access structure

old 

import schrodinger.trajectory.cmsstructure as cmsstructure
import schrodinger.structutils.analyze as analyze

cms_st = cmsstructure.read_cms(model_fname)
for a in cms_st.atom:
    print(a.index)
ligand_aids = analyze.evaluate_asl(cms_st, ligand_asl)
new 
import schrodinger.application.desmond.packages.topo as topo

_, cms_model = topo.read_cms(model_fname)
for a in cms_model.atom:
    print(a.index)
ligand_aids = cms_model.select_atom(ligand_asl)

Note that analyze.evaluate_asl does not respect PBC whereas cms_model.select_atom does.

access trajectory

old 

from schrodinger.trajectory.desmondsimulation import ChorusSimulation
from schrodinger.infra import desmond

tr = desmond.generic_trajectory(trajectory_directory)
dt = tr.frame_time(1) - tr.frame_time(0)

csim = ChorusSimulation(cms_filename, trajectory_directory)
for frame_index in xrange(csim.total_frame):
    fr = csim.getFrame(frame_index)
    st = fr.getStructure()

new 

import schrodinger.application.desmond.packages.traj as traj
import schrodinger.application.desmond.packages.topo as topo

_, cms_model = topo.read_cms(model_fname)
tr = traj.read_traj(trajectory_directory)
dt = tr[1].time - tr[0].time
for fr in tr:
    st = topo.update_fsys_ct(cms_model, fr).fsys_ct
    # you can use st = topo.update_fsys_ct(cms_model, fr) as well
    # since the properties of cms_model and its fsys_ct are in sync
Note that

  • although there is a correspondence of st = fr.getStructure(), it is likely not the way to go. See this paradigm.
  • there are two ways to update the cms_model 
    updated_cms = topo.update_fsys_ct(cms_model, fr)
updated_cms = topo.update_cms(cms_model, fr)

The difference is that update_cms not only updates full system ct, but also component cts.