schrodinger.application.matsci.equilibrium_md module¶

Equilibrium molecular dynamics classes/function shared by transport property calculations using Einstein and Green-Kubo methods. Added Onsager coefficient calculation using MS3, MS2 and MS1 methods. There is a bifurcation in workflow after displacement is calculated. We either compute stephan maxwell diffusion coefficient or self diffusion coefficient.

schrodinger.application.matsci.equilibrium_md.log_debug(msg)¶

Add a message to debug logger file.

Parameters:: msg (str) – The message to debug logging

schrodinger.application.matsci.equilibrium_md.get_core_num()¶

Return the number of the cores specified by users. None means not specified.

Returns:: the number of cores specified by users.
Return type:: int or None

schrodinger.application.matsci.equilibrium_md.get_reserves_cores_state(options)¶

Return the state of reserves cores so that some python standard library functions can have access to all CPU resources.

Parameters:: check_runtype (bool) – If true, the FLAG_RUN_TYPE in the options is checked
Returns:: True, if reserves_cores_state should be set as True to allow some python function to utilize multiple CPUs.
Return type:: bool

schrodinger.application.matsci.equilibrium_md.clearProps(cms_model, str_in_key='Diffusion')¶

Clear the diffusion related properties and should be called before new calculations.

Parameters:: cms_model ('schrodinger.application.desmond.cms.Cms') – A cms model to clear the properties

schrodinger.application.matsci.equilibrium_md.get_files(filename, ext)¶

Get all the files with same extension, if ext is provided.

Parameters:

filename (str) – file to be located and returned
ext (str or None) – extension to search files of the same type

Return type:

list of str

Returns:

list of filenames with path

schrodinger.application.matsci.equilibrium_md.check_finite_molecules(struct, atom_ids=None)¶

Check whether the molecules in structure are finite.

Parameters:

struct (schrodinger.structure.Structure) – the structure whose molecules will be checked
atom_ids (set of int, list of int, list of list, or None) – molecules sharing atoms with this set will be checked. If None, all the molecules are checked.

Returns:

message if any molecules are infinite

Return type:

string or None

schrodinger.application.matsci.equilibrium_md.get_md_results(basename, options, log, log_error, save_opts=None, smart_distribution=True)¶

From parsed options, setup and run md simulation.

Parameters:

basename (str) – basename for md simulation job
options (Named tuple) – The parsed command line option
log (function) – log information
log_error (function) – log error information and exit
smart_distribution (bool) – turn on / off the smart_distribution

Return type:

str, str, str

Returns:

output cms, trj folder, and enegrp_dat

schrodinger.application.matsci.equilibrium_md.setup_md_job(name_base, md_opts, enegrp_opts=None, save_opts=None, command_dir=None, **kwargs)¶

Write the .msj file, form the command, figure out the output filenames, and register files to backend for molecular dynamics simulations.

Note: if command_dir is not None, please call this method inside the command_dir as the returned ocms_name doesn’t have command_dir in the file path.

Parameters:

name_base (base name for the md job) – str
md_opts – ‘type.SimpleNamespace’
enegrp_opts (this data struct has attributes: energy_groups for the list of keywords for desmond energy_groups, interval for output time interval in ps, start for the output starting time in ps. If None, no enegrp file is generated.) – ‘type.SimpleNamespace’ or None
save_opts (this data struct has boolean attributes to save files likes: msj, ene, multisim_log, ocms, log, trj, cfg, write_velocity, enegrp, last, autocorrelation_file, zip_outputs, viscosity_file. If None, use default settings to decide the files to be copied back.) – ‘type.SimpleNamespace’ or None
command_dir (this is the path from the job start dir to the subjob dir. The setup function is expected to run in the subjob setup stage, and thus the subjob dir should be passed. If there is only one master job (no sub dir), current dir is used. In addition, the returned file paths are the the basename, and then users need to form the full file path when they decide to run in subfolder or master folder directly.) – str

Return type:

‘type.SimpleNamespace’

Returns:

data struct with cmd command to submit md, output cms, trj folder, enegrp file, jobname

schrodinger.application.matsci.equilibrium_md.type_model_file(arg, model_formats=None)¶

Validate that the argument is a file that contains a model.

Parameters:

arg (str) – the filename
model_formats (list of str) – the supported formats of the model

Raises:

ArgumentTypeError – when the file cannot be open by cms or structure reader

Returns:

filename with path

Return type:

str

schrodinger.application.matsci.equilibrium_md.add_md_basic_argument(parser, model_formats=None)¶

Add necessary parser arguments for setting up a MD simulation.

