Command Line Interface
¶
Note
Please feel free to ✎ improve this page or to 🕮 ask questions about this page .
Installation ¶
To install Leruli CLI, run this command in your terminal:
$ pip install -U leruli
This is the preferred method to install Leruli CLI, as it will always install the most recent stable release.
If you don’t have pip installed, this Python installation guide can guide you through the process.
Leruli CLI ¶
Use leruli.com from both command line and within Python code: a convenience wrapper around the corresponding API .
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'}
Cheminformatics ¶
leruli canonical-formula ¶
Canonicalize a sum formula.
leruli canonical-formula [OPTIONS] FORMULA
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- FORMULA ¶
-
Required argument
leruli canonical-graph ¶
Canonicalize a graph.
leruli canonical-graph [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-formula ¶
Obtain a formula from a graph.
leruli graph-to-formula [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-geometry ¶
Molecular geometry from a graph.
leruli graph-to-geometry [OPTIONS] GRAPH
Options
- --format <format> ¶
-
File format for output, defaults to XYZ.
- Options
-
XYZ | PDB | SDF
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-solvation-energy ¶
Estimate the free energy of solvation.
leruli graph-to-solvation-energy [OPTIONS] GRAPH SOLVENT TEMPERATURES
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
- --quiet ¶
-
Hide progress bar.
Arguments
- GRAPH ¶
-
Required argument
- SOLVENT ¶
-
Required argument
- TEMPERATURES ¶
-
Required argument
leruli graph-to-image ¶
Structure formula as image file.
leruli graph-to-image [OPTIONS] GRAPH FILENAME
Options
- --version <version> ¶
-
Request specific API version.
- --angle <angle> ¶
-
Rotation angle.
- --format <format> ¶
-
File format for output, defaults to SVG.
- Options
-
SVG | PNG | PDF
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
- FILENAME ¶
-
Required argument
Chemical Space ¶
leruli formula-to-cost ¶
Obtain a cost estimate for a molecule.
leruli formula-to-cost [OPTIONS] FORMULA BASISSET
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- FORMULA ¶
-
Required argument
- BASISSET ¶
-
Required argument
leruli graph-to-name ¶
Obtain a name from a graph.
leruli graph-to-name [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli name-to-graph ¶
Obtain a graph from a name.
leruli name-to-graph [OPTIONS] NAME
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- NAME ¶
-
Required argument
leruli formula-to-graphs ¶
Find molecular graphs of a given sum formula.
leruli formula-to-graphs [OPTIONS] FORMULA
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- FORMULA ¶
-
Required argument
Physical Chemistry ¶
leruli graph-to-boiling-point ¶
Estimate a boiling point in deg C.
leruli graph-to-boiling-point [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-melting-point ¶
Estimate a melting point in deg C.
leruli graph-to-melting-point [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-logp ¶
Estimate a logP.
leruli graph-to-logp [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-logd ¶
Estimate a logD.
leruli graph-to-logd [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
leruli graph-to-pka ¶
Estimate a pKa.
leruli graph-to-pka [OPTIONS] GRAPH
Options
- --version <version> ¶
-
Request specific API version.
- --reference ¶
-
Print references for the result.
Arguments
- GRAPH ¶
-
Required argument
Cloud Compute ¶
leruli task-get ¶
Get the status of a job in the queue.
leruli task-get [OPTIONS] [BUCKET]
Arguments
- BUCKET ¶
-
Optional argument
leruli task-prune ¶
Deletes the input/output files of a bucket.
leruli task-prune [OPTIONS] [BUCKET]
Arguments
- BUCKET ¶
-
Optional argument
leruli task-publish-code ¶
Uploads a local docker image to the queue.
leruli task-publish-code [OPTIONS] CODE VERSION
Arguments
- CODE ¶
-
Required argument
- VERSION ¶
-
Required argument
leruli task-status ¶
Get the status of a job in the queue.
leruli task-status [OPTIONS] [JOBID]
Arguments
- JOBID ¶
-
Optional argument
leruli task-submit ¶
Submit a job to the Leruli queue. This is a paid feature requiring an API secret, which can be obtained from info @ leruli . com .
leruli task-submit [OPTIONS] CODE VERSION COMMAND...
Options
- --memory <memory> ¶
-
Memory limit in MB.
- --time <time> ¶
-
Time limit in minutes.
- --cores <cores> ¶
-
Number of cores to allocate.
Arguments
- CODE ¶
-
Required argument
- VERSION ¶
-
Required argument
- COMMAND ¶
-
Required argument(s)