The Solv@TUM database contains a collection of experimentally measured partition coefficients for a large number of molecular solutes in non-aqueous solvents. The database is aimed at providing reference data for e.g. the parameter fitting of effective solvation models. The data has been compiled from the works of Abraham, Acree and co-workers and will be regularly updated as new data becomes available. Each entry is provided with the respective literature reference, all publications are listed in solvatum/data/solvatum_references.bib. The actual database (solvatum/data/solvatum.sdf) is given as a single structure data file (sdf).
For a simple and fast access to the data one can use the user interface, which is written in the Python programming language.
The installation and usage of this user interface is described in the following sections.
The Solv@TUM interface currently only supports Python 2.7.
Installation requires OpenBabel and its Python Interface Pybel.
Some functions will optionally use pandas, bibtexparser and ase.
To handle the sdf-format we are using the OpenBabel chemistry library and its Python interface 'pybel'. This has to be installed before you can install the Solv@TUM database interface. Installation guidelines can be found here:
We recommend to install Pybel/OpenBabel with the conda package manager, because then no manual installation of OpenBabel is necessary. For this just type
$ conda install -c openbabel openbabel
in your command line.
The latest stable release can be downloaded and installed with
$ rsync rsync://m1452571_001@138.246.224.34/m1452571_001/solvatum-1.0.0.zip .
$ pip install solvatum-1.0.0.zip
(password for download: m1452571_001)
For a manual download go to https://mediatum.ub.tum.de/1452571.
Open a Python prompt and type in:
>>> from solvatum.ui import Database
>>> d = Database()With this command the database gets initialized. Now all solvents or solutes can be listed with:
>>> print d.solvents
>>> print d.solutesOne can filter for one solvent, solute or both:
>>> d.filtering(solvent='chloroform')
>>> d.filtering(solute='hexane')
>>> d.filtering(solvent='chloroform', solute='hexane')
{'deltaG_solv': -0.16979, 'logK': 2.87}The output of the first lines is a dictionary with molecule specific propperties and a list with all corresponding solutes and solvents, respectively. The output of the latter, is a dictionary with the logK value and the solvation free energy calculated from it. The unit of the solvation free energy is per default eV, but one can switch to kcal/mol or J with
>>> d.energy_unit='kcal/mol'
{'deltaG_solv': -3.92, 'logK': 2.87}With
>>> d.get_molecule_properties(<molecule>)all properties (data) which are stored in the database, except the logK values, are shwon (e.g. formula, InChI, name, mean polarizability, dipole moment, etc.). Adding new properties is simple done with
>>> d.add_property(<molecule>, <property_name>, <property_value>)>>> d.one_mol_from_sdf(<solute>)returns the pybel.Molecule object of a given solute molecule. To that you can apply any Pybel or OpenBabel method.
If you are using the Atomic Simulation Environment (ASE) the database interface can directly convert the pybel.Molecule object to an ASE Atomas object with:
>>> d.mol_to_ase(<molecule>)The database interface also provides the possibility to draw depictions of the molecules:
>>> d.draw(<molecule>)This method take the keywords 'save=True', for saving a png figure of the depiction and 'notebook=True' for showing the depiction inline in jupyter notebooks.
There is a known issue in Pybel in the drawing functionality, which was already reported and is also fixed in the officiall Pybel source code. But by installing Pybel with conda or PIP and not directly from source it is possible that the following error still appears:
ImportError: Tkinter or Python Imaging Library not found, but is required for image display. See installation instructions for more information.
For this we provided a fixed version of pybel.py. Just locate your installation path of Pybel and replace the files.