pygromos.gromos package¶

Subpackages¶

pygromos.gromos.pyGromosPP package

Submodules¶

pygromos.gromos.compile_gromos module¶

pygromos.gromos.compile_gromos._configure_gromosPP_autotools(build_dir: str, binary_dir: Optional[str] = None, with_omp: bool = False, with_debug: bool = False, verbose: bool = True, _timing_dict: dict = {})[source]¶

Setting the configurations for the compiling gromosPP process. (uses autotools)

Parameters

build_dir (str) – directory, that should be used for building
binary_dir (str, optional) – directory in which the binaries should be written to, by default None
with_omp (bool, optional) – should gromosPP be compiled with omp, by default False
with_debug (bool, optional) – set gromos debug flag, by default False
verbose (bool, optional) – compiling is fun, I can tell you more!, by default True
_timing_dict (dict, optional) – structure for storing timings of process, by default {}

pygromos.gromos.compile_gromos._configure_gromosXX_autotools(build_dir: str, binary_dir: Optional[str] = None, with_cuda_dir: Optional[str] = None, with_omp: bool = False, with_mpi: bool = False, with_debug: bool = False, verbose: bool = True, _timing_dict: dict = {})[source]¶

Setting the configurations for the compiling gromosXX process. (uses autotools)

Parameters

build_dir (str) – directory, that should be used for building
binary_dir (str, optional) – directory in which the binaries should be written to, by default None
with_cuda_dir (str, optional) – use the following cuda path and activate cuda support, by default None
with_omp (bool, optional) – should gromosXX be compiled with omp - Warning dont combine wiht mpi!, by default False
with_mpi (bool, optional) – should gromosXX be compiled wiht mpi - Warning dont combine with omp!, by default False
with_debug (bool, optional) – set gromos debug flag, by default False
verbose (bool, optional) – compiling is fun, I can tell you more!, by default True
_timing_dict (dict, optional) – structure for storing timings of process, by default {}

Raises

ValueError – if wrong value was passed

pygromos.gromos.compile_gromos._make_clean(build_dir: str, nCore: int = 1, verbose: bool = True, _timing_dict: dict = {}, _timing_prefix: str = '')[source]¶

This function triggers make clean and removes the build_dir.

Parameters

build_dir (str) – directory prepared for make.
nCore (int, optional) – how many cores for each make command?, by default 1
verbose (bool, optional) – cleaning, cleaning, every thing gets so shiny and I can sing!, by default True
_timing_dict (dict, optional) – structure for storing timings of process, by default {}
_timing_prefix (str, optional) – prefix for timing keys, by default “”

pygromos.gromos.compile_gromos._make_compile(build_dir: str, nCore: int = 1, verbose: bool = True, _timing_dict: dict = {}, _timing_prefix: str = '')[source]¶

This function triggers make and make install in the build_dir.

Parameters

build_dir (str) – directory prepared for make.
nCore (int, optional) – how many cores for each make command?, by default 1
verbose (bool, optional) – make, make things and talk loudly about it! , by default True
_timing_dict (dict, optional) – structure for storing timings of process, by default {}
_timing_prefix (str, optional) – prefix for timing keys, by default “”

pygromos.gromos.compile_gromos.default_install(nCores: int = 1, _timing_dict: dict = {}, verbose: bool = False)[source]¶

pygromos.gromos.compile_gromos.install_gromos(root_dir: Optional[str] = None, nCore: int = 3, gromosXX_with_mpi: bool = False, gromosXX_with_omp: bool = False, gromosXX_with_cuda: Optional[str] = None, gromosPP_with_omp=False, gromosPP_with_debug: bool = False, gromosXX_with_debug: bool = False, do_compile: bool = True, do_clean: bool = True, recompile: bool = False, recompile_from_scratch: bool = False, _do_gromosPP: bool = True, _do_gromosXX: bool = True, _timing_dict: dict = {}, verbose: bool = True)[source]¶

Install the gromos simulation packages. As a helper: to get the dependencies right, install and activate the provided pygromos environments!

