MolOrient

In computational chemistry molecules are sets of atoms where each atom is often represented by a point in a three-dimensional Cartesian space. The coordinates for each atom ultimately depend on the definition of the axis system, including the distance and relative orientation with respect to the molecule. For many problems, what matters is not the absolute Cartesian coordinates of the atoms, but rather their relative positions, i.e., the distances and angles among them. Since the relative positions of the atoms are invariant to a translation and rotation of the axis system, this means that Cartesian coordinates do NOT define a unique representation of the molecule.

The lack of uniqueness, complicates:

• using molecules as data descriptors such as in machine learning
• uniquely defining integration grids for density functional theory
• standardizing direction-dependent properties such as multipole moments, polarizabilities, etc.
• assigning symmetry labels
• reusing/restarting calculations (need to know how the intermediate quantities are oriented)
• comparing structures

One solution is to standardize the axis system. MolOrient is a Python package for aligning molecules with a standardized axis systems.

Features

• Completely reproducible orientation standardization. MolOrient relies on arbitrary-length fixed-precision arithmetic to ensure results contain a user- specified number of significant figures.
• Built-in support for Standard Nuclear Orientation, as well as NWChem's standard orientation.
• Easy to add other standards.

Installation

MolOrient is on the Python Package Index, so installation is straightforward.

pip install molorient

Example Usage

Standard Nuclear Orientation (SNO)

MolOrient reads a molecule in .xyz format and does not accept other chemical file formats. For example, water.xyz:

3
Water
O 0.0000000 0.0000000 0.1168520
H 0.0000000 0.7546680 -0.4674100
H 0.0000000 -0.7546680 -0.4674100

To put it in Standard Nuclear Orientation, run:

molorient water.xyz

SNO is the default orientation, so --sno is optional; molorient water.xyz --sno gives the same result. To change the precision, add --precision N, where N is an integer, otherwise the default is 6 significant figures. MolOrient will then write the new file as water_standardized.xyz. Here is the result at 6 significant figures:

3
Standardized geometry by MolOrient
O 0.000000 0.116852 0.000000
H -0.754668 -0.467410 0.000000
H 0.754668 -0.467410 0.000000

NWChem Orientation

To use NWChem's orientation, pass the --nwchem flag:

molorient water.xyz --nwchem

MolOrient will, again, write the new file as water_standardized.xyz. Here is the result at 6 significant figures:

3
Standardized geometry by MolOrient (NWChem orientation)
O 0.000000 0.000000 0.116852
H -0.754668 0.000000 -0.467410
H 0.754668 0.000000 -0.467410

Resources

• Documentation
• Contributor Guidelines
• Code of Conduct

Acknowledgments

Work at the Ames National Laboratory was supported by the U.S. Department of Energy Office of Science, Science Undergraduate Laboratory Internships (SULI) program under its contract with Iowa State University, Contract No. DE-AC02-07CH11358. John Lewis is grateful to the DOE for the assistantship and for the opportunity to participate in the SULI program.