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)