Structure data I/O (sknano.io)

Introduction

The sknano.io package provides the main data structures for dealing with input/output streams of various types of structure data file formats.

Contents

LAMMPS data I/O (sknano.io.lammps_data)

sknano.io.lammps_data Module

LAMMPS data format (sknano.io.lammps_data)

Classes

DATA	alias of DATAData
DATAData([fpath])	Class for reading and writing StructureData in LAMMPS data format.
DATAReader(fpath[, atom_style, bond_style, ...])	StructureData class for reading LAMMPS data file format.
DATAWriter	StructureWriter class for writing LAMMPS data file format.
DATAFormatter([atom_style, bond_style, ...])	StructureDataFormatter class the LAMMPS data format spec.
DATAError	Exception class for DATAData IO Errors.
DATAIO	alias of DATAData
DATAIOReader	alias of DATAReader
DATAIOWriter	alias of DATAWriter
DATAIOError	alias of DATAError
DATAIOFormatter	alias of DATAFormatter
DATAFormatSpec	alias of DATAFormatter
DATAConverter([infile, outfile])	StructureDataConverter class for converting LAMMPS data.
DATA2XYZConverter(datafile, **kwargs)	DATAConverter class for converting to xyz format.
LAMMPSDATA	alias of DATAData
LAMMPSDATAReader	alias of DATAReader
LAMMPSDATAWriter	alias of DATAWriter
LAMMPSDATAFormatter	alias of DATAFormatter
LAMMPSDATAFormatSpec	alias of DATAFormatter
LAMMPSDATAIOError	alias of DATAError
LAMMPSDATA2XYZConverter	alias of DATA2XYZConverter

Class Inheritance Diagram

LAMMPS dump I/O (sknano.io.lammps_dump)

sknano.io.lammps_dump Module

LAMMPS dump format (sknano.io.lammps_dump)

Classes

DUMP	alias of DUMPData
DUMPData(*args, **kwargs)	Class for reading and writing structure data in LAMMPS dump format.
DUMPReader(*args[, autoread, ...])	Class for reading LAMMPS dump file format.
DUMPWriter	Class for writing LAMMPS dump chemical file format.
DUMPError	Exception class for DUMPData I/O errors.
DUMPFormatter([style, dumpattrs, ...])	Class defining the structure file format for LAMMPS dump.
DUMPIO	alias of DUMPData
DUMPIOReader	alias of DUMPReader
DUMPIOWriter	alias of DUMPWriter
DUMPIOError	alias of DUMPError
DUMPIOFormatter	alias of DUMPFormatter

Class Inheritance Diagram

pdb I/O (sknano.io.pdb)

sknano.io.pdb Module

PDB format (sknano.io.pdb)

Classes

PDB	alias of PDBData
PDBData([fpath])	Class for reading and writing structure data in PDB data format.
PDBReader(fpath[, formatter])	Class for reading pdb chemical file format.
PDBWriter	Class for writing pdb chemical file format.
PDBFormatter([records])	Class defining the structure file format for PDB data.
PDBError	Exception class for PDBData I/O errors.
PDBIO	alias of PDBData
PDBIOReader	alias of PDBReader
PDBIOWriter	alias of PDBWriter
PDBIOFormatter	alias of PDBFormatter
PDBIOError	alias of PDBError
PDBFormatSpec	alias of PDBFormatter

Class Inheritance Diagram

xyz I/O (sknano.io.xyz)

sknano.io.xyz Module

XYZ format (sknano.io.xyz)

Classes

XYZ	alias of XYZData
XYZData([fpath])	Class for reading and writing StructureData in xyz format.
XYZReader(fpath[, formatter])	StructureData class for reading xyz chemical file format.
XYZWriter	StructureWriter class for writing xyz chemical file format.
XYZFormatter([format_string])	StructureDataFormatter class defining properties for xyz format.
XYZConverter(**kwargs)	StructureDataConverter class for converting xyz data.
XYZError	Exception class for XYZData IO errors.
XYZIO	alias of XYZData
XYZIOReader	alias of XYZReader
XYZIOWriter	alias of XYZWriter
XYZIOFormatter	alias of XYZFormatter
XYZIOConverter	alias of XYZConverter
XYZIOError	alias of XYZError
XYZFormatSpec	alias of XYZFormatter
XYZ2DATAConverter(xyzfile, **kwargs)	XYZConverter for converting to LAMMPS data format.

