PDBReader

class sknano.io.PDBReader(fpath, formatter=None, **kwargs)

Bases: sknano.io.StructureIO

Class for reading pdb chemical file format.

Parameters:fpath (str) – pdb structure file

Attributes

atoms	Structure Atoms.
basis	Structure BasisAtoms.
comment_line	Comment line.
crystal_cell	Structure CrystalCell.
fmtstr	Format string.
lattice	Structure Crystal3DLattice.
lattice_shift	Lattice displacement vector.
scaling_matrix	CrystalCell.scaling_matrix.
structure	An alias to self.
unit_cell	Structure UnitCell.

Methods

clear()	Clear list of StructureMixin.atoms.
make_supercell(scaling_matrix[, wrap_coords])	Make supercell.
read()	Read PDB file.
read_data(*args, **kwargs)	Read LAMMPS Data file.
read_dump(*args, **kwargs)	Read LAMMPS Dump file.
read_pdb(*args, **kwargs)	Read PDB file.
read_xyz(*args, **kwargs)	Read XYZ file.
rotate(**kwargs)	Rotate crystal cell lattice, basis, and unit cell.
todict()	Return dict of constructor parameters.
transform_lattice(scaling_matrix[, ...])	Transform structure lattice.
translate(t[, fix_anchor_points])	Translate crystal cell lattice, basis, and unit cell.
write(*args, **kwargs)	Write structure data to file.
write_data(**kwargs)	Write LAMMPS data file.
write_dump(**kwargs)	Write LAMMPS dump file.
write_pdb(**kwargs)	Write pdb file.
write_xyz(**kwargs)	Write xyz file.

Methods Summary

read()

Read PDB file.

Methods Documentation

read()

Read PDB file.