Parameters

root_dir (str) – this dir contains the gromosXX and the gromosPP git repositories
nCore (int, optional) – how many cores should be used to compile?, by default 1
gromosXX_with_cuda_dir (str, optional) – use the following cuda path and activate cuda support, by default None
gromosXX_with_omp (bool, optional) – should gromosXX be compiled with omp - Warning dont combine wiht mpi!, by default False
gromosXX_with_mpi (bool, optional) – should gromosXX be compiled wiht mpi - Warning dont combine with omp!, by default False
gromosPP_with_omp (bool, optional) – should gromosPP be compiled with omp, by default False
gromosPP_with_debug (bool, optional) – set gromosPP debug flag, by default False
gromosXX_with_debug (bool, optional) – set gromosXX debug flag, by default False
do_compile (bool, optional) – compile the programms, by default True
do_clean (bool, optional) – clean up and remove the programs (can be used together with do_compile to get a clean start), by default False
recompile (bool, optional) – recompile the programs with make, by default False
recompile_from_scratch (bool, optional) – recompile with configure and make, by default False
_do_gromosPP (bool, optional) – install the gromosPP program, by default True
_do_gromosXX (bool, optional) – install the gromosXX program, by default True
_timing_dict (dict, optional) – structure for storing timings of process, by default {}
verbose (bool, optional) – compiling is fun, I can tell you more!, by default True

pygromos.gromos.gromosBashSyntaxParser module¶

class pygromos.gromos.gromosBashSyntaxParser.gromosBashSyntaxParser[source]¶

Bases: object

Helper class to parse general gromos bash syntax

all methods should be static

static atomSliceParser()[source]¶

static moleculeSliceParser()[source]¶

static multiplyArgumentParser(args: Union[str, List[str]], multiplier: Union[int, List[int]] = 1) → str[source]¶

Parser for multiplier syntax to gromos scripts

example: com_top @topo 1:Protein 2:Na 2:Cl 100:SPC …..

Parameters

args (str or list(str)) – The actual argument which should be multiplied (ex. top)
multiplier (int or list(int)) – the multiplier for each argument provided in args

pygromos.gromos.gromosPP module¶

FUNCTIONLIB: wrapper for gromos++ Description:

This file contains python wrappers for the bash commandline of gromos++

Author: Benjamin Schroeder

class pygromos.gromos.gromosPP.GromosPP(gromosPP_bin_dir: Optional[str] = None, _check_binary_paths: bool = True, verbose: bool = False)[source]¶

Bases: pygromos.gromos.gromosPP._gromosPPbase

This is the class represents gromosPP.

binstr, optional: This is the path to the folder containing the binaries of gromosPP If None, the bash enviroment variables will be used.

class pygromos.gromos.gromosPP._gromosPPbase(gromosPP_bin_dir: Optional[str] = None, _check_binary_paths: bool = True, verbose: bool = False)[source]¶

Bases: pygromos.gromos._gromosClass._gromosClass

GromosPP

This is the gromosPP baseclass. This should be inherited by a concrete class that might reimplement some new features, that are version dependent.

binstr, optional: This is the path to the folder containing the binaries of gromosPP. If None, the bash enviroment variables will be used.

__init__(gromosPP_bin_dir: Optional[str] = None, _check_binary_paths: bool = True, verbose: bool = False)[source]¶

Constructing a gromosPP object.

Parameters

bin (Union[str, None], optional) – This is the path to the folder containing the binaries of gromosXX. If None, the bash enviroment variables will be used.
_dont_check_binary (bool, optional) – This flag removes the checks of the binary presence for this obj. This can make sense if system access is slow!, by default False - checks will be made

add_hydrogens(in_cnf_path: str, in_top_path: str, out_cnf_path: str, tolerance: float = 0.1, periodic_boundary_condition: str = 'v', gathering: str = 'cog', _binary_name: str = 'gch') → str[source]¶

This function protonates a coordinate file.

