HTMD can handle a large amount of simulations. Simulation lists allow to create a simple list containing all relevant information about the simulations to later perform any type of analysis.
acelleralivehtmd.simlist.Frame(sim, piece, frame)¶Bases: object
Class used for referencing a specific frame of a Sim object object.
frame¶piece¶sim¶htmd.simlist.Sim(simid, parent, input, trajectory, molfile, numframes=None)¶Bases: object
Information class for a single simulation.
Do not use directly. Objects of this class are constructed by the simlist() and simfilter() functions.
This class is used for storing information on simulations. This information includes the path to the simulation,
the path to a structure file (pdb) which corresponds to the simulation, the folder containing the input files used
to generate the simulation (useful for adaptive), the parent of the simulation (if it was filtered it will point to
the original simulation) and a unique simulation id.
copy()¶htmd.simlist.simfilter(sims, outfolder, filtersel, njobs=None)¶Filters a list of simulations generated by simlist()
This function takes as input a list of simulations produced by simList and writes new trajectories containing only the desired atoms in a new directory.
sims (list) – A simulation list produced by the simList function
outfolder (str) – The folder in which to write the modified trajectories
filtersel (str) – Atom selection string describing the atoms we want to keep. See more here
njobs (int) – Number of parallel jobs to spawn for filtering of trajectories. If None it will use the default from htmd.config.
fsims – A list of filtered simulations
np.ndarray of Sim objects
Example
>>> sims = simlist(glob('data/*/'), glob('input/*/structure.pdb'))
>>> fsims = simfilter(sims, 'filtered', filtersel='not water')
htmd.simlist.simlist(datafolders, topologies, inputfolders=None)¶Creates a list of simulations
datafolders (str list) – A list of directories, each containing a single trajectory
topologies (str list) – A list of topology files or folders containing a topology file corresponding to the trajectories in dataFolders. Can also be a single string to a single structure which corresponds to all trajectories.
inputfolders (optional, str list) – A list of directories, each containing the input files used to produce the trajectories in dataFolders
sims – A list of simulations
np.ndarray of Sim objects
Examples
>>> simlist(glob('./test/data/*/'), glob('./test/input/*/'), glob('./test/input/*/'))
>>> simlist(glob('./test/data/*/'), glob('./test/input/*/*.pdb'), glob('./test/input/*/'))
htmd.simlist.simmerge(simlist1, simlist2)¶Merges two simlists by updating their simid fields