def main():
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description="Compress given configuration.")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument('outfile', type=str, nargs=1, help='minified file')
parser.add_argument('-a', action='store_true', help='Discard a vectors.')
parser.add_argument(
'-p',
type=int,
nargs=1,
help=
'Round positions and orientations to the specified number of digits.')
args = parser.parse_args()
traj_file = args.trajectory[0]
out = args.outfile[0]
# get the number of configurations
n_confs = cal_confs(traj_file)
try: # make sure there is no out file
remove(out)
except:
pass
with ErikReader(traj_file) as reader:
for i in range(n_confs):
print(i + 1, ":", n_confs)
# Erik reader ignores velocities
system = reader.read()
if args.p: # round positions
system.positions = round(system.positions, args.p[0])
system.a1s = round(system.a1s, args.p[0])
system.a3s = round(system.a3s, args.p[0])
if args.a: # discard a vectors
system.a1s -= system.a1s
system.a3s -= system.a3s
# output conf
system.write_append(out)
def main():
#read data from files
parser = argparse.ArgumentParser(prog = path.basename(__file__), description="Compare the bonds found at each trajectory with the intended design")
parser.add_argument('inputfile', type=str, nargs=1, help="The inputfile used to run the simulation")
parser.add_argument('trajectory', type=str, nargs=1, help="The trajecotry file to compare against the designed pairs")
parser.add_argument('designed_pairs', type=str, nargs=1, help="The file containing the desired nucleotides pairings in the format \n a b\nc d")
parser.add_argument('output_file', type=str, nargs=1, help="name of the file to save the output json overlay to")
parser.add_argument('-p', metavar='num_cpus', nargs=1, type=int, dest='parallel', help="(optional) How many cores to use")
#run system checks
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "numpy"])
args = parser.parse_args()
inputfile = args.inputfile[0]
traj_file = args.trajectory[0]
designfile = args.designed_pairs[0]
outfile = args.output_file[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
top_file = get_input_parameter(inputfile, "topology")
if "RNA" in get_input_parameter(inputfile, "interaction_type"):
environ["OXRNA"] = "1"
else:
environ["OXRNA"] = "0"
num_confs = cal_confs(traj_file)
with open(designfile, 'r') as file:
pairs = file.readlines()
if not parallel:
print("INFO: Computing base pairs in {} configurations using 1 core.".format(num_confs), file=stderr)
r = LorenzoReader2(traj_file,top_file)
tot_bonds, tot_missbonds, out_array, confid = bond_analysis(r, pairs, inputfile, num_confs)
try:
_ = tot_bonds #this will fail if DNAnalysis failed.
except:
print("ERROR: DNAnalysis encountered an error and could not analyze the trajectory")
exit(1)
if parallel:
print("INFO: Computing base pairs in {} configurations using {} cores.".format(num_confs, n_cpus), file=stderr)
out = parallelize_lorenzo_onefile.fire_multiprocess(traj_file, top_file, bond_analysis, num_confs, n_cpus, pairs, inputfile)
tot_bonds = 0
tot_missbonds = 0
out_array = np.zeros(len(open(top_file, 'r').readlines())-1)
confid = 0
for i in out:
if i[0] is not None:
tot_bonds += i[0]
tot_missbonds += i[1]
#out_array += i[2]
confid += i[3]
else:
print("WARNING: Some configurations were invalid and not included in the analysis. Please check the logs", file=stderr)
#tot_bonds = sum((i[0] for i in out if i[0] != None))
#tot_missbonds = sum((i[1] for i in out if i[1] != None))
out_array = sum((i[2] for i in out if len(i[2]) > 0))
#confid = sum((i[3] for i in out if i[3] != None))
print("\nSummary:\navg bonds: {}\navg_missbonds: {}".format(tot_bonds/(int(confid)),tot_missbonds/int(confid)))
print("INFO: Writing bond occupancy data to {}".format(outfile))
with open(outfile, "w+") as file:
file.write("{\n\"occupancy\" : [")
file.write(str(out_array[0]/int(confid)))
for n in out_array[1:]:
file.write(", {}".format(n/int(confid)))
file.write("] \n}")
def main():
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description=
"Calculate differences between structures and automatically apply DBSCAN to retrieve clusters"
)
parser.add_argument('inputfile',
type=str,
nargs=1,
help="The inputfile used to run the simulation")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
args = parser.parse_args()
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "numpy", "matplotlib"])
traj_file = args.trajectory[0]
inputfile = args.inputfile[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
top_file = get_input_parameter(inputfile, "topology")
if "RNA" in get_input_parameter(inputfile, "interaction_type"):
environ["OXRNA"] = "1"
else:
environ["OXRNA"] = "0"
num_confs = cal_confs(traj_file)
import UTILS.base #this needs to be imported after the model type is set
r2 = LorenzoReader2(traj_file, top_file)
#how do you want to get your eRMSDs? Do you need to do the time-consuming calculation or is it done and you have a pickle?
