mdgo.volume module

Computes the volume for each ligand or active site in a file.

In ligand mode, the volume of the entire structure is calculated. The -x, -y, -z, -xsize, -ysize and -zsize options are ignored.

In active site mode, the unoccupied volume within a cube is calculated. The center of the cube is defined by the -x, -y and -z options, and the size of the cube is defined by the -xsize, -ysize and -zsize options.

mdgo.volume.parse_command_line()[source]

The command line parser helper function.

Usage:

python volume.py -xyz <input_xyz> [options]

mdgo.volume.get_max_dimensions(mol)[source]

Calculates the dimension of a Molecule

Parameters

mol (Molecule) – A Molecule object.

Return type

Tuple[float, float, float, float, float, float]

Returns

xmin, xmax, ymin, ymax, zmin, zmax

mdgo.volume.set_max_dimensions(x=0.0, y=0.0, z=0.0, x_size=10.0, y_size=10.0, z_size=10.0)[source]

Set the max dimensions for calculating active site volume.

Parameters

  • x (float) – X center for volume grid. Default to 0.0.

  • y (float) – Y center for volume grid. Default to 0.0.

  • z (float) – Y center for volume grid. Default to 0.0.

  • x_size (float) – X side length for volume grid. Default to 10.0.

  • y_size (float) – Y side length for volume grid. Default to 10.0.

  • z_size (float) – Z side length for volume grid. Default to 10.0.

Return type

Tuple[float, float, float, float, float, float]

Returns

x_min, x_max, y_min, y_max, z_min, z_max

mdgo.volume.round_dimensions(x_min, x_max, y_min, y_max, z_min, z_max, mode='lig')[source]

Round dimensions to a larger box size (+ buffer).

Parameters

  • x_min (float) – x min.

  • x_max (float) – x max.

  • y_min (float) – y min.

  • y_max (float) – y max.

  • z_min (float) – z min.

  • z_max (float) – z max.

  • mode (str) – “lig” or “act” mode. Default to “lig”.

Return type

Tuple[float, float, float, float, float, float]

Returns

x0, x1, y0, y1, z0, z1

mdgo.volume.dsq(a1, a2, a3, b1, b2, b3)[source]

Squared distance between a and b

Parameters

  • a1 (float) – x coordinate of a

  • a2 (float) – y coordinate of a

  • a3 (float) – z coordinate of a

  • b1 (float) – x coordinate of b

  • b2 (float) – y coordinate of b

  • b3 (float) – z coordinate of b

Return type

float

Returns

squared distance

mdgo.volume.get_dimensions(x0, x1, y0, y1, z0, z1, res=0.1)[source]

Mesh dimensions in unit of res.

Parameters

  • x0 (float) – x min.

  • x1 (float) – x max.

  • y0 (float) – y min.

  • y1 (float) – y max.

  • z0 (float) – z min.

  • z1 (float) – z max.

  • res (float) – Resolution of the mesh to use in Å

Return type

Tuple[int, int, int]

Returns

xsteps, ysteps, zsteps

mdgo.volume.make_matrix(x_num, y_num, z_num)[source]

Make a matrix of None with specified dimensions.

Parameters

  • x_num (int) – x dimension.

  • y_num (int) – y dimension.

  • z_num (int) – z dimension.

Return type

ndarray

Returns

matrix

mdgo.volume.get_radii(radii_type='Bondi')[source]

Get a radii dict by type.

Parameters

radii_type (str) – The radii type. Valid types are “Bondi”, “Lange”, and “pymatgen”. Default to “Bondi”.

Return type

Dict[str, float]

Returns

A radii dict.

mdgo.volume.fill_volume_matrix(mol, x0, x1, y0, y1, z0, z1, res, matrix, radii_type, exclude_h=True)[source]

This method perform the mesh point filling algorithm on a given matrix.

Parameters

  • mol (Molecule) – The Molecule object to calculate volume.

  • x0 (float) – x min.

  • x1 (float) – x max.

  • y0 (float) – y min.

  • y1 (float) – y max.

  • z0 (float) – z min.

  • z1 (float) – z max.

  • res (float) – Resolution of the mesh to use when estimating molar volume, in Å

  • matrix (ndarray) – The mesh matrix to perform mesh point filling.

  • radii_type (str) – The radii type. Valid types are “Bondi”, “Lange”, and “pymatgen”. Default to “Bondi”.

  • exclude_h (bool) – Whether to exclude H when estimating molar volume. Default to True.

Return type

ndarray

Returns

The filled matrix.

mdgo.volume.get_occupied_volume(matrix, res, name=None, molar_volume=True)[source]

Get the occupied volume of the molecule in the box.

Parameters

  • matrix (ndarray) – The filled mesh matrix.

  • res (float) – Resolution of the mesh in Å.

  • name (Optional[str]) – The name of the molecule

  • molar_volume – Whether to return molar_volume, otherwise molecular volume. Default to True.

Return type

float

Returns

Volume

mdgo.volume.get_unoccupied_volume(matrix, res, name=None, molar_volume=True)[source]

Get the unoccupied volume of the molecule in the box.

Parameters

  • matrix (ndarray) – The filled mesh matrix.

  • res (float) – Resolution of the mesh in Å.

  • name (Optional[str]) – The name of the molecule

  • molar_volume – Whether to return molar_volume, otherwise molecular volume. Default to True.

Return type

float

Returns

Volume

mdgo.volume.molecular_volume(mol, name=None, res=0.1, radii_type='Bondi', molar_volume=True, exclude_h=True, mode='lig', x_cent=0.0, y_cent=0.0, z_cent=0.0, x_size=10.0, y_size=10.0, z_size=10.0)[source]

Estimate the molar volume in cm^3/mol or volume in Å^3

Parameters

  • mol (Union[str, Molecule]) – Molecule object or path to .xyz or other file that can be read by Molecule.from_file()

  • name (Optional[str]) – String representing the name of the molecule, e.g. “NaCl”

  • res (float) – Resolution of the mesh to use when estimating molar volume, in Å

  • radii_type (str) – “Bondi”, “Lange”, or “pymatgen”. Bondi and Lange vdW radii are compiled in this package for H, B, C, N, O, F, Si, P, S, Cl, Br, and I. Choose ‘pymatgen’ to use the vdW radii from pymatgen.Element, which are available for most elements and reflect the latest values in the CRC handbook.

  • molar_volume (bool) – Whether to return molar volume. If false, then return volume. Default to True (molar volume).

  • exclude_h (bool) – Whether to exclude H atoms during the calculation. Default to True.

  • mode (str) – In ligand mode (“lig”), the volume of the entire structure is calculated. In active site mode (“act”), the unoccupied volume within a cube is calculated. Default to “lig”.

  • x_cent (float) – X center for volume grid. Default to 0.0.

  • y_cent (float) – Y center for volume grid. Default to 0.0.

  • z_cent (float) – Z center for volume grid. Default to 0.0.

  • x_size (float) – X side length for volume grid. Default to 10.0.

  • y_size (float) – Y side length for volume grid. Default to 10.0.

  • z_size (float) – Z side length for volume grid. Default to 10.0.

Return type

float

Returns

The molar volume in cm^3/mol or volume in Å^3.