def _loadMols(self, i, rel, molfile, wrapsel, alignsel, refmol):
frames = self.data.rel2sim(rel)
mol = Molecule(molfile)
trajs = np.empty(0, dtype=str)
frs = np.empty(0, dtype=int)
for f in frames:
trajs = np.append(trajs, f.sim.trajectory[f.piece])
frs = np.append(frs, f.frame)
mol.read(trajs, frames=frs)
if len(wrapsel) > 0:
mol.wrap(wrapsel)
if refmol is not None:
mol.align(alignsel, refmol=refmol)
return mol
def _loadMols(self, rel, molfile, wrapsel, alignsel, refmol, simlist):
frames = self.data.rel2sim(rel, simlist=simlist)
mol = Molecule(molfile)
trajs = np.empty(0, dtype=str)
frs = np.empty(0, dtype=int)
for f in frames:
trajs = np.append(trajs, f.sim.trajectory[f.piece])
frs = np.append(frs, f.frame)
mol.read(trajs, frames=frs)
if len(wrapsel) > 0:
mol.wrap(wrapsel)
if (refmol is not None) and (alignsel is not None):
mol.align(alignsel, refmol=refmol)
return mol
def viewStates(self, protein=None, ligand=None, nsamples=20):
from htmd.projections.metric import _singleMolfile
from htmd.molecule.molecule import Molecule
from htmd.vmdviewer import getCurrentViewer
(single, molfile) = _singleMolfile(self.data.simlist)
if not single:
raise RuntimeError('Can'
't visualize states without unique molfile')
viewer = getCurrentViewer()
colors = [0, 1, 3, 4, 5, 6, 7, 9]
print('Active set includes macrostates: {}'.format(
self.hmm.active_set))
# dtraj = np.vstack(self.hmm.discrete_trajectories_full)
res = self.hmm.sample_by_observation_probabilities(nsamples)
refmol = Molecule(molfile)
for i, s in enumerate(self.hmm.active_set):
mol = Molecule(molfile)
mol.coords = []
mol.box = []
# idx = np.where(dtraj == i)[0]
# samples = np.random.choice(idx, 20)
# frames = self.data.abs2sim(samples)
frames = self.data.rel2sim(res[i])
for f in frames:
mol._readTraj(f.sim.trajectory[f.piece],
frames=[f.frame],
append=True)
mol.wrap('protein')
mol.align('protein', refmol=refmol)
viewer.loadMol(mol, name='hmm macro ' + str(s))
if ligand is not None:
viewer.rep('ligand',
sel=ligand,
color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
def viewStates(self, protein=None, ligand=None, nsamples=20):
from htmd.projections.metric import _singleMolfile
from htmd.molecule.molecule import Molecule
from htmd.vmdviewer import getCurrentViewer
(single, molfile) = _singleMolfile(self.data.simlist)
if not single:
raise RuntimeError('Can''t visualize states without unique molfile')
viewer = getCurrentViewer()
colors = [0, 1, 3, 4, 5, 6, 7, 9]
print('Active set includes macrostates: {}'.format(self.hmm.active_set))
# dtraj = np.vstack(self.hmm.discrete_trajectories_full)
res = self.hmm.sample_by_observation_probabilities(nsamples)
refmol = Molecule(molfile)
for i, s in enumerate(self.hmm.active_set):
mol = Molecule(molfile)
mol.coords = []
mol.box = []
# idx = np.where(dtraj == i)[0]
# samples = np.random.choice(idx, 20)
# frames = self.data.abs2sim(samples)
frames = self.data.rel2sim(res[i])
for f in frames:
mol._readTraj(f.sim.trajectory[f.piece], frames=[f.frame], append=True)
mol.wrap('protein')
mol.align('protein', refmol=refmol)
viewer.loadMol(mol, name='hmm macro ' + str(s))
if ligand is not None:
viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
if protein is not None:
viewer.rep('protein')
viewer.send('start_sscache')
Ra=226.00, Ac=227.00, Th=232.04, Pa=231.04, U=238.03,
Np=237.00, Pu=244.00, Am=243.00, Cm=247.00, Bk=247.00,
Cf=251.00, Es=252.00, Fm=257.00, Md=258.00, No=259.00,
Lr=262.00, Rf=261.00, Db=262.00, Sg=266.00, Bh=264.00,
Hs=269.00, Mt=268.00)
mol = mol.copy()
mol.filter(sel, _logger=False)
mol.wrap("protein")
mol.center()
mass = np.array([_atomic_mass[i] for i in mol.element])
t_mass = np.sum(mass)
center_of_mass = np.sum(mol.coords * mass[:, None, None], axis=0) / t_mass
dist_from_com = np.sqrt(np.sum((mol.coords - center_of_mass)**2, axis=1))
rg = np.sqrt(np.sum(mass[: , None] * dist_from_com**2, axis=0) / t_mass)
return rg[:, None]
if __name__ == '__main__':
from htmd.molecule.molecule import Molecule
# from htmd.projections.metric import Metric
# met_rg = Metric(sim)
mol = Molecule("./ref_files/MD_trajectory/structure.pdb")
mol.read("./ref_files/MD_trajectory/structure.psf")
mol.read("./ref_files/MD_trajectory/output.xtc")
mol.wrap("protein")
mol.align("protein")
met = metricRG(mol)