Parameters

in_cnf_path (str)
in_top_path (str)
out_cnf_path (str)
tolerance (float, optional)
periodic_boundary_condition (str, optional)
gathering (str, optional)
_binary_name (str, optional)

Return type

out_cnf_path

amber2gromos(ambertop: str, solvent: str, ljscaling: float = 2.0, chargegroups: str = None, atomic_chargegroups: bool = False, out_path: str = 'topology.top', _binary_name: str = 'amber2gromos', verbose: bool = False)[source]¶

Parameters

ambertop (str) – path to AMBER molecular topology file
solvent (str) – path to GROMOS topology file with solvent
ljscaling (float, optional) – scaling factor for LJ parameters (default: 2.0)
atomic_chargegroups (bool, optional) – assign each atom to its own chargegroup (default: False)
chargegroups (str, optional) – path to chargegroup file
_binary_name (str, otpional) – binary name of gromosPP programm (default: amber2gromos)

Returns

converted GROMOS topology

Return type

str

build_box(in_top_path: str, in_cnf_path: str, out_cnf_path: str = '', periodic_boundary_condition: str = 'r', nmolecule: int = 1, dens: float = 1.0, _binary_name: str = 'build_box', verbose: bool = False, return_command_only: bool = False) → str[source]¶

cog(in_top_path: str, in_trcs: Union[str, List[str]], out_file_path: str, atom_selection: str = None, outformat: str = None, cog_com: str = None, add_repl: str = None, solv: str = None, nthframe: str = None, pbc: str = 'r cog', _binary_name: str = 'cog', verbose: bool = False) → str[source]¶

Parameters

in_top_path (str) – path to topo file
in_trcs (str) – path to trc files
out_file_path (str) – outpath
atom_selection (str, optional) – atomspecifier(s) for which to calculate cog/com
outformat (str, optional) – output coordinates format
cog_com (str, optional) – calculate centre of geometry (cog) or mass (com); default: cog
add_repl (str, optional) – add (add) the cog/com or replace (repl) the solutes; default: repl
solv (str, optional) – include solvent in outcoordinates
nthframe (str, optional) – write every nth frame (default: 1)
_binary_name (str, otpional) – binary name of gromosPP programm (default: cog)

Returns

output_path of the generated csv file

Return type

str

com_top(in_topo_paths: Union[str, List[str]], topo_multiplier: Union[int, List[int]] = 1, out_top_path: str = 'combined_out.top', take_topology_params_of_file: int = 1, take_solvent_parameters_of_file: int = 1, _binary_name: str = 'com_top') → str[source]¶

Combine multiple topologies :Parameters: * in_topo_paths ((str or List[str]))

out_top_path (str, optional)

take_topology_params_of_file (int, optional)

take_solvent_parameters_of_file (int, optional)

_binary_name (str, optional)

Returns: output file_path
Return type: str

See also

make_top: For more information checkout the Gromos Manual

dfmult(in_endstate_file_paths: List[str], in_reference_state_file_path: str, out_file_path: str = 'dfmult_temp.out', temperature: float = 298, _binary_name: str = 'dfmult', verbose: bool = False) → str[source]¶

This funciton wraps dfmult of the gromos suite, it is used to calculate the free energy of a EDS simulation.

Parameters

in_endstate_file_paths (List[str]) – potentials energy of single state (get with ene Ana)
in_reference_state_file_path (str) – potential energy of reference State (get with ene Ana)
out_file_path (str, optional)
temperature (float, optional)
_binary_name (str, optional)
verbose (bool, optional)

Returns

out_put file path

Return type

str

ene_ana(in_ene_ana_library_path: str, in_en_file_paths: str, in_properties: str, out_energy_folder_path: str, out_files_prefix: str = None, out_files_suffix: str = None, in_topo: str = None, time: float = None, single_file: bool = False, return_outstat_also: bool = False, verbose: bool = False, _binary_name: str = 'ene_ana', workdir: bool = False) → Union[List[str], str][source]¶

This is a wrapper for ene_ana.
ene_ana is a tool to extract energy properties from a x.tre file.

