servalcat 0.4.100__cp311-cp311-win_amd64.whl → 0.4.105__cp311-cp311-win_amd64.whl

servalcat/__init__.py

@@ -6,5 +6,5 @@ This software is released under the
 Mozilla Public License, version 2.0; see LICENSE.
 """
 
-__version__ = '0.4.100'
-__date__ = '2025-01-22'
+__version__ = '0.4.105'
+__date__ = '2025-03-26'

servalcat/refine/refine.py

@@ -7,6 +7,7 @@ Mozilla Public License, version 2.0; see LICENSE.
 """
 from __future__ import absolute_import, division, print_function, generators
 import os
+import time
 import re
 import gemmi
 import numpy
@@ -221,7 +222,16 @@ def write_stats_json_safe(stats, json_out):
     out_tmp = json_out + ".part"
     with open(out_tmp, "w") as ofs:
         json.dump(tmp, ofs, indent=2)
-    os.replace(out_tmp, json_out)
+    for i in range(10):
+        try:
+            # On Windows, this fails when another process open the file
+            os.replace(out_tmp, json_out)
+            break
+        except PermissionError:
+            logger.writeln(f"{json_out} locked. retrying..")
+            time.sleep(0.5)
+    else:
+        raise RuntimeError(f"Cannot write {json_out}")
     logger.writeln(f"Refinement statistics saved: {json_out}")
 # write_stats_json_safe()
 

servalcat/refine/refine_spa.py

@@ -150,8 +150,8 @@ def main(args):
         topo = None
         if args.hydrogen == "all":
             logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
-            args.hydrogen = "yes"
-        elif args.hydrogen == "no":
+        if args.hydrogen != "yes":
+            args.hydrogen = "no"
             st.remove_hydrogens()
         for i, cra in enumerate(st[0].all()):
             cra.atom.serial = i + 1
@@ -300,8 +300,7 @@ def main(args):
     if args.hklin:
         return
     # Calc Fo-Fc (and updated) maps
-    diffmap_prefix = "{}_diffmap".format(args.output_prefix)
-    calc_fofc(refiner.st, st_expanded, maps, monlib, ".mmcif", args, diffmap_prefix=diffmap_prefix)
+    calc_fofc(refiner.st, st_expanded, maps, monlib, ".mmcif", args, diffmap_prefix=args.output_prefix)
     
     # Final summary
     adpstats_txt = ""
@@ -320,8 +319,8 @@ def main(args):
     if args.mask_for_fofc:
         map_peaks_str = """\
 List Fo-Fc map peaks in the ASU:
-servalcat util map_peaks --map {diffmap_prefix}_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
-""".format(prefix=args.output_prefix, diffmap_prefix=diffmap_prefix)
+servalcat util map_peaks --map {prefix}_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
+""".format(prefix=args.output_prefix)
     else:
         map_peaks_str = "WARNING: --mask_for_fofc was not given, so the Fo-Fc map was not normalized."
 
@@ -343,7 +342,7 @@ Weight used: {final_weight:.3e}
              If you want to change the weight, give larger (looser restraints)
              or smaller (tighter) value to --weight=.
              
-Open refined model and {diffmap_prefix}.mtz with COOT:
+Open refined model and {prefix}_maps.mtz with COOT:
 coot --script {prefix}_coot.py
 
 Open refined model, map and difference map with ChimeraX/ISOLDE:
@@ -358,7 +357,6 @@ chimerax {prefix}_chimerax.cxc
            adpstats=adpstats_txt.rstrip(),
            final_weight=args.weight,
            prefix=args.output_prefix,
-           diffmap_prefix=diffmap_prefix,
            map_peaks_msg=map_peaks_str))
 
 # main()

servalcat/refine/refine_xtal.py

@@ -24,11 +24,15 @@ b_to_u = utils.model.b_to_u
 def add_arguments(parser):
     parser.description = "program to refine crystallographic structures"
     parser.add_argument("--hklin", required=True)
+    parser.add_argument('--hklin_free',
+                        help='Input MTZ file for test flags')
     parser.add_argument("-d", '--d_min', type=float)
     parser.add_argument('--d_max', type=float)
     parser.add_argument('--nbins', type=int, 
                         help="Number of bins (default: auto)")
     parser.add_argument("--labin", help="F,SIGF,FREE input")
+    parser.add_argument('--labin_free',
+                        help='MTZ column of --hklin_free')
     parser.add_argument('--free', type=int,
                         help='flag number for test set')
     parser.add_argument('--model', required=True,
@@ -128,7 +132,7 @@ def main(args):
     elif utils.fileio.is_mmhkl_file(hklin):
         hklin = utils.fileio.read_mmhkl(hklin)
         labin = decide_mtz_labels(hklin)
-        
+    software_items = utils.fileio.software_items_from_mtz(hklin)
     try:
         hkldata, sts, fc_labs, centric_and_selections, args.free = process_input(hklin=hklin,
                                                                                  labin=labin,
@@ -141,7 +145,10 @@ def main(args):
                                                                                  use="work" if args.use_work_in_est else "test",
                                                                                  max_bins=30,
                                                                                  keep_charges=args.keep_charges,
-                                                                                 allow_unusual_occupancies=args.allow_unusual_occupancies)
+                                                                                 allow_unusual_occupancies=args.allow_unusual_occupancies,
+                                                                                 hklin_free=args.hklin_free,
+                                                                                 labin_free=args.labin_free)
+
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
@@ -161,12 +168,13 @@ def main(args):
     if args.unrestrained:
         monlib = gemmi.MonLib()
         topo = None
-        h_change = gemmi.HydrogenChange.NoChange
-        if args.hydrogen == "all":
-            logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
-        elif args.hydrogen == "no":
-            st.remove_hydrogens()
+        if args.hydrogen == "yes":
+            h_change = gemmi.HydrogenChange.NoChange
+        else:
             h_change = gemmi.HydrogenChange.Remove
+            st.remove_hydrogens()
+            if args.hydrogen == "all":
+                logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
         for i, cra in enumerate(st[0].all()):
             cra.atom.serial = i + 1
     else:
@@ -235,6 +243,7 @@ def main(args):
                                weight_adjust_bond_rmsz_range=args.target_bond_rmsz_range,
                                stats_json_out=args.output_prefix + "_stats.json")
     update_meta(st, stats[-1], ll)
+    st.meta.software = software_items + st.meta.software
     refiner.st.name = args.output_prefix
     utils.fileio.write_model(refiner.st, args.output_prefix, pdb=True, cif=True, hout=args.hout)
     if params["write_trajectory"]:
@@ -253,12 +262,12 @@ def main(args):
 
