propka.atom

Atom

The Atom class contains all atom information found in the PDB file.

Classes

Atom([line])

Atom class - contains all atom information found in the PDB file
class propka.atom.Atom(line: str | None = None)[source]

Atom class - contains all atom information found in the PDB file

Changed in version 3.4.0: make_input_line() and get_input_parameters() have been removed as reading/writing PROPKA input is no longer supported.

count_bonded_elements(element)[source]

Count number of bonded atoms with same element.

Parameters:

element – element type for test.

Returns:

number of bonded atoms.

get_bonded_elements(element)[source]

Get bonded atoms with same element.

Parameters:

element – element type for test.

Returns:

array of bonded atoms.

get_bonded_heavy_atoms()[source]

Get the atoms bonded to this one that aren’t hydrogen.

Returns:

list of atoms.

get_tidy_label()[source]

Returns a ‘tidier’ atom label for printing the new pdbfile

TODO - this could/should be a @property method/attribute

Returns:

String with label

is_atom_within_bond_distance(other_atom, max_bonds, cur_bond)[source]

Check if <other_atom> is found within <max_bonds> bonds of self.

Parameters:

  • other_atom – atom to check

  • max_bonds – number of bonds to check for other atom bonding to self

Returns:

Boolean for atom bond distance

make_conect_line()[source]

PDB line for bonding within this molecule.

Returns:

String with PDB line.

make_copy()[source]

Make a copy of this atom.

Returns:

Another atom object copy of this one.

make_mol2_line(id_)[source]

Create MOL2 line.

Format: 1 S1 3.6147 2.0531 1.4795 S.3 1 noname -0.1785

TODO - this could/should be a @property method/attribute

Returns:

String with MOL2 line.

make_pdb_line()[source]

Create PDB line.

TODO - this could/should be a @property method/attribute TODO - figure out difference between make_pdb_line, and make_pdb_line2

Returns:

String with PDB line.

set_group_type(type_: str)[source]

Set group type of atom.

Parameters:

type – group type of atom

set_properties(line: str | None)[source]

Line from PDB file to set properties of atom.

Parameters:

line – PDB file line

set_property(numb: int | None = None, name: str | None = None, res_name: str | None = None, chain_id: str | None = None, res_num: int | None = None, x: float | None = None, y: float | None = None, z: float | None = None, occ: str | None = None, beta: str | None = None)[source]

Set properties of the atom object.

Parameters:

  • numb – Atom number

  • name – Atom name

  • res_name – residue name

  • chain_id – chain ID

  • res_num – residue number

  • x – atom x-coordinate

  • y – atom y-coordinate

  • z – atom z-coordinate

  • occ – atom occupancy

  • beta – atom temperature factor