if not parallel:
r1 = LorenzoReader2(traj_file, top_file)
eRMSDs = get_eRMSDs(r1, r2, inputfile, traj_file, top_file, num_confs)
if parallel:
out = parallelize_lorenzo_onefile.fire_multiprocess(traj_file,
top_file,
get_eRMSDs,
num_confs,
n_cpus,
r2,
inputfile,
traj_file,
top_file,
matrix=True)
eRMSDs = np.sum((i for i in out), axis=0)
#eRMSDs = pickle.load(open('tmp_eRMSDs', 'rb'))
#the eRMSD matrix is actually only half a matrix
for ni, i in enumerate(eRMSDs):
for nj, j in enumerate(i):
eRMSDs[nj][ni] = j
if ni == nj:
eRMSDs[ni][nj] = 0
#since calculating the eRMSDs are so time-consuming to calculate we're gonna pickle it to iterate the DBSCAN later.
with open("tmp_eRMSDs", "wb") as file:
pickle.dump(eRMSDs, file)
###############################################################################################################
#Next, we're going to perform a DBSCAN on that matrix of eRMSDs to find clusters of similar structures
perform_DBSCAN(eRMSDs, num_confs, traj_file, inputfile, "precomputed", 12,
8)
def main():
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description=
"Calculates a principal component analysis of nucleotide deviations over a trajectory"
)
parser.add_argument('inputfile',
type=str,
nargs=1,
help="The inputfile used to run the simulation")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument(
'meanfile',
type=str,
nargs=1,
help='The mean structure .json file from compute_mean.py')
parser.add_argument(
'outfile',
type=str,
nargs=1,
help='the name of the .json file where the PCA will be written')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument(
'-c',
metavar='cluster',
dest='cluster',
action='store_const',
const=True,
default=False,
help="Run the clusterer on each configuration's position in PCA space?"
)
args = parser.parse_args()
check_dependencies(["python", "numpy", "Bio"])
traj_file = args.trajectory[0]
inputfile = args.inputfile[0]
mean_file = args.meanfile[0]
outfile = args.outfile[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
#-c makes it run the clusterer on the output
cluster = args.cluster
top_file = get_input_parameter(inputfile, "topology")
if "RNA" in get_input_parameter(inputfile, "interaction_type"):
environ["OXRNA"] = "1"
else:
environ["OXRNA"] = "0"
import UTILS.base #this needs to be imported after the model type is set
num_confs = cal_confs(traj_file)
if mean_file.split(".")[-1] == "json":
with open(mean_file) as file:
align_conf = load(file)['g_mean']
elif mean_file.split(".")[-1] == "dat":
fetch_np = lambda conf: np.array([n.cm_pos for n in conf._nucleotides])
with LorenzoReader2(mean_file, top_file) as reader:
s = reader._get_system()
align_conf = fetch_np(s)
cms = np.mean(align_conf,
axis=0) #all structures must have the same center of mass
align_conf -= cms
#Compute the deviations
if not parallel:
r = LorenzoReader2(traj_file, top_file)
deviations_matrix = get_pca(r, align_conf, num_confs)
if parallel:
out = parallelize_lorenzo_onefile.fire_multiprocess(
traj_file, top_file, get_pca, num_confs, n_cpus, align_conf)
deviations_matrix = np.concatenate([i for i in out])
#now that we have the deviations matrix we're gonna get the covariance and PCA it
#note that in the future we might want a switch for covariance vs correlation matrix because correlation (cov/stdev so all diagonals are 1) is better for really floppy structures
pca = PCA(n_components=3)
pca.fit(deviations_matrix)
transformed = pca.transform(deviations_matrix)
#THIS IS AS FAR AS I GOT
import matplotlib.pyplot as plt
print("INFO: Saving scree plot to scree.png", file=stderr)
plt.scatter(range(0, len(evalues)), evalues, s=25)
plt.xlabel("component")
plt.ylabel("eigenvalue")
plt.savefig("scree.png")
print(
"INFO: Creating coordinate plot from first three eigenvectors. Saving to coordinates.png",
file=stderr)
#if you want to weight the components by their eigenvectors
#mul = np.einsum('ij,i->ij',evectors[0:3], evalues[0:3])
mul = evectors
#reconstruct configurations in component space
out = np.dot(deviations_matrix, mul).astype(float)
#make a quick plot from the first three components
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.scatter(out[:, 0], out[:, 1], out[:, 2], c='g', s=25)
plt.savefig("coordinates.png")
#Create an oxView overlay showing the first SUM components
SUM = 1
print(
"INFO: Change the number of eigenvalues to sum and display by modifying the SUM variable in the script. Current value: {}"
.format(SUM),
file=stderr)
weighted_sum = np.zeros_like(evectors[0])
for i in range(0, SUM): #how many eigenvalues do you want?
weighted_sum += evalues[i] * evectors[i]
prep_pos_for_json = lambda conf: list(list(p) for p in conf)
with catch_warnings(
): #this produces an annoying warning about casting complex values to real values that is not relevant
simplefilter("ignore")
output_vectors = weighted_sum.reshape(int(weighted_sum.shape[0] / 3),
3).astype(float)
with open(outfile, "w+") as file:
file.write(dumps({"pca": prep_pos_for_json(output_vectors)}))
#If we're running clustering, feed the linear terms into the clusterer
if cluster:
print("INFO: Mapping configurations to component space...",
file=stderr)
#If you want to cluster on only some of the components, uncomment this
#out = out[:,0:3]
from clustering import perform_DBSCAN
labs = perform_DBSCAN(out, num_confs, traj_file, inputfile,
"euclidean", 12, 8)
def main():
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description="Fit vectors to every duplex in the structure")
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument('inputfile',
type=str,
nargs=1,
help="The inputfile used to run the simulation")
parser.add_argument('trajectory',
type=str,
nargs=1,
help="The trajectory file from the simulation")
parser.add_argument('-o',
'--output',
metavar='output_file',
type=str,
nargs=1,
help='name of the file to write the angle list to')
args = parser.parse_args()
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "numpy"])
#Process command line arguments:
inputfile = args.inputfile[0]
traj_file = args.trajectory[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
#-o names the output file
if args.output:
outfile = args.output[0]
else:
outfile = "angles.txt"
print("INFO: No outfile name provided, defaulting to \"{}\"".format(
outfile),
file=stderr)
#Get relevant parameters from the input file
top_file = get_input_parameter(inputfile, "topology")
if "RNA" in get_input_parameter(inputfile, "interaction_type"):
environ["OXRNA"] = "1"
else:
environ["OXRNA"] = "0"
#Calculate the number of configurations.
