From bc6fa3811b22e5001913b4cec8226d42b97c9ef9 Mon Sep 17 00:00:00 2001 From: Rick Sexton Date: Wed, 14 Feb 2024 22:17:11 -0700 Subject: [PATCH] changed _create_traj to use lipid resids instead of indices --- basicrta/weighted_density.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/basicrta/weighted_density.py b/basicrta/weighted_density.py index e674344..c549249 100644 --- a/basicrta/weighted_density.py +++ b/basicrta/weighted_density.py @@ -33,7 +33,7 @@ def __init__(self, gibbs, contacts, n=None): def _create_data(self): if os.path.exists(f'{self.gibbs.residue}/den_write_data_all.npy') and \ - self.N is not None: + self.N is not None: tmp = np.load(f'{self.gibbs.residue}/den_write_data_all.npy') wf, wl, wi = (tmp[:, 0].astype(int), tmp[:, 1].astype(int), tmp[:, 2:]) @@ -91,8 +91,8 @@ def _create_traj(self): with mda.Writer(self.trajname, len(write_ag.atoms)) as W: for i, ts in tqdm(enumerate(self.u.trajectory[wf]), total=self.N, desc='writing trajectory'): - W.write(self.ag1.atoms + - self.ag2.residues[wl[i]].atoms) + W.write(self.ag1 + + self.ag2.select_atoms(f'resid {wl[i]}').atoms) def compute_weighted_densities(self):