Class Inheritance Diagram

Reference/API

sknano.io Package

Classes

DATA	alias of DATAData
DATA2XYZConverter(datafile, **kwargs)	DATAConverter class for converting to xyz format.
DATAConverter([infile, outfile])	StructureDataConverter class for converting LAMMPS data.
DATAData([fpath])	Class for reading and writing StructureData in LAMMPS data format.
DATAError	Exception class for DATAData IO Errors.
DATAFormatSpec	alias of DATAFormatter
DATAFormatter([atom_style, bond_style, ...])	StructureDataFormatter class the LAMMPS data format spec.
DATAIO	alias of DATAData
DATAIOError	alias of DATAError
DATAIOFormatter	alias of DATAFormatter
DATAIOReader	alias of DATAReader
DATAIOWriter	alias of DATAWriter
DATAReader(fpath[, atom_style, bond_style, ...])	StructureData class for reading LAMMPS data file format.
DATAWriter	StructureWriter class for writing LAMMPS data file format.
DUMP	alias of DUMPData
DUMPData(*args, **kwargs)	Class for reading and writing structure data in LAMMPS dump format.
DUMPError	Exception class for DUMPData I/O errors.
DUMPFormatter([style, dumpattrs, ...])	Class defining the structure file format for LAMMPS dump.
DUMPIO	alias of DUMPData
DUMPIOError	alias of DUMPError
DUMPIOFormatter	alias of DUMPFormatter
DUMPIOReader	alias of DUMPReader
DUMPIOWriter	alias of DUMPWriter
DUMPReader(*args[, autoread, ...])	Class for reading LAMMPS dump file format.
DUMPWriter	Class for writing LAMMPS dump chemical file format.
LAMMPSDATA	alias of DATAData
LAMMPSDATA2XYZConverter	alias of DATA2XYZConverter
LAMMPSDATAFormatSpec	alias of DATAFormatter
LAMMPSDATAFormatter	alias of DATAFormatter
LAMMPSDATAIOError	alias of DATAError
LAMMPSDATAReader	alias of DATAReader
LAMMPSDATAWriter	alias of DATAWriter
PDB	alias of PDBData
PDBData([fpath])	Class for reading and writing structure data in PDB data format.
PDBError	Exception class for PDBData I/O errors.
PDBFormatSpec	alias of PDBFormatter
PDBFormatter([records])	Class defining the structure file format for PDB data.
PDBIO	alias of PDBData
PDBIOError	alias of PDBError
PDBIOFormatter	alias of PDBFormatter
PDBIOReader	alias of PDBReader
PDBIOWriter	alias of PDBWriter
PDBReader(fpath[, formatter])	Class for reading pdb chemical file format.
PDBWriter	Class for writing pdb chemical file format.
StructureData([fpath, fname, formatter])	Base class for structure data file input and output.
StructureDataConverter([infile, outfile])	Abstract base class for converting structure data.
StructureDataError	Base class for StructureData errors.
StructureDataFormatter(*args[, verbose, debug])	Base class for defining a format specification.
StructureDataMixin	Mixin class providing I/O methods for structure data.
StructureDataReader	Structure data reader base class.
StructureDataReaderMixin	Mixin class for reading structure data.
StructureDataWriter	Structure data writer base class.
StructureDataWriterMixin	Mixin class for saving structure data.
StructureFormatSpec	alias of StructureDataFormatter
StructureIO	alias of StructureData
StructureIOConverter	alias of StructureDataConverter
StructureIOError	alias of StructureDataError
StructureIOFormatter	alias of StructureDataFormatter
StructureIOMixin	alias of StructureDataMixin
StructureIOReader	alias of StructureDataReader
StructureIOReaderMixin	alias of StructureDataReaderMixin
StructureIOWriter	alias of StructureDataWriter
StructureIOWriterMixin	alias of StructureDataWriterMixin
StructureReader	alias of StructureDataReader
StructureReaderMixin	alias of StructureDataReaderMixin
StructureWriter	alias of StructureDataWriter
StructureWriterMixin	alias of StructureDataWriterMixin
XYZ	alias of XYZData
XYZ2DATAConverter(xyzfile, **kwargs)	XYZConverter for converting to LAMMPS data format.
XYZConverter(**kwargs)	StructureDataConverter class for converting xyz data.
XYZData([fpath])	Class for reading and writing StructureData in xyz format.
XYZError	Exception class for XYZData IO errors.
XYZFormatSpec	alias of XYZFormatter
XYZFormatter([format_string])	StructureDataFormatter class defining properties for xyz format.
XYZIO	alias of XYZData
XYZIOConverter	alias of XYZConverter
XYZIOError	alias of XYZError
XYZIOFormatter	alias of XYZFormatter
XYZIOReader	alias of XYZReader
XYZIOWriter	alias of XYZWriter
XYZReader(fpath[, formatter])	StructureData class for reading xyz chemical file format.
XYZWriter	StructureWriter class for writing xyz chemical file format.

Class Inheritance Diagram

sknano.io.tokenizers Package

Classes

PDBTokenizer()

PDB Record tokenizer.

Class Inheritance Diagram