Inconsistent behaviour of toVector for Python-wrapped array-like atom properties

[lohedges]

Ideally all array-like atom properties would behave in the same way, i.e. you could call .toVector() to return a Python list (or even numpy array) in an appropriate default unit. This works for the coordinates property, but doesn't for velocity.

For example, using BioSimSpace to load:

import BioSimSpace as BSS

system = BSS.IO.readMolecules(["pickled_system.gro", "pickled_system.top"])

coords = system._sire_object.property("coordinates")

print(coords, coords.isAnArray()
SireMol::AtomCoords() True

print(coords.toVector())
[( 2.87, -1.99, 0.94 ), ( 1.52, -2.32, 0.71 ), ( 0.51, -1.38, 0.98 ), ( 0.79, -0.17, 1.57 ), ( 2.09, 0.17, 1.8 ), ( 3.15, -0.75, 1.54 ), ( 4.55, -0.43, 1.88 ), ( 3.7, -2.65, 0.72 ), ( 1.36, -3.26, 0.19 ), ( -0.53, -1.59, 0.73 ), ( -0.03, 0.5, 1.8 ), ( 2.23, 1.14, 2.27 ), ( 5.04, 0.02, 1.02 ), ( 4.65, 0.24, 2.74 ), ( 5.15, -1.33, 2.09 ), ( 2.87, -1.99, 0.94 ), ( 1.52, -2.32, 0.71 ), ( 0.51, -1.38, 0.98 ), ( 0.79, -0.17, 1.57 ), ( 2.09, 0.17, 1.8 ), ( 3.15, -0.75, 1.54 ), ( 4.55, -0.43, 1.88 ), ( 3.7, -2.65, 0.72 ), ( 1.36, -3.26, 0.19 ), ( -0.53, -1.59, 0.73 ), ( -0.03, 0.5, 1.8 ), ( 2.23, 1.14, 2.27 )]

vels = system._sire_object.property("coordinates")
print(vels, vels.isAnArray()

AtomProperty<SireMol::Velocity3D>( [ ( 1.2e-05 angstrom fs-1, 0 angstrom fs-1, -1.8e-05 angstrom fs-1 ),( 6e-06 angstrom fs-1, -5e-06 angstrom fs-1, 2e-06 angstrom fs-1 ),( 4e-06 angstrom fs-1, -5e-06 angstrom fs-1, 4e-06 angstrom fs-1 ),( -5e-06 angstrom fs-1, -8e-06 angstrom fs-1, 6e-06 angstrom fs-1 ),( -3e-06 angstrom fs-1, 0 angstrom fs-1, -1.4e-05 angstrom fs-1 ),( -3e-06 angstrom fs-1, 1e-06 angstrom fs-1, -1.5e-05 angstrom fs-1 ),( 1.9e-05 angstrom fs-1, 0 angstrom fs-1, -9e-06 angstrom fs-1 ),( 2.3e-05 angstrom fs-1, 1.5e-05 angstrom fs-1, -2.5e-05 angstrom fs-1 ),( 2.3e-05 angstrom fs-1, 0 angstrom fs-1, -1.2e-05 angstrom fs-1 ),( 2e-06 angstrom fs-1, 7e-06 angstrom fs-1, 1e-06 angstrom fs-1 ),( -1.2e-05 angstrom fs-1, -2e-05 angstrom fs-1, 1.6e-05 angstrom fs-1 ),( -3.3e-05 angstrom fs-1, 6e-06 angstrom fs-1, -1.6e-05 angstrom fs-1 ),( -3e-06 angstrom fs-1, -8e-06 angstrom fs-1, -2.6e-05 angstrom fs-1 ),( 3e-06 angstrom fs-1, 0 angstrom fs-1, -6e-06 angstrom fs-1 ),( 2e-06 angstrom fs-1, -1.5e-05 angstrom fs-1, -2.1e-05 angstrom fs-1 ),( 1.2e-05 angstrom fs-1, 0 angstrom fs-1, -1.8e-05 angstrom fs-1 ),( 6e-06 angstrom fs-1, -5e-06 angstrom fs-1, 2e-06 angstrom fs-1 ),( 4e-06 angstrom fs-1, -5e-06 angstrom fs-1, 4e-06 angstrom fs-1 ),( -5e-06 angstrom fs-1, -8e-06 angstrom fs-1, 6e-06 angstrom fs-1 ),( -3e-06 angstrom fs-1, 0 angstrom fs-1, -1.4e-05 angstrom fs-1 ),( -3e-06 angstrom fs-1, 1e-06 angstrom fs-1, -1.5e-05 angstrom fs-1 ),( 1.9e-05 angstrom fs-1, 0 angstrom fs-1, -9e-06 angstrom fs-1 ),( 2.3e-05 angstrom fs-1, 1.5e-05 angstrom fs-1, -2.5e-05 angstrom fs-1 ),( 2.3e-05 angstrom fs-1, 0 angstrom fs-1, -1.2e-05 angstrom fs-1 ),( 2e-06 angstrom fs-1, 7e-06 angstrom fs-1, 1e-06 angstrom fs-1 ),( -1.2e-05 angstrom fs-1, -2e-05 angstrom fs-1, 1.6e-05 angstrom fs-1 ),( -3.3e-05 angstrom fs-1, 6e-06 angstrom fs-1, -1.6e-05 angstrom fs-1 ) ] ) True

print(vels.toVector())
TypeError: No to_python (by-value) converter found for C++ type: QVector<SireMaths::Vector3D<SireUnits::Dimension::PhysUnit<0, 1, -1, 0, 0, 0, 0> > >

Presumably the SireMol::AtomCoords type is handling the to toVector() conversion. There is a Siremol::AtomVelocities type, but casting the velocity above to this type makes no difference.

[lohedges]

Looking at the source code for AtomVelocities, it looks like the class hasn't been fleshed out. There is no cpp file with implementation details, as there is for AtomCoords.

[chryswoods]

AtomVelocities does have a toVector function. This is defined in atomproperty.hpp. Most AtomProperty-derived classes use the default implementation from atomproperty.hpp. AtomCoords is different, as it required lots of special cases, so ended up being a concrete manual specialisation of AtomProperty<Vector>.

The error message is saying that there isn't an automatic converter defined to convert a QVector<Velocity3D> from a C++ class to a Python class. This is because I'd forgotten to add the converter in SireMol_containers.cpp.

I have added more converters including the Velocity3D converter into the feat_2023_0 version of this file. You can merge this across, or just add the one-line addition to the devel version, e.g.

register_list< QVector<Velocity3D> >();

(remembering to #include "SireMol/atomvelocities.h" at the top of this file so that Velocity3D is defined)

[lohedges]

Brilliant, thanks for this. I'll add this to devel tomorrow and test.