schrodinger.application.desmond.ene_utils module

class schrodinger.application.desmond.ene_utils.EneGrpProp

Bases: object

Class that contains the information in a Desmond .enegrp (energy group) file

RAW_POTENTIAL = 'en'
POTENTIAL_ENERGY = 'E_p'
KINETIC_ENERGY = 'E_k'
EXTENDED_ENERGY = 'E_x'
PRESSURE = 'P'
VOLUME = 'V'
DISP_CORR = 'Dispersion_Correction'
ENERGY_CORR = 'Self_Energy_Correction'
CHARGE_CORR = 'Net_Charge_Correction'
GBL_FORCE = 'Global_Force_Sum'
DRIFT_VEL = 'Kinetic'
PAIR_ELEC = 'pair_elec'
PAIR_VDW = 'pair_vdw'
BOND_ENERGY = 'stretch'
ANGLE_ENERGY = 'angle'
DIHED_ENERGY = 'dihedral'
FAR_EXCLUSION = 'far_exclusion'
NON_BONDED_ELEC = 'nonbonded_elec'
NON_BONDED_VDW = 'nonbonded_vdw'
FAR_TERMS = 'far_terms'
TOTAL_ENERGY = 'Total'
VIRIAL = 'Virial'
KINETIC_TENSOR = 'K.E.tensor'
PRESS_TENSOR = 'Pressure_Tensor'
SIM_BOX = 'Simulation_Box'
class schrodinger.application.desmond.ene_utils.ENEGRP_VALUE(time, value)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

count(value, /)

Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

time

Alias for field number 0

value

Alias for field number 1

schrodinger.application.desmond.ene_utils.parse_ene_file(filename=None, fileobj=None, prop=None, gcmc=False)

Parse data from a Desmond .ene file. All the data from the file can be returned in a dictionary, or just the data from a single property can be returned in a list.

Parameters

  • filename (str) – The name of the .ene file to read

  • fileobj (file or io.BufferedReader) – The open file object for the .ene file. Only one of filename or fileobj should be supplied. If both are given, filename will take precedence. io.BufferedReader objects come from tarfile.extractfile, for instance. Note - in Python 3, open file objects are io.TextIOWrapper

  • prop (str) – If given, should match one of the properties in the ene file header (such as ‘V’). The return value will be a list of values for this property only

  • gcmc (bool) – Whether to parse GMCM or a standard MD file

Return type

dict, dict, or list, list or dict or list

Returns

If prop is not specified, the return value is a dict if gcmc is False, otherwise two dicts. Keys are property names from the ene header (without units, such as ‘V’) and values are lists of floating point values for that property in the order obtained from the .ene file. If prop is specified, the return value is a list if gcmc is False, otherwise two lists of those property values in the order found in the .ene file.

Raises

  • ValueError – If a line of unknown format is found while reading the file, or if neither filename or fileobj is specified.

  • TypeError – If prop is supplied but does not match a property in the header line

schrodinger.application.desmond.ene_utils.get_density_from_ene(ene_file, struct, fraction=0.2)

Parse the volume from the ene file and compute the density from it. The density is averaged over the last fraction of frames.

Parameters

  • ene_file (str) – The name of the file to read in.

  • struct (schrodinger.structure.Structure) – The structure to compute the density for

  • fraction (float) – The fraction of frames to average the density over. For instance, use 0.20 to compute the density over the final 20% of frames. Use the special value 0 to just use the final density. With fraction=0, the returned standard deviation is 0.

Return type

(float, float)

Returns

The mean density and standard deviation of the density.

Raises

IOError – If unable to read the volumes from the ene file (from get_prop_from_ene method)

schrodinger.application.desmond.ene_utils.get_prop_from_ene(ene_file, prop, fraction=0.2, reciprocal=False, include_first=False, average=True)

Parse the ene file and compute mean and std for a specific property. The property is averaged over the last fraction of frames.

Parameters

  • ene_file (str) – The name of the file to read in.

  • prop (str) – The name of the property to read in

  • fraction (float) – The fraction of frames to average the density over. For instance, use 0.20 to compute the prop over the final 20% of frames. Use the special value 0 to just use the final density. With fraction=0, the returned standard deviation is 0.

  • reciprocal (bool) – If True, the mean and std will be done on the reciprocal of the property values.

  • include_first (bool) – If true, the first entry of the ene file will be included in averaging.

  • average (bool) – If true, the average and std of the property will be returned. If false, then a list of the values will be returned.

Return type

(float, float) or list

Returns

The mean property and standard deviation of the property or the list of values if average=False. (or the reciprocal ones if reciprocal=True)

Raises

  • IOError – If unable to read the volumes from the ene file

  • ValueError – If data have zeros, and the reciprocal of them are requested.

schrodinger.application.desmond.ene_utils.get_cutoff(length: int, percent: float)

Get cutoff given length and percent

Parameters

  • length – Length

  • percent – Percent for the cutoff

Return int

Cutoff (minimum 1)

schrodinger.application.desmond.ene_utils.parse_enegrp_file(enegrp_fn, props=['angle', 'stretch', 'Net_Charge_Correction', 'dihedral', 'Dispersion_Correction', 'Kinetic', 'Self_Energy_Correction', 'E_x', 'far_exclusion', 'far_terms', 'Global_Force_Sum', 'E_k', 'K.E.tensor', 'nonbonded_elec', 'nonbonded_vdw', 'pair_elec', 'pair_vdw', 'E_p', 'P', 'Pressure_Tensor', 'en', 'Simulation_Box', 'Total', 'Virial', 'V'])

Parse data from a Desmond *enegrp.dat file. All the data from the file can be returned in a dictionary where key is the property name and values are dict, key is the time and values are the property value at that time.

Parameters

enegrp_fn (str) – name of enegrp file to read

Props list props

list of properties to parse. Check ALL_ENEGRP_PROPS for the list of supported properties.

Return type

dict

Returns

dictionary where key is the property name and values are namedtuple. The namedtuple has two fields, time and value. The value is the value for the property at that timestep. Value at the timestep can be a float or a list depending on the property.

schrodinger.application.desmond.ene_utils.get_ptensor_from_enegrp(enegrp_fn, percent_to_avg, log=None)

Extract and calculate average pressure from an energy group file.

Parameters

  • enegrp_fn (str) – Energy group filename

  • percent_to_avg (float) – Percent to use when averaging pressure tensor

  • log (method) – Log method

Return type

numpy.array()

Returns

Averaged pressure tensor

schrodinger.application.desmond.ene_utils.get_lattice_param_from_enegrp(enegrp_fn, percent_to_avg)

Extract and calculate average lattice parameter from an energy group file.

Parameters

  • enegrp_fn (str) – Energy group filename

  • percent_to_avg (float) – Percent to use when averaging lattice parameter

Raises

IOError – fail in reading enegrp file

Return type

numpy.ndarray

Returns

Averaged lattice parameters matrix