PyMoVE

Library and utilities for training volume estimation models with PyMoVE. Capable of calculating the solvent accessible surface area of a molecule using a marching cubes algorithm optimized for molecules.

This library is published to accompany the following peer-review article. Please cite this article for any work that makes use of the PyMoVE library.

Bier, I., & Marom, N. (2020). Machine Learned Model for Solid Form Volume Estimation Based on Packing-Accessible Surface and Molecular Topological Fragments. The Journal of Physical Chemistry A, 124(49), 10330-10345.

doi.org/10.1021/acs.jpca.0c06791

ResearchGate

Installation

It's highly recommended to start from an Anaconda distribution of Python, which can be found here.

Current full installation requires running two setup.py scripts. This will be modified in the near future. This is because the algorithm that enables the project marching cube algorithm relys on Numba compilation to run efficiently. The algorithm is still accessible and built in pure Python if a user cannot compile with Numba for any reason. But will require some changes. Please open an issue on github if these changes are required for you.

Running the following commands installs the complete PyMoVE library:

python setup.py install
python setup_numba.py install

After installation, basic usage of the solid-form volume prediction can be obtained through the command-line.

$ pymove examples/Example_Structures/molecules/benzene.xyz
Predicted Solid-Form Volume of benzene: 119.93509896777675

Basic Functionality

Fundament Objects

There are two fundamental types of objects in pymove.

Structure

The Structure object is the definition of a class in Python that stores the geometry of a molecule or crystal structure, its struct_id and its properties, such DFT energy, lattice parameters, space group, or structural descriptor.

StructDict

The StructDict is a Python dictionary of structure objects. The key for each Structure is its struct_id in the dictionary. pymove will work with any Python dict that has been defined in this way and does not require any other special class.

The fundamental file for pymove is the Structure.json file format. This is the same file format for Genarris/GAtor. json file formats are a standard way of storing information that look and behave a lot like a Python dictionary. You should never have to create a Structure.json file from scratch. Rather, use the pymove.io functionality to convert a FHI-aims geometry file, for example, to a Structure.json file.

Analysis functions in pymove will accept either a Structure or a StructDict. The function will tailor the task they perform based on whether they recieve a pymove.Structure object or a Python dict object. Because of this, the same commands that analyze a single Structure can be used for the analysis of a collection of structures.

Input/Output

The input and output capabilities, often just called io, is one of the core functionality of pymove that enables users to be more productive. pymove reads Structure.json files using built in functions and uses ASE.io to read other file types that are then to pymove.Structure objects in memory. pymove will automatically detect how to read a file based on the file's file extension. However, the user may also explicity define the file type.

io

To use this functionality add the following line to the top of a Python script:

from pymove.io import read,write 

read(struct_path, file_format="")

The read function has one required argument, the struct_path. This is the path to either a file or a directory. The functionality of read will change depending on if it detects the path is a file or a directory.

• File: The file will be read into memory and returned as a Structure object.
• Directory: All of the files in the directory will be attemped to be read into memory. Each file in the directory will be automatically detected for its file type. This means that even a folder containing a heterogenous mixture of file types will all be read into memory. The Structures will be returned as a StructDict. The struct_id will be assigned by struct_id contained in the Structure.json file. If the filetype is not a Structure.json, then a struct_id will be created for it using the filename without its file extension.

The file_format is an optional argument. If file_format is specified pymove will assume all of the files it attempts to load are this format. This functionality is important if the files are missing the correct file extension for one reason or another. If you manage your files correctly, this option should rarely be needed.

write(path, struct_obj, file_format="json", overwrite=False)

Let's go throught the arguments for the write function.

• path: Path to the location where you would like the struct_obj to be saved. If the struct_obj is a Structure, this should be the path to a single file. If the struct_obj is a StructDict, then the path will be the location of a folder.
• struct_obj: Either a Structure or a StructDict. The write function will automatically detect the object type.
• file_format: By default, the file format is for a Structure.json file. This can be changed to geo or aims for a FHI-aims file format or to any of the accepted ASE file formats.
• overwrite: Be default, if a file already exists with the same name, write will throw an Exception. This is so the user cannot overwrite files by accident. Only if overwrite=True will write replace existing files.

Maybe you can now see the power of the read and write capabilities. It is trivial for the user to read in thousands of CIF or FHI-aims geometry files and convert them all to Structure.json file formats. This can even be done from a Python terminal because it's so easy. For example, if we have geometry files in a directory named geometry_folder that we want to convert to Structure.json files, we can type:

>>> from pymove.io import read,write
>>> struct_dict = read("geometry_folder")
>>> write("json_folder", struct_dict, file_format="json")

Examples

The examples directory steps though all features of the PyMoVE library. These are:

1. Finding molecules from the molecular crystal structure
2. Calculating the packing factor of molecular crystals
3. Calculating the topological fragment descriptor

4. Calculating the packing accessible surface

5. Model training & testing and evaluating volumes using the pre-trained model