servalcat 0.4.88__cp311-cp311-win_amd64.whl → 0.4.99__cp311-cp311-win_amd64.whl

servalcat/xtal/sigmaa.py

@@ -30,6 +30,8 @@ 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('--spacegroup',
+                        help='Override space group')
     parser.add_argument('--labin',
                         help='MTZ column for F,SIGF,FREE')
     parser.add_argument('--free', type=int,
@@ -77,7 +79,7 @@ def calc_r_and_cc(hkldata, centric_and_selections, twin_data=None):
     has_int = "I" in hkldata.df
     has_free = "FREE" in hkldata.df
     stats = hkldata.binned_df.copy()
-    stats["n_obs"] = 0
+    stats[["n_obs", "n_all"]] = 0
     if has_free:
         stats[["n_work", "n_free"]] = 0
     rlab = "R1" if has_int else "R"
@@ -105,6 +107,7 @@ def calc_r_and_cc(hkldata, centric_and_selections, twin_data=None):
 
     for i_bin, idxes in hkldata.binned():
         stats.loc[i_bin, "n_obs"] = numpy.sum(numpy.isfinite(obs[idxes]))
+        stats.loc[i_bin, "n_all"] = len(idxes)
         if has_free:
             for j, suf in ((1, "work"), (2, "free")):
                 idxes2 = numpy.concatenate([sel[j] for sel in centric_and_selections[i_bin]])
@@ -1018,10 +1021,9 @@ def smooth_params(hkldata, D_labs, smoothing): # XXX twin_data
 # smooth_params()
 
 def expected_F_from_int(Io, sigIo, k_ani, DFc, eps, c, S):
-    if c == 0: # acentric
-        k_num, k_den = 0.5, 0.
-    else:
-        k_num, k_den = 0., -0.5
+    k_num = numpy.repeat(0.5 if c == 0 else 0., Io.size) # 0.5 if acentric
+    k_den = k_num - 0.5
+    if numpy.isscalar(c): c = numpy.repeat(c, Io.size)
     to = Io / sigIo - sigIo / (c+1) / k_ani**2 / S / eps
     tf = k_ani * numpy.abs(DFc) / numpy.sqrt(sigIo)
     sig1 = k_ani**2 * S * eps / sigIo
@@ -1088,15 +1090,23 @@ def calculate_maps_twin(hkldata, b_aniso, fc_labs, D_labs, twin_data, centric_an
                 Io[tohide] = numpy.nan
     
     twin_data.est_f_true(Io, sigIo)
-    F_true = numpy.asarray(twin_data.f_true_max)
     Ds = twin_data.ml_scale_array()
     DFc = (twin_data.f_calc * Ds).sum(axis=1)
     exp_ip = numpy.exp(numpy.angle(DFc)*1j)
     Ft = numpy.asarray(twin_data.f_true_max)
     m = twin_data.calc_fom()
-    fwt = numpy.where(numpy.asarray(twin_data.centric) == 0,
-                      2 * m * Ft * exp_ip - DFc, m * Ft * exp_ip)
-    delfwt = m * Ft * exp_ip - DFc
+    Fexp = twin_data.expected_F(Io, sigIo)
+    if 1:
+        fwt = numpy.where(numpy.asarray(twin_data.centric) == 0,
+                          2 * m * Ft * exp_ip - DFc,
+                          m * Ft * exp_ip)
+        delfwt = m * Ft * exp_ip - DFc
+    else: # based on "more accurate" evaluation of <m|F|>
+        fwt = numpy.where(numpy.asarray(twin_data.centric) == 0,
+                          2 * Fexp * exp_ip - DFc,
+                          m * Fexp * exp_ip)
+        delfwt = Fexp * exp_ip - DFc
+
     sel = numpy.isnan(fwt)
     fwt[sel] = DFc[sel]
     
