schemarecomb.pdb_structure.Atom

class schemarecomb.pdb_structure.Atom(serial_num, name, alt_loc, res_name, chain, res_index, insertion_code, x, y, z, occup, temp, segment, element, charge)

Atom within a PDB structure.

This class is basically a one-to-one conversion of ‘ATOM’ lines in PDB files. The primary constructor is Atom.from_line() to allow for easy parsing of PDB files. For schemarecomb, the important attributes are res_name, res_index, x, y, and z.

Initalization parameters and attributes are equivalent for this class.

Parameters

• serial_num (int) – Atom serial number.

• name (str) – Atom name.

• alt_loc (str) – Alternate location indicator.

• res_name (str) – Residue name.

• chain (str) – Chain identifier.

• res_index (int) – Residue index within the structure..

• insertion_code (str) – Code for insertions of residues.

• x (float) – X orthogonal Angstrom coordinate.

• y (float) – Y orthogonal Angstrom coordinate.

• z (float) – Z orthogonal Angstrom coordinate.

• occup (float) – Occupancy.

• temp (float) – Temperature factor.

• segment (str) – Segment identifier.

• element (str) – Element symbol.

• charge (str) – Charge.