htmd.projections.metric module#
- class htmd.projections.metric.Metric(simulations, skip=1, metricdata=None)#
Bases:
object
Class for calculating projections of a simlist.
- Parameters
simulations (list) – A list of simulations produced by
simlist
skip (int) – Frame skipping. Setting i.e. to 3 will keep only every third frame of each simulation.
metricdata (
MetricData
object) – If a MetricData object is passed in the constructor, Metric will try to update it by only adding simulations which don’t exist in it yet.
Examples
>>> metr = Metric(sims) >>> metr.set(MetricSelfDistance('protein and name CA', metric='contacts')) >>> data = metr.project() >>> >>> # Or define your own function which accepts as first argument a Molecule object. Further arguments are passed as >>> # function/argument tuples >>> def foo(mol, ref): >>> from moleculekit.util import molRMSD >>> mol.wrap('protein') >>> mol.align('protein and name CA', refmol=ref) >>> return molRMSD(mol, ref, mol.atomselect('protein and name CA'), ref.atomselect('protein and name CA')) >>> >>> metr = Metric(sims) >>> metr.set( (foo, (ref,)) ) >>> data2 = metr.project()
Methods
Attributes
- getMapping(mol)#
Returns the description of each projected dimension.
- Parameters
mol (
Molecule
object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.- Returns
map – A DataFrame containing the descriptions of each dimension
- Return type
DataFrame
object
- project(njobs=None)#
Applies all projections stored in Metric on all simulations.
- Parameters
njobs (int) – Number of parallel jobs to spawn for projection of trajectories. Take care that this can use large amounts of memory as multiple trajectories are loaded at once. If None it will use the default from htmd.config.
- Returns
data – Returns a MetricData object containing the projected data.
- Return type
MetricData object
- set(projection)#
Sets the projection to be applied to the simulations.
- Parameters
projection (function or
Projection
object or list of objects) – A function or projection or a list of projections/functions which to use on the simulations