num_confs = cal_confs(traj_file)
r0 = LorenzoReader2(traj_file, top_file)
r0._get_system()
#launch find_angle using the appropriate number of threads to find all duplexes.
if not parallel:
print(
"INFO: Fitting duplexes to {} configurations using 1 core.".format(
num_confs),
file=stderr)
r = LorenzoReader2(traj_file, top_file)
duplexes_at_step = find_angles(r, inputfile, num_confs)
if parallel:
print("INFO: Fitting duplexes to {} configurations using {} cores.".
format(num_confs, n_cpus),
file=stderr)
duplexes_at_step = []
out = parallelize_lorenzo_onefile.fire_multiprocess(
traj_file, top_file, find_angles, num_confs, n_cpus, inputfile)
[duplexes_at_step.extend(i) for i in out]
if [] in duplexes_at_step:
print(
"WARNING: Some configurations were invalid and not included in the analysis. Please check the log to view the error",
file=stderr)
#print duplexes to a file
print(
"INFO: Writing duplex data to {}. Use duplex_angle_plotter to graph data"
.format(outfile),
file=stderr)
output = open(outfile, 'w')
output.write(
"time\tduplex\tstart1\tend1\tstart2\tend2\taxisX\taxisY\taxisZ\thel_pos\n"
)
for i in range(0, len(duplexes_at_step)):
for j in range(0, len(duplexes_at_step[i])):
line = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t[{},{},{}]\n'.format(
duplexes_at_step[i][j].time, duplexes_at_step[i][j].index,
duplexes_at_step[i][j].start1, duplexes_at_step[i][j].end1,
duplexes_at_step[i][j].start2, duplexes_at_step[i][j].end2,
duplexes_at_step[i][j].axis[0], duplexes_at_step[i][j].axis[1],
duplexes_at_step[i][j].axis[2],
duplexes_at_step[i][j].final_hel_pos[0],
duplexes_at_step[i][j].final_hel_pos[1],
duplexes_at_step[i][j].final_hel_pos[2])
output.write(line)
output.close()
def main():
parser = argparse.ArgumentParser(
prog=os.path.basename(__file__),
description="Computes the mean structure of a trajectory file")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument('-o',
'--output',
metavar='output_file',
nargs=1,
help='The filename to save the mean structure to')
parser.add_argument(
'-f',
'--format',
metavar='<json/oxDNA/both>',
nargs=1,
help=
'Output format for the mean file. Defaults to json. Options are \"json\", \"oxdna/oxDNA\", and \"both\"'
)
parser.add_argument(
'-d',
'--deviations',
metavar='deviation_file',
nargs=1,
help='Immediatley run compute_deviations.py from the output')
parser.add_argument(
'-i',
metavar='index_file',
dest='index_file',
nargs=1,
help=
'Compute mean structure of a subset of particles from a space-separated list in the provided file'
)
parser.add_argument(
'-a',
'--align',
metavar='alignment_configuration',
nargs=1,
help='The id of the configuration to align to, otherwise random')
args = parser.parse_args()
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "Bio", "numpy"])
#get file names
traj_file = args.trajectory[0]
parallel = args.parallel
if parallel:
from oxDNA_analysis_tools.UTILS import parallelize_erik_onefile
n_cpus = args.parallel[0]
#-f defines the format of the output file
outjson = False
outoxdna = False
if args.format:
if "json" in args.format:
outjson = True
if "oxDNA" in args.format or "oxdna" in args.format:
outoxdna = True
if "both" in args.format:
outjson = True
outoxdna = True
if outjson == outoxdna == False:
print(
"ERROR: unrecognized output format\nAccepted formats are \"json\", \"oxDNA/oxdna\", and \"both\"",
file=stderr)
exit(1)
else:
print("INFO: No output format specified, defaulting to oxDNA",
file=stderr)
outoxdna = True
#-o names the output file
if args.output:
outfile = args.output[0]
else:
if outjson and not outoxdna:
ext = ".json"
elif outjson and outoxdna:
ext = ".json/.dat"
elif outoxdna and not outjson:
ext = ".dat"
outfile = "mean{}".format(ext)
print("INFO: No outfile name provided, defaulting to \"{}\"".format(
outfile),
file=stderr)
#-d will run compute_deviations.py when this script is completed.
dev_file = None
if args.deviations:
dev_file = args.deviations[0]
#-i will make it only run on a subset of nucleotides.