     # Write mtz file
     if ll.twin_data:
-        labs = ["F_est", "F_exp", "FOM"]
+        labs = ["F_est", "F_exp"]
     elif is_int:
-        labs = ["I", "SIGI", "FOM"]
+        labs = ["I", "SIGI", "F_est"]
     else:
-        labs = ["FP", "SIGFP", "FOM"]
-    labs.extend(["FWT", "DELFWT", "FC"])
+        labs = ["FP", "SIGFP"]
+    labs.extend(["FOM", "FWT", "DELFWT", "FC"])
     if "FAN" in hkldata.df:
         labs.append("FAN")
     if not args.no_solvent:

servalcat/refmac/refmac_wrapper.py

@@ -33,6 +33,8 @@ def add_arguments(parser):
     parser.add_argument('--keep_original_output', action='store_true', help="with .org extension")
     parser.add_argument("--keep_entities", action='store_true',
                         help="Do not override entities")
+    parser.add_argument("--tls_addu", action='store_true',
+                        help="Write prefix_addu.mmcif where TLS contribution is added to aniso U. Don't use this with 'tlso addu' keyword.")
     parser.add_argument('--prefix', help="output prefix")
     parser.add_argument("-v", "--version", action="version",
                         version=logger.versions_str())
@@ -222,7 +224,7 @@ def get_output_model_names(xyzout):
     return pdb, mmcif
 # get_output_model_names()
 
-def modify_output(pdbout, cifout, fixes, hout, cispeps, keep_original_output=False):
+def modify_output(pdbout, cifout, fixes, hout, cispeps, software_items, keep_original_output=False, tls_addu=False):
     st = utils.fileio.read_structure(cifout)
     st.cispeps = cispeps
     if os.path.exists(pdbout):
@@ -256,11 +258,37 @@ def modify_output(pdbout, cifout, fixes, hout, cispeps, keep_original_output=Fal
     # add servalcat version
     if len(st.meta.software) > 0 and st.meta.software[-1].name == "refmac":
         st.meta.software[-1].version += f" (refmacat {servalcat.__version__})"
+    st.meta.software = software_items + st.meta.software
     
     suffix = ".org"
     os.rename(cifout, cifout + suffix)
     utils.fileio.write_mmcif(st, cifout, cifout + suffix)
 
+    if tls_addu:
+        doc_ref = gemmi.cif.read(cifout + suffix)
+        tls_groups = {int(x.id): x for x in st.meta.refinement[0].tls_groups}
+        tls_details = doc_ref[0].find_value("_ccp4_refine_tls.details")
+        if tls_groups and gemmi.cif.as_string(tls_details) == "U values: residual only":
+            st2 = st.clone()
+            for cra in st2[0].all():
+                tlsgr = tls_groups.get(cra.atom.tls_group_id)
+                if cra.atom.tls_group_id > 0 and tlsgr is not None:
+                    if not cra.atom.aniso.nonzero():
+                        u = cra.atom.b_iso * utils.model.b_to_u
+                        cra.atom.aniso = gemmi.SMat33f(u, u, u, 0, 0, 0)
+                    u_from_tls = gemmi.calculate_u_from_tls(tlsgr, cra.atom.pos)
+                    cra.atom.aniso += gemmi.SMat33f(*u_from_tls.elements_pdb())
+                    cra.atom.b_iso = cra.atom.aniso.trace() / 3. * utils.model.u_to_b
+            cifout2 = cifout[:cifout.rindex(".")] + "_addu" + cifout[cifout.rindex("."):]
+            doc_ref[0].set_pair("_ccp4_refine_tls.details", gemmi.cif.quote("U values: with tls added"))
+            utils.fileio.write_mmcif(st2, cifout2, cif_ref_doc=doc_ref)
+        else:
+            if not tls_groups:
+                msg = "TLS group definition not found in the model"
+            else:
+                msg = "TLS already applied to the U values"
+            logger.writeln(f"Error: --tls_addu requested, but {msg}.")
+
     if st.has_d_fraction:
         st.store_deuterium_as_fraction(False) # also useful for pdb
         logger.writeln("will write a H/D expanded mmcif file")
@@ -313,6 +341,11 @@ def main(args):
     # TODO what if restin is given or make cr prepared is given?
     # TODO check make pept/link/suga/ss/conn/symm/chain
 
+    if "hklin" in opts: # for history
+        software_items = utils.fileio.software_items_from_mtz(opts["hklin"])
+    else:
+        software_items = []
+    
     # Process model
     crdout = None
     refmac_fixes = None
@@ -380,7 +413,8 @@ def main(args):
     if xyzin is not None:
         pdbout, cifout = get_output_model_names(opts.get("xyzout"))
         if os.path.exists(cifout):
-            modify_output(pdbout, cifout, refmac_fixes, keywords["make"].get("hout"), cispeps, args.keep_original_output)
+            modify_output(pdbout, cifout, refmac_fixes, keywords["make"].get("hout"), cispeps,
+                          software_items, args.keep_original_output, args.tls_addu)
 # main()
 
 def command_line():

servalcat/spa/fofc.py

@@ -357,7 +357,7 @@ def write_files(hkldata, map_labs, grid_start, stats_str,
             hkldata2.translate(lab, -shifts)
         hkldata = hkldata2
         
