gromacs.tools – Gromacs commands classes

A Gromacs command class produces an instance of a Gromacs tool command ( gromacs.core.GromacsCommand), any argument or keyword argument supplied will be used as default values for when the command is run.

Classes has the same name of the corresponding Gromacs tool with the first letter capitalized and dot and dashes replaced by underscores to make it a valid python identifier. Gromacs 5 tools are also aliased to their Gromacs 4 tool names (e.g, sasa to g_sas) for backwards compatibility.

The list of tools to be loaded is configured with the tools and groups options of the ~/.gromacswrapper.cfg file. Guesses are made if these options are not provided.

In the following example we create two instances of the gromacs.tools.Trjconv command (which runs the Gromacs trjconv command):

from gromacs.tools import Trjconv

trjconv = tools.Trjconv()
trjconv_compact = tools.Trjconv(ur='compact', center=True, boxcenter='tric', pbc='mol',
                                input=('protein','system'))

The first one, trjconv, behaves as the standard commandline tool but the second one, trjconv_compact, will by default create a compact representation of the input data by taking into account the shape of the unit cell. Of course, the same effect can be obtained by providing the corresponding arguments to trjconv but by naming the more specific command differently one can easily build up a library of small tools that will solve a specific, repeatedly encountered problem reliably. This is particularly helpful when doing interactive work.

Multi index

It is possible to extend the tool commands and patch in additional functionality. For example, the GromacsCommandMultiIndex class makes a command accept multiple index files and concatenates them on the fly; the behaviour mimics Gromacs’ “multi-file” input that has not yet been enabled for all tools.

class gromacs.tools.GromacsCommandMultiIndex(**kwargs)

Command class that accept multiple index files.

It works combining multiple index files into a single temporary one so that tools that do not (yet) support multi index files as input can be used as if they did.

It creates a new file only if multiple index files are supplied.

gromacs.tools.merge_ndx(*args)

Takes one or more index files and optionally one structure file and returns a path for a new merged index file.

Parameters:args – index files and zero or one structure file Returns:path for the new merged index file

Helpers

gromacs.tools.tool_factory(clsname, name, driver, base=<class 'gromacs.core.GromacsCommand'>)

Factory for GromacsCommand derived types.

gromacs.tools.load_v4_tools()

Load Gromacs 4.x tools automatically using some heuristic.

Tries to load tools (1) in configured tool groups (2) and fails back to automatic detection from GMXBIN (3) then to a prefilled list.

Also load any extra tool configured in ~/.gromacswrapper.cfg

Returns:dict mapping tool names to GromacsCommand classes

gromacs.tools.load_v5_tools()

Load Gromacs 2018/2016/5.x tools automatically using some heuristic.

Tries to load tools (1) using the driver from configured groups (2) and falls back to automatic detection from GMXBIN (3) then to rough guesses.

In all cases the command gmx help is ran to get all tools available.

Returns:dict mapping tool names to GromacsCommand classes

gromacs.tools.find_executables(path)

Find executables in a path.

Searches executables in a directory excluding some know commands unusable with GromacsWrapper.

Parameters:path – dirname to search for Returns:list of executables

gromacs.tools.make_valid_identifier(name)

Turns tool names into valid identifiers.

Parameters:name – tool name Returns:valid identifier

exception gromacs.tools.GromacsToolLoadingError

Raised when no Gromacs tool could be found.

