mooonpy.molspace.molspace module

class mooonpy.molspace.molspace.Molspace(filename='', **kwargs)

Bases: object

Initializes a Molspace instance

This class can be called via:

• Full namespace syntax : mooonpy.molspace.molspace.Molspace()

• Aliased namespace syntax : mooonpy.Molspace()

Initialization Parameters

filenamestr, optional

An optional filename to read and initialize a Molspace() instance with molecular system information (e.g. atoms, bonds, force field parameters …). Supported file extensions:

• LAMMPS datafile .data

• Tripos mol2 file .mol2

• SYBL mol file .mol

If no filename is provided the Molspace instance will be generated with no molecular system information.

Attributes

Nint

The order of the filter. For ‘bandpass’ and ‘bandstop’ filters, the resulting order of the final second-order sections (‘sos’) matrix is 2*N, with N the number of biquad sections of the desired system.

Wnarray_like

The critical frequency or frequencies. For lowpass and highpass filters, Wn is a scalar; for bandpass and bandstop filters, Wn is a length-2 sequence.

Methods

Nint

The order of the filter. For ‘bandpass’ and ‘bandstop’ filters, the resulting order of the final second-order sections (‘sos’) matrix is 2*N, with N the number of biquad sections of the desired system.

add_type_labels(labels)

Adds type labels for atom types and use 1st instance for each BADI type label

could refactor the composition to a function somewhere

bonds_from_distances(periodicity: str = 'ppp')

Resets the bonds in a molecular system, based in interatomic distances and valences of atoms. The cutoff distances are set based on the summation of vdw radii per element involved in the bond. Each atom’s valence is respected (e.g. the maximum number of allowable bonded atoms to a carbon atom is 4).

Example:

>>> import mooonpy
>>> my_molecule = mooonpy.molspace('detda.data')
>>> my_molecule.bonds_from_distances(periodicity='fff')

Note

Before using this command the element per-atom info and element per-mass info need to be updated by running “my_molecule.update_elements()”.

Parameters:

periodicity (str) – Optional for setting the periodicity of the model, where f=fixed and p=periodic. Each position is a face (e.g. periodicity=’fpp’ is fixed on X-faces and periodic in Y- and Z-faces)

Returns:

None

Return type:

None

compute_ADI()

compute_BADI_by_type(periodicity='ppp', comp_bond=True, comp_angle=True, comp_dihedral=True, comp_improper=True)

compute_bond_length(periodicity='ppp')

compute_pairs(cutoff, whitelist=None, blacklist=None, algorithm='DD_13', periodicity='ppp')

Compute pairwise distances within cutoff between atoms

copy()

find_cumulative_neighs()

find_rings(ring_sizes: tuple[int] = (3, 4, 5, 6, 7))

Finds all rings in the current Molspace instance. The size of rings searched for is set in the ring_sizes parameter.

Example:

>>> import mooonpy
>>> my_molecule = mooonpy.molspace('detda.mol2')
>>> rings = my_molecule.find_rings(ring_sizes=(3,4,5,6,7))
>>> print(rings)
[(1, 2, 3, 4, 5, 6)]

Note

Each ring will be sorted in the order it was traversed in the graph and will be in the canonical form (e.g., canonical=(1,2,3) vs non_canonical=(2,3,1)).

Parameters:

ring_sizes (tuple[int]) – Tuple containing ring sizes to search for in graph

Returns:

rings

Return type:

list[tuple[int]]

generate_graph()

read_files(filename, dsect=['all'], steps=Ellipsis)

Read files into Molspace Currently supports .data and .dump files.

Parameters:

• filename (str or Path) – path to file to read

• dsect (list) – Sections of data file to read, see mooonpy.molspace._files_io.read_lmp_data for more details

• steps (list or int) – Steps in dump file to read see mooonpy.molspace._files_io.read_lmp_dump for more details

Returns:

Modifies self in-place if data or single step, returns dict if multiple steps

Return type:

None or dict

Example:

>>> from mooonpy import Molspace
>>> MyPath = Path('Project/Monomers/DETDA.data')
>>> mol = Molspace(MyPath, dsect=['all'])
>>> MyPath2 = Path('Project/Monomers/DETDA.dump')
>>> series = Molspace(MyPath2, steps=None)

remove_atoms(atom_ids)

make smart and remove from some?

update_elements(type2mass=None, type2element=None)

Updates every per-atom .element attribute with the element type for that atom.

Example:

>>> import mooonpy
>>> my_molecule = mooonpy.molspace('detda.data')
>>> my_molecule.update_elements()

Note

This will also update the per-mass .element attribute in ff.masses dictionary as well.

Parameters:

• type2mass (dict[int, float]) – Optional for setting the atom type to mass map (e.g. type2mass={1: 12.01115, 2: 1.008}). If not provided this will be generated from the masses section.

• type2element (dict[int, str]) – Optional for setting the atom type to mass map (e.g. type2element={1: ‘C’, 2: ‘H’}). If not provided this will be generated from the masses section and interally defined periodic table.

Returns:

None

Return type:

None

write_files(filename, atom_style='full')