def process_file(traj, top_file, resname, report, outputFilename, format_out,
new_report, epoch):
start = time.time()
sasa_values = calculateSASA(traj, top_file, resname)
header = ""
if not new_report:
try:
reportFilename = glob.glob(report)[0]
except IndexError:
raise IndexError("File %s not found" % report)
if outputFilename != reportFilename:
reportFilename = outputFilename
with open(reportFilename) as f:
header = f.readline().rstrip()
if not header.startswith("#"):
header = ""
reportFile = utilities.loadtxtfile(f)
fixedReport = analysis_utils.extendReportWithRmsd(
reportFile, sasa_values)
else:
indexes = np.array(range(sasa_values.shape[0]))
fixedReport = np.concatenate((indexes[:, None], sasa_values[:, None]),
axis=1)
with open(outputFilename, "w") as fw:
if header:
fw.write("%s\tSASA\n" % header)
else:
fw.write("# Step\tSASA\n")
np.savetxt(fw, fixedReport, fmt=format_out, delimiter="\t")
end = time.time()
print("Took %.2fs to process" % (end - start), traj)
def calculate_rmsd_traj(nativePDB, resname, symmetries, rmsdColInReport, traj, reportName, top, epoch, outputFilename, fmt_str, new_report):
top_proc = None
if top is not None:
top_proc = utilities.getTopologyFile(top)
rmsds = utilities.getRMSD(traj, nativePDB, resname, symmetries, topology=top_proc)
if new_report:
fixedReport = np.zeros((rmsds.size, 2))
fixedReport[:, 0] = range(rmsds.size)
fixedReport[:, 1] = rmsds
header = ""
else:
with open(reportName) as f:
header = f.readline().rstrip()
if not header.startswith("#"):
header = ""
reportFile = utilities.loadtxtfile(reportName)
if rmsdColInReport > 0 and rmsdColInReport < reportFile.shape[1]:
reportFile[:, rmsdColInReport] = rmsds
fixedReport = reportFile
else:
fixedReport = analysis_utils.extendReportWithRmsd(reportFile, rmsds)
with open(outputFilename, "w") as fw:
if header:
fw.write("%s\tRMSD\n" % header)
else:
fw.write("# Step\tRMSD\n")
np.savetxt(fw, fixedReport, fmt=fmt_str)
def process_file(report, outputFilename, format_out, new_report, epoch,
energy_column):
try:
reportFilename = glob.glob(report)[0]
except IndexError:
raise IndexError("File %s not found" % report)
with open(reportFilename) as f:
header = f.readline().rstrip()
if not header.startswith("#"):
header = ""
reportFile = utilities.loadtxtfile(f)
energy_values = reportFile[:, energy_column]
energy_values = preprocessing.scale(energy_values)
if not new_report:
if outputFilename != reportFilename:
reportFile = utilities.loadtxtfile(outputFilename)
fixedReport = analysis_utils.extendReportWithRmsd(
reportFile, energy_values)
else:
header = ""
indexes = np.array(range(energy_values.shape[0]))
fixedReport = np.concatenate(
(indexes[:, None], energy_values[:, None]), axis=1)
with open(outputFilename, "w") as fw:
if header:
fw.write("%s\tEnergy\n" % header)
else:
fw.write("# Step\tEnergy\n")
np.savetxt(fw, fixedReport, fmt=format_out, delimiter="\t")