BFEE2.templates_gromacs

This is the interface for generating Gromacs input files.

class BFEE2.templates_gromacs.BFEEGromacs.BFEEGromacs(structureFile, topologyFile, ligandOnlyStructureFile, ligandOnlyTopologyFile, baseDirectory=None, structureFormat='pdb', ligandOnlyStructureFileFormat='pdb')[source]

Bases: object

The entry class for handling gromacs inputs in BFEE.

logger

logger object for debugging

Type:: logging.Logger

handler

output stream of the debug output

Type:: logging.StreamHandler

baseDirectory

output directory of the generated files

Type:: str

structureFile

filename of the structure file (either in PDB or GRO format) of the protein-ligand binding complex

Type:: str

topologyFile

filename of the GROMACS topology file of the protein-ligand binding complex

Type:: str

ligandOnlyStructureFile

filename of the structure file (either in PDB or GRO format) of the ligand-only system

Type:: str

system

MDAnalysis universe of the protein-ligand binding system

Type:: MDAnalysis.core.universe

ligandOnlySystem

MDAnalysis universe of the ligand-only system

Type:: MDAnalysis.core.universe

basenames

subdirectory names of all eight steps

Type:: str

ligand

selected HEAVY ATOMS of the ligand in the protein-ligand binding complex. This attribute does not exist until the call of setLigandHeavyAtomsGroup.

Type:: MDAnalysis.core.groups.AtomGroup

ligandOnly

selected HEAVY ATOMS of the ligand in the ligand-only system. This attribute does not exist until the call of setLigandHeavyAtomsGroup.

Type:: MDAnalysis.core.groups.AtomGroup

protein

selected HEAVY ATOMS of the protein in the protein-ligand binding complex. This attribute does not exist until the call of setProteinHeavyAtomsGroup.

Type:: MDAnalysis.core.groups.AtomGroup

solvent

selected atoms of the solvents in the protein-ligand binding complex. This attribute does not exist until the call of setSolventAtomsGroup.

Type:: MDAnalysis.core.groups.AtomGroup

temperature

the temperature of simulations (default : 300.0)

Type:: float

generate000()[source]: generate files for running an equilibrium simulation

generate001()[source]: generate files for determining the PMF along the RMSD of the ligand with respect to its bound state

generate002()[source]: generate files for determining the PMF along the pitch (theta) angle of the ligand

generate003()[source]: generate files for determining the PMF along the roll (phi) angle of the ligand

generate004()[source]: generate files for determining the PMF along the yaw (psi) angle of the ligand

generate005()[source]: generate files for determining the PMF along the polar theta angle of the ligand relative to the protein

generate006()[source]: generate files for determining the PMF along the polar phi angle of the ligand relative to the protein

generate007()[source]: generate files for determining the PMF along the distance between the the ligand and the protein

generate008()[source]: generate files for determining the PMF along the RMSD of the ligand with respect to its unbound state

generateGromacsIndex(outputFile)[source]: generate a GROMACS index file for atom selection in Colvars

saveStructure(outputFile, selection='all')[source]

a helper method for selecting a group of atoms and save it

Parameters:

outputFile (str) – filename of the output file
selection (str, optional) – MDAnalysis atom selection string. Defaults to ‘all’.

Raises:

SelectionError – if the selection corresponds to nothing

setLigandHeavyAtomsGroup(selection)[source]

select the heavy atoms of the ligand in both the protein-ligand complex: and the ligand-only systems

Parameters:: selection (str) – MDAnalysis atom selection string
Raises:: SelectionError – if the selection corresponds to nothing

setProteinHeavyAtomsGroup(selection)[source]

select the heavy atoms of the protein

Parameters:: selection (str) – MDAnalysis atom selection string
Raises:: SelectionError – if the selection corresponds to nothing

setSolventAtomsGroup(selection)[source]

select the solvent atoms

Parameters:: selection (str) – MDAnalysis atom selection string
Raises:: SelectionError – if the selection corresponds nothing

setTemperature(newTemperature)[source]

set the temperature

Parameters:: newTemperature (float) – new value of the temperature

exception BFEE2.templates_gromacs.BFEEGromacs.SelectionError(arg)[source]: Bases: RuntimeError

