Molecule#

class pyjess.Atom#

A single atom in a molecule.

Added in version 0.4.0: Equality, hashing and pickle protocol support.

classmethod load(file)#

Load an atom from the given file.

Parameters:: file (file-like object) – A file-like object opened in text mode to read the atom from.

classmethod loads(text)#

Load an atom from the given string.

Parameters:: text (str, bytes or bytearray) – The atom line to read the atom metadata from.

__init__(*, serial, name, residue_name, chain_id, residue_number, x, y, z, occupancy=0.0, temperature_factor=0.0, altloc=' ', insertion_code=' ', segment='', element='', charge=0)#

Create a new atom.

Raises:

MemoryError – When the system allocator fails to allocate enough memory for the atom storage.
ValueError – When either of the name, residue_name, segment, element or chain_id strings is too long.

copy()#

Create a copy of this atom.

Returns:: Atom – A newly allocated atom with identical attributes.

Added in version 0.4.0.

dump(file, format='pdb')#

Write the atom to a file.

Parameters:

file (file-like object) – A file opened in text mode where the atom will be written.
format (str) – The format in which to write the hit. Currently only supports pdb, which writes the hits in the same format as Jess.

Added in version 0.9.0.

dumps(format='pdb')#

Write the atom to a string.

Parameters:: format (str) – The format in which to write the atom. Currently only supports pdb, which writes the hits in the same format as Jess.

Added in version 0.9.0.

transform(matrix)#

Apply a geometric transformation to the atom coordinates.

Parameters:: matrix (Mat4) – A 4x4 matrix in homogeneous coordinates describing the transformation to apply.

Added in version 0.10.0.

altloc#

The alternate location indicator for the atom.

Type:: str

chain_id#

The identifier of the chain the atom belongs to.

Type:: str

charge#

The atom charge.

Type:: int

element#

The element symbol.

Type:: str

insertion_code#

The code for insertion of residues.

Type:: str

name#

The atom name.

Type:: str

occupancy#

The atom occupancy.

Type:: float

residue_name#

The residue name.

Type:: str

residue_number#

The residue sequence number.

Type:: int

segment#

The segment identifier.

Type:: str

serial#

The atom serial number.

Type:: int

temperature_factor#

The atom temperature factor.

Type:: float

x#

The atom coordinate in the 1st dimension.

Type:: float

y#

The atom coordinate in the 2nd dimension.

Type:: float

z#

The atom coordinate in the 3rd dimension.

Type:: float

class pyjess.Molecule#

A molecule structure, as a sequence of Atom objects.

Added in version 0.2.2: Support identifiers of arbitrary length.

Added in version 0.4.0: Equality, hashing and pickle protocol support.

classmethod from_biopython(structure, id=None, date=None, name=None)#

Create a new Molecule from a Bio.PDB.Structure.

Parameters:

structure (Bio.PDB.Structure or Bio.PDB.Model) – The Biopython object containing the structure data.
id (str or None) – The identifier to give to the newly created molecule. If None given, will use the value of structure.id.
date (datetime.date or None) – The deposition date to give to the newly created molecule.
name (str or None) – The name to give to the newly created molecule.

Returns:

Molecule – A molecule object suitable for using in Jess.query.

Added in version 0.7.0.

classmethod from_biotite(atom_array, id=None, date=None, name=None)#

Create a new Molecule from a biotite.structure.AtomArray.

Parameters:

atom_array (biotite.structure.AtomArray) – The biotite object containing the structure data.
id (str or None) – The id to give to the newly created molecule.
date (datetime.date or None) – The deposition date to give to the newly created molecule.
name (str or None) – The name to give to the newly created molecule.

Returns:

Molecule – A molecule object suitable for using in Jess.query.

Caution

If loading data with the biotite.structure.io.pdb.PDBFile module, ensure that you are requesting all atoms and all extra fields in get_structure:

db_file = PDBFile.read("data/1AMY.pdb")
structure = pdb_file.get_structure(
    altloc="all",
    extra_fields=["atom_id", "b_factor", "occupancy", "charge"],
)
molecule = Molecule.from_biotite(structure[0])

Added in version 0.7.0.

classmethod from_gemmi(model, id=None, date=None, name=None)#

Create a new Molecule from a gemmi.Model.

Parameters:

structure (gemmi.Model) – The gemmi object containing the structure data.
id (str or None) – The identifier to give to the newly created molecule.
date (datetime.date or None) – The deposition date to give to the newly created molecule.
name (str or None) – The name to give to the newly created molecule.

Returns:

Molecule – A molecule object suitable for using in Jess.query.

Added in version 0.7.0.

classmethod load(file, format='detect', *, id=None, date=None, name=None, ignore_endmdl=False, use_author=False, skip_hetatm=False)#

Load a molecule from a PDB file.

Parameters:

file (str, os.PathLike, or file-like object) – Either the path to a file, or a file-like object opened in text mode containing a molecule.
format (str) – The format to parse the file. Supported formats are: pdb for the Protein Data Bank format, cif for Crystallographic Information File format (additionally requires the gemmi module), or detect to attempt auto-detection (the default).

Keyword Arguments:

id (str, optional) – The identifier of the molecule. If None given, the parser will attempt to extract it from the HEADER line (for PDB files) or the block name (for CIF files).
date (datetime.date, optional) – The deposition date of the structure. If None given, the parser will attempt to extract it from the HEADER line (for PDB files) or the earliest revision data (for CIF files).
name (str, optional) – The name of the structure. If None given, the parser will attempt to extract it from the HEADER line (for PDB files) or the _struct_keywords.pdbx_keywords (for CIF files).
ignore_endmdl (bool) – Pass True to make the parser read all the atoms from the PDB file. By default, the parser only reads the atoms of the first model, and stops at the first ENDMDL line - or for CIF files stops if the PDB model > 1.
use_author (bool) – Pass True to use the author-defined labels while parsing CIF files, e.g. read the chain name from _atom_site.auth_asym_id rather than _atom_site.label_asym_id. Ignored for PDB files.
skip_hetatm (bool) – Pass True to skip parsing of heteroatoms (HETATM) in the input file.

Returns:

Molecule – The molecule parsed from the PDB file.