Parameters:

parser (argparse.ArgumentParser) – The parser to add additional options
model_formats (list of str) – the supported formats of the model

Return type:

‘argparse._ArgumentGroup’

Returns:

argparse ArgumentGroup with MD setting options

schrodinger.application.matsci.equilibrium_md.add_md_output_argument(parser, extra_options)¶

Add parser arguments to record output information for MD simulations.

Parameters:

parser (argparse.ArgumentParser) – The parser to add additional options
extra_options (extra options can be added according to these keywords) – list of str

Return type:

‘argparse._ArgumentGroup’

Returns:

argparse ArgumentGroup with MD output recording information

schrodinger.application.matsci.equilibrium_md.add_analysis_argument(parser, extra_options)¶

Add parser arguments for analysis.

Parameters:

parser (argparse.ArgumentParser) – The parser to add additional options
extra_options (extra options can be added according to these keywords) – list of str

Return type:

‘argparse._ArgumentGroup’

Returns:

argparse ArgumentGroup with analysis options

schrodinger.application.matsci.equilibrium_md.add_parser_opts(parser, final_prop, mid_prop, use_tau=True, extra_options=None, model_formats=None)¶

Add all necessary parser arguments for setting up a MD simulation and optional arguments for certain green-kubo property calculation.

Parameters:

parser (argparse.ArgumentParser) – The parser for error information
final_prop (the final property needs to be calculated) – str
mid_prop (the property needs to be calculated before the final prop) – str
use_tau (Tau limits are added, if True) – bool
extra_options (extra options can be added according to these keywords) – None or list of str
model_formats (list of str) – the supported formats of the model

Return type:

‘argparse._ArgumentGroup’, ‘argparse._ArgumentGroup’, ‘argparse._ArgumentGroup’

Returns:

argparse ArgumentGroups with setting options

schrodinger.application.matsci.equilibrium_md.check_options(options, parser, option_flag, min_data_point, check_tau=True, check_gpu=False)¶

Validate the options.

Parameters:

options (Named tuple) – The parsed command line options
parser (argparser.ArgumentParser) – parser to log error information
option_flag (str) – time interval is defined by this flag
min_data_point (int) – minimum required data point
check_tau (bool) – validate tau range against available time range
check_gpu (bool) – check GPU/CPU resource availability. For a remote host, -gpu flag requires a GPU host, and no -gpu flag requires a CPU HOST. For localhost and no job control, only check whether GPU resource is available when -gpu flag exists.

schrodinger.application.matsci.equilibrium_md.check_tau_options(options, parser, option_flag, min_data_point)¶

Validate the Tau options.

Parameters:

options (Named tuple) – The parsed command line options
parser (argparser.ArgumentParser) – parser to log error information
option_flag (str) – time interval is defined by this flag
min_data_point (int) – minimum required data point

class schrodinger.application.matsci.equilibrium_md.Model(filename)¶

Bases: object

Wrapper around a structure.

__init__(filename)¶

Parameters:: filename (str) – file path pointing to a cms or mae file.

load()¶: Load a model.

setProperty(key, value)¶

Set the property to the model.

Parameters:

key (str) – property name
value (str, float, int) – the value of the property

property property¶

Return the model property.

Returns:: a dictionary
Return type:: dict

getExtension()¶

Return the extension of the filename.

Returns:: the extension of the filename
Return type:: str

getStruct()¶

Return the ‘structure.Structure’ object.

Returns:: structure of the model
Return type:: ‘structure.Structure’

class schrodinger.application.matsci.equilibrium_md.MaeModel(filename)¶

Bases: Model

Wrapper around Structure.

load()¶: Load a model from the mae file.

setProperty(key, value)¶

Set the property to the mae model.

Parameters:

key (str) – property name
value (str, float, int) – the value of the property

removeTrajProp()¶: Remove the trajectory property.

write(fname, wam_type=22)¶

Write the model into a file with the source_path and feature’s WAM

Parameters:

fname (str) – filename to write out the model.
wam_type (str) – default WAM type

class schrodinger.application.matsci.equilibrium_md.CmsModel(filename)¶

Bases: Model

Wrapper around Cms.

load()¶: load a model from a cms file.

setProperty(key, value)¶

Set the property to the cms model.

Parameters:

key (str) – property name
value (str, float, int) – the value of the property

removeTrajProp()¶: Remove the trajectory property.

write(fname, wam_type=22)¶

Write the model into a file with the source_path and feature’s WAM

Parameters:

fname (str) – filename to write out the model.
wam_type (str) – default WAM type

setWam(wam_type=22)¶

Set the feature’s WAM for the model.

Parameters:: wam_type (str) – default WAM type

getStruct()¶

Return the ‘structure.Structure’ object.

