Fix issues #296, #297, and #298

[lohedges]

This PR closes #296 by setting and SDF tags as properties of the RDKit molecule during conversion. (The SDF metada is stored internally in Sire as a sdf_data property on molecule.) On conversion back to Sire, all non-internal properties of a RDKit molecule are now stored as an rdkit_data property. We can't write back to sdf_data, since the RDKit molecule doesn't tag where the properties come from, e.g. were they set when loading from SDF, or otherwise, so there is no clean separation of what data came from where. A user could allow these tags to be used when writing to SDF by using the property map, e.g. by remapping sdf_data to rdkit_data. In any case, the main use case here is the ability to convert an SDF molecule to RDKit, then later write to SDF using RDKit and retain all of the tags in the original file, which this does.

The PR also closes #297 by setting the MolName of any molecule loaded from SDF to the name in that file. Currently it takes a default molecule name of MOL. There is also a name molecular property that is set, but CI failures made me realise that this can also be used for other information, e..g. the neopentane-methane merged system appeared to have some kind of atom selection as the name property.

In [1]: import sire as sr

In [2]: mols = sr.load_test_files("neo_meth_scratch.bss")


In [3]: mols[0].property("name0")
Out[3]:
SireMol::AtomStringProperty( size=17
0: C1
1: C2
2: C3
3: C4
4: C5
...
12: H13
13: H14
14: H15
15: H16
16: H17
)

The PR also closes #298 by adding special handling for velocity records when the number of atoms in an AMBER RST7 file is 2 or less. If so, then the velocity line could be blank if no data is present. (There is a check to see how many lines should be exist if velocities are present, which this passes, but the line contains no data.) I'm not sure what parser is adding a blank line at the end, but it is part of the Exs pipeline.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[chryswoods]

Look good :-)