PDBData

class sknano.io.pdb.PDBData(fpath=None)

Bases: sknano.io.pdb.PDBReader

Class for reading and writing structure data in PDB data format.

Parameters:fpath (str, optional) –

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([pdbfile, atoms, mode, comment_line])	Write pdb 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

write([pdbfile, atoms, mode, comment_line])

Write pdb file.

Methods Documentation

write(pdbfile=None, atoms=None, mode='w', comment_line=None, **kwargs)

Write pdb file.

Parameters:

• pdbfile ({None, str}, optional) –
• atoms (Atoms, optional) –
• mode ({'w', 'a'}, optional) –