Returns:: structure of the model
Return type:: ‘structure.Structure’

schrodinger.application.matsci.equilibrium_md.get_model(filename)¶

Get the model from a cms or mae file.

Parameters:: filename (str) – file path pointing to a cms or mae file.
Returns:: the model in the file.
Return type:: ‘CmsModel’ or ‘MaeModel’

class schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase(input_cms, logger=False)¶

Bases: object

This is a base class for equilibrium MD subclass, and should be not be instantiated directly.

__init__(input_cms, logger=False)¶

Parameters:

input_cms (cms input file) – str
logger (loggerobj.logger prints to logfilename; None prints to stdout; False mutes logging and raises errors) – logging.Logger, None or False

log(msg, **kwargs)¶

Add a message to the log file in driver mode, or ignore the logging in module mode.

Parameters:: msg (str) – The information message

Additional keyword arguments are passed to the textlogger.log_msg function

log_error(msg)¶

Exit with the error printed in driver mode, or raise the error in module mode.

Parameters:: str (msg) – The error message
Raise:: RuntimeError in module mode

checkSetTimeInterval(time_intervals=None)¶

Time interval must be the same for all trajectery.

Parameters:: time_intervals (list or None) – time intervals between every two frames.

checkConstantVol(allow_npt=True)¶

Calculate volume and check whether it changes.

Parameters:: allow_npt (bool) – allow volume to change, if True

calDensity()¶: Caluate the average system density.

savePropAndCms(cms_out=None, wam_type=None)¶

Save properties to cms model, delete trj information if needed, and write out cms file.

Parameters:

cms_out (str) – name of the output cms.
wam_type (int or None) – One of the enums defined in workflow_action_menu.h if the results should have a Workflow Action Menu in Maestro

class schrodinger.application.matsci.equilibrium_md.TrjBase(input_cms, logger=False)¶

Bases: EquilibriumMdBase

This is a base class for equilibrium MD subclass that uses trajectory, and should be not be instantiated directly.

readTrj(make_whole=False)¶

Read trj frames from trj folder.

Parameters:: make_whole (bool) – if True, bond across PBCs are fixed so that two bonded particles won’t be on opposite sides of the system

trajFrames(make_whole=False)¶

Fix pbc bonds (if needed), yield the trajectory frame, and garbage-collect to release the occupied memory.

Parameters:: make_whole (bool) – if True, bond across PBCs are fixed so that two bonded particles won’t be on opposite sides of the system
Return type:: schrodinger.application.desmond.packages.traj.frame
Returns:: a trajectory frame

checkTau(frame_num, min_tau_data_point)¶

Check whether trj frame number is large enough.

Parameters:

frame_num (number of total data point) – int
min_tau_data_point (minimum requested data) – int

checkVel()¶: Check whether each frame contains velocity information.

class schrodinger.application.matsci.equilibrium_md.MsdTrajBase(options, **kwargs)¶

Bases: TrjBase

Trajectory base class for Mean squared displacement method.

ATOM = 'atom'¶

METHOD = 'MSD'¶

X = 'x'¶

Y = 'y'¶

Z = 'z'¶

TAU_PS = 'Tau(ps)'¶

MSD_ANG2 = 'MSD(angstrom^2)'¶

STDEV_ANG2 = 'Std Dev(angstrom^2)'¶

Y_HEADERS = ['MSD(angstrom^2)', 'Std Dev(angstrom^2)']¶

CSV_HEADER_3D = ['Tau(ps)', '3D MSD(angstrom^2)', '3D Std Dev(angstrom^2)']¶

ANISO_DIMS = ['1D', '1D', '2D', '2D']¶

CSV_HEADER_PLANE = ['1D MSD(angstrom^2)', '1D Std Dev(angstrom^2)', '2D MSD(angstrom^2)', '2D Std Dev(angstrom^2)']¶

AXES = ['x', 'x', 'y', 'y', 'z', 'z']¶

CSV_HEADER_AXIS = ['x MSD(angstrom^2)', 'x Std Dev(angstrom^2)', 'y MSD(angstrom^2)', 'y Std Dev(angstrom^2)', 'z MSD(angstrom^2)', 'z Std Dev(angstrom^2)']¶

