Merge branch 'master' of https://github.com/stefsmeets/edtools

edtools/extract_xds_info.py

@@ -13,24 +13,24 @@ class xds_parser(object):
  def __init__(self, filename):
  super(xds_parser, self).__init__()
  self.ios_threshold = 0.8
- 
+
  self.filename = Path(filename).resolve()
  self.d = self.parse()
- 
+
  def parse(self):
  ios_threshold = self.ios_threshold
 
  fn = self.filename
- 
+
  f = open(fn, "r")
- 
+
  in_block = False
  block = []
- 
+
  d = {}
 
  cell, spgr = None, None
- 
+
  for line in f:
  if line.startswith(" SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION"):
  in_block = True
@@ -63,41 +63,41 @@ def parse(self):
  line = next(f)
  inp = line.split()
  resolution_range = float(inp[0]), float(inp[1])
- 
+
  if in_block:
  if line:
  block.append(line.strip("\n"))
 
  d["ISa"] = ISa
  d["Boverall"] = Boverall
- 
+
  dmin = 999
- 
+
  for line in block:
  inp = line.split()
  if len(inp) != 14:
  continue
- 
+
  try:
  res = float(inp[0])
  except ValueError:
  res = inp[0]
  if res != "total":
  continue
- 
+
  res = float(inp[0]) if inp[0] != "total" else inp[0]
  ntot, nuniq, completeness = int(inp[1]), int(inp[2]), float(inp[4].strip("%"))
  ios, rmeas, cchalf = float(inp[8]), float(inp[9].strip("%")), float(inp[10].strip("*"))
- 
+
  if ios < ios_threshold and res != "total":
  continue
- 
+
  if (res != "total") and (res < dmin):
  shell = (dmin, res)
  dmin = res
- 
+
  d[res] = {"ntot": ntot, "nuniq": nuniq, "completeness": completeness, "ios": ios, "rmeas": rmeas, "cchalf": cchalf}
- 
+
  if dmin == 999:
  return
 
@@ -123,7 +123,7 @@ def parse(self):
  nframes = datarange[1] - datarange[0]
  rotationrange = nframes * osc_angle
  d["rot_range"] = rotationrange
- 
+
  return d
 
  @staticmethod
@@ -152,7 +152,7 @@ def integration_info(self, sequence=0, outer_shell=True, filename=False):
 
  if k == 0:
  s += self.info_header()
- 
+
  dmax, dmin = d["res_range"]
 
  s += "{k: 4d} {dmax: 6.2f}{dmin: 6.2f}{ntot: 8d}{nuniq: 8d}{completeness: 8.1f}{ios: 8.2f}{rmeas: 8.1f}{cchalf: 8.1f}{ISa: 8.2f}{Boverall: 8.2f}".format(
@@ -255,7 +255,7 @@ def cells_to_yaml(ps, fn="cells.yaml"):
 
 
 def gather_xds_ascii(ps, min_completeness=10.0, min_cchalf=90.0, gather=False):
- """Takes a list of `xds_parser` instances and gathers the 
+ """Takes a list of `xds_parser` instances and gathers the
  corresponding `XDS_ASCII.HKL` files into the current directory.
  The data source and numbering scheme is summarized in the file `filelist.txt`.
  """
@@ -292,9 +292,9 @@ def gather_xds_ascii(ps, min_completeness=10.0, min_cchalf=90.0, gather=False):
 
 
 def lattice_to_space_group(lattice):
- return { 'aP': 1, 'mP': 3, 'mC': 5, 'mI': 5, 
+ return { 'aP': 1, 'mP': 3, 'mC': 5, 'mI': 5,
  'oP': 16, 'oC': 21, 'oI': 23, 'oF': 22,
- 'tP': 75, 'tI': 79, 'hP':143, 'hR':146, 
+ 'tP': 75, 'tI': 79, 'hP':143, 'hR':146,
  'cP':195, 'cF':196, 'cI':197 }[lattice]
 
 
@@ -322,14 +322,55 @@ def evaluate_symmetry(ps):
 
  return lattice_to_space_group(c_score.most_common()[0][0])
 
+def parse_xparm_for_uc(fn):
+ with open(fn, "r") as f:
+ f.readline()
+ f.readline()
+ f.readline()
+
+ line = f.readline().split()
+ uc = line[1:]
+ uc = [float(i) for i in uc]
+ return uc
+
+def cells_to_yaml_xparm(uc, fn="cells_xparm.yaml"):
+ import yaml
+ ds = []
+ for i, p in enumerate(uc):
+ i += 1
+ d = {}
+
+ d["directory"] = str(Path(p[1]).parent.resolve())
+
+ """get rotation range from XDS.INP"""
+ xdsinp = Path(p[1]).parent / "XDS.INP"
+ with open(xdsinp, "r") as f:
+ for line in f:
+ if line.startswith("DATA_RANGE="):
+ datarange = list(map(float, line.strip("\n").split()[1:]))
+ elif line.startswith("OSCILLATION_RANGE="):
+ osc_angle = float(line.strip("\n").split()[1])
+
+ rr = osc_angle * (datarange[1] - datarange[0] + 1)
+
+ d["number"] = i
+ d["rotation_range"] = rr
+ d["raw_unit_cell"] = p[0]
+ d["space_group"] = "P1"
+ d["weight"] = 1
+ ds.append(d)
+
+ yaml.dump(ds, open(fn, "w"))
+
+ print(f"Wrote {i} cells to file {fn}")
 
