parser.add_argument('-e',
'--last_it',
dest="last_iteration",
type=int,
default=-1,
help="Last iteration to use.")
parser.add_argument('-v',
'--verbose',
action="store_true",
dest="verbose",
help="Print information for every iteration")
args = parser.parse_args()
logger = Logger(args.logdir)
iterations = logger.loadIterations(args.first_iteration,
args.last_iteration,
verbose=True)
VERBOSE = args.verbose
total_count = 0
for iteration in iterations:
total_iteration_segments = 0
active_bins = 0
inactive_bins = 0
for this_bin in iteration:
this_number_of_segments = this_bin.getNumberOfSegments()
if this_bin.getSampleRegion():
active_bins += 1
total_count += this_number_of_segments
total_iteration_segments += this_number_of_segments
# Initialize
print(
'\033[1mCalculating PMF\033[0m (Free Energy is given in kcal/mol at 298K).'
)
args = parser.parse_args()
if args.plot:
import matplotlib.pyplot as plt
# failproofing for segment plotting
if args.first_iteration == args.last_iteration and \
args.plot_segments:
raise Exception("Need more than 1 iteration for --segments\n")
#get the actual Iteration from logger module
logger = Logger(args.logdir)
iterations = logger.loadIterations(begin=args.first_iteration,
end=args.last_iteration)
# load md module
if not args.input_md_conf:
args.input_md_conf = logger.loadConfigFile(iterations[0].getId())
md_module = MD_module(args.input_md_conf, debug=False)
# Load cpptraj input file as one string with linebreaks and delete the last line break
try:
cpptraj_lines_file = open(args.cpptraj_lines_file_path, 'r')
except:
print('Error: could not open ' + args.cpptraj_lines_file_path)
cpptraj_lines = ''
for line in cpptraj_lines_file:
cpptraj_lines = cpptraj_lines + line
cpptraj_lines = cpptraj_lines[0:-1]
# Initialize
print(
'\033[1mCalculating Bin Free Energies\033[0m (Free Energy is given in kcal/mol at 298K).'
)
args = parser.parse_args()
last_iteration = args.last_iteration
first_iteration = args.first_iteration
logger = Logger(args.logdir)
if last_iteration < 0:
last_iteration = logger.getLastIterationId()
n_iterations = last_iteration - first_iteration + 1
#initialize bin probability evolution array with size of last frame number_of_bins
iteration = logger.loadIterations(logger.getLastIterationId(),
logger.getLastIterationId())[0]
n_bins = iteration.getNumberOfBins()
bin_probabilities = numpy.zeros(
[n_iterations, iteration.getNumberOfBins(), 2], float)
for i in range(0, len(bin_probabilities[:, 0, 0])):
for j in range(0, len(bin_probabilities[0, :, 0])):
for k in range(0, 2):
bin_probabilities[i, j, k] = 0
for i in range(first_iteration, last_iteration):
print(i)
iteration = logger.loadIterations(i, i)[0]
i = i - first_iteration
for j in range(iteration.getNumberOfBins()):
bin_probabilities[i, j, 0] = iteration.bins[j].getProbability()
if bin_probabilities[i, j, 0] > 0.0:
