4.1.1. propka.atom¶
4.1.1.1. Atom¶
The Atom
class contains all atom information found in the PDB file.
Classes
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Atom class - contains all atom information found in the PDB file |
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class
propka.atom.
Atom
(line=None)[source]¶ Atom class - contains all atom information found in the PDB file
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count_bonded_elements
(element)[source]¶ Count number of bonded atoms with same element.
- Parameters
element – element type for test.
- Returns
number of bonded atoms.
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get_bonded_elements
(element)[source]¶ Get bonded atoms with same element.
- Parameters
element – element type for test.
- Returns
array of bonded atoms.
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get_bonded_heavy_atoms
()[source]¶ Get the atoms bonded to this one that aren’t hydrogen.
- Returns
list of atoms.
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get_input_parameters
()[source]¶ Extract the input parameters stored in the occupancy and b-factor fields in input files
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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
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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
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make_conect_line
()[source]¶ PDB line for bonding within this molecule.
- Returns
String with PDB line.
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make_input_line
()[source]¶ PDB line for this atom.
TODO - Could be @property method/attribute TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
- Returns
String with PDB-format line.
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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.
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make_pdb_line
()[source]¶ Create PDB line.
TODO - this could/should be a @property method/attribute TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
- Returns
String with PDB line.
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make_pdb_line2
(numb=None, name=None, res_name=None, chain_id=None, res_num=None, x=None, y=None, z=None, occ=None, beta=None)[source]¶ Create a PDB line.
TODO - this could/should be a @property method/attribute TODO - figure out difference between make_pdb_line, make_input_line,
and make_pdb_line2
- Returns
String with PDB line.
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set_properties
(line)[source]¶ Line from PDB file to set properties of atom.
- Parameters
line – PDB file line
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set_property
(numb=None, name=None, res_name=None, chain_id=None, res_num=None, x=None, y=None, z=None, occ=None, beta=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
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