-    dump_to_mtz(hkldata, map_labs, "{}.mtz".format(output_prefix))
+    dump_to_mtz(hkldata, map_labs, "{}_maps.mtz".format(output_prefix))
     if stats_str: open("{}_Fstats.log".format(output_prefix), "w").write(stats_str)
 # write_files()
 
@@ -458,15 +458,15 @@ def main(args):
 
     py_out = "{}_coot.py".format(args.output_prefix)
     write_coot_script(py_out, model_file=args.model,
-                      mtz_file=args.output_prefix+".mtz",
+                      mtz_file=args.output_prefix+"_maps.mtz",
                       contour_fo=None if mask is None else 1.2,
                       contour_fofc=None if mask is None else 3.0,
                       ncs_ops=ncs_org)
-    logger.writeln("\nOpen model and diffmap.mtz with COOT:")
+    logger.writeln("\nOpen model and diffmap mtz with COOT:")
     logger.writeln("coot --script " + py_out)
     if mask is not None:
         logger.writeln("\nWant to list Fo-Fc map peaks? Try:")
-        if omit_h_electron:
+        if args.omit_h_electron:
             logger.writeln("servalcat util map_peaks --map {}_normalized_fofc_flipsign.mrc --model {} --abs_level 4.0".format(args.output_prefix, args.model))
         else:
             logger.writeln("servalcat util map_peaks --map {}_normalized_fofc.mrc --model {} --abs_level 4.0".format(args.output_prefix, args.model))

servalcat/spa/run_refmac.py

@@ -125,7 +125,7 @@ def add_arguments(parser):
     group = parser.add_mutually_exclusive_group()
     group.add_argument('--mask_for_fofc', help="Mask file for Fo-Fc map calculation")
     group.add_argument('--mask_radius_for_fofc', type=float, help="Mask radius for Fo-Fc map calculation")
-    parser.add_argument('--trim_fofc_mtz', action="store_true", help="diffmap.mtz will have smaller cell (if --mask_for_fofc is given)")
+    parser.add_argument('--trim_fofc_mtz', action="store_true", help="maps mtz will have smaller cell (if --mask_for_fofc is given)")
     parser.add_argument("--fsc_resolution", type=float,
                         help="High resolution limit for FSC calculation. Default: Nyquist")
 
@@ -312,7 +312,7 @@ def calc_fofc(st, st_expanded, maps, monlib, model_format, args, diffmap_prefix=
     # Create Coot script
     spa.fofc.write_coot_script("{}_coot.py".format(args.output_prefix),
                                model_file="{}.pdb".format(args.output_prefix), # as Coot is not good at mmcif file..
-                               mtz_file="{}.mtz".format(diffmap_prefix),
+                               mtz_file="{}_maps.mtz".format(diffmap_prefix),
                                contour_fo=None if mask is None else 1.2,
                                contour_fofc=None if mask is None else 3.0,
                                ncs_ops=st.ncs)
@@ -364,7 +364,7 @@ Weight used: {final_weight}
              If you want to change the weight, give larger (looser restraints)
              or smaller (tighter) value to --weight_auto_scale=.
              
-Open refined model and diffmap.mtz with COOT:
+Open refined model and maps mtz with COOT:
 coot --script {prefix}_coot.py
 
 Open refined model, map and difference map with ChimeraX/ISOLDE:

servalcat/utils/commands.py

@@ -330,7 +330,7 @@ def symmodel(args):
     map_and_start = None
     if args.map:
         logger.writeln("Reading cell from map")
-        map_and_start = fileio.read_ccp4_map(args.map)
+        map_and_start = fileio.read_ccp4_map(args.map, header_only=True)
         st.cell = map_and_start[0].unit_cell
     elif args.cell:
         st.cell = gemmi.UnitCell(*args.cell)
@@ -388,7 +388,7 @@ def helical_biomt(args):
     map_and_start = None
     if args.map:
         logger.writeln("Reading cell from map")
-        map_and_start = fileio.read_ccp4_map(args.map)
+        map_and_start = fileio.read_ccp4_map(args.map, header_only=True)
         st.cell = map_and_start[0].unit_cell
     elif args.cell:
         st.cell = gemmi.UnitCell(*args.cell)
@@ -1307,7 +1307,7 @@ def mask_from_model(args):
     st = fileio.read_structure(args.model) # TODO option to (or not to) expand NCS
     if args.selection:
         gemmi.Selection(args.selection).remove_not_selected(st)
-    gr, grid_start, _ = fileio.read_ccp4_map(args.map)
+    gr, grid_start, _ = fileio.read_ccp4_map(args.map, header_only=True)
     mask = maps.mask_from_model(st, args.radius, soft_edge=args.soft_edge, grid=gr)
     maps.write_ccp4_map(args.output, mask, grid_start=grid_start)
 # mask_from_model()
@@ -1367,7 +1367,7 @@ def map2mtz(args):
 
 def sm2mm(args):
     if args.output_prefix is None:
-        args.output_prefix = fileio.splitext(args.files[0])[0]
+        args.output_prefix = os.path.basename(fileio.splitext(args.files[0])[0])
     st, mtz = fileio.read_small_molecule_files(args.files)
     if st is not None:
         fileio.write_model(st, prefix=args.output_prefix, pdb=True, cif=True)

servalcat/utils/fileio.py

@@ -18,6 +18,7 @@ import subprocess
 import gemmi
 import numpy
 import gzip
+import traceback
 
 def splitext(path):
     if path.endswith((".bz2",".gz")):
@@ -66,14 +67,15 @@ def check_model_format(xyzin):
         return ".pdb"
 # check_model_format()
 
