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.

KE()

add_type_labels(labels, per_atom_comment=False)

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

build_old2new(mode='contiguous', offset=0, start=1, keep=None)

Build an (old2new, new2old) mapping for use with remap_ids().

See mooonpy.molspace.remap.build_old2new() for parameter details.

combine(other, vect=None, move_mode='offset', offset_types=False, assign_clusters=True)

Append other into self in place. other’s atom ids are shifted by self’s current max(atoms) so they don’t collide. Coordinates of the shifted copy are translated via Atoms.move() before merging.

Parameters:

• other (Molspace) – Molspace to append. Not mutated.

• vect (tuple[float, float, float] or None) – Displacement applied to other before merging. None skips translation.

• move_mode (str) – Mode passed to Atoms.move(). Defaults to 'offset'.

• offset_types (bool) – If True, other’s atom-type integers are shifted by max(self.ff.masses) and the corresponding mass entries are merged into self.ff.masses with the shifted keys. This is needed when the two systems use unrelated type tables (e.g. combining raw monomers from independent atom_typing runs). For systems that already share the same FF (e.g. post-BRM data files), leave it False so types stay aligned.

• assign_clusters (bool) – Re-run cluster identification after merge.

Returns:

The id offset applied to other’s atom ids.

Return type:

int

compute_ADI()

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

Apply this command mol.ff.has_type_labels = True or mol.add_type_labels(labels) To make dict keys type labels

compute_bond_length(periodicity='ppp')

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

Compute pairwise distances within cutoff between atoms

contiguous(start=1)

Renumber atoms start..start+N-1 in current insertion order, in place. Returns the old2new dict.

copy(deepcopy=False)

Return a fully independent copy of this Molspace (independence verified in tests/test_molspace_copy.py).

Factory classes and defaults are frozen at construction, so the copy references the SAME factory/lookup instances by design; all mutable state is rebuilt fresh.

Parameters:

deepcopy (bool) – if True, use the copy.deepcopy fallback (same result, ~6-8x slower; for cross-checking only).

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()

min_image_unwrap(changeimg=True)

Make every molecule whole under the minimum-image convention, in place.

Walks each bonded cluster outward from the atom nearest the box center and shifts every neighbor to its minimum-image position relative to the atom it was reached from, so no bond spans more than half the box. Restricted- triclinic safe: the minimum image is taken in fractional space (consistent with Atoms.wrap()), then converted back through the box h-matrix.

Parameters:

• mol – Molspace modified in place (needs .atoms, .atoms.box, bonds).

• changeimg – If True, update each shifted atom’s image flags so the canonical wrapped position is preserved (unwrapped = stored + h.image stays invariant; Atoms.wrap() will still recover the cell).

reachable(start_id, depth)

Flat-set bond-graph reachability from start_id up to depth bonds (inclusive of start_id). Thin wrapper around mooonpy.molspace.graph_theory.interface.find_reachable_neighbors().

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)

remap_ids(old2new)

Renumber and/or slice atom ids in place using old2new.

Any current atom whose id is not a key in old2new is dropped, along with any bond/angle/dihedral/improper entry that references it. Container Python identities and surviving per-atom/per-bond object identities are preserved. See mooonpy.molspace.remap.

remove_atoms(atom_ids)

make smart and remove from some?

slice(keep_ids, renumber=True)

Drop every atom whose id is not in keep_ids, in place. By default the surviving atoms are renumbered contiguously from 1. Returns the old2new dict.

temp()

update_atoms(atoms, whitelist=None, blacklist=None, box=True)

Map per atom information from other atoms instance to this molspace

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')