def plot_pair_fits(pair, fits, use_agg=False, ylims=(0, 1)):
if use_agg:
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
for state, fit in fits[pair].items():
ax.plot(fit, label=state)
ax.set_xlabel('step')
ax.set_ylabel('relative fit')
ax.set_ylim(ylims)
ax.legend(loc='best')
ax.set_title(pair)
tpl.timize(ax)
fig.tight_layout()
fig.savefig('figures/%s-fit.pdf' % pair, transparent=True)
plt.close('all')
def plot_pair_at_state(t1, t2, state, step, target_dir,
potentials_dir='./potentials', rdf_dir='./rdfs', use_agg=False,
to_angstrom=6.0, to_kcalpermol=0.1, lw=None):
"""Plot the RDFs (target and CG) and potential on the same plot for a given pair at a
given state.
Args
----
t1 : str
The first type in the pair
t2 : str
The second type in the pair
state : str
The name of the state
target_dir : str
Path to target RDFs
potentials_dir : str
Path to potentials from MS IBI optimization
rdf_dir : str
Path to RDFs from MS IBI optimization
use_agg : bool
Use Agg backend if true, may be useful for clusters with no display
to_angstrom : float
Multiply distance units by this to get into Angstrom
to_kcalpermol : float
Multiple energy units by this to get into kcal/mol
Returns
-------
Nothing - prints plots in './figures'
"""
if use_agg:
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
pot_name = 'step{step}.pot.{t1}-{t2}.txt'.format(**locals())
pot_file = os.path.join(potentials_dir, pot_name)
rdf_name = '{t1}-{t2}-{state}.txt'.format(**locals())
rdf_file = os.path.join(target_dir, rdf_name)
try:
potential = np.loadtxt(pot_file)
except:
raise IOError('File not found: {pot_file}'.format(**locals()))
try:
rdfs = [np.loadtxt(rdf_file)]
except:
raise IOError('File not found: {rdf_file}'.format(**locals()))
potential[:, 0] *= to_angstrom
potential[:, 1] *= to_kcalpermol
rdfs[0][:, 0] *= to_angstrom
rdf_name = 'pair_{t1}-{t2}-state_{state}-step{step}.txt'.format(**locals())
rdf_file = os.path.join(rdf_dir, rdf_name)
rdfs.append(np.loadtxt(rdf_file))
rdfs[1][:, 0] *= to_angstrom
for rdf, label in zip(rdfs, ['Target', 'CG']):
if lw:
ax.plot(rdf[:, 0], rdf[:, 1], label=label, lw=lw)
else:
ax.plot(rdf[:, 0], rdf[:, 1], label=label)
ax.set_xlabel(u'r, \u00c5')
ax.set_ylabel('g(r)')
ax.set_ylim(bottom=0)
ax.set_xlim(left=0)
ax.set_title('{t1}-{t2}, {state}'.format(**locals()))
pot_ax = ax.twinx()
pot_ax.plot(potential[:, 0], potential[:, 1], "#0485d1")
pot_ax.set_ylabel('V(r), kcal/mol')
pot_ax.set_ylim(bottom=1.1*np.amin(potential[5:, 1]))
pot_ax.set_ylim(top=-1.1*np.amin(potential[5:, 1]))
pot_ax.set_xlim(left=0)
ax.set_xlim(right=rdfs[0][-1, 0])
extra = [[potential[-1, 0], ax.get_xlim()[1]], [0, 0]]
pot_ax.plot(extra[0], extra[1], '#0485d1')
ax.legend(loc=0)
tpl.timize(ax)
tpl.timize(pot_ax, legend=False, grid=False)
fig.tight_layout()
if not os.path.exists('figures'):
os.makedirs('figures')
fig.savefig('figures/{t1}-{t2}-{state}-step{step}.pdf'.format(**locals()),
transparent=True)
plt.close('all')