#The index file is a space-separated list of particle IDs
if args.index_file:
index_file = args.index_file[0]
with open(index_file, 'r') as f:
indexes = f.readline().split()
try:
indexes = [int(i) for i in indexes]
except:
print(
"ERROR: The index file must be a space-seperated list of particles. These can be generated using oxView by clicking the \"Download Selected Base List\" button"
)
else:
with ErikReader(traj_file) as r:
indexes = list(range(len(r.read().positions)))
# The reference configuration which is used to define alignment
align_conf = []
#calculate the number of configurations in the trajectory
num_confs = cal_confs(traj_file)
# if we have no align_conf we need to chose one
# and realign its cms to be @ 0,0,0
if align_conf == []:
align = None
if args.align:
align = args.align[0]
align_conf_id, align_poses = pick_starting_configuration(
traj_file, num_confs, align)
# we are just interested in the nucleotide positions
align_conf = align_poses.positions[indexes]
#Actually compute mean structure
if not parallel:
print(
"INFO: Computing mean of {} configurations with an alignment of {} particles using 1 core."
.format(num_confs, len(align_conf)),
file=stderr)
r = ErikReader(traj_file)
mean_pos_storage, mean_a1_storage, mean_a3_storage, intermediate_mean_structures, processed_frames = compute_mean(
r, align_conf, indexes, num_confs)
#If parallel, the trajectory is split into a number of chunks equal to the number of CPUs available.
#Each of those chunks is then calculated seperatley and the result is summed.
if parallel:
print(
"INFO: Computing mean of {} configurations with an alignment of {} particles using {} cores."
.format(num_confs, len(align_conf), n_cpus),
file=stderr)
out = parallelize_erik_onefile.fire_multiprocess(
traj_file, compute_mean, num_confs, n_cpus, align_conf, indexes)
mean_pos_storage = np.sum(np.array([i[0] for i in out]), axis=0)
mean_a1_storage = np.sum(np.array([i[1] for i in out]), axis=0)
mean_a3_storage = np.sum(np.array([i[2] for i in out]), axis=0)
intermediate_mean_structures = []
[intermediate_mean_structures.extend(i[3]) for i in out]
processed_frames = sum((i[4] for i in out))
# finished task entry
print("INFO: processed frames total: {}".format(processed_frames),
file=stderr)
#Convert mean structure to a json file
mean_file = dumps({
"i_means":
intermediate_mean_structures,
"g_mean":
prep_pos_for_json(mean_pos_storage / processed_frames),
"a1_mean":
prep_pos_for_json(
[normalize(v) for v in (mean_a1_storage / processed_frames)]),
"a3_mean":
prep_pos_for_json(
[normalize(v) for v in (mean_a3_storage / processed_frames)]),
"p_frames":
processed_frames,
"ini_conf": {
"conf": prep_pos_for_json(align_conf),
"id": align_conf_id
}
})
#Save the mean structure to the specified output file.
if outjson or dev_file:
#save output as json format
if outoxdna == True:
#if making both outputs, automatically set file extensions.
jsonfile = outfile.split(".")[0] + ".json"
else:
jsonfile = outfile
print("INFO: Writing mean configuration to", jsonfile, file=stderr)
with open(jsonfile, "w") as file:
file.write(mean_file)
if outoxdna:
#save output as oxDNA .dat format
if outjson == True:
#if making both outputs, automatically set file extensions.
outname = outfile.split(".")[0] + ".dat"
else:
outname = outfile
from oxDNA_analysis_tools.mean2dat import make_dat
make_dat(loads(mean_file), outname)
#If requested, run compute_deviations.py using the output from this script.
if dev_file:
print("INFO: launching compute_deviations.py", file=stderr)
#this is probably horrible practice, but to maintain the ability to call things from the command line, I cannot pass arguments between main() calls.
#so instead we're gonna spoof a global variable to make it look like compute_deviations was called explicitally
argv.clear()
argv.extend([
'compute_deviations.py', '-o', dev_file, "-r",
dev_file.split('.')[0] + "_rmsd.png", "-d",
dev_file.split('.')[0] + "_rmsd_data.json"
])
if args.index_file:
argv.append("-i")
argv.append(index_file)
if parallel:
argv.append("-p")
argv.append(str(n_cpus))
argv.append(jsonfile)
argv.append(traj_file)
from oxDNA_analysis_tools import compute_deviations
from sys import executable
print(executable)
print(argv)
compute_deviations.main()
#compute_deviations needs the json meanfile, but its not useful for visualization
#so we dump it
if not outjson:
print("INFO: deleting {}".format(jsonfile), file=stderr)
from os import remove
remove(jsonfile)
print(time.time() - start_t)
def main():
#handle commandline arguments
#the positional arguments for this are:
# 1. the mean structure from compute_mean.py in json format
# 2. the trajectory from which to compute the centroid
# 3. the name of the file to write out the centroid to. Should be a .dat because oxView uses file extensions
parser = argparse.ArgumentParser(
prog=os.path.basename(__file__),
description=
"Compute the RMSD of each nucleotide from the mean structure produced by compute_mean.py"
)
parser.add_argument(
'mean_structure',
type=str,
nargs=1,
help="The mean structure .json file from compute_mean.py")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument('-o',
'--output',
metavar='output_file',
nargs=1,
help='The filename to save the centroid to')
parser.add_argument(
'-i',
metavar='index_file',
dest='index_file',
nargs=1,
help=
'Compute mean structure of a subset of particles from a space-separated list in the provided file'
)
args = parser.parse_args()
#system check
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "Bio", "numpy"])
#-o names the output file
if args.output:
outfile = args.output[0].strip()
else:
outfile = "centroid.dat"
print("INFO: No outfile name provided, defaulting to \"{}\"".format(
outfile),
file=stderr)
#prepare the data files and calculate how many configurations there are to run
traj_file = args.trajectory[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
num_confs = cal_confs(traj_file)
#-i will make it only run on a subset of nucleotides.