-def write_mmcif(st, cif_out, cif_ref=None):
+def write_mmcif(st, cif_out, cif_ref=None, cif_ref_doc=None):
     """
     Refmac fails if _entry.id is longer than 80 chars including quotations
     """
     st_new = st.clone()
     logger.writeln("Writing mmCIF file: {}".format(cif_out))
-    if cif_ref:
-        logger.writeln("  using mmCIF metadata from: {}".format(cif_ref))
+    if cif_ref or cif_ref_doc:
+        if cif_ref:
+            logger.writeln("  using mmCIF metadata from: {}".format(cif_ref))
         groups = gemmi.MmcifOutputGroups(False)
         groups.group_pdb = True
         groups.ncs = True
@@ -88,18 +90,19 @@ def write_mmcif(st, cif_out, cif_ref=None):
         groups.conn = True
         groups.software = True
         groups.auth_all = True
-        # FIXME is this all? 
-        try:
-            doc = read_cif_safe(cif_ref)
-        except Exception as e:
-            # Sometimes refmac writes a broken mmcif file..
-            logger.error("Error in mmCIF reading: {}".format(e))
-            logger.error("  Give up using cif reference.")
-            return write_mmcif(st, cif_out)
+        # FIXME is this all?
+        if cif_ref:
+            try:
+                cif_ref_doc = read_cif_safe(cif_ref)
+            except Exception as e:
+                # Sometimes refmac writes a broken mmcif file..
+                logger.error("Error in mmCIF reading: {}".format(e))
+                logger.error("  Give up using cif reference.")
+                return write_mmcif(st, cif_out)
             
-        blocks = list(filter(lambda b: b.find_loop("_atom_site.id"), doc))
+        blocks = list(filter(lambda b: b.find_loop("_atom_site.id"), cif_ref_doc))
         if len(blocks) == 0:
-            logger.writeln("No _atom_site found in {}".format(cif_ref))
+            logger.writeln("No _atom_site found in reference")
             logger.writeln("  Give up using cif reference.")
             return write_mmcif(st, cif_out)
         block = blocks[0]
@@ -108,7 +111,7 @@ def write_mmcif(st, cif_out, cif_ref=None):
         block.find_mmcif_category("_atom_sites.").erase()
         st_new.update_mmcif_block(block, groups)
         if "_entry.id" in st_new.info: st_new.info["_entry.id"] = st_new.info["_entry.id"][:78]
-        doc.write_file(cif_out, options=gemmi.cif.Style.Aligned)
+        cif_ref_doc.write_file(cif_out, options=gemmi.cif.Style.Aligned)
     else:
         st_new.name = st_new.name[:78] # this will become _entry.id
         if "_entry.id" in st_new.info: st_new.info["_entry.id"] = st_new.info["_entry.id"][:78]
@@ -162,17 +165,20 @@ def read_shifts_txt(shifts_txt):
     return ret
 # read_shifts_txt()
 
-def read_ccp4_map(filename, setup=True, default_value=0., pixel_size=None, ignore_origin=True):
-    m = gemmi.read_ccp4_map(filename)
-    g = m.grid
+def read_ccp4_map(filename, header_only=False, setup=True, default_value=0., pixel_size=None, ignore_origin=True):
+    if header_only:
+        m = gemmi.read_ccp4_header(filename)
+    else:
+        m = gemmi.read_ccp4_map(filename)
     grid_cell = [m.header_i32(x) for x in (8,9,10)]
     grid_start = [m.header_i32(x) for x in (5,6,7)]
     grid_shape = [m.header_i32(x) for x in (1,2,3)]
     axis_pos = m.axis_positions()
     axis_letters = ["","",""]
     for i, l in zip(axis_pos, "XYZ"): axis_letters[i] = l
-    spacings = [1./g.unit_cell.reciprocal().parameters[i]/grid_cell[i] for i in (0,1,2)]
-    voxel_size = [g.unit_cell.parameters[i]/grid_cell[i] for i in (0,1,2)]
+    cell = gemmi.UnitCell(*(m.header_float(x) for x in range(11,17)))
+    spacings = [1./cell.reciprocal().parameters[i]/grid_cell[i] for i in (0,1,2)]
+    voxel_size = [cell.parameters[i]/grid_cell[i] for i in (0,1,2)]
     origin = [m.header_float(x) for x in (50,51,52)]
     label = m.header_str(57, 80)
     label = label[:label.find("\0")]
@@ -181,7 +187,7 @@ def read_ccp4_map(filename, setup=True, default_value=0., pixel_size=None, ignor
     logger.writeln("    Map mode: {}".format(m.header_i32(4)))
     logger.writeln("       Start: {:4d} {:4d} {:4d}".format(*grid_start))
     logger.writeln("       Shape: {:4d} {:4d} {:4d}".format(*grid_shape))
-    logger.writeln("        Cell: {} {} {} {} {} {}".format(*g.unit_cell.parameters))
+    logger.writeln("        Cell: {} {} {} {} {} {}".format(*cell.parameters))
     logger.writeln("  Axis order: {}".format(" ".join(axis_letters)))
     logger.writeln(" Space group: {}".format(m.header_i32(23)))
     logger.writeln("     Spacing: {:.6f} {:.6f} {:.6f}".format(*spacings))
@@ -195,9 +201,17 @@ def read_ccp4_map(filename, setup=True, default_value=0., pixel_size=None, ignor
     logger.writeln("       Label: {}".format(label))
     logger.writeln("")
 
