leruli 22.1.6

Features

Cheminformatics

• graph-to-solvation-energy: Estimate the free energy of solvation in kcal/mol.

• graph-to-geometry: Returns an approximate 3D geometry from a given graph input.

• graph-to-formula: Calculates the chemical formula in the Hill system given a graph representation like SMILES.

• canonical-formula: Expands nested or ill-ordered chemical formulas to conform to the Hill system.)

• canonical-graph: Returns a canonical version of the input graph-based representation.

Chemical space

• formula-to-graphs: Returns a list of up to 12 known molecules that are relevant for the given sum formula.

• graph-to-name: SMILES string to IUPAC name

• name-to-graph: IUPAC or trivial name to SMILES

Compute

• formula-to-cost: Estimates the resources required for a single point calculation of a given sum formula and basis set.

• graph-to-boiling-point: Predicts a boiling point in deg C.

• graph-to-logD: Predicts logD.

• graph-to-logP: Predicts logP.

• graph-to-melting-point: Predicts a melting point in deg C.

• graph-to-pKa: Predicts the pKa.

Images

• graph-to-image: Renders a molecule as SVG, PNG, or PDF

Arguments and usage are explained in the documentation.

Examples for command line usage

$ leruli name-to-graph acetone
CC(=O)C

$ leruli graph-to-geometry "CC(=O)C"
10
Generated with https://api.leruli.com/latest/references/BCE2020,BEG2019,rdkit/bibtex
C -1.27026192165113 0.14084775426444 0.00476447523142
C 0.02515865734774 -0.50330451875543 -0.42395679691615
C 1.2579793305529 0.10253815475833 0.20100853006798
O 0.07157373218152 -1.42176383766864 -1.19973295254716
H -1.22116019071807 1.21731682582838 -0.14125628889309
H -1.4330436431626 -0.04892803967934 1.06432799065161
H -2.10110516465872 -0.27062142792271 -0.56236052059465
H 1.38126815602784 1.12055904935252 -0.16250100941439
H 2.13759306261 -0.4780527025027 -0.06252115184424
H 1.15199798147051 0.14140874232516 1.28222772425865

$ leruli graph-to-formula "CC(=O)C"
C3H6O

$ leruli graph-to-solvation-energy CC water 298,300,400,200
  Temperature [K]  Energy of solvation [kcal/mol]
-----------------  --------------------------------
              200  N/A
              298  0.8636409650058766
              300  0.902919806812065
              400  1.9950388437192126

Examples for usage in Python

Load the library

>>> import leruli

Get a SMILES string from a molecule name.

>>> leruli.name_to_graph("acetone")
{'graph': 'CC(=O)C', 'reference': 'wikidata'}

Get a geometry for given molecular graph.

>>> print(leruli.graph_to_geometry('CC(=O)C', "XYZ")['geometry'])
10
Generated with https://api.leruli.com/latest/references/BCE2020,BEG2019,rdkit/bibtex
C -1.27026192165113 0.14084775426444 0.00476447523142
C 0.02515865734774 -0.50330451875543 -0.42395679691615
C 1.2579793305529 0.10253815475833 0.20100853006798
O 0.07157373218152 -1.42176383766864 -1.19973295254716
H -1.22116019071807 1.21731682582838 -0.14125628889309
H -1.4330436431626 -0.04892803967934 1.06432799065161
H -2.10110516465872 -0.27062142792271 -0.56236052059465
H 1.38126815602784 1.12055904935252 -0.16250100941439
H 2.13759306261 -0.4780527025027 -0.06252115184424
H 1.15199798147051 0.14140874232516 1.28222772425865

Get the sum formula from a molecular graph.

>>> leruli.graph_to_formula("CC=O")
{'formula': 'C2H4O', 'reference': 'M2013,rdkit'}