Parameters

in_ene_ana_library_path (str)
in_en_file_paths (str)
in_properties (str) –

this str should name the properties, that shall be written out. For the variable names, check the ene_ana lib.
(e.g.: “solvtemp1 e1 eR”)
out_energy_folder_path (str) – give the path to an directory, where the output should be stored in.
out_files_prefix (None or str, optional)
out_files_suffix (None or str, optional)
in_topo (None or str, optional)
time (None or float, optional)
single_file (bool, optional) – if used a single csv is generated. the return value gets the file_path(str).
verbose (bool, optional)
_binary_name (str, optional)

Returns

if single_file used, return = str

Return type

List[str] or str

filter(out_filter_path: str, in_coord_path: str, in_top_path: str, atom_selection: Optional[str] = None, periodic_boundary_condition: str = 'r cog', cutoff: Optional[float] = None, pairlist: Optional[str] = None, select: str = '1:a', reject: Optional[str] = None, time: Optional[int] = None, dt: Optional[int] = None, outformat: Optional[str] = None, _binary_name: str = 'filter') → str[source]¶

This wrapper uses filter to reduce a given trajectory to a selection of atoms. By default, only the first residue (1:a) is retained.

Parameters

out_filter_path (str)
in_coord_path (str)
in_top_path (str)
atom_selection (str, optional)
periodic_boundary_condition (str, optional)
cutoff (float, optional)
pairlist (str, optional)
select (str, optional)
reject (str, optional)
time (int, optional)
dt (int, optional)
outformat (str, optional)
_binary_name (str, optional)

Returns

returns out_filter_path

Return type

str

frameout(in_top_path: str, in_coord_path: str, periodic_boundary_condition: str, out_file_path: str = None, out_file_format: str = None, single_file: bool = None, gather: Union[int, str] = None, include: str = 'SOLUTE', reference_structure_path: str = None, atomsfit: str = None, frames: int = None, time: int = None, dt: int = None, notimeblock: bool = None, _binary_name: str = 'frameout', verbose: bool = False) → str[source]¶

this wrapper wraps frameout.
frameout is a tool, that can be used for example to convert gromos coordinate files or to recenter them or …. Optional parameters are not used in the command, when they are None!

Parameters

in_top_path (str)
in_coord_path (str)
periodic_boundary_condition (str)
out_file_path (None or str, optional)
out_file_format (None or str, optional)
single_file (None or bool, optional)
gather (None or int or str optional)
include (None or str, optional) – ALL that also includes the solvent. SOLUTE this option filters the Solvent out of the output file. (default) alternative gromos selection synthax can be used.
reference_structure_path (None or str, optional) – This path should provide a refrence position for atom fitting.
atomsfit (None or str, optional) – This option can be used to fit all frames to one reference structure. The selection Syntax follow the Gromos manual (e.g. “1:a” - aligns all frames to the first molecule and all its atoms) requires reference_sturcture_path.
frames (None or int, optional)
time (None or float, optional)
dt (None or float, optional)
notimeblock (None or bool, optional)
_binary_name (str, optional)
verbose (bool, optional)

Returns

out_file_path

Return type

str

gch(in_cnf_path: str, in_top_path: str, out_cnf_path: str, tolerance: float = 0.1, periodic_boundary_condition: str = 'v', gathering: str = 'cog', _binary_name: str = 'gch') → str[source]¶

This function adds reasonable hydrogenpositions a coordinate file.

Parameters

in_cnf_path (str)
in_top_path (str)
out_cnf_path (str)
tolerance (float, optional)
periodic_boundary_condition (str, optional)
gathering (str, optional)
_binary_name (str, optional)

Return type

out_cnf_path

ion(in_top_path: str, in_cnf_path: str, out_cnf_path: str, periodic_boundary_condition: str = 'v', negative: list = None, positive: list = None, potential: float = 0.8, mindist: float = 0.8, random_seed: int = None, exclude: str = None, _binary_name: str = 'ion', verbose: bool = False) → str[source]¶

When simulating a charged solute in solution, one may wish to include counter-ions in the molecular system in order to obtain a neutral system, or a system with a specific ionic strength. The program ion can replace solvent molecules by atomic ions by placing the ion at the position of the first atom of a solvent molecule. Substitution of solvent molecules by positive or negative ions can be performed by selecting the solvent positions with the lowest or highest Coulomb potential, respectively, or by random selection. In order to prevent two ions being placed too close together, a sphere around each inserted ion can be specified from which no solvent molecules will be substituted by additional ions. In addition, the user can specify specific water molecules that should not be considered for replacement.

