ligning.characterization¶

Charaterization funcions

class ligning.characterization.Characterize(P: Polymer)¶

polymer characterization object

cal_MW() → float¶

calculate the molecular weight

Returns: Molecular weight of the polymer
Return type: float

cal_all(cal_MW=False, print_flag=True)¶

Main count function

Parameters

cal_MW (bool, optional) – flag to calculate molecular weight, by default False
print_flag (bool, optional) – flag to print all properties, by default True

cal_branching() → float¶

calculate the branching coefficient

Returns: branching_coeff – the branching coefficient: ratio of branched monomers to total monomers
Return type: float

count_OCH3() → float¶

count the number of -OCH3 group

Returns: OCH3_count – -OCH3 counts
Return type: float

count_OH() → float¶

count the number of available -OH3 group

Returns: OH_count – -OH counts
Return type: float

count_connections() → dict¶

Count the number of connections of each monomer

Returns: connections_count – the number of connections
Return type: dict

count_linkages() → dict¶

count the type of linkages

Returns: linkages_count – the linkage type counts
Return type: dict

count_monomers() → int¶

count the total number of monomers, i.e. the polymer size

Returns: monomer_count – the polymer size
Return type: float

count_types() → dict¶

count the monomer types

Returns: mtype_count – the monomer type counts
Return type: dict

get_counts(additional: Optional[bool] = False, cal_MW: Optional[bool] = False) → nparray¶

Get the count array for a polymer

Parameters: additional (Optional[bool], optional) – include additional metrics, by default False
Returns: counts – counts array
Return type: nparray

get_metrics(additional: Optional[bool] = False, cal_MW: Optional[bool] = False) → nparray¶

Get the metrics array for a polymer

Parameters: additional (Optional[bool], optional) – include additional metrics, by default False
Returns: metrics – metrics array
Return type: nparray

class ligning.characterization.CharacterizeGraph(G: nxgraph)¶

polymer charaterization object

cal_MW() → float¶

calculate the molecular weight

Returns: Molecular weight of the polymer
Return type: float

cal_all(cal_MW=False, print_flag=True)¶

Main count function

Parameters

cal_MW (bool, optional) – flag to calculate molecular weight, by default False
print_flag (bool, optional) – flag to print all properties, by default True

cal_metrics(cal_MW: Optional[bool] = False) → nparray¶

calculate the 10 by 1 metrics array

Returns: metrics – metrics array
Return type: nparray

count_OCH3() → float¶

count the number of -OCH3 group

Returns: OCH3_count – -OCH3 counts
Return type: float

count_OH() → float¶

count the number of available -OH3 group

Returns: OH_count – -OH counts
Return type: float

count_linkages() → dict¶

count the type of linkages

Returns: linkages_count – the linkage type counts
Return type: dict

count_monomers() → float¶

count the total number of monomers, i.e. the polymer size

Returns: monomer_count – the polymer size
Return type: float

count_types() → dict¶

count the monomer types

Returns: mtype_count – the monomer type counts
Return type: dict

class ligning.characterization.Population(population: List[Polymer], name: Optional[str] = 'lignin_x', InputPath: Optional[str] = '/home/docs/checkouts/readthedocs.org/user_builds/ligningraphs/checkouts/latest/docs/source', ResultsName: Optional[str] = 'results', TrialIndex: Optional[str] = None)¶

Characterize a population of polymers

analyze()¶: Analyze the population Output the data and stats both in csv files

characterize_all()¶: Characterize each individual polymer

get_counts(additional: Optional[bool] = False)¶

Get the metrics matrix for the entire population

Parameters: additional (Optional[bool], optional) – include additional metrics, by default False
Returns: metrics – metrics matrix
Return type: nparray

get_metrics_mean(additional: Optional[bool] = False)¶

Get the metrics matrix for the entire population

Parameters: additional (Optional[bool], optional) – include additional metrics, by default False
Returns: metrics – metrics mean array
Return type: nparray

ligning.characterization.get_counts_polymer(P: Polymer, additional: Optional[bool] = False, cal_MW: Optional[bool] = False) → Tuple[nparray, int, float]¶

Get the counts array for a polymer

Parameters

P (Polymer) – polymer object
additional (Optional[bool], optional) – include additional metrics, by default False
cal_MW (bool, optional) – flag to calculate molecular weight, by default False

Returns

counts_P (nparray) – the counts array
monomer_count (int) – the number of monomers
MW (float) – the molecular weight

ligning.characterization.get_metrics_polymer(P: Polymer, additional: Optional[bool] = False, cal_MW: Optional[bool] = False) → Tuple[nparray, int, float]¶

Get the metrics and count for a polymer

Parameters

P (Polymer) – polymer object
additional (Optional[bool], optional) – include additional metrics, by default False
cal_MW (bool, optional) – flag to calculate molecular weight, by default False

Returns

metrics_P (nparray) – the metrics array
monomer_count (int) – the number of monomers
MW (float) – the molecular weight