#The index file is a space-separated list of particle IDs
if args.index_file:
index_file = args.index_file[0]
with open(index_file, 'r') as f:
indexes = f.readline().split()
try:
indexes = [int(i) for i in indexes]
except:
print(
"ERROR: The index file must be a space-seperated list of particles. These can be generated using oxView by clicking the \"Download Selected Base List\" button"
)
else:
with ErikReader(traj_file) as r:
indexes = list(range(len(r.read().positions)))
# load mean structure
mean_file = args.mean_structure[0]
if mean_file.split(".")[-1] == "json":
with open(mean_file) as file:
mean_structure = load(file)['g_mean'][indexes]
elif mean_file.split(".")[-1] == "dat":
with ErikReader(mean_file) as reader:
s = reader.read()
mean_structure = s.positions[indexes]
print("INFO: mean structure loaded", file=stderr)
#Calculate centroid, in parallel if available
if not parallel:
print(
"INFO: Computing centroid from the mean of {} configurations using 1 core."
.format(num_confs),
file=stderr)
r = ErikReader(traj_file)
centroid, centroid_a1s, centroid_a3s, centroid_rmsf, centroid_time = compute_centroid(
r, mean_structure, indexes, num_confs)
#If parallel, the trajectory is split into a number of chunks equal to the number of CPUs available.
#Each of those chunks is then calculated seperatley and the results are compiled .
if parallel:
print(
"INFO: Computing centroid from the mean of {} configurations using {} cores."
.format(num_confs, n_cpus),
file=stderr)
candidates = []
rmsfs = []
a1s = []
a3s = []
ts = []
out = parallelize_erik_onefile.fire_multiprocess(
traj_file, compute_centroid, num_confs, n_cpus, mean_structure,
indexes)
[candidates.append(i[0]) for i in out]
[rmsfs.append(i[3]) for i in out]
[a1s.append(i[1]) for i in out]
[a3s.append(i[2]) for i in out]
[ts.append(i[4]) for i in out]
min_id = rmsfs.index(min(rmsfs))
centroid = candidates[min_id]
centroid_a1s = a1s[min_id]
centroid_a3s = a3s[min_id]
centroid_time = ts[min_id]
centroid_rmsf = rmsfs[min_id]
print(
"INFO: Centroid configuration found at configuration t = {}, RMSF = {}"
.format(centroid_time, centroid_rmsf),
file=stderr)
from oxDNA_analysis_tools.mean2dat import make_dat
make_dat(
{
'g_mean': centroid,
'a1_mean': centroid_a1s,
'a3_mean': centroid_a3s
}, outfile)
def main():
#handle commandline arguments
#the positional arguments for this are:
# 1. the mean structure from compute_mean.py in json format
# 2. the trajectory from which to compute the deviations
from sys import argv
print(argv)
parser = argparse.ArgumentParser(
prog=os.path.basename(__file__),
description=
"Compute the RMSD of each nucleotide from the mean structure produced by compute_mean.py"
)
parser.add_argument(
'mean_structure',
type=str,
nargs=1,
help="The mean structure .json file from compute_mean.py")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument(
'-o',
'--output',
metavar='output_file',
nargs=1,
help='The filename to save the deviations json file to')
parser.add_argument(
'-i',
metavar='index_file',
dest='index_file',
nargs=1,
help=
'Compute mean structure of a subset of particles from a space-separated list in the provided file'
)
parser.add_argument('-r',
metavar='rmsd_plot',
dest='rmsd_plot',
nargs=1,
help='The name of the file to save the RMSD plot to.')
parser.add_argument(
'-d',
metavar='rmsd_data',
dest='rmsd_data',
nargs=1,
help='The name of the file to save the RNSD data in json format.')
args = parser.parse_args()
#system check
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "Bio", "numpy", "matplotlib"])
#-o names the output file
if args.output:
outfile = args.output[0].strip()
if not outfile.split(".")[-1] == 'json':
outfile += ".json"
else:
outfile = "devs.json"
print("INFO: No outfile name provided, defaulting to \"{}\"".format(
outfile),
file=stderr)
#prepare the data files and calculate how many configurations there are to run
traj_file = args.trajectory[0]
parallel = args.parallel
if parallel:
from oxDNA_analysis_tools.UTILS import parallelize_erik_onefile
n_cpus = args.parallel[0]
num_confs = cal_confs(traj_file)
#-i will make it only run on a subset of nucleotides.