Parameters

in_top_path (str) – the path to the input topology file (.top)
in_cnf_path (str) – the path to the input coordinate file (.cnf), to which the ions shall be added
out_cnf_path (str) – the path to the resulting coordinate (.cnf) file
periodic_boundary_condition (str, optional) – describes the boundary condition of the given system in the cnf. (r - rectangle, v - vacuum, ). a gathering method can be optionally added with a whitespace seperation., by default “v”
negative (list, optional) – the first element of the list is the number of ions and the second element of the list is the type of ion, optionally a third element can be passed giving the residue name, by default None
positive (list, optional) – the first element of the list is the number of ions and the second element of the list is the type of ion, optionally a third element can be passed giving the residue name, by default None
potential (float, optional) – cutoff for potential calculation[nm], by default 0.8
mindist (float, optional) – minimum distance between ions[nm], by default 0.8
random_seed (int, optional) – provide the used random seed, by default None
exclude (str, optional) – if you want to exclude solvent molecules, define a gromos selection here, by default None
_binary_name (str, optional) – the program name, by default “ion”
verbose (bool, optional) – stay a while and listen, by default False

Returns

returns the resulting cnf-file path

Return type

str

jval(in_top_path: str, in_jval_path: str, in_traj_path: Union[str, List[str]], out_path: str, pbc: str = 'v', gathering: str = 'cog', timeseries: bool = False, rmsd: bool = False, time: float = None, _binary_name: str = 'jval', verbose: bool = False)[source]¶

Parameters

in_top_path (str) – topology path
in_jval_path (str) – jval specification path
in_traj_path (str) – coordinate file
out_path (str) – path to the output file
pbc (str, optional) – default: v periodic boundary condition of the coordinates:

v - vacuum r - rectangular box
gathering (str, optional) – default: cog how the coordinates shall be gathered before the calculation:

cog - center of geometry com - center of mass
timeseries (bool, optional)
rmsd (bool, optional)
time ((Number, str), optional)

Returns

str – out_path
NotImplemented
—————
time (float, float (time, dt))

make_top(out_top_path: str, in_building_block_lib_path: str, in_parameter_lib_path: str, in_sequence: str, in_solvent: str = 'H2O', _binary_name: str = 'make_top') → str[source]¶

This wrapper uses make_top to generate a topology file.

Parameters

out_top_path (str)
in_building_block_lib_path (str)
in_parameter_lib_path (str)
in_sequence (str)
in_solvent (str, optional)
additional_options (str, optional)

Returns

returns out_file_path

Return type

str

noe(in_top_path: str, in_noe_path: str, in_traj_path: str, out_path: str, pbc: str = 'v', gathering: str = 'cog', _binary_name: str = 'noe', verbose: bool = False) → str[source]¶

Parameters

in_top_path (str) – topology path
in_noe_path (str) – output path of prep_noe
in_traj_path (str) – coordinate file
out_path (str) – path to the output file
pbc (str, optional) – default: v periodic boundary condition of the coordinates:

v - vacuum r - rectangular box
gathering (str, optional) – default: cog how the coordinates shall be gathered before the calculation:

cog - center of geometry com - center of mass

Returns

str – out_path
NotImplemented
—————
time (float, float (time, dt))

pdb2gromos(in_pdb_path: str, in_top_path: str, out_cnf_path: str = None, in_lib_path: str = '/home/mlehner/PyGromosTools/pygromos/data/pdb2g96.lib', _binary_name: str = 'pdb2g96', verbose: bool = False) → str[source]¶

This is a wrapper for pdb2gromos. It executes the gromosPP binary.

Parameters

in_pdb_path (str)
in_top_path (str)
in_lib_path (str, optional) – The lib can be used as a look up table for residues or atoms etc. - see gromos manual
out_cnf_path (str, optional) – The out_cnf is the path for the output file. if not given, the pdb basename and dir is taken as default.
_binary_name (str, optional)
verbose (bool, optional)

Returns

Returns out_cnf path

Return type

str

pdb2seq(in_pdb_path: str, out_path: str = '', pH: float = 7.4, select: str = 'ALL', gff: str = '54a7', add_head: str = 'NH3+', add_tail: str = 'COO-', _binary_name: str = 'pdb2seq') → str[source]¶

This function is translating a pdb into a sequence file, that can be used to generate for example topologies.

