean masks indicating the chains to which the given atom indices belong.
get_chain_starts_for	For each given atom index, get the index that points to the start of the chain that atom belongs to.
get_chain_positions	For each given atom index, obtain the position of the chain corresponding to this index in the input array.
chain_iter	Iterate over all chains in an atom array (stack).
get_chains	Get the chain IDs of an atom array (stack).
get_chain_count	Get the amount of chains in an atom array (stack).
chain_iter	Iterate over all chains in an atom array (stack).

Molecule level utility

get_molecule_indices	Get an index array for each molecule in the given structure.
get_molecule_masks	Get a boolean mask for each molecule in the given structure.
molecule_iter	Iterate over each molecule in a input structure.

Structure comparison

average	Calculate an average structure.
rmsd	Calculate the RMSD between two structures.
rmspd	Calculate the RMSD of atom pair distances for given structures relative to those found in a reference structure.
rmsf	Calculate the RMSF between two structures.

General analysis

sasa	Calculate the Solvent Accessible Surface Area (SASA) of a protein.
hbond	Find hydrogen bonds in a structure using the Baker-Hubbard algorithm.
hbond_frequency	Get the relative frequency of each hydrogen bond in a multi-model structure.
partial_charges	Compute the partial charge of the individual atoms comprised in a given AtomArray depending on their electronegativity.
density	Compute the density of the selected atoms.

Proteins

dihedral_backbone	Measure the characteristic backbone dihedral angles of a chain.
annotate_sse	Calculate the secondary structure elements (SSEs) of a peptide chain based on the P-SEA algorithm.

Nucleic acids

Edge	This enum type represents the interacting edge for a given base.
GlycosidicBond	This enum type represents the relative glycosidic bond orientation for a given base pair.
map_nucleotide	Map a nucleotide to one of the 5 common bases Adenine, Guanine, Thymine, Cytosine, and Uracil.
base_pairs	Use DSSR criteria to find the base pairs in an AtomArray.
base_stacking	Find pi-stacking interactions between aromatic rings in nucleic acids.
pseudoknots	Identify the pseudoknot order for each base pair in a given set of base pairs.
base_pairs_edge	Get the interacting edges for given base pairs in an AtomArray according to the Leontis-Westhof nomenclature.
base_pairs_glycosidic_bond	Calculate the glycosidic bond orientation for given base pairs in an AtomArray according to the Leontis-Westhof nomenclature.
dot_bracket	Represent a nucleic acid strand in dot-bracket-letter-notation (DBL-notation).
dot_bracket_from_structure	Represent a nucleic-acid-strand in dot-bracket-letter-notation (DBL-notation).
base_pairs_from_dot_bracket	Extract the base pairs from a nucleic-acid-strand in dot-bracket-letter-notation (DBL-notation).

Miscellaneous

BadStructureError	Indicates that a structure is not suitable for a certain operation.
CellList	This class enables the efficient search of atoms in vicinity of a defined location.
IncompleteStructureWarning	Indicates that a structure is not complete.
UnexpectedStructureWarning	Indicates that a structure was not expected.
coord	Get the atom coordinates of the given array.
to_sequence	Convert each chain in a structure into a sequence.

Subpackages

biotite.structure.info	A subpackage for obtaining all kinds of chemical information about atoms and residues, including masses, radii, bonds, etc.
biotite.structure.io	A subpackage for reading and writing structure related data.
biotite.structure.io.mol	The MOL format is used to depict atom positions and bonds for small molecules.
biotite.structure.io.xtc	This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format.
biotite.structure.io.netcdf	This subpackage is used for reading and writing trajectories in the AMBER NetCDF format.
biotite.structure.io.dcd	This subpackage is used for reading and writing trajectories in the CDC format used by software like CHARMM, OpenMM and NAMD.
biotite.structure.io.gro	This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the Gro format used by the gromacs software package.
biotite.structure.io.pdb	This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the popular PDB format.
biotite.structure.io.trr	This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR format.
biotite.structure.io.pdbqt	This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the PDBQT format used by the AutoDock software series.
biotite.structure.io.pdbx	This subpackage provides support for the the modern PDBx file formats.
biotite.structure.alphabet	A subpackage for converting structures to structural alphabet sequences.
biotite.structure.graphics	A subpackage for visualizing structure related objects.