 def main():
  import argparse
 
  description = "Program to consolidate data from a large series of data sets from a serial crystallography experiment."
  parser = argparse.ArgumentParser(description=description,
  formatter_class=argparse.RawDescriptionHelpFormatter)
- 
+
  parser.add_argument("args",
  type=str, nargs="*", metavar="FILE",
  help="List of CORRECT.LP files or list of directories. If a list of directories is given "
@@ -344,44 +385,61 @@ def main():
  action="store_true", dest="gather",
  help="Gather XDS_ASCII.HKL files in local directory.")
 
+ parser.add_argument("-x", "--xparm",
+ action="store_true", dest="xparm",
+ help="extract unit cell info from XPARM.XDS instead of CORRECT.LP. NOTE!! Only aimed for first step clustering.")
+
  parser.set_defaults(match=None)
- 
+
  options = parser.parse_args()
 
  match = options.match
  gather = options.gather
+ xparm = options.xparm
  args = options.args
 
- fns = parse_args_for_fns(args, name="CORRECT.LP", match=match)
-
- xdsall = []
- for fn in fns:
- try:
- p = xds_parser(fn)
- except UnboundLocalError as e:
- print(e)
- continue
- else:
- if p and p.d:
- xdsall.append(p)
-
- for i, p in enumerate(xdsall):
- i += 1
- print(p.cell_info(sequence=i))
-
- print(xds_parser.info_header())
- for i, p in enumerate(xdsall):
- i += 1
- print(p.integration_info(sequence=i, filename=True))
-
- cells_to_excel(xdsall)
- # cells_to_cellparm(xdsall)
- cells_to_yaml(xdsall)
+ if xparm:
+ fns = parse_args_for_fns(args, name="XPARM.XDS", match=match)
+ foundCells_and_Path = []
+
+ for fn in fns:
+ uc = parse_xparm_for_uc(fn)
+ foundCells_and_Path.append([uc, fn])
+
+ cells_to_yaml_xparm(uc = foundCells_and_Path, fn = "cells_xparm.yaml")
+ print("Cell information from XPARM.XDS parsed to cells_xparm.yaml")
+
+ else:
+ fns = parse_args_for_fns(args, name="CORRECT.LP", match=match)
+
+ xdsall = []
+ for fn in fns:
+ try:
+ p = xds_parser(fn)
+ except UnboundLocalError as e:
+ print(e)
+ continue
+ else:
+ if p and p.d:
+ xdsall.append(p)
+
+ for i, p in enumerate(xdsall):
+ i += 1
+ print(p.cell_info(sequence=i))
+
+ print(xds_parser.info_header())
+ for i, p in enumerate(xdsall):
+ i += 1
+ print(p.integration_info(sequence=i, filename=True))
+
+ cells_to_excel(xdsall)
+ # cells_to_cellparm(xdsall)
+ cells_to_yaml(xdsall)
 
- gather_xds_ascii(xdsall, gather=gather)
+  gather_xds_ascii(xdsall, gather=gather)
 
- evaluate_symmetry(xdsall)
- print("\n ** the score corresponds to the total number of indexed reflections.")
+  evaluate_symmetry(xdsall)
+  print("\n ** the score corresponds to the total number of indexed reflections.")
 
 
 if __name__ == '__main__':

edtools/find_cell.py

@@ -370,7 +370,7 @@ def main():
  action="store_true", dest="use_radian_for_clustering",
  help="Use radians for unit cell clustering (to downweight the difference in angles)")
 
- parser.add_argument("-r", "--use_sine_for_angles",
+ parser.add_argument("-s", "--use_sine_for_angles",
  action="store_true", dest="use_sine_for_clustering",
  help="Use sine for unit cell clustering (to disambiguousize the difference in angles)")
 

edtools/make_shelx.py

@@ -19,7 +19,7 @@
 def comp2dict(composition):
  """Takes composition: Si20 O10, returns dict of atoms {'Si':20,'O':10}"""
  import re
- composition = " ".join(composition)
+ composition = "".join(composition)
  pat = re.compile('([A-z]+|[0-9]+)')
  m = re.findall(pat, composition)
  return dict(zip(m[::2], map(int,m[1::2])))

edtools/update_xds.py

@@ -155,10 +155,6 @@ def main():
  action="store", type=float, dest="StrongPixel",
  help="Parameter used for strong pixel threshold")
 
- parser.add_argument("--match",
- action="store", type=str, dest="match",
- help="Include the XDS.INP files only if they are in the given directories (i.e. --match SMV_reprocessed)")
-
  parser.add_argument("-it", "--indexingNumberThreshold",
  action="store", type=float, dest="indexingNumberThreshold",
  help="Parameter to tune the threshold for percentage of spots that is indexed")