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 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.G_spatial

class gromacs.tools.G_g_anaeig

class gromacs.tools.G_g_spol

class gromacs.tools.G_g_mindist

class gromacs.tools.G_filter

class gromacs.tools.Genrestr

class gromacs.tools.G_g_cluster

class gromacs.tools.G_g_traj

class gromacs.tools.G_g_nmtraj

class gromacs.tools.Trjcat

class gromacs.tools.G_g_luck

class gromacs.tools.G_helixorient

class gromacs.tools.G_gyrate

class gromacs.tools.G_densmap

class gromacs.tools.G_g_confrms

class gromacs.tools.G_g_pme_error

class gromacs.tools.G_g_clustsize

class gromacs.tools.G_g_energy

class gromacs.tools.G_nmens

class gromacs.tools.Grompp

class gromacs.tools.G_g_sorient

class gromacs.tools.G_dist

class gromacs.tools.Trjconv

class gromacs.tools.G_g_select

class gromacs.tools.G_cluster

class gromacs.tools.G_sgangle

class gromacs.tools.G_g_disre

class gromacs.tools.G_g_angle

class gromacs.tools.G_anaeig

class gromacs.tools.G_g_rmsf

class gromacs.tools.Genion

class gromacs.tools.G_gmxdump

class gromacs.tools.G_sham

class gromacs.tools.G_protonate

class gromacs.tools.G_enemat

class gromacs.tools.G_density

class gromacs.tools.G_sigeps

class gromacs.tools.G_nmeig

class gromacs.tools.G_g_tcaf

class gromacs.tools.Tpbconv

class gromacs.tools.G_tcaf

class gromacs.tools.Mdrun_d

class gromacs.tools.Genbox

class gromacs.tools.G_rms

class gromacs.tools.G_current

class gromacs.tools.G_dielectric

class gromacs.tools.G_g_chi

class gromacs.tools.G_msd

class gromacs.tools.G_g_anadock

class gromacs.tools.G_g_densmap

class gromacs.tools.G_disre

class gromacs.tools.G_analyze

class gromacs.tools.Mdrun

class gromacs.tools.G_g_analyze

class gromacs.tools.G_g_sgangle

class gromacs.tools.G_g_dielectric

class gromacs.tools.G_confrms

class gromacs.tools.Trjorder

class gromacs.tools.G_principal

class gromacs.tools.G_g_polystat

class gromacs.tools.G_g_velacc

class gromacs.tools.G_g_rotacf

class gromacs.tools.G_rdf

class gromacs.tools.G_anadock

class gromacs.tools.G_g_helix

class gromacs.tools.G_g_morph

class gromacs.tools.G_hbond

class gromacs.tools.G_g_kinetics

class gromacs.tools.G_g_sigeps

class gromacs.tools.G_g_sham

class gromacs.tools.G_g_nmeig

class gromacs.tools.Gmxdump

class gromacs.tools.G_h2order

class gromacs.tools.G_traj

class gromacs.tools.G_g_bar

class gromacs.tools.G_g_order

class gromacs.tools.G_x2top

class gromacs.tools.G_g_vanhove

class gromacs.tools.G_g_enemat

class gromacs.tools.G_dih

class gromacs.tools.G_g_saltbr

class gromacs.tools.Gmxcheck

class gromacs.tools.G_mindist

class gromacs.tools.G_sas

class gromacs.tools.G_g_dyndom

class gromacs.tools.G_g_current

class gromacs.tools.G_g_rmsdist

class gromacs.tools.G_nmtraj

class gromacs.tools.G_g_gyrate

class gromacs.tools.G_g_bundle

class gromacs.tools.G_g_covar

class gromacs.tools.G_bond

class gromacs.tools.G_covar

class gromacs.tools.G_g_dih

class gromacs.tools.Editconf

class gromacs.tools.Pdb2gmx

class gromacs.tools.G_g_sas

class gromacs.tools.G_g_lie

class gromacs.tools.G_helix

class gromacs.tools.Mk_angndx

class gromacs.tools.G_mdmat

class gromacs.tools.Eneconv

class gromacs.tools.G_g_rotmat

class gromacs.tools.G_energy

class gromacs.tools.G_rmsdist

class gromacs.tools.G_tpbconv

class gromacs.tools.G_clustsize

class gromacs.tools.G_g_protonate

class gromacs.tools.G_dipoles

class gromacs.tools.G_lie

class gromacs.tools.G_g_hbond

class gromacs.tools.Xpm2ps

class gromacs.tools.G_rama

class gromacs.tools.G_wham

class gromacs.tools.G_vanhove

class gromacs.tools.G_rotacf

class gromacs.tools.G_g_spatial

class gromacs.tools.G_g_rama

class gromacs.tools.G_luck

class gromacs.tools.G_spol

class gromacs.tools.G_g_membed

class gromacs.tools.G_pme_error

class gromacs.tools.G_g_tune_pme

class gromacs.tools.Make_edi

class gromacs.tools.G_angle

class gromacs.tools.G_potential

class gromacs.tools.G_g_mdmat

class gromacs.tools.G_g_dist

class gromacs.tools.G_select

class gromacs.tools.G_gmxcheck

class gromacs.tools.G_g_nmens

class gromacs.tools.G_g_filter

class gromacs.tools.G_velacc

class gromacs.tools.G_g_dipoles

class gromacs.tools.G_g_x2top

class gromacs.tools.G_g_wheel

class gromacs.tools.G_rotmat

class gromacs.tools.G_g_potential

class gromacs.tools.G_polystat

class gromacs.tools.G_genbox

class gromacs.tools.G_bundle

class gromacs.tools.G_order

class gromacs.tools.G_g_density

class gromacs.tools.G_g_wham

class gromacs.tools.G_g_helixorient

class gromacs.tools.G_g_bond

class gromacs.tools.G_g_rms

class gromacs.tools.G_saltbr

class gromacs.tools.G_g_msd

class gromacs.tools.Do_dssp

class gromacs.tools.G_bar

class gromacs.tools.G_g_h2order

class gromacs.tools.G_wheel

class gromacs.tools.Make_ndx

class gromacs.tools.G_mk_angndx

class gromacs.tools.G_dyndom

class gromacs.tools.Genconf

class gromacs.tools.G_tune_pme

class gromacs.tools.G_g_rdf

class gromacs.tools.G_kinetics

class gromacs.tools.G_morph

class gromacs.tools.G_chi

class gromacs.tools.G_membed

class gromacs.tools.G_sorient

class gromacs.tools.G_rmsf

class gromacs.tools.G_g_principal