def plot_all_fits(filename, use_agg=False, ylims=(-1, -1)):
"""Plot fitness function vs. iteration for each pair at each state
Args
----
filename : str
Name of file from which to read.
use_agg : bool
Use Agg backend if True - may be useful on clusters with no display
ylims : iterable, len=2
Set the ylimits of the f_fit axes - useful for comparing plots of different pairs
Returns
-------
Nothing is returned, but plots are made for each pair.
If the directory './figures' does not exist, it is created, and the figures
are saved in that directory with the name 'type1-type2-fit.pdf'.
The filename should where the optimization output was redirected, as the
format is determined by the MSIBI.optimize() function.
"""
fits = parse_logfile(filename)
if not os.path.exists('figures'):
os.makedirs('figures')
for pair in fits:
plot_pair_fits(pair, fits, use_agg, ylims)
def plot_all_fits(filename, use_agg=False, ylims=(-1, -1)):
"""Plot fitness function vs. iteration for each pair at each state
Args
----
filename : str
Name of file from which to read.
use_agg : bool
Use Agg backend if True - may be useful on clusters with no display
ylims : iterable, len=2
Set the ylimits of the f_fit axes - useful for comparing plots of different pairs
Returns
-------
Nothing is returned, but plots are made for each pair.
If the directory './figures' does not exist, it is created, and the figures
are saved in that directory with the name 'type1-type2-fit.pdf'.
The filename should where the optimization output was redirected, as the
format is determined by the MSIBI.optimize() function.
"""
fits = parse_logfile(filename)
if not os.path.exists('figures'):
os.makedirs('figures')
for pair in fits:
plot_pair_fits(pair, fits, use_agg, ylims)
def test_all_pairs_same_number_of_states():
filename = get_fn('opt.out')
logfile_info = parse_logfile(filename)
assert (len(logfile_info) == 15)
for pair, states in logfile_info.items():
assert len(states) == 4
for state, f_fits in states.items():
assert (len(f_fits) == 8)
def test_all_pairs_same_number_of_states():
filename = get_fn('opt.out')
logfile_info = parse_logfile(filename)
assert(len(logfile_info) == 15)
for pair, states in logfile_info.items():
assert len(states) == 4
for state, f_fits in states.items():
assert(len(f_fits) == 8)
def plot_all_rdfs(logfile_name,
target_dir,
potentials_dir='./potentials',
rdf_dir='./rdfs',
step=-1,
use_agg=False,
to_angstrom=1.0,
to_kcalpermol=1,
lw=None):
"""Plot the RDF vs. the target for each pair at each state
Args
----
fits : dict
Dict with {pairs: {states: fits}}, as returned from parse_logfile
target-dir : str
path (relative or absolute) to target RDFs
potentials_dir : str
path (relative or absolute) to potentials from optimization
step : int
Print RDFs and potentials from this step
use_agg : bool
True to use Agg backend, may be useful on clusters with no display
Returns
-------
Nothing is returned, but figures are plotted in './figures'
The target rdfs are expected to have the format 'target-dir/type1-type2-state.txt'
"""
if not os.path.exists('figures'):
os.makedirs('figures')
logfile_info = parse_logfile(logfile_name)
for pair, state in logfile_info.items():
for state, fits in state.items():
if step == -1:
step = len(fits) - 1
type1 = pair.split('-')[0]
type2 = pair.split('-')[1]
plot_pair_at_state(type1,
type2,
state,
step,
target_dir,
potentials_dir,
rdf_dir,
use_agg,
to_angstrom,
to_kcalpermol,
lw=lw)
def animate_all_pairs_states(logfile_name, target_dir,
potentials_dir='./potentials', rdf_dir = './rdfs', step=-1,
use_agg=False, to_angstrom=6.0, to_kcalpermol=0.1, n_skip=1):
"""Plot the RDF vs. the target for each pair at each state
Args
----
fits : dict
Dict with {pairs: {states: fits}}, as returned from parse_logfile
target-dir : str
path (relative or absolute) to target RDFs
potentials_dir : str
path (relative or absolute) to potentials from optimization
step : int
Print RDFs and potentials from this step
use_agg : bool
True to use Agg backend, may be useful on clusters with no display
n_skip : int
Set ylimits on RDF plot with RDFs after n_skip
Returns
-------
Nothing is returned, but figures are plotted in './animations'
The target rdfs are expected to have the format 'target-dir/type1-type2-state.txt'
"""
if not os.path.exists('animations'):
os.makedirs('animations')
logfile_info = parse_logfile(logfile_name)
for pair, state in logfile_info.items():
for state, fits in state.items():
if step == -1:
step = len(fits)
type1 = pair.split('-')[0]
type2 = pair.split('-')[1]
animate_pair_at_state(type1, type2, state, step, target_dir,
potentials_dir, rdf_dir, use_agg, to_angstrom,
to_kcalpermol, n_skip)
from msibi_utils.plot_fit import plot_all_fits
from msibi_utils.animate_rdf import animate_all_pairs_states
from msibi_utils.parse_logfile import parse_logfile
from msibi_utils.find_best_iterations import find_best_iterations
logfile = 'charmm_bi/6-12-18.log'
log_info = parse_logfile(logfile)
best_iterations = find_best_iterations(logfile)
print(best_iterations)
plot_all_fits(logfile, use_agg=True, ylims=(0, 1))
animate_all_pairs_states(
logfile,
"charmm_bi/rdfs",
potentials_dir="charmm_bi/potentials",
rdf_dir="charmm_bi/rdfs",
potentials2_dir="charmm_bulk_debi_flhe_dspc/potentials",
rdf2_dir="charmm_bulk_debi_flhe_dspc/rdfs",
use_agg=True)