mooonpy package

class mooonpy.Molspace(filename='', **kwargs)[source]

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)[source]

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')[source]

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()[source]
compute_BADI_by_type(periodicity='ppp', comp_bond=True, comp_angle=True, comp_dihedral=True, comp_improper=True)[source]
compute_bond_length(periodicity='ppp')[source]
compute_pairs(cutoff, whitelist=None, blacklist=None, algorithm='DD_13', periodicity='ppp')[source]

Compute pairwise distances within cutoff between atoms

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

Finds all rings in the current Molspace instance. The size of rings searched for is set in the 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()[source]
read_files(filename, dsect=['all'])[source]
update_elements(type2mass=None, type2element=None)[source]

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')[source]
class mooonpy.Path(string: str | Path)[source]

Bases: str

As computational scientists, half our jobs is file management and manipulation, the Path class contains several aliases for the os.path and glob.glob modules to make processing data easier. All mooonpy functions internally use this class for inputs of files or folders. Relevant strings are converted to path on entering functions

Examples

A copy of the code used in these examples is avalible in rootmooonpyexamplestoolspath_utilsexample_Path.py

Basic Path Operations
>>> project_path = Path('Project/Data/Analysis')
>>> filename = Path('results.txt')
>>> full_path = project_path / filename
>>> print(full_path)
Project\Data\Analysis\results.txt
>>> print(abs(full_path))
root\mooonpy\examples\tools\path_utils\Project\Data\Analysis\results.txt
Path Parsing
>>> sample_path = Path('experiments/run_001/data.csv.gz')
>>> print(sample_path.dir())
experiments\run_001
>>> print(sample_path.basename())
data.csv.gz
>>> print(sample_path.root())
data.csv
>>> print(sample_path.ext())
.gz
Extension Manipulation
>>> data_file = Path('analysis/results.txt')
>>> print(data_file.new_ext('.json'))
analysis\results.json
>>> print(data_file.new_ext('.txt.gz'))
analysis\results.txt.gz
File Existence
>>> current_file = Path(__file__)
>>> fake_file = Path('nonexistent.txt')
>>> print(bool(current_file))
True
>>> print(bool(fake_file))
False
Wildcard Matching
>>> txt_pattern = Path('temp_dir/*.txt')
>>> print(txt_pattern.matches())
['test1.txt', 'test2.txt']
>>> for file in Path('temp_dir/*'):
...     print(file.basename())
data.csv
readme.md
test1.txt
test2.txt
Recent File Finding
>>> pattern = Path('temp_dir/*.txt')
>>> print(pattern.recent())
newest_file.txt
>>> print(pattern.recent(oldest=True))
old_file.txt
Smart File Opening
>>> mypath = Path('data.txt')
>>> with mypath.open('w') as f:
...     f.write('Hello World')
# Creates regular file
>>> compressed_path = Path('data.txt.gz')
>>> # compressed_path.open() would use gzip automatically
# Would automatically handle gzip compression
** Absolute Path Conversion **
>>> rel_path = Path('data/file.txt')
>>> print(abs(rel_path))
root\mooonpy\examples\tools\path_utils\data\file.txt

Todo

__truediv__ __bool__ __abs__ and __iter__ docstrings in config?

basename() → Path[source]

Split Path to filename and extention.

Alias for os.path.basename

Returns:

Path of file

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> print(MyPath.basename())
'DETDA.mol'
dir() → Path[source]

Split Path to directory.

Alias for os.path.dirname.

Returns:

Path to directory

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> print(MyPath.dir())
'Project\Monomers'
ext() → Path[source]

Split Path to just extention.

Alias for os.path.basename and os.path.splitext.

Returns:

extention as Path

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> print(MyPath.ext())
'.mol'
matches(whitelist_ext=None, blacklist_ext=None) → List[Path][source]

Finds matching paths with a * (asterisk) wildcard character.

Returns:

List of matching Paths

Return type:

List[Path]

Example:
>>> from mooonpy import Path
>>> MyWildcard = Path('*.mol')
>>> print(Path.matches(MyWildcard))
[Path('DETDA.mol'), Path('DEGBF.mol')]
new_ext(ext: str | Path) → Path[source]

Replace extension on a Path with a new extension.

Parameters:

ext (str or Path) – new extension including delimeter.

Returns:

replaced Path

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> print(MyPath.new_ext('.data'))
'Project/Monomers/DETDA.data'
open(mode='r', encoding='utf-8')[source]

Open path with smart_open

Parameters:

  • mode (str) – Open mode, usually ‘r’ or ‘a’

  • encoding (str) – File encoding

Returns:

opened file as object

Return type:

File Object

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> MyFileObj = MyPath.open(mode='r')
recent(oldest: bool = False) → Path | None[source]

Find wildcard matches and return the Path of the most recently modified file.

Parameters:

oldest (bool) – Reverses direction and finds least recently modified file.

Returns:

Path of most recently modified file

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyWildcard = Path('Template_*.lmpmol')
>>> print(Path.recent())
'Template_1_v10_final_realthistime.lmpmol'
>>> print(Path.recent(oldest=True))
'Template_1.lmpmol'
root() → Path[source]

Split Path to filename with no extention.

Alias for os.path.basename and os.path.splitext.

Returns:

Path of filename

Return type:

Path

Example:
>>> from mooonpy import Path
>>> MyPath = Path('Project/Monomers/DETDA.mol')
>>> print(MyPath.root())
'DETDA'
class mooonpy.Thermospace(**kwargs)[source]

Bases: ColTable

Class to hold data found in LAMMPS logs. Data is organized into columns

classmethod basic_read(file: Path | str, silence_error_line: bool = False) → Thermospace[source]
join_restart(restart, step_col='Step', restart_step_ind=0, this_step_ind=None)[source]

Appends data from a restarted thermospace to the current one. Uses (step_col, restart_step_ind) as the start of the appended section, and finds the last matching (step_col, this_step_ind) and overwrites after that

step_col is the column used for indexing, defaults to ‘Step’ but ‘v_Time’ may also be used

restart_step_ind = 0 uses 0th index step, and so on this_step_ind = None uses last matching value

sect(sect_string: str | range | list | int | None = None, priority='off') → ColTable[source]

Subpackages

Submodules