run_dirs = []
for ii in range(20):
run_dirs.append('/DESRES-Trajectory_pnas2011a-A-'+str(ii)+'-no-water-no-lipid/pnas2011a-A-'+str(ii)+'-no-water-no-lipid')
dir_top = '/home/shenglan/topologies'
times_path = parent_dir+run_dirs[0]+'/'+run_dirs[0].split('/')[-1]+'_times.csv'
LOAD_STRIDE = 10
colors = np.array([x for x in 'bgrcmykbgrcmykbgrcmykbgrcmyk'])
colors = np.hstack([colors] * 20)
#load list of mdtraj objects
simulations = []
for this_run_dir in run_dirs:
simulations.append(util.load_trajs(this_run_dir,parent_dir,dir_top,load_stride = LOAD_STRIDE))
#track atoms in ligands
inds =[] #indices of Cs in the aromatic ring
atoms_in_ring = ['C8','C9','C10','C11','C12','C13']
ligands = [residue for residue in simulations[0][0].topology.chain(1).residues][:-1]
for ligand in ligands:
iis = [atom.index for atom in simulations[0][0].topology.chain(1).atoms if atom.name in atoms_in_ring
and atom.residue == ligand]
inds.append(iis)
#track residue Aps113
first_res = str(simulations[0][0].topology.chain(0).residue(0))
import re
match = re.match(r"([a-z]+)([0-9]+)", first_res, re.I)
if match:
run_dirs.append('/DESRES-Trajectory_pnas2011a-C-' + str(ii) +
'-no-water-no-lipid/pnas2011a-C-' + str(ii) +
'-no-water-no-lipid')
dir_top = '/home/shenglan/topologies'
times_path = parent_dir + run_dirs[0] + '/' + run_dirs[0].split(
'/')[-1] + '_times.csv'
LOAD_STRIDE = None
N_CLUSTER = 1000
#load list of mdtraj objects
simulations = []
for this_run_dir in run_dirs:
simulations.append(
util.load_trajs(this_run_dir,
parent_dir,
dir_top,
load_stride=LOAD_STRIDE))
#track atoms in ligands
inds_N = [] #indices of N atom
atoms_to_track = ['N']
ligands = ['ALP%d' % (ii + 1) for ii in range(10)]
for ligand in ligands:
iis = [
atom.index for atom in simulations[0][0].topology.chain(0).atoms if
atom.element.symbol in atoms_to_track and str(atom.residue) == ligand
]
inds_N.append(iis)
inds_all = [] #indices of all atoms, separated by ligands
dir_top = '/home/shenglan/topologies'
times_path = parent_dir + run_dirs[0] + '/' + run_dirs[0].split(
'/')[-1] + '_times.csv'
files = []
for this_file in os.listdir(parent_dir + run_dirs[0]):
if this_file.endswith('.dcd'):
files.append(this_file)
files = sorted(files)
LOAD_STRIDE = 10000
test_run = run_dirs[0]
test_traj = util.load_trajs(test_run,
parent_dir,
dir_top,
load_stride=LOAD_STRIDE)
inds_N = [] #indices of N atom
atoms_to_track = ['N']
ligands = ['ALP%d' % (ii + 1) for ii in range(10)]
print ligands
print test_traj[0].topology.chain(0).atom(4667).residue
for ligand in ligands:
iis = [
atom.index for atom in test_traj[0].topology.chain(0).atoms if
atom.element.symbol in atoms_to_track and str(atom.residue) == ligand
]
inds_N.append(iis)
for ii in range(number_of_sims):
run_dirs.append('/DESRES-Trajectory_pnas2011a-C-'+str(ii)+'-no-water-no-lipid/pnas2011a-C-'+str(ii)+'-no-water-no-lipid')
dir_top = '/home/shenglan/topologies'
times_path = parent_dir+run_dirs[0]+'/'+run_dirs[0].split('/')[-1]+'_times.csv'
files = []
for this_file in os.listdir(parent_dir+run_dirs[0]):
if this_file.endswith('.dcd'):
files.append(this_file)
files = sorted(files)
LOAD_STRIDE = 10000
test_run = run_dirs[0]
test_traj = util.load_trajs(test_run,parent_dir,dir_top,load_stride = LOAD_STRIDE)
inds_N =[] #indices of N atom
atoms_to_track =['N']
ligands = ['ALP%d'%(ii+1) for ii in range(10)]
print ligands
print test_traj[0].topology.chain(0).atom(4667).residue
for ligand in ligands:
iis = [atom.index for atom in test_traj[0].topology.chain(0).atoms if atom.element.symbol in atoms_to_track
and str(atom.residue)==ligand]
inds_N.append(iis)
# inds_N = [[atom.index] for atom in test_traj[0].topology.chain(0).atoms if atom.element.symbol in atoms_to_track
# and atom.residue.name== 'ALP']
print inds_N