#The index file is a space-separated list of particle IDs
if args.index_file:
index_file = args.index_file[0]
with open(index_file, 'r') as f:
indexes = f.readline().split()
try:
indexes = [int(i) for i in indexes]
except:
print(
"ERROR: The index file must be a space-seperated list of particles. These can be generated using oxView by clicking the \"Download Selected Base List\" button"
)
else:
with ErikReader(traj_file) as r:
indexes = list(range(len(r.read().positions)))
#-r names the file to print the RMSD plot to
if args.rmsd_plot:
plot_name = args.rmsd_plot[0]
else:
plot_name = 'rmsd.png'
# -d names the file to print the RMSD data to
if args.rmsd_data:
data_file = args.rmsd_data[0]
# load mean structure
mean_structure_file = args.mean_structure[0]
with open(mean_structure_file) as file:
mean_data = loads(file.read())
mean_structure = np.array(mean_data["g_mean"])
indexed_mean_structure = mean_structure[indexes]
print("INFO: mean structure loaded", file=stderr)
#Calculate deviations, in parallel if available
if not parallel:
print(
"INFO: Computing deviations from the mean of {} configurations with an alignment of {} particles using 1 core."
.format(num_confs, len(indexed_mean_structure)),
file=stderr)
r = ErikReader(traj_file)
deviations, RMSDs = compute_deviations(r, mean_structure,
indexed_mean_structure, indexes,
num_confs)
#If parallel, the trajectory is split into a number of chunks equal to the number of CPUs available.
#Each of those chunks is then calculated seperatley and the results are compiled .
if parallel:
print(
"INFO: Computing deviations from the mean of {} configurations with an alignment of {} particles using {} cores."
.format(num_confs, len(indexed_mean_structure), n_cpus),
file=stderr)
deviations = []
RMSDs = []
out = parallelize_erik_onefile.fire_multiprocess(
traj_file, compute_deviations, num_confs, n_cpus, mean_structure,
indexed_mean_structure, indexes)
[deviations.extend(i[0]) for i in out]
[RMSDs.extend(i[1]) for i in out]
#compute_deviations() returns the deviation of every particle in every configuration
#take the mean of the per-configuration deviations to get the RMSF
rmsfs = np.sqrt(np.mean(np.square(np.array(deviations)), axis=0)) * 0.8518
#write the deviations to a json file
print("INFO: writing deviations to {}".format(outfile), file=stderr)
with open(outfile, "w") as file:
file.write(dumps({"RMSF (nm)": rmsfs.tolist()}))
#plot RMSDs
print("INFO: writing RMSD plot to {}".format(plot_name), file=stderr)
plt.plot(RMSDs)
plt.axhline(np.mean(RMSDs), color='red')
plt.xlabel('Configuration')
plt.ylabel('RMSD (nm)')
plt.savefig(plot_name)
#print RMSDs
print("INFO: writing RMSD data to {}".format(data_file), file=stderr)
if args.rmsd_data:
with open(data_file, 'w') as f:
f.write(dumps({"RMSD (nm)": RMSDs}))
def main():
parser = argparse.ArgumentParser(
prog=os.path.basename(__file__),
description="Computes the deviations in the backbone torsion angles")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument(
'topology',
type=str,
nargs=1,
help="The topology file associated with the trajectory file")
parser.add_argument('outfile',
type=str,
nargs=1,
help='The file name for the output .json file.')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
args = parser.parse_args()
#run system checks
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "numpy"])
top_file = args.topology[0]
traj_file = args.trajectory[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
num_confs = cal_confs(traj_file)
r = LorenzoReader2(traj_file, top_file)
if not parallel:
torsions, dihedrals = get_internal_coords(r, num_confs)
if parallel:
out = parallelize_lorenzo_onefile.fire_multiprocess(
traj_file, top_file, get_internal_coords, num_confs, n_cpus)
# Out Dims: 1 Processor, 2 Torsion or Dihedrals, 3 Specific list of torsions listed by conf
torsions = np.concatenate([out[i][0] for i in range(n_cpus)], axis=1)
dihedrals = np.concatenate([out[i][1] for i in range(n_cpus)], axis=1)
torsion_mean = np.mean(torsions, axis=1).tolist()
dihedral_mean = np.mean(dihedrals, axis=1).tolist()
#make something akin to a ramachandran plot for DNA origami??
import matplotlib.pyplot as plt
plt.scatter(torsion_mean[1:], dihedral_mean)
plt.xlabel("torsion_angle")
plt.ylabel("dihedral_angle")
plt.show()
torsion_mean.insert(0, torsion_mean[0])
torsion_mean.insert(0, torsion_mean[0])
with open(args.outfile[0], "w") as file:
file.write(dumps({"torsion": torsion_mean}))
def main():
#at 2.5 you start to see the hard edges caused by end-loops and see some loop interactions
cutoff_distance = 2.5
#get commandline arguments
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description=
"Calculate molecular contacts, and assembles an average set of contacts based on MDS"
)
parser.add_argument('inputfile',
type=str,
nargs=1,
help="The inputfile used to run the simulation")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument(
'meanfile',
type=str,
nargs=1,
help='the name of the .dat file where the mean will be written')
parser.add_argument(
'devfile',
type=str,
nargs=1,
help='the name of the .json file where the devs will be written')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
#process commandline arguments
args = parser.parse_args()
traj_file = args.trajectory[0]
inputfile = args.inputfile[0]
meanfile = args.meanfile[0]
devfile = args.devfile[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
top_file = get_input_parameter(inputfile, "topology")
if "RNA" in get_input_parameter(inputfile, "interaction_type"):
environ["OXRNA"] = "1"
else:
environ["OXRNA"] = "0"
from oxDNA_analysis_tools.config import check_dependencies
check_dependencies(["python", "numpy"])
#get the number of configurations in the trajectory
num_confs = cal_confs(traj_file)
#Get the mean distance to all other particles
if not parallel:
print(
"INFO: Computing interparticle distances of {} configurations using 1 core."
.format(num_confs),
file=stderr)
r = LorenzoReader2(traj_file, top_file)
cartesian_distances = get_mean(r, inputfile, num_confs)
mean_distance_map = cartesian_distances * (1 / (num_confs))
if parallel:
print(
"INFO: Computing interparticle distances of {} configurations using {} cores."
.format(num_confs, n_cpus),
file=stderr)
out = parallelize_lorenzo_onefile.fire_multiprocess(
traj_file, top_file, get_mean, num_confs, n_cpus, inputfile)
cartesian_distances = np.sum(np.array([i for i in out]), axis=0)
mean_distance_map = cartesian_distances * (1 / (num_confs))
#Making a new configuration file from scratch is hard, so we're just going to read in one and then overwrite the positional information
r = LorenzoReader2(traj_file, top_file)
output_system = r._get_system()
#make heatmap of the summed distances
#make_heatmap(mean_distance_map)
masked_mean = np.ma.masked_array(mean_distance_map,
~(mean_distance_map < cutoff_distance))
#I tried to use DGSOL to analytically solve this, but origamis were too big
#f = open('test_dist.nmr', 'w+')
#for i, line in enumerate(masked_mean):
# for j, dist in enumerate(line):
# if dist != "--" and dist != 0 and i < j:
# if j%2 == 0:
# f.write("{}\t{}\t1\t1\t{}\t{}\tn\tn\tn\tn\n".format(i+1, j+1, dist, dist))
# else:
# f.write("{}\t{}\t1\t1\t{}\t{}\tn\tn\tn\tn\n".format(j+1, i+1, dist, dist))
#super_cutoff_ids = mean_distance_map > cutoff_distance
#mean_distance_map[super_cutoff_ids] = 0
#sparse_map = csr_matrix(mean_distance_map)
print("INFO: fitting local distance data", file=stderr)
#Many embedding algorithms were tried...
#from sklearn.manifold import LocallyLinearEmbedding
#from megaman.geometry import Geometry
#from scipy.sparse import csr_matrix
#geom = Geometry()
#geom = Geometry(adjacency_kwds={'radius':cutoff_distance})#, laplacian_kwds={'scaling_epps':cutoff_distance})
#geom.set_data_matrix(masked_mean)
#geom.set_adjacency_matrix(masked_mean)
#from megaman.embedding import LocallyLinearEmbedding
#lle = LocallyLinearEmbedding(n_neighbors=5, n_components=3, eigen_solver='arpack', max_iter=3000)
#lle = LocallyLinearEmbedding(n_components=3, eigen_solver='arpack', geom=geom)
#out_coords = lle.fit_transform(masked_mean, input_type='adjacency')
#out_coords = lle.fit_transform(masked_mean)
#init = np.array([p.cm_pos for p in out_conf._nucleotides])
#Run multidimensional scaling on the average distances to find average positions
from sklearn.manifold import MDS
mds = MDS(n_components=3,
metric=True,
max_iter=3000,
eps=1e-12,
dissimilarity="precomputed",
n_jobs=1,
n_init=1)
out_coords = mds.fit_transform(
masked_mean) #, init=init) #this one worked best
#Overwrite the system we made earlier with the coordinates calculated via MDS
for i, n in enumerate(output_system._nucleotides):
n.cm_pos = out_coords[i]
n._a1 = np.array([0, 0, 0])
n._a3 = np.array(
[0, 0, 0]
) #since the orientation vectors are all 0, this cannot be used in a simulation, but the viewer will handle it
#Write the mean structure out as a new .dat and .top pair
output_system.print_lorenzo_output("{}.dat".format(meanfile),
"{}.top".format(meanfile))
print("INFO: wrote output files: {}.dat, {}.top".format(
meanfile, meanfile),
file=stderr)
#Loop through the trajectory again and calculate deviations from the average distances
print(
"INFO: Computing distance deviations of {} configurations using 1 core."
.format(num_confs),
file=stderr)
if not parallel:
r = LorenzoReader2(traj_file, top_file)
devs = get_devs(r, masked_mean, inputfile, cutoff_distance, num_confs)
if parallel:
print(
"INFO: Computing distance deviations of {} configurations using {} cores."
.format(num_confs, n_cpus),
file=stderr)
out = parallelize_lorenzo_onefile.fire_multiprocess(
traj_file, top_file, get_devs, num_confs, n_cpus, masked_mean,
inputfile, cutoff_distance)
devs = np.sum(np.array([i for i in out]), axis=0)
#Dump the deviations to an oxView overlay file
devs = np.ma.masked_array(
devs,
~(devs != 0.0)) #mask all the 0s so they don't contribute to the mean
devs *= (1 / num_confs)
devs = np.mean(devs, axis=0)
devs = np.sqrt(devs)
with open(devfile + ".json", "w") as file:
file.write(dumps({"contact deviation": list(devs)}))
print("INFO: wrote file {}.json".format(devfile), file=stderr)
def main():
parser = argparse.ArgumentParser(
prog=path.basename(__file__),
description=
"Calculates a principal component analysis of nucleotide deviations over a trajectory"
)
parser.add_argument('inputfile',
type=str,
nargs=1,
help="The inputfile used to run the simulation")
parser.add_argument('trajectory',
type=str,
nargs=1,
help='the trajectory file you wish to analyze')
parser.add_argument(
'meanfile',
type=str,
nargs=1,
help='The mean structure .json file from compute_mean.py')
parser.add_argument(
'outfile',
type=str,
nargs=1,
help='the name of the .json file where the PCA will be written')
parser.add_argument('-p',
metavar='num_cpus',
nargs=1,
type=int,
dest='parallel',
help="(optional) How many cores to use")
parser.add_argument(
'-c',
metavar='cluster',
dest='cluster',
action='store_const',
const=True,
default=False,
help="Run the clusterer on each configuration's position in PCA space?"