Parameters

in_pdb_path (str)
out_path (str, optional) – out_path for output File
pH (float, optional)
select (str, optional)
gff (str,optional) – which Gromos ForceField
add_head (str, optional) – protein N-term capping with this group.
add_tail (str,optional) – protein C-term capping with this group
_binary (str, optional)

Returns

out_path

Return type

str

prep_eds(in_top_paths: List[str], number_of_eds_states: int, param_top_index: int = 1, solv_top_index: int = 1, out_file_path: str = 'dev', _binary_name: str = 'prep_eds', verbose: bool = False) → Tuple[str, str][source]¶

prepare eds topology.

Parameters

in_top_paths (List[str])
number_of_eds_states (int)
param_top_index (int, optional)
solv_top_index (int, optional)
out_file_path (str, optional) – output path without file ending. (prefix)
_binary_name (str, optional)
verbose (bool, optional)

Returns

out_top, out_ptp

Return type

tuple[str,str]

prep_noe(in_top_path: str, in_noe_path: str, in_library_path: str, out_path: str, dish: float = 0.1, disc: float = 0.153, title: str = 'NOE', _binary_name: str = 'prep_noe', in_correction_path: str = None, verbose: bool = False) → str[source]¶

Parameters

in_top_path (str) – molecular topology file
in_noe_path (str) – NOE specification file
in_library_path (str) – NOE specification library
out_path (str) – path to the output file
dish (float, optional) – carbon-hydrogen distance; default: 0.1 nm
disc (float, optional) – carbon-carbon distance; default: 0.153 nm
title (str, optional) – NOE title for output, default: “NOE”
correction (str, optional) – Correction file -> <correction_file> [correction type]

Returns

str – path to the output file
NotImplemented
——-
parsetype (<1,2,3>) –

Choices are:
1: Upper bound == first number 2: Upper bound == first + third number (most common, default) 3: Upper bound == first - second number (commonly the lower bound)
action (<add> or <substraction> = add)
filter (discard nNOE’s above a certain distance[nm] = 10000 nm)
factor (conversion factor ang to nm , = 10)

ran_box(in_top_path: str, in_cnf_path: str, out_cnf_path: str = '', periodic_boundary_condition: str = 'r', nmolecule: int = 1, dens: float = 1.0, threshold: float = None, layer: bool = False, boxsize: float = None, fixfirst: bool = False, seed: float = None, _binary_name: str = 'ran_box', verbose: bool = False, return_command_only: bool = False) → str[source]¶

red_top(in_top_path: str, atom_selection: str, out_top_path: str, _binary_name: str = 'red_top') → str[source]¶

red_top is a gromos tool to reduce a gromos tool to a certain selection.

Parameters

in_top_path (str)
atom_selection (str)
out_top_path (str)
_binary_name (str, optional)

Returns

out_top_path

Return type

str

rgyr(out_rgyr_path: str, in_coord_path: str, in_top_path: str, atom_selection: str = '1:a', periodic_boundary_condition: str = 'r cog', time: Optional[int] = None, dt: Optional[int] = None, mass_weighted: bool = False, _binary_name: str = 'rgyr') → str[source]¶

This wrapper uses rgyr to compute the radius of gyration for a given atom selection.

Parameters

out_rgyr_path (str)
in_coord_path (str)
in_top_path (str)
atom_selection (str, optional)
periodic_boundary_condition (str, optional)
time (int, optional)
dt (int, optional) – mass_weighted:bool, optional _binary_name: str, optional

Returns

returns out_rgyr_path

Return type

str

rmsd(in_top_path: str, in_trcs: Union[str, List[str]], atom_selection: str, out_file_path: str, pbc: str = 'r', _binary_name: str = 'rmsd') → str[source]¶

