meld.system.pdb_writer.PDBWriter

class meld.system.pdb_writer.PDBWriter(atom_numbers, atom_names, residue_numbers, residue_names)

Bases: object

Convert states into PDB format

__init__(atom_numbers, atom_names, residue_numbers, residue_names)

Initialize a PDBWriter

Parameters

• atom_numbers (List[int]) – number for each atom

• atom_names (List[str]) – name for each atom

• residue_numbers (List[int]) – residue number for each atom

• residue_names (List[str]) – residue name for each atom

Methods

__init__(atom_numbers, atom_names, ...)	Initialize a PDBWriter
get_pdb_string(coordinates, stage)	Get pdb representation for coordinates

get_pdb_string(coordinates, stage)

Get pdb representation for coordinates

Parameters

• coordinates (ndarray) – n_atoms x 3 array

• stage (int) – stage number to record in pdb

Return type

str

Returns

string representation in pdb format