Package schrodinger :: Package application :: Package desmond :: Module fepana

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Module fepana

Tools for various FEP-related analyses.

Classes

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TimeSanityException

DeltaEnergy

FreeEnergyContrib

Functions

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_float_range(start, stop, step, closed=True)
Return evenly spaced float values from start to stop.

get_energy_table(fname, term_list)
columns: (0, 0) (0, 1) (1, 1) ...

get_global_quantity(fname, quantity_list)

get_mean(ene, index=-1, data_structure='table')
Returns (mean, std_error, std_dev,).

parse_eneseq(eneseq_fname, column)
Parses a eneseq file and returns a list of number lists.

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)

run_bennett(bar, begin_time=100.0, end_time=-1.0, nresamples=None)

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')

are_times_insane(begin_time, end_time)
Are the given begin and end times reasonable?

get_delta_time(begin_time, end_time, delta_time, window=0)

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.

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.

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.

cleanup_time(begin_time, end_time, last_time, delta_time, window=0)

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

read_dE_file(dE_fname, time_range=[0.0, inf])

calc_work_prob_distr(energy, energy_range=None)

calc_forward_reversed_work_overlap(dE0, dE1)

calc_lambda_window_overlap(dE_fname0, dE_fname1, time_range)

plot_lambda_window_overlap(dE_fname0, dE_fname1, out_fname=None, legend=None, time_range=[0.0, inf], filename=None, reporter=None)

calc_lambda_sim_matrix(num_lambda, *gibbs_dname, **kw)

_get_pathway_helper(pathway, mat)

get_pathway(mat)

print_pathway(pathway)

calc_convergence_rate(first_length, last_length, length_incr, traj_start, traj_end, n_win, dir='.', temperature=300.0, random_seed=2111839)

calc_contrib(fname, cfg_fname)

correct_restr(egout0, egout1, fname_out)

long_range_dispersion_energy(r_cut, c6, rho)
r_cut: cutoff radius (Angstrom).

get_field_from_log(field, fname)

get_number_density_from_cms(model)
Returns a tuple of elements as follows: 1.

get_average_box_volume(fname)
'fname' must be a *_simbox.dat file.

calc_long_range_dispersion_energy(model, atom_list, log_fname=None, simbox_fname=None, cfg_fname=None, r_cut=-1, average_coefficient=-1)

calc_free_energy_for_abfe_cross_link(restr, temperature=300.0)
Calculates correction for the cross link restraints in absolute binding free energy simulations.

calc_free_energy_for_abfe_cross_link_xu(restr, temperature=300.0)
Calculates correction for the cross link restraints in absolute binding free energy simulations.

violate_midpoint(model, atom, r_clone2)
`atom' is a list of atom indices and Nones.

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.

Variables

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model = cms.Cms("wu20090927T224119_2-out.cms")

lig_atom = model.select_atom("atom.num 902-919")

r_clone = 5.0

model_fname = "wu20090927T224119_2-out.cms"

traj_fname = "wu20090927T224119_2_trj"

stretch = [cms.Restrain([1, 2,], 5.0, 5.1),]

angle = [cms.Restrain([1, 2, 3], 5.0, 67.5), cms.Restrain([1, ...

torsion = [cms.Restrain([1, 2, 3, 4], 5.0,-113.0), cms.Restrai...

table = get_global_quantity("test_enegrp.dat", ["V"])

mean = get_mean(table ["V"], data_structure= "array")

mat = calc_lambda_sim_matrix(4, "cis", "trans", mat_fname= "ma...

data = calc_freeenergy_stime_function(".", 12)

cms_fname = sys.argv [1]

trj_dir = sys.argv [2]

asl = "all"

__package__ = 'schrodinger.application.desmond'

Function Details

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_float_range(start, stop, step, closed=True)

Return evenly spaced float values from start to stop.

Parameters:

start - First value in the range
stop - Last value in the range if closed, first value outside of the range if not closed.
step - The size of the step between elements of the result range.
closed - Should stop be included in the range?

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]

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.

_get_pathway_helper(pathway, mat)

Parameters:

pathway - a list of tuples. Each tuple consists of three elements: structure name, free energy, and probability.

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)

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

calc_free_energy_for_abfe_cross_link(restr, 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.

calc_free_energy_for_abfe_cross_link_xu(restr, 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( -eta kr (r - r0)^2 )
    \Prod_{i = 1, 2   } \int_0^\pi d        heta_i \sin     heta_i exp( -eta ka (  heta_i -        heta_{i0})^2 )
    \Prod_{i = 1, 2, 3} \int_{\psi_{i0} - \pi}^{\psi_{i0} + \pi} d\psi_i exp( -eta kd (\psi_i - \psi_{i0})^2 )
The integration over theta is approximated by integration over {-\inf, \inf}.

Variables Details

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angle

Value:

[cms.Restrain([1, 2, 3], 5.0, 67.5), cms.Restrain([1, 2, 3], 5.0, 84.5
),]

torsion

Value:

[cms.Restrain([1, 2, 3, 4], 5.0,-113.0), cms.Restrain([1, 2, 3, 4], 5.
0,-82.0), cms.Restrain([1, 2, 3, 4], 5.0,-169.0),]

mat

Value:

calc_lambda_sim_matrix(4, "cis", "trans", mat_fname= "matrix")