PDBData¶
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class
sknano.io.pdb.
PDBData
(fpath=None)[source] [edit on github][source]¶ 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
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write
(pdbfile=None, atoms=None, mode='w', comment_line=None, **kwargs)[source] [edit on github][source]¶ Write pdb file.
Parameters: - pdbfile ({None, str}, optional) –
- atoms (
Atoms
, optional) – - mode ({'w', 'a'}, optional) –
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