htmd.simlist module¶

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.

class htmd.simlist.Frame(sim, piece, frame)¶

Bases: object

Class used for referencing a specific frame of a Sim object object.

Parameters

sim (Sim object) – The simulation.
piece (int) – Which trajectory piece the frame corresponds to.
frame (int) – The frame of the specific trajectory piece.

frame¶

piece¶

sim¶

class 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.

simid¶

A unique simulation ID

Type: int

parent¶

The parent of the simulations

Type: Sim object

input¶

The path to the input folder which generated this simulation

Type: str

trajectory¶

A list of trajectory files

Type: list

molfile¶

The path to the structural information about the simulation. Usually a PDB file

Type: str

numframes¶

Number of frames in trajectories

Type: list

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.

Parameters

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.

Returns

fsims – A list of filtered simulations

Return type

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

Parameters

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

Returns

sims – A list of simulations

Return type

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

Parameters

simlist1 (numpy array of Sim objects) – First list
simlist2 (numpy array of Sim objects) – Second list

Returns

newlist – A new list containing all simulations

Return type

np.ndarray of Sim objects