+    if header_only:
+        grid = gemmi.FloatGrid(*grid_cell if setup else grid_shape) # waste of memory, but unavoidable for now
+        grid.set_unit_cell(cell)
+        grid.spacegroup = gemmi.find_spacegroup_by_number(m.header_i32(23))
+    else:
+        grid = m.grid
+
     if setup:
-        if default_value is None: default_value = float("nan")
-        m.setup(default_value)
+        if not header_only:
+            if default_value is None: default_value = float("nan")
+            m.setup(default_value)
         grid_start = [grid_start[i] for i in axis_pos]
         
     if pixel_size is not None:
@@ -207,13 +221,13 @@ def read_ccp4_map(filename, setup=True, default_value=0., pixel_size=None, ignor
             pixel_size = [pixel_size, pixel_size, pixel_size]
             
         logger.writeln("Overriding pixel size with {:.6f} {:.6f} {:.6f}".format(*pixel_size))
-        orgc = m.grid.unit_cell.parameters
+        orgc = grid.unit_cell.parameters
         new_abc = [orgc[i]*pixel_size[i]/voxel_size[i] for i in (0,1,2)]
-        m.grid.unit_cell = gemmi.UnitCell(new_abc[0], new_abc[1], new_abc[2],
-                                          orgc[3], orgc[4], orgc[5])
-        logger.writeln(" New cell= {:.1f} {:.1f} {:.1f} {:.1f} {:.1f} {:.1f}".format(*m.grid.unit_cell.parameters))
+        new_cell = gemmi.UnitCell(new_abc[0], new_abc[1], new_abc[2], orgc[3], orgc[4], orgc[5])
+        grid.set_unit_cell(new_cell)
+        logger.writeln(" New cell= {:.1f} {:.1f} {:.1f} {:.1f} {:.1f} {:.1f}".format(*grid.unit_cell.parameters))
 
-    return [m.grid, grid_start, grid_shape]
+    return [grid, grid_start, grid_shape]
 # read_ccp4_map()
 
 def read_halfmaps(files, pixel_size=None, fail=True):
@@ -267,6 +281,19 @@ def is_mmhkl_file(hklin):
     # otherwise cannot decide
 # is_smhkl()
 
+def software_items_from_mtz(hklin):
+    try:
+        if type(hklin) is gemmi.Mtz:
+            mtz = hklin
+        else:
+            mtz = gemmi.read_mtz_file(hklin, with_data=False)
+        return gemmi.get_software_from_mtz_history(mtz.history)
+    except:
+        logger.writeln(f"Failed to read software info from {hklin}")
+        logger.writeln(traceback.format_exc())
+        return []
+# software_items_from_mtz()
+
 def read_map_from_mtz(mtz_in, cols, grid_size=None, sample_rate=3):
     mtz = read_mmhkl(mtz_in)
     d_min = mtz.resolution_high() # TODO get resolution for column?
@@ -551,9 +578,16 @@ def read_shelx_ins(ins_in=None, lines_in=None, ignore_q_peaks=True): # TODO supp
             if len(sp) > 11:
                 u = list(map(float, sp[6:12]))
                 site.aniso = gemmi.SMat33d(u[0], u[1], u[2], u[5], u[4], u[3])
-                #TODO site.u_iso needs to be set?
+                site.u_iso = sum(u[:3]) / 3.
             else:
                 site.u_iso = float(sp[6])
+                if site.u_iso < 0:
+                    # most recently defined non-hydrogen atom
+                    u_p = next((s.u_iso for s in reversed(ss.sites) if not s.element.is_hydrogen), None)
+                    if u_p is not None:
+                        site.u_iso *= -u_p
+                    else:
+                        logger.writeln(f"WARNING: parent atom not found for {site.label}")
 
             ss.add_site(site)
 
@@ -693,20 +727,21 @@ def read_small_molecule_files(files):
     # first pass - find structure
     for filename in files:
         ext = splitext(filename)[1]
-        if ext in (".cif", ".res", ".ins"):
+        if ext in (".cif", ".res", ".ins", ".pdb", ".ent", ".mmcif"):
             try:
                 st = read_structure(filename)
             except:
                 continue
             logger.writeln("Coordinates read from: {}".format(filename))
-            if ext == ".cif":
-                b = gemmi.cif.read(filename).sole_block()
-                res_str = b.find_value("_shelx_res_file")
-            else:
-                res_str = open(filename).read()
-            if res_str:
-                _, info = read_shelx_ins(lines_in=res_str.splitlines())
-                hklf = info["hklf"]
+            if ext in (".cif", ".res", ".ins"):
+                if ext == ".cif":
+                    b = gemmi.cif.read(filename).sole_block()
+                    res_str = b.find_value("_shelx_res_file")
+                else:
+                    res_str = open(filename).read()
+                if res_str:
+                    _, info = read_shelx_ins(lines_in=res_str.splitlines())
+                    hklf = info["hklf"]
     if st is None:
         logger.writeln("ERROR: coordinates not found.")
         return None, None
@@ -733,12 +768,16 @@ def read_sequence_file(f):
     # TODO needs improvement
     # return a list of [name, sequence]
     ret = []
-    for l in open(f):
+    for i, l in enumerate(open(f)):
         l = l.strip()
         if l.startswith(">"):
             name = l[1:].strip()
             ret.append([name, ""])
         elif l:
             if not ret: ret.append(["", ""])
-            ret[-1][1] += l.replace("*", "").replace("-", "").upper()
+            tmp = l.replace("*", "").replace("-", "").upper()
+            r = re.search("[^A-Z]", tmp)
+            if r:
+                raise RuntimeError(f"Invalid character in the sequence file: {f}:{i+1}")
+            ret[-1][1] += tmp
     return ret

servalcat/utils/model.py

@@ -494,9 +494,10 @@ def filter_contacting_ncs(st, cutoff=5.):
     st.setup_cell_images()
     ns = gemmi.NeighborSearch(st[0], st.cell, cutoff*2).populate() # This is considered crystallographic cell if not 1 1 1. Undesirable result may be seen.
     cs = gemmi.ContactSearch(cutoff)
+    cs.twice = True # since we need all image_idx
     cs.ignore = gemmi.ContactSearch.Ignore.SameAsu
     results = cs.find_contacts(ns)
-    indices = set([r.image_idx for r in results])
+    indices = {r.image_idx for r in results}
     logger.writeln(" contacting copies: {}".format(indices))
     ops = [st.ncs[i-1] for i in indices] # XXX is this correct? maybe yes as long as identity operator is not there
     st.ncs.clear()

servalcat/utils/symmetry.py

@@ -39,8 +39,11 @@ def update_ncs_from_args(args, st, map_and_start=None, filter_contacting=False,
     ncsops = ncsops_from_args(args, st.cell, map_and_start=map_and_start, st=st,
                               helical_min_n=helical_min_n, helical_max_n=helical_max_n)
 
