Working with TopologyAttributes

Richard Gowers edited this page Dec 29, 2015 · 2 revisions

TopologyAttributes (TA) are used to define static information in the Universe.

Creating a new TopologyAttribute

Should a Topology require a TopologyAttribute that doesn't currently exist, these can be easily made....

The transplant system

All attributes added to the Topology object are automatically added to the namespace of all Groups (AtomGroup, ResidueGroup and SegmentGroup) and components (Atom, Residue & Segment). It is also possible to make a TA supply arbitrary methods and properties to these classes, done via the transplant system.

To do this, the desired method is defined inside the TopologyAttribute. A defaultdict called transplants is defined, and a tuple containing the method's name and the method is appended to the list of methods. Transplants may be defined at either the atom, residue, segment, atomgroup, residuegroup or segmentgroup levels.

class MyAttribute(TopologyAttribute):
    # <normal TA code>
    transplants = defaultdict(list)

    def mass_multiplier(ag, value):
        """Multiply the mass of each item by *value*"""
        return ag.masses * value

    transplants['atomgroup'].append(('multimass', mass_multiplier))

# Creates the following method:

It is also possible to add in properties as well as methods:

class MyAttribute(TopologyAttribute):
    # <normal TA code>
    transplants = defaultdict(list)

    def mass_doubler(ag):
        """Returns double the mass of each item"""
        return ag.masses * 2

    transplants['atomgroup'].append(('doublemass', property(mass_doubler, None, None, mass_multiplier.__doc__)))

# Creates the following method:

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Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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