def main():
parser = argparse.ArgumentParser()
parser.add_argument('-p', '--project', default='ProjectInfo.h5')
parser.add_argument('-a', '--assignments', default='Data/Assignments.h5')
args = parser.parse_args()
a = Serializer.LoadData(args.assignments)
p = Project.LoadFromHDF(args.project)
maxx, maxy, minx, miny = -np.inf, -np.inf, np.inf, np.inf
n_states = np.max(a) + 1
x = np.concatenate([p.LoadTraj(i)['XYZList'][:, 0, 0] for i in range(p['NumTrajs'])])
y = np.concatenate([p.LoadTraj(i)['XYZList'][:, 0, 1] for i in range(p['NumTrajs'])])
a = np.concatenate([a[i, :] for i in range(p['NumTrajs'])])
plot_v(minx=np.min(x), maxx=np.max(x), miny=np.min(y), maxy=np.max(y))
colors = ['b', 'r', 'm', 'c', 'g']
for j in xrange(n_states):
w = np.where(a == j)[0]
pp.scatter(x[w], y[w], marker='x', c=colors[j], label='State %d' % j,
edgecolor=colors[j], alpha=0.5)
pp.legend()
pp.show()
the structures of each of the cluster centers. Produced using Cluster.py.''',
default='Data/Gens.lh5')
parser.add_argument('output_dir', default='PDBs')
args = parser.parse_args()
if -1 in args.states:
print "Ripping PDBs for all states"
args.states = 'all'
if args.conformations_per_state == -1:
print "Getting all PDBs for each state"
args.conformations_per_state = 'all'
atom_indices = np.loadtxt(args.lprmsd_atom_indices, np.int)
assignments = Serializer.LoadData(args.assignments)
project = Project.load_from_hdf(args.project)
if args.lprmsd_permute_atoms == 'None':
permute_indices = None
else:
permute_indices = ReadPermFile(args.lprmsd_permute_atoms)
if args.lprmsd_alt_indices == 'None':
alt_indices = None
else:
alt_indices = np.loadtxt(args.lprmsd_alt_indices, np.int)
run(project, assignments, args.conformations_per_state, args.states,
args.output_dir, args.generators, atom_indices, permute_indices,
alt_indices, args.total_memory_gb)
import sys, os
import numpy as np
import scipy.io
from msmbuilder import arglib
from msmbuilder import Serializer
from msmbuilder import MSMLib
Assignments = Serializer.LoadData("%s" % (sys.argv[1]))
NumStates = max(Assignments.flatten()) + 1
LagTime = sys.argv[2]
Counts = MSMLib.GetCountMatrixFromAssignments(Assignments,
NumStates,
LagTime=LagTime,
Slide=True)
scipy.io.mmwrite('%s' % (sys.argv[3]), Counts)