)
args = parser.parse_args()
check_dependencies(["python", "numpy", "Bio"])
traj_file = args.trajectory[0]
inputfile = args.inputfile[0]
mean_file = args.meanfile[0]
outfile = args.outfile[0]
parallel = args.parallel
if parallel:
n_cpus = args.parallel[0]
#-c makes it run the clusterer on the output
cluster = args.cluster
num_confs = cal_confs(traj_file)
if mean_file.split(".")[-1] == "json":
with open(mean_file) as file:
align_conf = load(file)['g_mean']
elif mean_file.split(".")[-1] == "dat" or mean_file.split(
".")[-1] == "conf" or mean_file.split(".")[-1] == "oxdna":
with ErikReader(mean_file) as reader:
align_conf = reader.read().positions
else:
print(
"ERROR: {} is an unrecognized file type. \nThe mean structure must either be provided as an oxDNA configuration file with the extension .dat, .conf or .oxdna or as the .json file produced by compute_mean.py.",
file=stderr)
exit(1)
cms = np.mean(align_conf,
axis=0) #all structures must have the same center of mass
align_conf -= cms
#Compute the deviations
if not parallel:
r = ErikReader(traj_file)
covariation_matrix = get_cov(r, align_conf, num_confs)
if parallel:
out = parallelize_erik_onefile.fire_multiprocess(
traj_file, get_cov, num_confs, n_cpus, align_conf)
covariation_matrix = np.sum([i for i in out], axis=0)
covariation_matrix /= (num_confs - 1)
#now that we have the covatiation matrix we're going to use eigendecomposition to get the principal components.
#make_heatmap(covariance)
print("INFO: calculating eigenvectors", file=stderr)
evalues, evectors = np.linalg.eig(
covariation_matrix) #these eigenvalues are already sorted
evectors = evectors.T #vectors come out as the columns of the array
print("INFO: eigenvectors calculated", file=stderr)
import matplotlib.pyplot as plt
print("INFO: Saving scree plot to scree.png", file=stderr)
plt.scatter(range(0, len(evalues)), evalues, s=25)
plt.xlabel("component")
plt.ylabel("eigenvalue")
plt.savefig("scree.png")
total = sum(evalues)
running = 0
i = 0
while running < 0.9:
running += (evalues[i] / total)
i += 1
print("90% of the variance is found in the first {} components".format(i))
#if you want to weight the components by their eigenvectors
#mul = np.einsum('ij,i->ij',evectors, evalues)
mul = evectors
#reconstruct configurations in component space
#because we donlist't save the difference matrix, this involves running through the whole trajectory again
if not parallel:
r = ErikReader(traj_file)
coordinates = change_basis(r, align_conf, mul, num_confs)
if parallel:
out = parallelize_erik_onefile.fire_multiprocess(
traj_file, change_basis, num_confs, n_cpus, align_conf, mul)
coordinates = np.concatenate([i for i in out])
#make a quick plot from the first three components
print(
"INFO: Creating coordinate plot from first three eigenvectors. Saving to coordinates.png",
file=stderr)
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.gca(projection='3d')
ax.scatter(coordinates[:, 0],
coordinates[:, 1],
coordinates[:, 2],
c='g',
s=25)
plt.savefig("coordinates.png")
#Create an oxView overlays for the first N components
N = 3
prep_pos_for_json = lambda conf: list(list(p) for p in conf)
print(
"INFO: Change the number of eigenvalues to sum and display by modifying the N variable in the script. Current value: {}"
.format(N),
file=stderr)
for i in range(0, N): #how many eigenvalues do you want?
try:
if outfile.split(".")[1] != "json":
raise Exception
f = outfile.split(".")[0] + str(i) + "." + outfile.split(".")[1]
except:
print(
"ERROR: oxView overlays must have a '.json' extension. No overlays will be produced",
file=stderr)
break
out = np.sqrt(evalues[i]) * evectors[i]
with catch_warnings(
): #this produces an annoying warning about casting complex values to real values that is not relevant
simplefilter("ignore")
output_vectors = out.reshape(int(out.shape[0] / 3),
3).astype(float)
with open(f, "w+") as file:
file.write(dumps({"pca": prep_pos_for_json(output_vectors)}))
#If we're running clustering, feed the linear terms into the clusterer
if cluster:
print("INFO: Mapping configurations to component space...",
file=stderr)
#If you want to cluster on only some of the components, uncomment this
#out = out[:,0:3]
from oxDNA_analysis_tools.clustering import perform_DBSCAN
labs = perform_DBSCAN(coordinates, num_confs, traj_file, inputfile,
"euclidean", 12, 8)
