pygen_structures.mol_containers.atom module

Module containing the Atom class, used to store PDB/PSF data and represent it directly as a PSF/PDB atom line.

This is in a separate, dependency free class to encourage re-use.

class pygen_structures.mol_containers.atom.Atom(record: str = 'ATOM', atom_serial: int = 0, atom_name: str = 'OH2', alt_locator: str = ' ', residue_name: str = 'TIP3', chain: str = ' ', residue_number: int = 0, insertion_code: str = ' ', x: float = 0.0, y: float = 0.0, z: float = 0.0, occupancy: float = 1.0, beta_factor: float = 0.0, segment_id: str = '0', element_symbol: (<class 'str'>, None) = None, formal_charge: int = 0, atom_type: str = '', partial_charge: float = 0.0, mass: float = 0.0)

Bases: object

A class to hold the information present in a PDB/PSF atom. Atom objects are directly representable as an atom line from a PDB or PSF file.

Parameters

  • record – “ATOM” or “HETATM” (PDB field)

  • atom_serial – the atom number (PDB and PSF field)

  • atom_name – the name of the atom in the residue (PDB & PSF field)

  • alt_locator – alternate location indicator (PDB field)

  • residue_name – name of the residue the atom is in (PDB & PSF field)

  • chain – identifier for chain (PDB field)

  • residue_number – residue sequence number (PDB & PSF field)

  • insertion_code – code for insertion of residues. This allows for branches, to a limited degree. e.g. 52 -> 52A -> 53. Not widely used (PDB field)

  • x – x position of atom /Angstroms (PDB field)

  • y – y position of atom /Angstroms (PDB field)

  • z – z position of atom /Angstroms (PDB field)

  • occupancy – occupancy of position from crystal structure. Generally used to indicate presence of multiple conformations (PDB field)

  • beta_factor – temperature factor. Indicates how much the position of the atom fluctuates with temperature (PDB field)

  • segment_id – segment identifier. Used by MD simulation programs to keep track of multiple molecules/groups of molecules. (PDB & PSF field)

  • element_symbol – chemical element in capitals (PDB field)

  • formal_charge – the formal charge on the atom (PDB field)

  • atom_type – the type of the atom. To be used by the forcefield when calculating bond/NB terms (PSF field)

  • partial_charge – the charge of the atom. To be used by the forcefield when calculating electrostatics (PSF field)

  • mass – mass of the atom. To be used by the forcefield to calculated acceleration from given force (PSF field)

classmethod from_pdb_line(line: str)

Instantiate the class from a line in a PDB file. This will not have the atom_type, partial_charge or mass.

Parameters

line – an ATOM/HETATM record from a pdb file.

to_pdb_line() → str

Create a PDB formatted atom record from the Atom. The fields are described in the class docstring.

Where atom serials exceed the 5 character limit, these are converted to hexadecimal.

Where residue numbers exceed the 4 character limit, these are wrapped around to 0.

to_psf_line() → str

Create a PDB formatted atom record from the Atom. The fields are described in the class docstring.