schrodinger.application.desmond.fepana module

Tools for various FEP-related analyses.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.fepana.get_energy_table(fname, term_list)

columns: (0, 0) (0, 1) (1, 1) … “total” rows : frame1, frame2, frame3, …

Separate table for each term. table[row][col]

schrodinger.application.desmond.fepana.get_global_quantity(fname, quantity_list)
schrodinger.application.desmond.fepana.get_mean(ene, index=-1, data_structure='table')

Returns (mean, std_error, std_dev,).

schrodinger.application.desmond.fepana.parse_eneseq(eneseq_fname, column)

Parses a eneseq file and returns a list of number lists. Each element of the returned list is a list, where the first element is the time, followed by numbers from the selected columns.

Parameters:
  • eneseq_fname – eneseq file name.
  • column – a list of column indices. Data of these columns will be returned.
schrodinger.application.desmond.fepana.init_bennett(dir, n_win=12, temperature=300.0, begin_time=100.0, end_time=-1.0, random_seed=2111839, result_file=None, nresamples=0, file_pattern='gibbs.%d.dE')
schrodinger.application.desmond.fepana.run_bennett(bar, begin_time=100.0, end_time=-1.0, nresamples=None)
schrodinger.application.desmond.fepana.run_bennett_orig(dir, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, random_seed=2111839, result_fname='result', description='Desmond bennett analysis')
schrodinger.application.desmond.fepana.are_times_insane(begin_time, end_time)

Are the given begin and end times reasonable?

schrodinger.application.desmond.fepana.get_delta_time(begin_time, end_time, delta_time, window=0)
schrodinger.application.desmond.fepana.calc_free_energy_time_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839)

Calculates the free energy as a function of time.

schrodinger.application.desmond.fepana.calc_free_energy_rtime_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839)

Calculates the free energy as a function of reversed time.

schrodinger.application.desmond.fepana.calc_free_energy_stime_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, window=500.0, random_seed=2111839)

Calculates the free energy as a function of time with sliding window.

schrodinger.application.desmond.fepana.calc_freeenergy_time_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839)

Calculates the free energy as a function of time.

schrodinger.application.desmond.fepana.calc_freeenergy_rtime_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839)

Calculates the free energy as a function of reversed time.

schrodinger.application.desmond.fepana.calc_freeenergy_stime_function(dir, last_time, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, window=500.0, random_seed=2111839)

Calculates the free energy as a function of time with sliding window.

exception schrodinger.application.desmond.fepana.TimeSanityException

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fepana', '__weakref__': <attribute '__weakref__' of 'TimeSanityException' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.fepana'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.desmond.fepana.cleanup_time(begin_time, end_time, last_time, delta_time, window=0)
schrodinger.application.desmond.fepana.calc_time_curve(dir, n_win, temperature, begin_time, end_time, random_seed, time_ranges)

Calculates the free energy as a function of time_ranges

class schrodinger.application.desmond.fepana.DeltaEnergy

Bases: object

__init__()

Initialize self. See help(type(self)) for accurate signature.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fepana', '__doc__': '\n\n ', '__init__': <function DeltaEnergy.__init__>, '__dict__': <attribute '__dict__' of 'DeltaEnergy' objects>, '__weakref__': <attribute '__weakref__' of 'DeltaEnergy' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.fepana'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.fepana.read_dE_file(dE_fname, time_range=[0.0, inf])
schrodinger.application.desmond.fepana.calc_work_prob_distr(energy, energy_range=None)
schrodinger.application.desmond.fepana.calc_forward_reversed_work_overlap(dE0, dE1)
schrodinger.application.desmond.fepana.calc_lambda_window_overlap(dE_fname0, dE_fname1, time_range)
schrodinger.application.desmond.fepana.plot_lambda_window_overlap(dE_fname0, dE_fname1, out_fname=None, legend=None, time_range=[0.0, inf], filename=None, reporter=None)
schrodinger.application.desmond.fepana.calc_lambda_sim_matrix(num_lambda, *gibbs_dname, **kw)
schrodinger.application.desmond.fepana.get_pathway(mat)
schrodinger.application.desmond.fepana.print_pathway(pathway)
schrodinger.application.desmond.fepana.calc_convergence_rate(first_length, last_length, length_incr, traj_start, traj_end, n_win, dir='.', temperature=300.0, random_seed=2111839)
class schrodinger.application.desmond.fepana.FreeEnergyContrib(coulomb=None, vdw=None, bonded=None)

Bases: object

__init__(coulomb=None, vdw=None, bonded=None)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.fepana', '__doc__': '\n\n ', '__init__': <function FreeEnergyContrib.__init__>, '__dict__': <attribute '__dict__' of 'FreeEnergyContrib' objects>, '__weakref__': <attribute '__weakref__' of 'FreeEnergyContrib' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.fepana'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.fepana.calc_contrib(fname, cfg_fname)
schrodinger.application.desmond.fepana.correct_restr(egout0, egout1, fname_out)
schrodinger.application.desmond.fepana.long_range_dispersion_energy(r_cut, c6, rho)

r_cut: cutoff radius (Angstrom). c6: average dispersion coefficient (kcal/mol * Angstrom**6). rho: number density (1/ Angstrom**3)

schrodinger.application.desmond.fepana.get_field_from_log(field, fname)
schrodinger.application.desmond.fepana.get_number_density_from_cms(model)

Returns a tuple of elements as follows: 1. the number density in the unit of 1 / Angstrom**3 2. number of atoms in the system 3. volume of the system

schrodinger.application.desmond.fepana.get_average_box_volume(fname)

‘fname’ must be a *_simbox.dat file.

schrodinger.application.desmond.fepana.calc_long_range_dispersion_energy(model, atom_list, log_fname=None, simbox_fname=None, cfg_fname=None, r_cut=-1, average_coefficient=-1)

Calculates correction for the cross link restraints in absolute binding free energy simulations. Reference: Boresch, Stefan, Franz Tettinger, Martin Leitgeb, and Martin Karplus.

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation. The Journal of Physical Chemistry B 107, no. 35 (September 2003): 9535-9551. http://pubs.acs.org/doi/abs/10.1021/jp0217839.

Note: We could not reproduce the numbers on the 5th row of Table 5 in the reference.

Calculates correction for the cross link restraints in absolute binding free energy simulations.

We use Huangfeng Xu’s formula. The partition function of the restraint terms is this:

Z = int dr r^2 exp( -beta kr (r - r0)^2 )
Prod_{i = 1, 2 } int_0^pi dtheta_i sintheta_i exp( -beta ka (theta_i - theta_{i0})^2 ) Prod_{i = 1, 2, 3} int_{psi_{i0} - pi}^{psi_{i0} + pi} dpsi_i exp( -beta kd (psi_i - psi_{i0})^2 )

The integration over theta is approximated by integration over {-inf, inf}.

schrodinger.application.desmond.fepana.violate_midpoint(model, atom, r_clone2)

`atom’ is a list of atom indices and Nones.

the model should be created by the topo.read_cms function `ligand’ is a list of ligand atoms’ indices.

schrodinger.application.desmond.fepana.calc_free_energy(dir, last_time: float, n_win: int, temperature: float, bennett_options: Dict, random_seed: int) → Dict

Return forward, reverse and slide energies.

schrodinger.application.desmond.fepana.plot_convergence(data, dG_fname, dF_fname_pattern, x_label, dF_color, dG_color='black', reporter=None) → Dict[str, Union[typing.List[str], str]]

process the data and write png files.

Return a dictionary with format {‘url’: url, ‘dF’: df, ‘dG’: dG_fname}