TAU_START_PROP = 'r_matsci_Diffusion_Coefficient_MSD_Tau_Start_(ns)'¶

TAU_END_PROP = 'r_matsci_Diffusion_Coefficient_MSD_Tau_End_(ns)'¶

VECTOR_DELIM = ','¶

VECTOR_DELIM_WITH_SPACE = ', '¶

NORMAL = 'Normal'¶

DIFFUSION_FILE_PROP = 's_matsci_Diffusion_MSD_File'¶

DIFFUSIVITY_VECTOR_PROP = 's_matsci_Diffusion_Coefficient_MSD_Normal'¶

DIFFUSIVITY_1D_PROP = 'r_matsci_Diffusion_Coefficient_1D_MSD_(m^2/s)'¶

DIFFUSIVITY_2D_PROP = 'r_matsci_Diffusion_Coefficient_2D_MSD_(m^2/s)'¶

DIFFUSIVITY_3D_PROP = 'r_matsci_Diffusion_Coefficient_3D_MSD_(m^2/s)'¶

DIFFUSIVITY_X_PROP = 'r_matsci_Diffusion_Coefficient_X_MSD_(m^2/s)'¶

DIFFUSIVITY_Y_PROP = 'r_matsci_Diffusion_Coefficient_Y_MSD_(m^2/s)'¶

DIFFUSIVITY_Z_PROP = 'r_matsci_Diffusion_Coefficient_Z_MSD_(m^2/s)'¶

STDEV = 'stdev'¶

SD_EXT = 'MSD_stdev'¶

DIFFUSIVITY_1D_SD_PROP = 'r_matsci_Diffusion_Coefficient_1D_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_2D_SD_PROP = 'r_matsci_Diffusion_Coefficient_2D_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_3D_SD_PROP = 'r_matsci_Diffusion_Coefficient_3D_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_X_SD_PROP = 'r_matsci_Diffusion_Coefficient_X_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_Y_SD_PROP = 'r_matsci_Diffusion_Coefficient_Y_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_Z_SD_PROP = 'r_matsci_Diffusion_Coefficient_Z_MSD_stdev_(m^2/s)'¶

DIFFUSIVITY_1D_R2_PROP = 'r_matsci_Diffusion_Coefficient_1D_MSD_R2'¶

DIFFUSIVITY_2D_R2_PROP = 'r_matsci_Diffusion_Coefficient_2D_MSD_R2'¶

DIFFUSIVITY_3D_R2_PROP = 'r_matsci_Diffusion_Coefficient_3D_MSD_R2'¶

DIFFUSIVITY_X_R2_PROP = 'r_matsci_Diffusion_Coefficient_X_MSD_R2'¶

DIFFUSIVITY_Y_R2_PROP = 'r_matsci_Diffusion_Coefficient_Y_MSD_R2'¶

DIFFUSIVITY_Z_R2_PROP = 'r_matsci_Diffusion_Coefficient_Z_MSD_R2'¶

class DIFFUSIVITY(diffusivity, std_dev, r2)¶

Bases: tuple

diffusivity¶: Alias for field number 0

r2¶: Alias for field number 2

std_dev¶: Alias for field number 1

ISOTROPIC = 'isotropic'¶

ANISOTROPIC = 'anisotropic'¶

ISOTROPIC_3D = 'isotropic:3D'¶

ANISOTROPIC_1D = 'anisotropic:1D'¶

ANISOTROPIC_2D = 'anisotropic:2D'¶

DIMENSION_MAP = {'anisotropic:1D': 1, 'anisotropic:2D': 2, 'isotropic:3D': 3}¶

DIFFUSION_PROPS_MAP = {1: DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_1D_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_1D_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_1D_MSD_R2'), 2: DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_2D_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_2D_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_2D_MSD_R2'), 3: DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_3D_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_3D_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_3D_MSD_R2'), 'x': DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_X_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_X_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_X_MSD_R2'), 'y': DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_Y_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_Y_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_Y_MSD_R2'), 'z': DIFFUSIVITY(diffusivity='r_matsci_Diffusion_Coefficient_Z_MSD_(m^2/s)', std_dev='r_matsci_Diffusion_Coefficient_Z_MSD_stdev_(m^2/s)', r2='r_matsci_Diffusion_Coefficient_Z_MSD_R2')}¶

DIFFUSION_COL_MAP = {1: (0, 3, 4), 2: (0, 5, 6), 3: (0, 1, 2), 'x': (0, 3, 4), 'y': (0, 5, 6), 'z': (0, 7, 8)}¶

__init__(options, **kwargs)¶

Parameters:: options (Named tuple) – The parsed command line options

static fitMsd(time_msd_std, start_idx, end_idx, dimension=3)¶

Fit the mean squared displacement

Parameters:

time_msd_std (numpy.ndarray) – first column is time in ps, second column is mean squared displacement in angstrom^2.
start_idx (int) – index to select the starting frame
end_idx (int) – index to select the ending frame
dimension (int) – 1 stands for 1D; 2 stands for 2D; 3 stands for 3D

Returns:

diffusivity coefficient in m^2/s, diffusivity_std in m^2/s, R-squared in linear regression

Return type:

float, float, float

classmethod vectorStr(vector)¶

Convert vector array to str format.