-    st.ncs.clear()
-    st.ncs.extend([x for x in ncsops if not x.tr.is_identity()])
+    st.ncs = [x for x in ncsops if not x.tr.is_identity()]
+    # To write identity op to the output model
+    idop_id = next((x.id for x in ncsops if x.tr.is_identity()), None)
+    if idop_id:
+        st.info["_struct_ncs_oper.id"] = idop_id
 
     if filter_contacting:
         model.filter_contacting_ncs(st)

servalcat/xtal/sigmaa.py

@@ -30,10 +30,14 @@ def add_arguments(parser):
     parser.description = 'Sigma-A parameter estimation for crystallographic data'
     parser.add_argument('--hklin', required=True,
                         help='Input MTZ file')
+    parser.add_argument('--hklin_free',
+                        help='Input MTZ file for test flags')
     parser.add_argument('--spacegroup',
                         help='Override space group')
     parser.add_argument('--labin',
-                        help='MTZ column for F,SIGF,FREE')
+                        help='MTZ columns of --hklin for F,SIGF,FREE')
+    parser.add_argument('--labin_free',
+                        help='MTZ column of --hklin_free')
     parser.add_argument('--free', type=int,
                         help='flag number for test set')
     parser.add_argument('--model', required=True, nargs="+", action="append",
@@ -97,6 +101,8 @@ def calc_r_and_cc(hkldata, centric_and_selections, twin_data=None):
     else:
         obs = obs_sqrt = hkldata.df.FP
         calc = calc_sqrt = Fc
+    if "CC*" in stats: # swap the positions
+        stats.insert(len(stats.columns)-1, "CC*", stats.pop("CC*"))
     if has_free:
         for lab in (cclab, rlab):
             for suf in ("work", "free"):
@@ -1037,6 +1043,7 @@ def calculate_maps_int(hkldata, b_aniso, fc_labs, D_labs, centric_and_selections
     nmodels = len(fc_labs)
     hkldata.df["FWT"] = 0j * numpy.nan
     hkldata.df["DELFWT"] = 0j * numpy.nan
+    hkldata.df["F_est"] = numpy.nan
     hkldata.df["FOM"] = numpy.nan # FOM proxy, |<F>| / <|F|>
     has_ano = "I(+)" in hkldata.df and "I(-)" in hkldata.df
     if has_ano:
@@ -1059,6 +1066,7 @@ def calculate_maps_int(hkldata, b_aniso, fc_labs, D_labs, centric_and_selections
             hkldata.df.loc[cidxes, "FWT"] = 2 * f * exp_ip - DFc[cidxes]
             hkldata.df.loc[cidxes, "DELFWT"] = f * exp_ip - DFc[cidxes]
             hkldata.df.loc[cidxes, "FOM"] = m_proxy
+            hkldata.df.loc[cidxes, "F_est"] = f
             if has_ano:
                 f_p, _ = expected_F_from_int(ano_data[cidxes,0], ano_data[cidxes,1],
                                              k_ani[cidxes], DFc[cidxes], eps[cidxes], c, S)
@@ -1159,9 +1167,32 @@ def decide_mtz_labels(mtz, find_free=True, require=None):
     return labin
 # decide_mtz_labels()
 
+def decide_spacegroup(sg_user, sg_st, sg_hkl):
+    assert sg_hkl is not None
+    ret = None
+    if sg_user is not None:
+        ret = sg_user
+        logger.writeln(f"Space group overridden by user. Using {ret.xhm()}")
+    else:
+        ret = sg_hkl
+        if sg_hkl != sg_st:
+            if sg_st and sg_st.laue_str() != sg_hkl.laue_str():
+                raise RuntimeError("Crystal symmetry mismatch between model and data")
+            logger.writeln("Warning: space group mismatch between model and mtz")
+            if sg_st and sg_st.laue_str() == sg_hkl.laue_str():
+                logger.writeln("         using space group from model")
+                ret = sg_st
+            else:
+                logger.writeln("         using space group from mtz")
+            logger.writeln("")
+
+    return ret
+# decide_spacegroup
+
 def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=None,
                   n_per_bin=None, use="all", max_bins=None, cif_index=0, keep_charges=False,
-                  allow_unusual_occupancies=False, space_group=None):
+                  allow_unusual_occupancies=False, space_group=None,
+                  hklin_free=None, labin_free=None):
     if labin: assert 1 < len(labin) < 6
     assert use in ("all", "work", "test")
 
@@ -1181,13 +1212,18 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
         assert len(xyzins) == 1
         assert not sts
         st, mtz = utils.fileio.read_small_molecule_files([hklin, xyzins[0]])
+        if None in (st, mtz):
+            raise SystemExit("Failed to read small molecule file(s)")
         sts = [st]
 
     for st in sts:
         utils.model.check_occupancies(st, raise_error=not allow_unusual_occupancies)
         