Parameters

in_top_path
in_trcs
atom_selection
out_file_path
pbc
_binary_name

rmsf(in_top_path: str, in_trcs: Union[str, List[str]], atom_selection: str, out_file_path: str, pbc: str = 'r', _binary_name: str = 'rmsf') → str[source]¶

this is a wrapper for gromosPP rmsf programm. (Root mean square fluctuation

Parameters

in_top_path (str) – path to topology file
in_trcs (Union[str, List[str]]) – Path OR paths to trc coordinate files
atom_selection (str) – selection of atoms
out_file_path – out path.
pbc (str) – periodic boundary condition of trc files
_binary_name (str) – binary name of gromos file

Returns

outpath of the traj

Return type

str

sasa(out_sasa_path: str, in_coord_path: str, in_top_path: str, atom_selection: str = '1:a', sasa_atoms: str = '1:a', probe: str = '4 1.4', periodic_boundary_condition: str = 'r cog', zslice: Optional[float] = None, time: Optional[int] = None, dt: Optional[int] = None, verbose: bool = False, _binary_name: str = 'sasa') → str[source]¶

This wrapper uses sasa to compute the solvent accessible surface area (SASA) for a given atom selection. By default, this is done for the first residue (1:a) with parameters for water (IAC type: 4, radius: 0.4 nm)

Parameters

out_sasa_path (str)
in_coord_path (str)
in_top_path (str)
atom_selection (str, optional)
sasa_atoms (str, optional)
probe (str, optional)
periodic_boundary_condition (str, optional)
zslice (float, optional)
time (int, optional)
dt (int, optional)
verbose (bool, optional)
_binary_name (str, optional)

Returns

returns out_sasa_path

Return type

str

sim_box(in_top_path: str, in_cnf_path: str, in_solvent_cnf_file_path: str, out_cnf_path: str = '', periodic_boundary_condition: str = 'r', gathering_method: str = None, minwall: float = 0.8, threshold: float = None, rotate: str = None, boxsize: bool = False, _binary_name: str = 'sim_box', verbose: bool = False) → str[source]¶

When simulating a molecule in solution or in a crystal containing solvent molecules, the atomic coordinates of the solvent molecules are to be generated, if they are not available from experiment. Program sim_box can solvate a solute in a pre-equilibrated box of solvent molecules. The file specifying the solvent configuration should contain a BOX block with the dimensions corresponding to the pre-equilibrated density. The solvent topology is read from the solvent block in the specified topology.

Parameters

in_top_path (str) – the path to the input topology file (.top)
in_cnf_path (str) – the path to the input coordinate file (.cnf), which shall be solvated
in_solvent_cnf_file_path (str) – the path to the input coordinate file of the solvent (.cnf), that shall be used to solvate (checkout pygromos.data.solvent_coordinates for templates)
out_cnf_path (str, optional) – the path to the resulting coordinate (.cnf) file, by default “”
periodic_boundary_condition (str, optional) – describes the boundary condition of the given system in the cnf. (r - rectangle, v - vacuum, ), by default “r”
gathering_method (str, optional) – the gathering method to be used, by default None
minwall (float, optional) – minimum solute to wall distance, by default 0.8
threshold (float, optional) – minimum solvent-solute distance, by default None -> 0.23 nm
rotate (str, optional) – rotate solute: biggest axis along z, second along y, by default None
boxsize (bool, optional) – use boxsize specified in solute coordinate file, by default False
_binary_name (str, optional) – name of the binary, by default “sim_box”
verbose (bool, optional) – stay a while and listen!, by default False

Returns

return the path to the resulting cnf path.

Return type

str

tser(in_trc_path: str, in_top_path: str, out_csv_path: str, property: str, periodic_boundary_condition: str = 'r', time: float = None, solvent: str = None, normalise_distribution: bool = False, skip_first_n_frames: int = 0, take_each_nth_frame: int = 1, _binary_name: str = 'tser') → str[source]¶

Tser is a gromos programm, that can analyze trajectories.