Parameters:: vector (1 x 3 array of floats) – a vector
Returns:: vector in str format
Return type:: str

getMsdHeader()¶

Get the MSD csv header.

Returns:: column labels separated by comma.
Return type:: str

setTauFrame(tau_start=None, tau_end=None)¶

Set Tau frame start and end limits.

Parameters:

float (tau_end) – the starting tau value in ps
float – the ending tau value in ps

setIsotropicMSD()¶: Set the isotropic 3d diffusion coefficients.

setPlaneMSD()¶: Set the anisotropic in-plane 2d diffusion coefficients.

setAxisMSD()¶: Set the anisotropic along-axis 1d diffusion coefficients.

class schrodinger.application.matsci.equilibrium_md.MultiToOneConverter(msd_files, jobname, options, save=True)¶

Bases: MsdTrajBase

The class to gather multiple files and merge them into one.

OUTFILE_EXT = '_msd.log'¶

ERR_MSG = 'No MSD files found.'¶

__init__(msd_files, jobname, options, save=True)¶

Parameters:

msd_files (list of str) – the msd files (with path) for diffusion data.
jobname (str) – the jobname
options (SimpleNamespace or namedtuple) – commandline options
save (bool) – If True, add output files to the backend

run()¶: Main function to load data, process data, and fit.

loadData(use_numpy=True)¶: Read in all msd files.

calculateMeanAndStd()¶: Calculate mean and std of the diffusion from multi runs.

writeMeanAndStd()¶: Write the mean and std of the diffusion.

combineTrace()¶: Combine the trace files from MSD diffusion calculations.

getMSDRelatedFiles(ext)¶

Get related files with given extension which are similar msd log file :param str ext: extension name

Return type:: list
Returns:: list of file names

class schrodinger.application.matsci.equilibrium_md.TrajectoryFrame(frame, ids, com_type='atom', vel=False)¶

Bases: object

Container of cms_model and trajectory frame with custom functions and storage

ATOM = 'atom'¶

COL_NUM_POS = 3¶

cms_model = None¶

msys_model = None¶

__init__(frame, ids, com_type='atom', vel=False)¶

Crease a TrajectoryFrame object, update gids, mass, and positions.

Parameters:

frame (traj.Frame) – One trajectory frame
ids (list) – atom id list [int1, int2…] or [(int1, int2…), (…)…]
com_type (string) – mass center of atoms within each com_type group
vel (bool) – velocity in trajectry frame is used to calculate system translation and shift the system before unwrapping displacements

setGids()¶: Get global ids of beads (atom or mass center) to extra positions and velocities.

setMass()¶: Set the mass of each bead (atom or mass center of atoms).

setGrpMass()¶: Set the total mass of each grouped atoms.

setFrame(frame)¶

Update trajectry, time, sel coordinates, box, and reduced positions.

Parameters:: frame (traj.Frame objects) – Trajectory

setXYZ()¶: Set the xyz coordinates obtaioned from trajectory frame. If -com_type != ATOM, the the center of mass is calculated first.

setBox()¶: Set the stored pbc box size.

reducedUnitNumpyPos()¶: Convert the XYZ in real unit to reduced unit.

momentum2Velocity()¶: Calculate the mean velocity of system using velocity information from trajectory frame.

class schrodinger.application.matsci.equilibrium_md.BaseDiffusivitiyAnalysis(options, jobname, command_dir='.', save=True, **kwargs)¶

Bases: MsdTrajBase

Base class for diffusivity analysis.

MIN_TAU_DATA_POINT_NUM = 10¶

COL_NUM_POS = 3¶

ATOM = 'atom'¶

MOLECULE = 'molecule'¶

MONOMER = 'monomer'¶

SMARTS = 'SMARTS'¶

DIFFUSION_FILE_EXT = '_msd.log'¶

DEFAULT_REF = 'all'¶

MAX_REDUCED_DISPLACEMENT = 0.45¶

INDICES = 'indices'¶

__init__(options, jobname, command_dir='.', save=True, **kwargs)¶

Parameters:

options (SimpleNamespace or namedtuple) – commandline options
jobname (str) – the jobname
command_dir (str) – the command dir with respect to the launch dir
save (bool) – If True, add output files to the backend
log (function to log information) – function
log_error (log error information and exit calculation) – function

setSelectionAndLoadTrj()¶: Set the atom selection and load trajectory.

setDisplacementTimeSerial()¶: Set the atom selection, time intervals, and displacements.

static isIterable(item)¶

Whether the input is iterable. Currently, list, set, and tuple are treated as iterable.