+    sg_use = decide_spacegroup(sg_user=gemmi.SpaceGroup(space_group) if space_group else None,
+                               sg_st=sts[0].find_spacegroup() if sts else None,
+                               sg_hkl=mtz.spacegroup)
     if not labin:
-        labin = decide_mtz_labels(mtz)
+        labin = decide_mtz_labels(mtz, find_free=hklin_free is None)
     col_types = {x.label:x.type for x in mtz.columns}
     if labin[0] not in col_types:
         raise RuntimeError("MTZ column not found: {}".format(labin[0]))
@@ -1197,10 +1233,30 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
                       "K": ("anomalous intensity", ["I(+)","SIGI(+)", "I(-)", "SIGI(-)"], ["K", "M", "K", "M"])}
     if col_types[labin[0]] not in labs_and_types:
         raise RuntimeError("MTZ column {} is neither amplitude nor intensity".format(labin[0]))
+    if col_types[labin[0]] == "J": # may be unmerged data
+        ints = gemmi.Intensities()
+        ints.set_data(mtz.cell, sg_use, mtz.make_miller_array(),
+                      mtz.array[:,mtz.column_labels().index(labin[0])],
+                      mtz.array[:,mtz.column_labels().index(labin[1])])
+        dtype = ints.prepare_for_merging(gemmi.DataType.Mean) # do we want Anomalous?
+        ints_bak = ints.clone() # for stats
+        ints.merge_in_place(dtype)
+        if (ints.nobs_array > 1).any():
+            mtz = ints.prepare_merged_mtz(with_nobs=False)
+            labin = mtz.column_labels()[3:]
+            col_types = {x.label:x.type for x in mtz.columns}
+            mult = ints.nobs_array.mean()
+            logger.writeln(f"Input data were merged (multiplicity: {mult:.2f}). Overriding labin={','.join(labin)}")
+        else:
+            ints_bak = None
+    else:
+        ints_bak = None
+        
     name, newlabels, require_types = labs_and_types[col_types[labin[0]]]
     logger.writeln("Observation type: {}".format(name))
     if len(newlabels) < len(labin): newlabels.append("FREE")
     hkldata = utils.hkl.hkldata_from_mtz(mtz, labin, newlabels=newlabels, require_types=require_types)
+    hkldata.sg = sg_use
     hkldata.mask_invalid_obs_values(newlabels)
     if newlabels[0] == "F(+)":
         hkldata.merge_anomalous(newlabels[:4], ["FP", "SIGFP"])
@@ -1211,13 +1267,7 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
 
     if hkldata.df.empty:
         raise RuntimeError("No data in hkl data")
-    
-    if space_group is None:
-        sg_use = None
-    else:
-        sg_use = gemmi.SpaceGroup(space_group)
-        logger.writeln(f"Space group overridden by user. Using {sg_use.xhm()}")
-    
+
     if sts:
         assert source in ["electron", "xray", "neutron"]
         for st in sts:
@@ -1227,23 +1277,8 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
             logger.writeln("Warning: unit cell mismatch between model and reflection data")
             logger.writeln("         using unit cell from mtz")
 
-        for st in sts: st.cell = hkldata.cell # mtz cell is used in any case
-
-        sg_st = sts[0].find_spacegroup() # may be None
-        if sg_use is None:
-            sg_use = hkldata.sg
-            if hkldata.sg != sg_st:
-                if st.cell.is_crystal() and sg_st and sg_st.laue_str() != hkldata.sg.laue_str():
-                    raise RuntimeError("Crystal symmetry mismatch between model and data")
-                logger.writeln("Warning: space group mismatch between model and mtz")
-                if sg_st and sg_st.laue_str() == hkldata.sg.laue_str():
-                    logger.writeln("         using space group from model")
-                    sg_use = sg_st
-                else:
-                    logger.writeln("         using space group from mtz")
-                logger.writeln("")
-            
         for st in sts:
+            st.cell = hkldata.cell # mtz cell is used in any case
             st.spacegroup_hm = sg_use.xhm()
             st.setup_cell_images()
 
@@ -1251,19 +1286,36 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
             utils.model.remove_charge(sts)
         utils.model.check_atomsf(sts, source)
 
-    if sg_use is not None:
-        hkldata.sg = sg_use
     hkldata.switch_to_asu()
     hkldata.remove_systematic_absences()
     #hkldata.df = hkldata.df.astype({name: 'float64' for name in ["I","SIGI","FP","SIGFP"] if name in hkldata.df})
-    d_min_data = hkldata.d_min_max(newlabels)[0]
-    if d_min is None and hkldata.d_min_max()[0] != d_min_data:
-        d_min = d_min_data
+    d_min_max_data = hkldata.d_min_max(newlabels)
+    if d_min is None and hkldata.d_min_max()[0] != d_min_max_data[0]:
+        d_min = d_min_max_data[0]
         logger.writeln(f"Changing resolution to {d_min:.3f} A")
     if (d_min, d_max).count(None) != 2:
         hkldata = hkldata.copy(d_min=d_min, d_max=d_max)
     if hkldata.df.empty:
         raise RuntimeError("No data left in hkl data")
+
+    if hklin_free is not None:
+        mtz2 = utils.fileio.read_mmhkl(hklin_free)
+        if labin_free and labin_free not in mtz2.column_labels():
+            raise RuntimeError(f"specified label ({labin_free}) not found in {hklin_free}")
+        if not labin_free:
+            tmp = utils.hkl.mtz_find_free_columns(mtz2)
+            if tmp:
+                labin_free = tmp[0]
+            else:
+                raise RuntimeError(f"Test flag label not found in {hklin_free}")
+        tmp = utils.hkl.hkldata_from_mtz(mtz2, [labin_free], newlabels=["FREE"])
+        tmp.sg = sg_use
+        tmp.switch_to_asu()
+        tmp.remove_systematic_absences()
+        tmp = tmp.copy(d_min=d_min_max_data[0], d_max=d_min_max_data[1])
+        hkldata.complete()
+        tmp.complete()
+        hkldata.merge(tmp.df[["H","K","L","FREE"]])
         
     hkldata.complete()
     hkldata.sort_by_resolution()
@@ -1271,7 +1323,7 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
     hkldata.calc_centric()
 
     if "FREE" in hkldata.df and free is None:
-        free = hkldata.guess_free_number(newlabels[0])
+        free = hkldata.guess_free_number(newlabels[0]) # also check NaN
 
     if n_bins is None:
         if n_per_bin is None:
@@ -1297,8 +1349,6 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
         logger.writeln("n_per_bin={} requested for {}. n_bins set to {}".format(n_per_bin, use, n_bins))
 
     hkldata.setup_binning(n_bins=n_bins)
-    logger.writeln("Data completeness: {:.2f}%".format(hkldata.completeness()*100.))
-
     fc_labs = ["FC{}".format(i)  for i, _ in enumerate(sts)]
 