BFEE2.templates_gromacs.BFEEGromacs.generateColvars(colvarsTemplate, outputPrefix, logger=None, **kwargs)[source]

generate a Colvars configuration file from a template suffixed with ‘.dat’

Parameters:

colvarsTemplate (str) – path to a colvars template
outputPrefix (str) – (no .dat extension) of the output Colvars configuration file
logger (Logging.logger, optional) – logger for debugging. Defaults to None.
**kwargs – additional arguments passed to safe_substitute()

BFEE2.templates_gromacs.BFEEGromacs.generateMDP(MDPTemplate, outputPrefix, timeStep, numSteps, temperature, pressure, colvarsFile, logger=None)[source]

generate a GROMACS mdp file from a template

Parameters:

MDPTemplate (str) – template MDP file with $dt and $nsteps
outputPrefix (str) – prefix (no .mdp extension) of the output MDP file
timeStep (float) – timestep for running the simulation
numSteps (int) – number of steps for running the simulation
temperature (float) – simulation temperature
pressure (float) – simulation pressure
logger (Logging.logger, optional) – logger for debugging. Defaults to None.

BFEE2.templates_gromacs.BFEEGromacs.generateShellScript(shellTemplate, outputPrefix, logger=None, **kwargs)[source]

generate a shell script from a template

Parameters:

shellTemplate (str) – path to a shell template
outputPrefix (str) – prefix (no .sh extension) of the output Colvars configuration file
logger (Logging.logger, optional) – logger for debugging. Defaults to None.
**kwargs – additional arguments passed to safe_substitute()

BFEE2.templates_gromacs.BFEEGromacs.get_cell(atom_positions)[source]

mimic the VMD script get_cell.tcl to calculate the cell units

Parameters:: atom_positions (numpy.array) – a numpy array containing the XYZ coordinates of N atoms. The shape should be (N, 3).
Returns:: a shape of (3,3) array contains periodic cell information
Return type:: Numpy.array

BFEE2.templates_gromacs.BFEEGromacs.mearsurePolarAngles(proteinCenter, ligandCenter)[source]

measure the polar angles between the protein and the ligand

Parameters:

proteinCenter (numpy.array) – center-of-mass of the protein
ligandCenter (numpy.array) – center-of-mass of the ligand

Returns:

a (theta, phi) tuple where theta and phi are measured in degrees

Return type:

tuple

BFEE2.templates_gromacs.BFEEGromacs.measure_center(atom_positions)[source]

mimic the VMD command “measure center”

Parameters:: atom_positions (numpy.array) – a numpy array containing the XYZ coordinates of N atoms. The shape should be (N, 3).
Returns:: a shape of (3,) array contains the geometric center
Return type:: Numpy.array

BFEE2.templates_gromacs.BFEEGromacs.measure_minmax(atom_positions)[source]

mimic the VMD command “measure minmax”

Parameters:

atom_positions (numpy.array) – a numpy array containing the XYZ coordinates of N atoms. The shape should be (N, 3).

Returns:

a shape of (2, 3) array, where the first subarray has the minimum: values in XYZ directions, and the second subarray has the maximum values in XYZ directions.

Return type:

Numpy.array

BFEE2.templates_gromacs.BFEEGromacs.scanGromacsTopologyInclude(gmxTopFile, logger=None)[source]

scan the files included by a gromacs topology file

Parameters:

gmxTopFile (str) – filename of the gromacs topology file
logger (Logging.logger, optional) – logger for debugging. Defaults to None.

Returns:

tuple:: a (list, list) tuple. The first list contains the absolute pathnames of included files. The second list contains the strings in the quotation marks for handling relative paths.
Logging.logger:: logger for debugging

Return type:

tuple