Parameters:: item – str, list, tuple, or other data type
Returns:: Whether the input is iterable
Return type:: bool

classmethod flatten(an_iterable_item)¶

Robust function to flatten list recursively.

Parameters:: an_iterable_item (list, tuple or set) – The iterable item to be flatten. (an iterable that describes the whole or part of the workflow)
Returns:: The flatten items in a list ([uniterable value 1, uniterable value 2, uniterable value 3 …])
Return type:: list of uniterable values (str or dict)

setMakeWholeState()¶

Set the make_whole state. If true, the bonds across the PBCs will be fixed before trajectory analysis. This happens when the mass center of a group covalently bonded atoms (e.g molecule) is needed.

Only set state here as make_whole on per-frame reduces peak memory usage

readTrj(make_whole=False)¶

See parent methods for docs.

make_whole removes the bond broken by PBC.

checkVel()¶: See parent methods for docs.

checkSetTimeInterval(time_intervals=None)¶: See parent methods for docs.

savePropAndCms()¶: See parent methods for docs.

getIdx(asl, com_type='atom', smarts_pattern=None)¶

Get atom indices from asl selection.

Parameters:

asl (str) – ASL search string.
com_type (string) – mass center of atoms within each com_type group is calculated
smarts_pattern (string) – SMARTS pattern

Return type:

list

Returns:

index of atoms that matche the asl string. [int1, int2…], if use_type == ATOM; [(int1, int2…), (…)…], if if use_com != ATOM

classmethod groupIdx(struct, atom_ids, com_type='atom', smarts_atom_list=None)¶

Group atoms according to com_type, or find the SMARTS matches within the atom selection.

Parameters:

struct (schrodinger.structure) – structure containing atoms
atom_ids (list) – atom id list of atom selection
com_type (string) – atom, molecule, monomer, or SMARTS as in COM_TYPE
smarts_atom_list (list) – [[a1, a2..],[b1, b2..]..], each sublist contains atom ids that match the SMARTS pattern.

Return type:

list

Returns:

[a1, a2, ..], if com_type=ATOM. [(a1, a2..), (c1, c2..)..], union of atom selection and SMARTS matches or each (..) is a subset of atom selection that belongs to one molecule or residue

setIds()¶: Evaluate asl string and save selected atom ids.

setFinalDisplacement()¶: Choose functions to get the displacement matrix if self.momentum=True, do recentering using ref atoms,

setFinalDisplacementCenter()¶: Calculate the displacement between adjacent trajectories, unwrap the coordinates, and correct the mass center.

setFinalDisplacementNoCenter()¶: Calculate the displacement between adjacent trajectories, unwrap the coordinates directly (no mass center shift).

getDisplacementFromConstTranslation(cur_frame, pre_frame)¶

Estimate the position shift between two frames by time x mean velocity.

Parameters:

cur_frame (traj.Frame objects) – current trajectory frame
pre_frame (traj.Frame objects) – previous trajectory frame

Return type:

list or None

Returns:

list of float (xyz coordinates), if vel=True

unwrapReducedDisplacement(cur_frame, pre_frame, cons_acceleration_shift=None)¶

Calculate wrapped XYZ displacement, shift the mass center, and unwrap displacement.

Parameters:

cur_frame (traj.Frame objects) – current trajectory frame
pre_frame (traj.Frame objects) – previous trajectory frame
cons_acceleration_shift (list of float) – xyz shift of mass center due to ref atom collective translation assuming constant acceleration

Return type:

numpy.matrix

Returns:

unwrapped coordinates MXN matrix in reduced unit after const momentum shift

getShiftVectorByRecenterMass(mass, adj_displacement)¶

Get the XYZ shift vetor of the unwrapped mass center (reduced unit).

Parameters:

mass (list) – list of atom mass
adj_displacement (numpy.matrix) – unwrapped displacement matrix in reduced unit

Return type:

list

Returns:

list of float

getAdjustedDisplacement(selected_adj_displacement, shift_centered_mass, box)¶

Get the “correct” displacement in xyz coordinates (real unit) for adjacent trajectory.

Parameters:

selected_adj_displacement (numpy.matrix) – wrapped adjacent trajectory displacement
shift_centered_mass (list) – vector to zero mass center of ref atoms
box (list) – list of float, the periodic boundary dimensions

Return type:

numpy.matrix

Returns:

MXN matrix in real unit, wrapped adjacent trajectory displacement

realUnitCoordinate(selected_adj_displacement, box)¶

Change reduced unit to real unit for displacement matrix.

