API

class scenario.Rule(rulename, probability, smarts)

Class to contain a metabolic rule

Parameters:
  • rulename – A string containing a unique name of the rule
  • probability – A probability value between 0 and 1 indicating the empirical success rate of the rule
  • smarts – A reaction smarts describing the chemical transformation of the rule
class scenario.Scenario(scenario)

Class to read and process metabolic scenario

Parameters:scenario – A list of lists, each representing a metabolic phase as [name_of_file_containing_rules, number_of_cycles_to_apply]
run(parentmol)
Parameters:parentmol – An RDKit molecule
Returns:A sygma.Tree object
class tree.Tree(parentmol=None)

Class to build and analyse a metabolic tree

Parameters:parentmol – An RDKit molecule
add_coordinates()

Add missing atomic coordinates to all metabolites

calc_scores()

Calculate probability scores for all metabolites

metabolize_all_nodes(rules, cycles=1)

Metabolize all nodes according to [rules], for [cycles] number of cycles

Parameters:
  • rules – List of rules
  • cycles – Integer indicating the number of subsequent steps to apply the rules
to_list(filter_small_fragments=True, parent_column='parent')

Generate a list of metabolites

Parameters:
  • filter_small_fragments – Boolean to activate filtering all metabolites with less then 15% of original atoms (of the parent)
  • parent_column – String containing the name for the column with the parent molecule
Returns:

A list of dictionaries for each metabolites, containing the SyGMa_metabolite (an RDKit Molecule), SyGMa_pathway and SyGMa_score, sorted by decreasing probability.
to_smiles(filter_small_fragments=True)

Generate a smiles list of metabolites

Parameters:filter_small_fragments – Boolean to activate filtering all metabolites with less then 15% of original atoms (of the parent)
Returns:A list of metabolites as list [[SyGMa_metabolite as smiles, SyGMa_score]] sorted by decreasing probability score.
write_sdf(file=<open file '<stdout>', mode 'w'>, filter_small_fragments=True)

Generate an SDFile with metabolites including the SyGMa_pathway and the SyGMa score as properties

Parameters:
  • file – The SDF file to write to
  • filter_small_fragments – Boolean to activate filtering all metabolites with less then 15% of original atoms (of the parent)
class treenode.TreeNode(mol, parent='', rule=None, score=None, pathway='')

Class containing a node of the SyGMa tree

Key mol:RDKit Molecule
Key parents:Dictonary {inchikey_of_parent: rulename_transforming_parent_to_self}
Key children:List of inchikeys of the child nodes
Key score:Value between 0 and 1
Key pathway:String describing the pathway from parent to self
Key n_original_atoms:
 Integer, number of atoms originating from parent or None if not yet determined
gen_coords()

Calculate 2D positions for atoms in self.mol without coordinates