     # Create a centric selection table for faster look up
@@ -1348,6 +1398,14 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
             stats.loc[i_bin, "n_test"] = n_test
             
     stats["completeness"] = stats["n_obs"] / stats["n_all"] * 100
+    logger.writeln("Data completeness: {:.2%}".format(stats["n_obs"].sum() / stats["n_all"].sum()))
+    if ints_bak is not None:
+        binner = gemmi.Binner()
+        binner.setup(n_bins, gemmi.Binner.Method.Dstar2, ints_bak)
+        bin_stats = ints_bak.calculate_merging_stats(binner, use_weights="X")
+        stats["CC1/2"] = [stats.cc_half() for stats in bin_stats]
+        hkldata.binned_df["CC*"] = numpy.sqrt(2 * stats["CC1/2"] / (1 + stats["CC1/2"]))
+    
     logger.writeln(stats.to_string())
     return hkldata, sts, fc_labs, centric_and_selections, free
 # process_input()
@@ -1551,7 +1609,9 @@ def main(args):
                                                                            use=args.use,
                                                                            max_bins=30,
                                                                            keep_charges=args.keep_charges,
-                                                                           space_group=args.spacegroup)
+                                                                           space_group=args.spacegroup,
+                                                                           hklin_free=args.hklin_free,
+                                                                           labin_free=args.labin_free)
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
@@ -1623,7 +1683,7 @@ def main(args):
     if twin_data:
         labs = ["F_est", "F_exp"]
     elif is_int:
-        labs = ["I", "SIGI"]
+        labs = ["I", "SIGI", "F_est"]
     else:
         labs = ["FP", "SIGFP"]
     labs.extend(["FOM", "FWT", "DELFWT", "FC", "DFC"])

servalcat/xtal/twin.py

@@ -37,11 +37,10 @@ def find_twin_domains_from_data(hkldata, max_oblique=5, min_alpha=0.05):
         nums.append([])
         rs = []
         for i_op, op in enumerate(ops):
+            cc = r = numpy.nan
             ii = numpy.array(twin_data.pairs(i_op, i_bin))
-            val = numpy.all(numpy.isfinite(Io[ii]), axis=1)
-            if numpy.sum(val) == 0:
-                cc = r = numpy.nan
-            else:
+            val = numpy.all(numpy.isfinite(Io[ii]), axis=1) if ii.size != 0 else []
+            if numpy.sum(val) != 0:
                 cc = numpy.corrcoef(Io[ii][val].T)[0,1]
                 r = numpy.sum(numpy.abs(Io[ii][val, 0] - Io[ii][val, 1])) / numpy.sum(Io[ii][val])
             ratio = (1 - numpy.sqrt(1 - cc**2)) / cc

{servalcat-0.4.100.dist-info → servalcat-0.4.105.dist-info}/METADATA

@@ -1,16 +1,16 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: servalcat
-Version: 0.4.100
+Version: 0.4.105
 Summary: Structure refinement and validation for crystallography and single particle analysis
 Author: Keitaro Yamashita, Garib N. Murshudov
 License: MPL-2.0
-Project-URL: Repository, https://github.com/keitaroyam/servalcat
+Project-URL: repository, https://github.com/keitaroyam/servalcat
 Requires-Python: >=3.8
 Requires-Dist: packaging
 Requires-Dist: numpy>=1.15
 Requires-Dist: scipy
 Requires-Dist: pandas>=1.1.0
-Requires-Dist: gemmi==0.7.0
+Requires-Dist: gemmi==0.7.1
 Description-Content-Type: text/markdown
 
 # Servalcat
@@ -40,7 +40,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.7.0](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.0). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
+The required GEMMI version is now [v0.7.1](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.1). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
 
 To use the Refmac5 related commands, you also need to install [CCP4](https://www.ccp4.ac.uk/). For "No Refmac5" commands, you may just need [the monomer library](https://github.com/MonomerLibrary/monomers) if CCP4 is not installed.
 

{servalcat-0.4.100.dist-info → servalcat-0.4.105.dist-info}/RECORD

@@ -1,45 +1,45 @@
-servalcat/__init__.py,sha256=bOvfsOFrPkgPBtZIILjkf4hYnPjPRDQYcfbDpTzod3k,242
+servalcat/__init__.py,sha256=h7BOGz-QcZhMfvflyNwkvrvZA4n4eOWgYklEDpKwUZo,242
 servalcat/__main__.py,sha256=XUM193aDwZAEQY02VzvZasAzD6AYEM-_A4wqy93KDWE,4190
-servalcat/ext.cp311-win_amd64.pyd,sha256=40LmEqSy1DI73pjCEWtd53GtpV4TNaQdDif5E7qlwq8,1335808
+servalcat/ext.cp311-win_amd64.pyd,sha256=Ff9-pb99ApU1n3klxqwvoAJXxwRGRJx2MAZJ6gh04_w,1326592
 servalcat/refine/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 servalcat/refine/cgsolve.py,sha256=Xz7EwGI-mr4nnbfARyfFjAqbJbPWGH9qNWQ0GpltDuc,3172
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{servalcat-0.4.100.dist-info → servalcat-0.4.105.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.10.7
+Generator: scikit-build-core 0.11.1
 Root-Is-Purelib: false
 Tag: cp311-cp311-win_amd64