Parameters:

selected_adj_displacement (numpy.matrix) – displacement matrix in reduced unit
box (list) – pbc box size

Return type:

numpy.matrix

Returns:

displacement matrix in real unit

setDisplacementLength()¶: Set the displacement matrix length.

class schrodinger.application.matsci.equilibrium_md.DiffusivityMsdAnalysis(options, jobname, command_dir='.', save=True, **kwargs)¶

Bases: BaseDiffusivitiyAnalysis

Main class that performs coordinate unwrap, displacement calculation, and diffusivity fit.

TRACE_FILE_EXT = '_trace.csv'¶

TRACE_HEADER = 'X1, Y1, Z1, X2, Y2, Z2, ...'¶

MAX_NUM_TRACE = 1000¶

__init__(options, jobname, command_dir='.', save=True, **kwargs)¶

Parameters:

options (SimpleNamespace or namedtuple) – commandline options
jobname (str) – the jobname
command_dir (str) – the command dir with respect to the launch dir
save (bool) – If True, add output files to the backend
log (function to log information) – function
log_error (log error information and exit calculation) – function

run()¶: Calculate unwrapped displacement, check time interval, and calculate diffusivity.

setSquaredDisplacementTimeserial()¶: Set the atom selection and load trajectory.

exportTrace()¶: Export trace to file

setSquaredDisplacement()¶: Loop over all adjacent displacement matrix to run MSD calculation

sdFromDisplacement(start_id)¶

Calculate the squared displacement from start_id trj frame to proper frame

Parameters:: start_id (int) – calculation starts from the frame of start_id

collectData()¶

Collect the msd and std from displacement matrix.

# Std is calculated from sqrt(E[X^2] - (E[X])^2) and X is the mean # squared displacement at one Tau (one time point pair) # https://en.wikipedia.org/wiki/Standard_deviation#Definition_of_population_values

saveMsdTxt()¶: Save MSD matrix: [time(ps), MSD(Angstrom^2), STD(Angstrom^2)]

setTauRange()¶: Set Tau start and end limits.

class schrodinger.application.matsci.equilibrium_md.MSDiffusivityMsdAnalysis(options, jobname, command_dir='.', save=True, **kwargs)¶

Bases: BaseDiffusivitiyAnalysis

Subclass of DiffusivityMsdAnalysis to calculate Onsager coefficient.

DIFFUSION_FILE_EXT = '_onsager.csv'¶

__init__(options, jobname, command_dir='.', save=True, **kwargs)¶

Parameters:

options (SimpleNamespace or namedtuple) – commandline options
jobname (str) – the jobname
command_dir (str) – the command dir with respect to the launch dir
save (bool) – If True, add output files to the backend
log (function to log information) – function
log_error (log error information and exit calculation) – function

run()¶: Run the analysis

checkTau(frame_num, min_tau_data_point)¶

Check the tau parameters for block averaging

Parameters:

frame_num (int) – The number of frames
min_tau_data_point (int) – The minimum number of data points

Return type:

bool

Returns:

True if tau parameters are valid else False

setMSDiffusionParams()¶: Set the Stephan maxwell mean squared displacement information.

setComponents()¶: Set the molecular components for the models.

static splitComponents(cms_model=None, ms_method='MS1', use_ctname_smiles=False)¶

Split the components of the system into different groups.

Parameters:

cms_model (cms.Cms) – the cms model
ms_method (str) – the method to generate the component name
use_ctname_smiles (bool) – If True, use the smiles string of the molecule as component name else use CATION, ANION and SOLVENT for component names.

Return type:

dict

Returns:

A dictionary with the name of species as key and Simplenamespace containing total number of species, molecule number of the species, total molecular weight of the species, charge and weight fraction

static getCompCtName(struct, method='MS1', use_ctname_smiles=False)¶

Get the component name based on the MS method.

Parameters:

struct (structure.Structure) – The input structure
method (str) – The method to generate the component name
use_ctname_smiles (bool) – If True, use the smiles string of the molecule as component name for MS1 method. If False, use CATION, ANION and SOLVENT for names.

Returns:

The component name

Return type:

str

computeOnsagerCoefficients()¶: Compute the displacement of each molecule center of mass

validateBlockTau()¶

Validate tau parameters for block averaging

Return type:: bool
Returns:: True if tau parameters are valid else False

computeOnsagerLambda()¶: Compute the average molecule displacement as a function of time

static getActiveCompPair(components, method='MS1', use_ctname_smiles=False)¶

Get the active component pairs for the calculation of onsager coefficient.

