improved integration of PROPKA into Python scripts

The two commits add the capability to run a PROPKA calculation from another Python script. At the moment the support is rudimentary in that one simply supplies the commandline options as a list to the new function `run.single()`:

```python
import propka.run
mol = propka.run.single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
```
Additionally, small changes were made so that instead of files, any kind of Python streams can be used. This improves the way PROPKA can be integrated into workflows whereby other code writes PDB structures to a StringIO object instead of to disk, and PROPKA reads its input from this memory buffer.