diffpy.structure.apps package

Script applications that use the diffpy.structure package.

Submodules

diffpy.structure.apps.transtru module

Translate structure file to different format.

Usage: transtru INFMT..OUTFMT strufile

Translates structure file strufile from INFMT to OUTFMT format and prints it to the screen. Use “-” as strufile to read from standard input. To save the translated file, use

transtru INFMT..OUTFMT strufile > strufile.out

Supported input and output structure formats are

  • INFMT: inputFormats

  • OUTFMT: outputFormats

Options:
-h, --help

Display this message.

-V, --version

Show script version.

diffpy.structure.apps.transtru.main()[source]
diffpy.structure.apps.transtru.usage(style=None)[source]

Show usage info, for style=="brief" show only first 2 lines.

diffpy.structure.apps.transtru.version()[source]

diffpy.structure.apps.anyeye module

Anyeye view structure file in atomeye.

Usage: anyeye [options] strufile

Anyeye understands more Structure formats than atomeye. It converts strufile to a temporary XCFG file which is opened in atomeye. See supported file formats: inputFormats

Options:
-f, --formula

Override chemical formula in strufile. The formula defines elements in the same order as in strufile, e.g., Na4Cl4.

-w, --watch

Watch input file for changes.

--viewer=VIEWER

The structure viewer program, by default “atomeye”. The program will be executed as “VIEWER structurefile”.

--formats=FORMATS

Comma-separated list of file formats that are understood by the VIEWER, by default "xcfg,pdb". Files of other formats will be converted to the first listed format.

-h, --help

Display this message and exit.

-V, --version

Show script version and exit.

diffpy.structure.apps.anyeye.cleanUp(pd)
diffpy.structure.apps.anyeye.clean_up(pd)[source]
diffpy.structure.apps.anyeye.convertStructureFile(pd)
diffpy.structure.apps.anyeye.convert_structure_file(pd)[source]
diffpy.structure.apps.anyeye.die(exit_status=0, pd={})[source]
diffpy.structure.apps.anyeye.loadStructureFile(filename, format='auto')

Load structure from specified file.

Parameters:

  • filename (str) – Path to the structure file.

  • format (str, Optional) – File format, by default “auto”.

Returns:

A tuple of (Structure, fileformat).

Return type:

tuple

diffpy.structure.apps.anyeye.load_structure_file(filename, format='auto')[source]

Load structure from specified file.

Parameters:

  • filename (str) – Path to the structure file.

  • format (str, Optional) – File format, by default “auto”.

Returns:

A tuple of (Structure, fileformat).

Return type:

tuple

diffpy.structure.apps.anyeye.main()[source]
diffpy.structure.apps.anyeye.parseFormula(formula)

Parse chemical formula and return a list of elements.

diffpy.structure.apps.anyeye.parse_formula(formula)[source]

Parse chemical formula and return a list of elements.

diffpy.structure.apps.anyeye.signalHandler(signum, stackframe)
diffpy.structure.apps.anyeye.signal_handler(signum, stackframe)[source]
diffpy.structure.apps.anyeye.usage(style=None)[source]

Show usage info, for style=="brief" show only first 2 lines.

diffpy.structure.apps.anyeye.version()[source]
diffpy.structure.apps.anyeye.watchStructureFile(pd)
diffpy.structure.apps.anyeye.watch_structure_file(pd)[source]

diffpy.structure.apps.vesta_viewer module

View structure file in VESTA.

Usage: vestaview [options] strufile

Vestaview understands more Structure formats than VESTA. It converts strufile to a temporary VESTA or CIF file which is opened in VESTA. See supported file formats: inputFormats

Options:
-f, --formula

Override chemical formula in strufile. The formula defines elements in the same order as in strufile, e.g., Na4Cl4.

-w, --watch

Watch input file for changes.

--viewer=VIEWER

The structure viewer program, by default “vesta”. The program will be executed as “VIEWER structurefile”.

--formats=FORMATS

Comma-separated list of file formats that are understood by the VIEWER, by default "vesta,cif". Files of other formats will be converted to the first listed format.

-h, --help

Display this message and exit.

-V, --version

Show script version and exit.

Notes

VESTA is the actively maintained successor to AtomEye. Unlike AtomEye, VESTA natively reads CIF, its own .vesta format, and several other crystallographic file types, so format conversion is only required for formats not in that set.

AtomEye XCFG format is no longer a default target format but the XCFG parser (P_xcfg) remains available in diffpy.structure.parsers for backward compatibility.

diffpy.structure.apps.vesta_viewer.clean_up(pd)[source]

Remove temporary file and directory created during conversion.

Parameters:

pd (dict) – The parameter dictionary that may contain "tmpfile" and "tmpdir" entries to be removed.

diffpy.structure.apps.vesta_viewer.convert_structure_file(pd)[source]

Convert strufile to a temporary file understood by the viewer.

On the first call, a temporary directory is created and stored in pd. Subsequent calls in watch mode reuse the directory.

The VESTA viewer natively reads .vesta and .cif files, so if the source is already in one of the formats listed in pd["formats"] and no formula override is requested, the file is copied unchanged. Otherwise the structure is loaded and re-written in the first format listed in pd["formats"].

Parameters:

pd (dict) – The parameter dictionary containing at minimum "strufile" and "formats" keys. It is modified in place to add "tmpdir" and "tmpfile" on the first call.

diffpy.structure.apps.vesta_viewer.die(exit_status=0, pd=None)[source]

Clean up temporary files and exit with exit_status.

Parameters:

  • exit_status (int, optional) – The exit code passed to sys.exit(), by default 0.

  • pd (dict, optional) – The parameter dictionary forwarded to clean_up().

diffpy.structure.apps.vesta_viewer.load_structure_file(filename, format='auto')[source]

Load structure from the specified file.

Parameters:

  • filename (str or Path) – The path to the structure file.

  • format (str, optional) – The file format, by default "auto".

Returns:

The loaded (Structure, fileformat) pair.

Return type:

tuple

diffpy.structure.apps.vesta_viewer.main()[source]

Entry point for the vestaview command-line tool.

diffpy.structure.apps.vesta_viewer.parse_formula(formula)[source]

Parse chemical formula and return a list of elements.

Parameters:

formula (str) – The chemical formula string such as "Na4Cl4" or "H2O".

Returns:

The ordered list of element symbols with repetition matching the formula.

Return type:

list of str

Raises:

RuntimeError – Raised when formula does not start with an uppercase letter or contains a non-integer count.

diffpy.structure.apps.vesta_viewer.signal_handler(signum, stackframe)[source]

Handle OS signals by reverting to the default handler and exiting.

On SIGCHLD the child exit status is harvested via os.wait(); on all other signals die() is called with exit status 1.

Parameters:

  • signum (int) – The signal number.

  • stackframe (frame) – The current stack frame. Unused.

diffpy.structure.apps.vesta_viewer.usage(style=None)[source]

Show usage info. for style=="brief" show only first 2 lines.

Parameters:

style (str, optional) – The usage display style.

diffpy.structure.apps.vesta_viewer.version()[source]

Print the script version.

diffpy.structure.apps.vesta_viewer.watch_structure_file(pd)[source]

Watch strufile for modifications and reconvert when changed.

Polls the modification timestamps of pd["strufile"] and pd["tmpfile"] once per second. When the source is newer, the file is reconverted via convert_structure_file().

Parameters:

pd (dict) – The parameter dictionary as used by convert_structure_file().