Parameters:

components (dict) – A dictionary containing smiles as key and information about the component as value
method (str) – The method to generate the component name
use_ctname_smiles (bool) – If True, use the smiles string of the molecule as component name for MS1 method. If False, use CATION, ANION and SOLVENT for names.

Return type:

list

Returns:

list of active component pairs for which onsager coefficient will be calculated

getPerWindowCoefficients(start_frame, end_frame)¶

Compute the average molecule displacement as a function of time for a defined time window

Parameters:

start_frame (int) – start frame of the time window
end_frame (int) – end frame of the time window

Return type:

numpy.ndarray

Returns:

average molecule displacement coefficient as a function of time

getMSCoeffcientMS1(disps_window)¶

Compute the Onsager coefficient based on MS1 method

Parameters:: disps_window (list[numpy.ndarray]) – list of displacement between each time step for every molecule. The array shape is [[t=0, nmol, 3], [t=1, nmol, 3], …].
Return type:: numpy.ndarray
Returns:: Onsager coefficient as a function of time

getMSCoeffcientMS2(disps_window)¶

Compute the Onsager coefficient based on MS2 method

Parameters:: disps_window (list[numpy.ndarray]) – list of displacement between each time step for every molecule. The array shape is [[t=0, nmol, 3], [t=1, nmol, 3], …].
Return type:: numpy.ndarray
Returns:: Onsager coefficient as a function of time

getMSCoefficientMS3(disps_window)¶

Compute the Onsager coefficient based on MS2 method

Parameters:: disps_window (list[numpy.ndarray]) – list of displacement between each time step for every molecule. The array shape is [[t=0, nmol, 3], [t=1, nmol, 3], …].
Return type:: numpy.ndarray
Returns:: Onsager coefficient as a function of time

static getActivePairFromModel(model)¶

Get the column name for the onsager coefficient

Parameters:: model (cms.Cms) – the cms model
Return type:: dict, list[tuple(str, str)]
Returns:: A dictionary containing smiles as key and information about the component as value and a list of active component pairs for which the onsager coefficient will be calculated.

static getColumnLabels(active_pairs)¶

Get column label for the onsager coefficient

Parameters:: active_pairs (list) – list of active component pairs for the label needs to be generated
Return type:: list[str]
Returns:: A list of column labels for the onsager coefficient

writeOnsagerCoefficients()¶: Write onsager coefficient to a file.

logComponentInfo()¶: Save the onsager coefficient to the project table and log to file.

class schrodinger.application.matsci.equilibrium_md.SingleMDJob(jobname, md_opts, enegrp_opts, save_opts, command_dir='.', **kwargs)¶

Bases: RobustSubmissionJob

Job class to submit a molecular dynamics simulation.

__init__(jobname, md_opts, enegrp_opts, save_opts, command_dir='.', **kwargs)¶

Parameters:

jobname (str) – The basename for the job
md_opts ('SimpleNamespace') – molecular dynamics options
enegrp_opts ('SimpleNamespace') – enegrp options
save_opts ('SimpleNamespace') – files to save
command_dir (str) – the job launch dir

setup()¶: Over write parent class method.

class schrodinger.application.matsci.equilibrium_md.MultiDriver(options, jobname_base, logger=None, smart_jdj=False)¶

Bases: object

Class to fire off multiple subjobs.

__init__(options, jobname_base, logger=None, smart_jdj=False)¶

Parameters:

options (Named tuple) – The parsed command line options
jobname_base (str) – base name of this job
logger (logging.Logger) – The logger for this builder
smart_jdj (bool) – whether to use smart distribution of jobs

run()¶: Run multiple calculation and perform ensemble average.

convertMultiToOne()¶: Convert data from files from multiple subjobs into one single file.

loadDataFromAllInOneFile()¶: Set the all-in-one file based on user input.

setUpQue()¶: Setup job queue.

initiateAndAddMdJobs(SingleMDJob=<class 'schrodinger.application.matsci.equilibrium_md.SingleMDJob'>, has_enegrp=False, additional_save_info=None, **kwargs)¶

Construct options, and initiate SingleMDJob jobs, and added them to jobdj.

Parameters:

SingleMDJob ('queue.JobControlJob') – instantiate this class to an object that can be added to jobdj
has_enegrp (bool) – if False, no enegrp file is generated.
additional_save_info ('types.SimpleNamespace') – additional information on what files to be copied back.

log(msg, **kwargs)¶

Add a message to the log file

Parameters:: msg (str) – The message to log

Additional keyword arguments are passed to the textlogger.log_msg function

log_error(msg)¶

Add a message to the log file and exit with an error code

Parameters:: msg (str) – The message to log

runSubjobs()¶: Run molecular dynamics jobs and Summarize the status of the runs.