Gromacs tools

class gromacs.tools.Dyecoupl

class gromacs.tools.G_spatial

class gromacs.tools.Sigeps

class gromacs.tools.Density

class gromacs.tools.Chi

class gromacs.tools.G_filter

class gromacs.tools.Genrestr

class gromacs.tools.Nmtraj

class gromacs.tools.Analyze

class gromacs.tools.Helixorient

class gromacs.tools.G_sans

class gromacs.tools.Trjcat

class gromacs.tools.G_densorder

class gromacs.tools.G_helixorient

class gromacs.tools.Velacc

class gromacs.tools.G_principal

class gromacs.tools.Spol

class gromacs.tools.G_densmap

class gromacs.tools.Confrms

class gromacs.tools.G_order

class gromacs.tools.G_nmens

class gromacs.tools.Grompp

class gromacs.tools.G_angle

class gromacs.tools.Editconf

class gromacs.tools.Bar

class gromacs.tools.Trjconv

class gromacs.tools.Clustsize

class gromacs.tools.G_sgangle

class gromacs.tools.G_pairdist

class gromacs.tools.G_dyecoupl

class gromacs.tools.G_hydorder

class gromacs.tools.Sasa

class gromacs.tools.Vanhove

class gromacs.tools.G_help

class gromacs.tools.Help

class gromacs.tools.Solvate

class gromacs.tools.Hydorder

class gromacs.tools.Enemat

class gromacs.tools.Genion

class gromacs.tools.G_sham

class gromacs.tools.Polystat

class gromacs.tools.G_enemat

class gromacs.tools.G_density

class gromacs.tools.G_sigeps

class gromacs.tools.Check

class gromacs.tools.Select

class gromacs.tools.Tpbconv

class gromacs.tools.G_tcaf

class gromacs.tools.Genbox

class gromacs.tools.Nmens

class gromacs.tools.G_rms

class gromacs.tools.Pairdist

class gromacs.tools.G_dielectric

class gromacs.tools.Spatial

class gromacs.tools.G_anadock

class gromacs.tools.H2order

class gromacs.tools.G_disre

class gromacs.tools.Wham

class gromacs.tools.Nmr

class gromacs.tools.Mdrun

class gromacs.tools.Densorder

class gromacs.tools.G_confrms

class gromacs.tools.Trjorder

class gromacs.tools.G_view

class gromacs.tools.Awh

class gromacs.tools.G_dos

class gromacs.tools.G_hbond

class gromacs.tools.Tune_pme

class gromacs.tools.Anadock

class gromacs.tools.G_rdf

class gromacs.tools.Rmsf

class gromacs.tools.Sans

class gromacs.tools.Rmsdist

class gromacs.tools.Saltbr

class gromacs.tools.G_rama

class gromacs.tools.Disre

class gromacs.tools.Rdf

class gromacs.tools.Gmxdump

class gromacs.tools.Gangle

class gromacs.tools.G_h2order

class gromacs.tools.G_traj

class gromacs.tools.Anaeig

class gromacs.tools.Dump

class gromacs.tools.G_rotacf

class gromacs.tools.Energy

class gromacs.tools.G_lie

class gromacs.tools.G_x2top

class gromacs.tools.G_nmeig

class gromacs.tools.Rotmat

class gromacs.tools.G_dist

class gromacs.tools.G_gyrate

class gromacs.tools.Gmxcheck

class gromacs.tools.G_mindist

class gromacs.tools.G_sas

class gromacs.tools.Convert_tpr

class gromacs.tools.G_nmtraj

class gromacs.tools.Helix

class gromacs.tools.Densmap

class gromacs.tools.Msd

class gromacs.tools.Sham

class gromacs.tools.G_covar

class gromacs.tools.Saxs

class gromacs.tools.Bundle

class gromacs.tools.Pdb2gmx

class gromacs.tools.Mindist

class gromacs.tools.G_helix

class gromacs.tools.Mk_angndx

class gromacs.tools.G_mdmat

class gromacs.tools.Sorient

class gromacs.tools.G_nmr

class gromacs.tools.Insert_molecules

class gromacs.tools.Morph

class gromacs.tools.G_energy

class gromacs.tools.Filter

class gromacs.tools.G_rmsdist

class gromacs.tools.Gyrate

class gromacs.tools.G_clustsize

class gromacs.tools.Mdmat

class gromacs.tools.G_dipoles

class gromacs.tools.Freevolume

class gromacs.tools.Rama

class gromacs.tools.Xpm2ps

class gromacs.tools.Rms

class gromacs.tools.G_wham

class gromacs.tools.G_vanhove

class gromacs.tools.G_anaeig

class gromacs.tools.Cluster

class gromacs.tools.G_spol

class gromacs.tools.Dyndom

class gromacs.tools.G_pme_error

class gromacs.tools.G_current

class gromacs.tools.Eneconv

class gromacs.tools.Make_edi

class gromacs.tools.Lie

class gromacs.tools.G_potential

class gromacs.tools.Angle

class gromacs.tools.X2top

class gromacs.tools.Pme_error

class gromacs.tools.Trajectory

class gromacs.tools.G_select

class gromacs.tools.G_insert_molecules

class gromacs.tools.Current

class gromacs.tools.G_velacc

class gromacs.tools.Potential

class gromacs.tools.Dipoles

class gromacs.tools.Tcaf

class gromacs.tools.G_rotmat

class gromacs.tools.G_polystat

class gromacs.tools.Wheel

class gromacs.tools.G_bundle

class gromacs.tools.G_dyndom

class gromacs.tools.Covar

class gromacs.tools.G_msd

class gromacs.tools.Dielectric

class gromacs.tools.G_cluster

class gromacs.tools.Distance

class gromacs.tools.G_saltbr

class gromacs.tools.Rotacf

class gromacs.tools.G_freevolume

class gromacs.tools.Do_dssp

class gromacs.tools.G_bar

class gromacs.tools.Nmeig

class gromacs.tools.Hbond

class gromacs.tools.Traj

class gromacs.tools.G_wheel

class gromacs.tools.G_analyze

class gromacs.tools.Make_ndx

class gromacs.tools.Dos

class gromacs.tools.Order

class gromacs.tools.View

class gromacs.tools.Genconf

class gromacs.tools.G_tune_pme

class gromacs.tools.G_saxs

class gromacs.tools.G_mk_angndx

class gromacs.tools.G_trajectory

class gromacs.tools.G_morph

class gromacs.tools.G_chi

class gromacs.tools.G_awh

class gromacs.tools.G_sorient

class gromacs.tools.G_rmsf

class gromacs.tools.Principal