"""Example format for Xplor Maps: 2 !NTITLE REMARKS FILENAME="" REMARKS scitbx.flex.double to Xplor map format 24 0 24 120 0 120 54 0 54 3.20420E+01 1.75362E+02 7.96630E+01 9.00000E+01 9.00000E+01 9.00000E+01 ZYX 0 -2.84546E-01-1.67775E-01-5.66095E-01-1.18305E+00-1.49559E+00-1.31942E+00 -1.01611E+00-1.00873E+00-1.18992E+00-1.02460E+00-2.72099E-01 5.94242E-01 -9999 0.0000E+00 1.0000E+00 That is: ...a blank line ...an integer giving the number of title lines, with mandatory !NTITLE ...title lines in %-264s format ...X, Y, and Z sections giving: sections per unit cell, in the given direction ordinal of first section in file ordinal of last section in file ...unit cell dimensions ...slow, medium, fast section order, always ZYX ...for each slow section, the section number ...sectional data in special fortran format shown ...-9999 ...map average and standard deviation """ from __future__ import absolute_import, division, print_function import iotbx.xplor.ext as ext from cctbx import miller from cctbx import maptbx from cctbx import uctbx from cctbx.array_family import flex import sys from six.moves import range from six.moves import zip class gridding(object): def __init__(self, n, first, last): self.n = tuple(n) self.first = tuple(first) self.last = tuple(last) for x,ni,fi,li in zip("XYZ",n,first,last): if (ni < 1 or fi > li): raise RuntimeError( "Illegal xplor map gridding for dimension %s: " "gridding=%d, first=%d, last=%d" % (x,ni,fi,li)) def format_9i8(self): result = "" for triple in zip(self.n,self.first,self.last): result += ("%8d"*3) % triple return result def as_flex_grid(self): return flex.grid(self.first, self.last, False) def is_compatible_flex_grid(self, flex_grid, is_p1_cell=False): if (flex_grid.nd() != 3): return False if (is_p1_cell is None): # XXX temporary flag allowing any cell self_as_flex_grid = self.as_flex_grid() if (flex_grid.origin() != self_as_flex_grid.origin()): return False if (flex_grid.last() != self_as_flex_grid.last()): return False elif (not is_p1_cell): self_as_flex_grid = self.as_flex_grid() if (flex_grid.origin() != self_as_flex_grid.origin()): return False if (flex_grid.last() != self_as_flex_grid.last()): return False else: if (not flex_grid.is_0_based()): return False if (flex_grid.focus() != self.n): return False return True class reader(object): def __init__(self, file_name, header_only=False): with open(file_name, "r") as f: f.readline() self.title_lines = [] ntitle = int(f.readline().strip().split("!")[0]) self.title_lines=[] for x in range(ntitle): line = f.readline().rstrip() self.title_lines.append(line) line = f.readline() values = [int(line[i:i+8]) for i in range(0,72,8)] self.gridding = gridding( n = [values[i] for i in range(0,9,3)], first = [values[i] for i in range(1,9,3)], last = [values[i] for i in range(2,9,3)]) line = f.readline() params = [float(line[i:i+12]) for i in range(0,72,12)] self.unit_cell = uctbx.unit_cell(params) order = f.readline().strip() assert order == "ZYX" if (header_only): self.data = None self.average = None self.standard_deviation = None else: ext_reader = ext.map_reader( file_name=file_name, n_header_lines=len(self.title_lines)+5, grid=self.gridding.as_flex_grid()) self.data = ext_reader.data self.average = ext_reader.average self.standard_deviation = ext_reader.standard_deviation def show_summary(self, out=None, prefix=""): if (out is None): out = sys.stdout print(prefix+"Title lines:", len(self.title_lines), file=out) for line in self.title_lines: print(prefix+" "+line.rstrip(), file=out) g = self.gridding print(prefix+"Gridding:", file=out) print(prefix+" n: ", g.n, file=out) print(prefix+" first:", g.first, file=out) print(prefix+" last: ", g.last, file=out) print(prefix+"Total number of data points:", self.data.size(), file=out) stats = maptbx.statistics(self.data) print(prefix+" min: %.6g" % stats.min(), file=out) print(prefix+" max: %.6g" % stats.max(), file=out) print(prefix+" mean: %.6g" % stats.mean(), file=out) print(prefix+" sigma: %.6g" % stats.sigma(), file=out) def writer(file_name, title_lines, unit_cell, gridding, data, is_p1_cell=False, average=-1, standard_deviation=-1): assert gridding.is_compatible_flex_grid( flex_grid=data.accessor(), is_p1_cell=is_p1_cell) with open(file_name, "w") as f: f.write("\n") f.write("%8d !NTITLE\n" % len(title_lines)) for line in title_lines: f.write("%-264s\n" % line) f.write("%s\n" % gridding.format_9i8()) if (is_p1_cell is None): # XXX temporary flag allowing any cell ext.map_writer( file_name=file_name, unit_cell=unit_cell, data=data, average=average, standard_deviation=standard_deviation) elif (not is_p1_cell): ext.map_writer( file_name=file_name, unit_cell=unit_cell, data=data, average=average, standard_deviation=standard_deviation) else: ext.map_writer( file_name=file_name, unit_cell=unit_cell, gridding_first=gridding.first, gridding_last=gridding.last, data=data, average=average, standard_deviation=standard_deviation) def cctbx_miller_fft_map_as_xplor_map( self, file_name, title_lines=["cctbx.miller.fft_map"], gridding_first=None, gridding_last=None, average=None, standard_deviation=None): if (gridding_first is None): gridding_first = (0,0,0) if (gridding_last is None): gridding_last = self.n_real() gridding_ = gridding( n=self.n_real(), first=gridding_first, last=gridding_last) data = self.real_map() if (average is None or standard_deviation is None): statistics = maptbx.statistics(data) if (average is None): average = statistics.mean() if (standard_deviation is None): standard_deviation = statistics.sigma() writer( file_name=file_name, title_lines=title_lines, unit_cell=self.unit_cell(), gridding=gridding_, data=data, is_p1_cell=True, average=average, standard_deviation=standard_deviation) # injecting miller.fft_map.as_xplor_map = cctbx_miller_fft_map_as_xplor_map