schrodinger.application.desmond.fepana module¶
Tools for various FEP-related analyses.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.desmond.fepana.
Restraint
(atom, ref, k)¶ Bases:
object
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__init__
(atom, ref, k)¶ Initialize self. See help(type(self)) for accurate signature.
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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]
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schrodinger.application.desmond.fepana.
get_global_quantity
(fname, quantity_list)¶
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schrodinger.application.desmond.fepana.
get_mean
(ene, index=-1, data_structure='table')¶ Returns (mean, std_error, std_dev,).
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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.
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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')¶
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schrodinger.application.desmond.fepana.
run_bennett
(bar, begin_time=100.0, end_time=-1.0, nresamples=None)¶
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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')¶
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schrodinger.application.desmond.fepana.
are_times_insane
(begin_time, end_time)¶ Are the given begin and end times reasonable?
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schrodinger.application.desmond.fepana.
get_delta_time
(begin_time, end_time, delta_time, window=0)¶
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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.
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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.
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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.
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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.
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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.
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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.
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exception
schrodinger.application.desmond.fepana.
TimeSanityException
¶ Bases:
Exception
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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schrodinger.application.desmond.fepana.
cleanup_time
(begin_time, end_time, last_time, delta_time, window=0)¶
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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
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class
schrodinger.application.desmond.fepana.
DeltaEnergy
¶ Bases:
object
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__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.fepana.
read_dE_file
(dE_fname, time_range=None)¶
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schrodinger.application.desmond.fepana.
calc_work_prob_distr
(energy, energy_range=None)¶
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schrodinger.application.desmond.fepana.
calc_forward_reversed_work_overlap
(dE0, dE1)¶
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schrodinger.application.desmond.fepana.
calc_lambda_window_overlap
(dE_fname0, dE_fname1, time_range)¶
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schrodinger.application.desmond.fepana.
plot_lambda_window_overlap
(dE_fname0, dE_fname1, out_fname=None, legend=None, time_range=None, filename=None, reporter=None)¶
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schrodinger.application.desmond.fepana.
calc_lambda_sim_matrix
(num_lambda, *gibbs_dname, **kw)¶
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schrodinger.application.desmond.fepana.
get_pathway
(mat)¶
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schrodinger.application.desmond.fepana.
print_pathway
(pathway)¶
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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)¶
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class
schrodinger.application.desmond.fepana.
FreeEnergyContrib
(coulomb=None, vdw=None, bonded=None)¶ Bases:
object
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__init__
(coulomb=None, vdw=None, bonded=None)¶
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schrodinger.application.desmond.fepana.
calc_contrib
(fname, cfg_fname)¶
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schrodinger.application.desmond.fepana.
correct_restr
(egout0, egout1, fname_out)¶
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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)
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schrodinger.application.desmond.fepana.
get_field_from_log
(field, fname)¶
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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
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schrodinger.application.desmond.fepana.
get_average_box_volume
(fname)¶ ‘fname’ must be a *_simbox.dat file.
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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)¶
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schrodinger.application.desmond.fepana.
calc_free_energy_for_abfe_cross_link
(restr: List[schrodinger.application.desmond.fepana.Restraint], temperature=300.0)¶ 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.
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schrodinger.application.desmond.fepana.
calc_free_energy_for_abfe_cross_link_xu
(restr: List[schrodinger.application.desmond.fepana.Restraint], temperature=300.0)¶ 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}.
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schrodinger.application.desmond.fepana.
calc_free_energy_correction_due_to_restraint
(r, fc, temperature) → float¶ Parameters: - r – Cross-link restraint to calculate the free energy correction for
- fc – Three force constants for the stretch, the angle, and the torsion restraints, respectively.
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schrodinger.application.desmond.fepana.
get_abfep_cross_link
(model, ligand, r_clone, traj_fname, first_frame=0, max_frame=256)¶ the model should be created by the topo.read_cms function `ligand’ is a list of ligand atoms’ indices.
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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.
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schrodinger.application.desmond.fepana.
plot_convergence
(data, dG_fname, dF_fname_pattern, x_label, dF_color, dG_color='black', reporter=None) → Dict[str, Union[List[str], str]]¶ process the
data
and write png files.Return a dictionary with format {‘url’: url, ‘dF’: df, ‘dG’: dG_fname}