imp.find_module('matplotlib')
matplotlib_found = True
import matplotlib.pyplot as plt
from matplotlib.colors import colorConverter as cc
import matplotlib.gridspec as gridspec
except ImportError:
matplotlib_found = False
#have to run parser twice, first just to get filename for loadProfile
#then have to run it after deciding what the correct dmax should be
#so that the voxel size, box size, nsamples, etc are set correctly
initparser = argparse.ArgumentParser(
description=
" A tool for refining an electron density map from solution scattering data",
formatter_class=argparse.RawTextHelpFormatter)
initargs = dopts.parse_arguments(initparser, gnomdmax=None)
q, I, sigq, dmax, isout = saxs.loadProfile(initargs.file, units=initargs.units)
if not initargs.force_run:
if min(q) != 0.0:
print("CAUTION: Minimum q value = %f " % min(q))
print("is not 0.0. It is STRONGLY recommended to include")
print("I(q=0) in your given scattering profile. You can use")
print("denss.fit_data.py to calculate a scattering profile fit")
print("which will include I(q=0), or you can also use the GNOM")
print("program from ATSAS to create a .out file.")
print()
print("If you are positive you would like to continue, ")
print("rerun with the --force_run option.")
sys.exit()
import saxstats.denssopts as dopts
import numpy as np
import sys, argparse, os
import logging
import imp
try:
imp.find_module('matplotlib')
matplotlib_found = True
import matplotlib.pyplot as plt
from matplotlib.colors import colorConverter as cc
import matplotlib.gridspec as gridspec
except ImportError:
matplotlib_found = False
parser = argparse.ArgumentParser(description="DENSS: DENsity from Solution Scattering.\n A tool for calculating an electron density map from solution scattering data", formatter_class=argparse.RawTextHelpFormatter)
args = dopts.parse_arguments(parser)
if args.rho_start is None:
print(" denss.refine.py requires a .mrc file to be given to the --rho_start option.")
sys.exit()
basename, ext = os.path.splitext(args.rho_start)
args.output = basename + '_refine'
args.rho_start, rho_side = saxs.read_mrc(args.rho_start)
rho_nsamples = args.rho_start.shape[0]
rho_voxel = rho_side/rho_nsamples
args.side = args.dmax*args.oversampling
matplotlib_found = True
import matplotlib.pyplot as plt
from matplotlib.colors import colorConverter as cc
import matplotlib.gridspec as gridspec
except ImportError:
matplotlib_found = False
### 引数の設定（python denss.py --option_a value_a --option_b value_bというように引数を渡す設定）
#have to run parser twice, first just to get filename for loadProfile
#then have to run it after deciding what the correct dmax should be
#so that the voxel size, box size, nsamples, etc are set correctly
initparser = argparse.ArgumentParser(
description=
" DENSS: DENsity from Solution Scattering.\n A tool for calculating an electron density map from solution scattering data",
formatter_class=argparse.RawTextHelpFormatter)
initargs = dopts.parse_arguments(initparser, gnomdmax=None) ### doptsは引数設定関数
q, I, sigq, dmax, isout = saxs.loadProfile(initargs.file, units=initargs.units)
if not initargs.force_run:
if min(q) != 0.0:
print "CAUTION: Minimum q value = %f " % min(q)
print "is not 0.0. It is STRONGLY recommended to include"
print "I(q=0) in your given scattering profile. You can use"
print "denss.fit_data.py to calculate a scattering profile fit"
print "which will include I(q=0), or you can also use the GNOM"
print "program from ATSAS to create a .out file."
print
print "If you are positive you would like to continue, "
print "rerun with the --force_run option."
sys.exit()
