def plot_dih(self, sel="protein", data=None):
"""Creates a plot of the standard deviation of the dihedral angles of the protein by macrostate
"""
from htmd.projections.metricdihedral import MetricDihedral
dih_metric = MetricDihedral(protsel=sel)
aux_plot(self.model, self.mol, plot_dihedral, metric=dih_metric, data=data, skip=self.skip, method=np.std,
save=self.out_folder + "/{}.png".format(self.plot_dihedral), chain_id="P1",
start_index=self.start_index)
def sasa_variation(self):
from htmd.projections.metricsasa import MetricSasa
labels = generate_labels(self.mol)
mol_contact_map_metric = MetricSasa(sel='protein', probeRadius=1.4, numSpherePoints=500, mode='residue')
mapping = mol_contact_map_metric.getMapping(self.mol)
aux_plot(self.model, self.mol, plot_contacts, metric=mol_contact_map_metric, normalize=False, skip=self.skip, method=np.mean,
mod=self.model, title="Contacts by residue", vmax=None,
plot=False, save=f'{self.out_folder}/no_sasa_test.png')
def plot_contact_map(self, name, selection="noh and protein", data=None, threshold=4):
"""Generate a residue-residue contact plot by macrostate given a VMD selection
Parameters
----------
name : str
Output name for the generated plot
selection : str, optional
VMD selection to create a matrix contact plot
threshold : int, optional
Threshold distance in angstrom to discrinate contact vs no-contact
"""
from htmd.projections.metricdistance import MetricDistance
contact_metric = MetricDistance(sel1=selection, sel2=selection,
groupsel1="residue", groupsel2="residue", threshold=threshold, metric="contacts")
mapping = contact_metric.getMapping(self.mol)
aux_plot(self.model, self.mol, contact_plot, metric=contact_metric, skip=self.skip, method=np.mean,
mapping=mapping, cols=2, rows=int(self.model.macronum/2)+self.model.macronum%2, data=data,
plot=False, save=f"{self.out_folder}/{name}.png")
def plot_mol_contact(self, data=None, sel1="noh and protein", sel2="noh and resname MOL", threshold=4):
"""Plot a molecule-residue contact map.
Parameters
----------
sel1 : str, optional
VMD selection. Grouped by residue.
sel2 : str, optional
VMD selection
threshold : int, optional
Threshold distance in angstrom to discrinate contact vs no-contact
"""
from htmd.projections.metricdistance import MetricDistance
# labels = generate_labels(self.mol)
mol_contact_map_metric = MetricDistance(sel1=sel1, sel2=sel2,
groupsel1="residue", groupsel2="all", threshold=5, metric="contacts")
# mapping = mol_contact_map_metric.getMapping(self.mol)
aux_plot(self.model, self.mol, plot_contacts, metric=mol_contact_map_metric, skip=self.skip, method=np.mean,
title="Contacts by residue", data=data,
plot=False, save=f'{self.out_folder}/{self.plot_mol_contacts}.png')
def plot_atom_mol_contact(self, data=None, sel1="noh and protein", sel2="noh and resname MOL", threshold=5):
"""Plot a molecule-residue contact map.
Parameters
----------
sel1 : str, optional
VMD selection. Grouped by residue.
sel2 : str, optional
VMD selection
threshold : int, optional
Threshold distance in angstrom to discrinate contact vs no-contact
"""
from htmd.projections.metricdistance import MetricDistance
label = ['M{}-{}%'.format(i, np.round(percent*100, 2)) for i, percent in enumerate(self.model.eqDistribution(plot=False))]
mol_contact_map_metric = MetricDistance(sel1=sel1, sel2=sel2,
groupsel1="residue", threshold=threshold, metric="contacts")
mapping = mol_contact_map_metric.getMapping(self.mol)
aux_plot(self.model, self.mol, contact_plot_by_atom, metric=mol_contact_map_metric,
skip=self.skip, method=np.mean, data=data,
mapping=mapping, label=label, save=f'{self.out_folder}/{self.plot_mol_contacts}_by_atom.png')