Parameters

in_trc_path (str)
in_top_path (str)
out_csv_path (str)
property (str)
periodic_boundary_condition (str, optional)
time (float, optional)
solvent (str, optional)
normalise_distribution (bool, optional)
skip_first_n_frames (int, optional)
take_each_nth_frame (int, optional)
_binary_name (str, optional)

Warning

missing options: @nots, @dist

Returns: out_csv_path
Return type: str

pygromos.gromos.gromosXX module¶

FUNCTIONLIB: wrapper for gromosXX Description:

This file contains python wrappers for the bash commandline of gromosXX

Author: Benjamin Schroeder

class pygromos.gromos.gromosXX.GromosXX(gromosXX_bin_dir: Optional[str] = None, _check_binary_paths: bool = True)[source]¶

Bases: pygromos.gromos.gromosXX._GromosXX

This is the class represents gromosXX.

binstr, optional: This is the path to the folder containing the binaries of gromosXX. If None, the bash enviroment variables will be used.

class pygromos.gromos.gromosXX._GromosXX(gromosXX_bin_dir: Optional[str] = None, _check_binary_paths: bool = True)[source]¶

Bases: pygromos.gromos._gromosClass._gromosClass

GromosXX

This is the gromosXX baseclass. This should be inherited by a concrete class that might reimplement some new features, that are version dependent.

binstr, optional: This is the path to the folder containing the binaries of gromosXX. If None, the bash enviroment variables will be used.

__init__(gromosXX_bin_dir: Optional[str] = None, _check_binary_paths: bool = True)[source]¶

Constructing a gromosXX object.

Parameters

gromosXX_bin_dir (str, optional) – This is the path to the folder containing the binaries of gromosXX. If None, the bash enviroment variables will be used.
_dont_check_binary (bool, optional) – This flag removes the checks of the binary presence for this obj. This can make sense if system access is slow!, by default False - checks will be made

md_run(in_topo_path: str, in_coord_path: str, in_imd_path: str, out_prefix: str, in_pert_topo_path: str = None, in_disres_path: str = None, in_posresspec_path: str = None, in_refpos_path: str = None, in_qmmm_path: str = None, nomp: int = 1, nmpi: int = 1, out_trc: bool = False, out_tre: bool = False, out_trv: bool = False, out_trf: bool = False, out_trs: bool = False, out_trg: bool = False, verbose: bool = False, _binary_name: str = 'md') → str[source]¶

This function is a wrapper for gromosXX md_mpi. You can directly execute the gromosXX md_mpi in a bash enviroment here.

Warning

Hybrid jobs are possible, but very difficult to implement correctly to Euler and performance gain is questionable. If OMP should be used, I suggest the md_run - function.

Parameters

in_topo_path (str) – This is the path to the input topology file (x.top)
in_coord_path (str) – This is the path to the input coordinate file (x.cnf)
in_imd_path (str) – This is the path to the input simulation parameter file (x.imd)
out_prefix (str) – This prefix, define the output name.
in_pert_topo_path (str, optional) – This is the path to the pertubation file (x.ptp)
in_disres_path (str, optional) – This is the path to the distance restraint file (x.dat)
in_posresspec_path (str, optional) – This is the path to the position restraint file (x.pos)
in_refpos_path (str, optional) – This is the path to the reference position file (x.rpf)
nomp (int, optional) – How many omp cores shall be used? Prerequesite, gromos was compiled with -enableOMP
nmpi (int, optional) – How many mpi cores shall be used? Prerequesite, gromos was compiled with -enableMPI (and suggested to have -disableOMP)
out_trc (bool, optional) – do you want to output a coordinate trajectory (x.trc) file? (needs also an output number in write block of imd!)
out_tre (bool, optional) – do you want to output a coordinate trajectory (x.trc) file? (needs also an output number in write block of imd!)
out_trs (bool, optional) – do you want to output a coordinate trajectory (x.trc) file? (needs also an output number in write block of imd!)
out_trg (bool, optional) – do you want to output the free energy trajectory (x.trg) file? (needs also an output number in write block of imd!)

Returns

returns the log_file_path of the simulation.

Return type

str

Raises

ChildProcessError – If the execution of the simulation fails, this error is raised.

pygromos.gromos package¶

Subpackages¶

Submodules¶

pygromos.gromos.compile_gromos module¶

pygromos.gromos.gromosBashSyntaxParser module¶

pygromos.gromos.gromosPP module¶

pygromos.gromos.gromosXX module¶

Module contents¶