openprattle 1.1.0

A convenience wrapper for seamlessly accessing the pybel library and obabel command-line tools

OpenPrattle

A command-line tool and python library that provides a seamless interface to both the Pybel library and obabel command-line tool.

Dependencies

Required

Openbabel >= 3.0.0

Python >= 3.9

Optional

JSON (for printing in JSON format with the --readable and --writable options)

pytest (for running the unit tests)

Usage

OpenPrattle provides both a python library and command-line tool.

Library

Files are interconverted using converter objects, each of which represents a supported backend. To automatically get a suitable converter object, use openprattle.Openbabel_converter.from_file():

from openprattle import Openbabel_converter

my_file = "Benzene.xyz"
converter = Openbabel_converter.from_file(input_file_path = my_file)

By default, the format of the input file is determined automatically from its extension. The format can be explicitly specified with input_file_type:

converter = Openbabel_converter.from_file(input_file_path = my_file, input_file_type = "xyz")

Openbabel_converter.from_file() will favour the Pybel backend if it is available, except when converting files in formats that are not supported by Pybel. To explicitly choose a backend, use the backend option:

converter = Openbabel_converter.from_file(
    input_file_path = my_file,
    input_file_type = "xyz",
    backend = "Pybel" # Either 'Pybel', 'Obabel', or 'Auto'
)

Or use the appropriate class directly.

from openprattle import Obabel_converter, Pybel_converter

my_file = "Benzene.xyz"
obabel = Obabel_converter(
    input_file_path = my_file
)
pybel = Pybel_converter(
    input_file_path = my_file
)

In addition to reading from a file path, all the converters can read from an open file descriptor using input_file:

with open("Benzene.xyz") as my_file:
    converter = Openbabel_converter.from_file(
        input_file = my_file,
        input_file_type = "xyz",
    )

Or from a memory buffer using input_file_buffer:

with open("Benzene.xyz") as my_file:
    buffer = my_file.read()

converter = Openbabel_converter.from_file(
    input_file_buffer = buffer,
    input_file_type = "xyz",
)

Whenever the input_file or input_file_buffer options are used, the file type must be specified with input_file_type.

Once an appropriate converter object has been obtained, the file can be converted by calling convert():

converter = Openbabel_converter.from_file(input_file_path = "Benzene.xyz")
converter.convert("cml", "Benzene.cml")

convert() can either write to a file (using output_file), or return the converted file as a buffer (if output_file is omitted):

converter = Openbabel_converter.from_file(input_file_path = "Benzene.xyz")
output_file = converter.convert("cml")
print(output_file)

A limited subset of formats support molecular charge and multiplicity information. These can be set using the charge and multiplicity options:

converter = Openbabel_converter.from_file(input_file_path = "Benzene.xyz")
converter.convert("cml", "Benzene.cml", charge = 1, multiplicity = 2)

The following is a non-exhaustive list of formats that do support charge and multiplicity:

• com (Gaussian input)
• dalmol (DALTON input)
• gau (Gaussian input)
• gjc (Gaussian input)
• gjf (Gaussian input)
• gzmat (Gaussian Z-Matrix Input)

Of these, only dalmol is both a readable and writable format.

[!IMPORTANT] Currently, OpenPrattle is not aware of which formats will preserve the specified charge and multiplicity. If an unsupported format is chosen, any charge and multiplicity information will be silently discarded.

Charge and multiplicity are only supported with the Pybel_converter backend. This means that to convert from a format that is not supported by Pybel (most noticeably ChemDraw's .cdx), two conversions should be performed in sequence:

from openprattle import Openbabel_converter, Pybel_converter

intermediate = Openbabel_converter.from_file(input_file_path = "Benzene.cdx").convert("xyz")
final = Pybel_converter(input_file_buffer = "intermediate", input_file_type = "xyz").convert(
    "com",
    charge = 1,
    multiplicity = 2
)

1D (eg, SMILES) and 2D (eg, ChemDraw) can be converted to 3D structures using Openbabel's gen3D option. Gen3D performs a rapid geometry optimisation using a molecular force field. While this is normally useful for generating a good starting geometry for further optimisations, it is rarely desirable for coordinates that are already in three-dimensions.

The default behaviour in OpenPrattle (gen3D = 'auto') is to convert geometries to three-dimensions so long as the coordinates are not already in 3D. The function to determine the input geometry dimensions is exposed by Pybel, but not by the obabel command-line tool. This means that automatic conversion with gen3D will only occur when using the Pybel backend, unless the input format is exclusively non-3D (such as ChemDraw's cdx).

The 3D conversion can be explicitly requested or disabled by using gen3D = True or gen3D = False respectively.

output = Openbabel_converter.from_file(input_file_path = "Benzene.cdx").convert(
    "xyz",
    gen3D = True
)

Command-line

The oprattle command-line tool has the following main syntax:

$ oprattle input_file [-i INPUT_FORMAT] [-o OUTPUT_FORMAT] -O OUTPUT_FILE

For example:

$ oprattle Benzene.xyz -O Benzene.cml

Explicit input and output formats can be specified using [-i INPUT_FORMAT] and [-o OUTPUT_FORMAT] respectively.

$ oprattle Benzene.file1 -i xyz -o cml -O Benzene.file2

Either (or both) of the input file and output file can be omitted to read from stdin or to write to stdout:

$ cat Benzene.xyz | oprattle i xyz -o cml

The backend can be chosen with the --backend option:

$ oprattle Benzene.cdx -O Benzene.cml --backend Obabel

Charge, multiplicity, and 3D conversion can be set using --charge, --multiplicity, and --gen3D respectively.

$ oprattle Benzene.cdx -O Benzene.cml --charge 1 --multiplicity 2 --gen3D True

The same caveats for charge, multiplicity, and gen3D apply as for the OpenPrattle library (see above).

To see a list of supported input and output formats, use the --readable and --writable options:

$ oprattle --readable
abinit     : ABINIT Output Format
acesout    : ACES output format
acr        : ACR format
...

$ oprattle --writable
acesin     : ACES input format
adf        : ADF cartesian input format
alc        : Alchemy format
...

Either --readable or --writable can be combined with --json (if the JSON library is available) to print the list of formats in JSON format:

$ oprattle --readable --json
"abinit": "ABINIT Output Format", "acesout": "ACES output format", "acr": "ACR format"...

Why?

On the surface, the pybel library and obabel tool appear to offer the same functionality. However, there are important instances where each offers functionality over the other. For example, pybel allows for the molecular charge and multiplicity to be set in some output formats, obabel does not. Conversely, obabel can read from ChemDraw (.cdx) files, while pybel cannot.

In addition, the programmer may not know ahead of time whether pybel and/or obabel will be available on the target system. OpenPrattle allows for this scenario.

Name?

A light-hearted pun; 'prattle' and 'babel' are approximate synonyms.

Licensing

OpenBabel is licensed under GPL 2.0. Because OpenPrattle depends on the pybel library, it too must be licensed under the GPL.