@@ -1105,7 +1115,8 @@ def calculate_maps_twin(hkldata, b_aniso, fc_labs, D_labs, twin_data, centric_an
     hkldata2.df["FWT"] = fwt
     hkldata2.df["DELFWT"] = delfwt
     hkldata2.df["FOM"] = m
-    hkldata2.df["F_est"] = F_true
+    hkldata2.df["F_est"] = Ft
+    hkldata2.df["F_exp"] = Fexp
     hkldata2.df["FC"] = twin_data.f_calc.sum(axis=1)
     hkldata2.df["DFC"] = DFc
     hkldata2.df[D_labs] = Ds
@@ -1116,7 +1127,7 @@ def calculate_maps_twin(hkldata, b_aniso, fc_labs, D_labs, twin_data, centric_an
 def merge_models(sts): # simply merge models. no fix in chain ids etc.
     st2 = sts[0].clone()
     del st2[:]
-    model = gemmi.Model("1")
+    model = gemmi.Model(1)
     for st in sts:
         for m in st:
             for c in m:
@@ -1153,7 +1164,7 @@ def decide_mtz_labels(mtz, find_free=True, require=None):
 
 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):
+                  allow_unusual_occupancies=False, space_group=None):
     if labin: assert 1 < len(labin) < 6
     assert use in ("all", "work", "test")
     assert n_bins or n_per_bin #if n_bins not set, n_per_bin should be given
@@ -1204,6 +1215,12 @@ 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:
@@ -1216,39 +1233,43 @@ def process_input(hklin, labin, n_bins, free, xyzins, source, d_max=None, d_min=
         for st in sts: st.cell = hkldata.cell # mtz cell is used in any case
 
         sg_st = sts[0].find_spacegroup() # may be 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("")
-
+        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.spacegroup_hm = sg_use.xhm()
             st.setup_cell_images()
-        hkldata.sg = sg_use
 
         if not keep_charges:
             utils.model.remove_charge(sts)
         utils.model.check_atomsf(sts, source)
 
+    if sg_use is not None:
+        hkldata.sg = sg_use
     if newlabels[0] == "FP":
         hkldata.remove_nonpositive(newlabels[0])
     hkldata.remove_nonpositive(newlabels[1])
     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
+        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")
-    d_min, d_max = hkldata.d_min_max()
         
     hkldata.complete()
     hkldata.sort_by_resolution()
@@ -1527,7 +1548,8 @@ def main(args):
                                                                            n_per_bin=n_per_bin,
                                                                            use=args.use,
                                                                            max_bins=30,
-                                                                           keep_charges=args.keep_charges)
+                                                                           keep_charges=args.keep_charges,
+                                                                           space_group=args.spacegroup)
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
@@ -1597,7 +1619,7 @@ def main(args):
 
     # Write mtz file
     if twin_data:
-        labs = ["F_est"]
+        labs = ["F_est", "F_exp"]
     elif is_int:
         labs = ["I", "SIGI"]
     else:
@@ -1613,7 +1635,7 @@ def main(args):
         labs.append("F_true_est")
     labs += D_labs + ["S"]
     mtz_out = args.output_prefix+".mtz"
-    hkldata.write_mtz(mtz_out, labs=labs, types={"FOM": "W", "FP":"F", "SIGFP":"Q", "F_est": "F"})
+    hkldata.write_mtz(mtz_out, labs=labs, types={"FOM": "W", "FP":"F", "SIGFP":"Q", "F_est": "F", "F_exp": "F"})
     return hkldata
 # main()
 if __name__ == "__main__":

servalcat/xtal/twin.py

@@ -23,7 +23,7 @@ def find_twin_domains_from_data(hkldata, max_oblique=5, min_alpha=0.05):
     if not ops:
         return
     twin_data = ext.TwinData()
-    twin_data.setup(hkldata.miller_array().to_numpy(), hkldata.df.bin, hkldata.sg, hkldata.cell, ops)
+    twin_data.setup(hkldata.miller_array(), hkldata.df.bin, hkldata.sg, hkldata.cell, ops)
     if "I" in hkldata.df:
         Io = hkldata.df.I.to_numpy()
     else:
@@ -37,14 +37,17 @@ def find_twin_domains_from_data(hkldata, max_oblique=5, min_alpha=0.05):
         for i_op, op in enumerate(ops):
             ii = numpy.array(twin_data.pairs(i_op, i_bin))
             val = numpy.all(numpy.isfinite(Io[ii]), axis=1)
-            cc = numpy.corrcoef(Io[ii][val].T)[0,1]
+            if numpy.sum(val) == 0:
+                cc = numpy.nan
+            else:
+                cc = numpy.corrcoef(Io[ii][val].T)[0,1]
             rr = (1 - numpy.sqrt(1 - cc**2)) / cc
             ratios.append(rr)
             ccs[-1].append(cc)
             nums[-1].append(len(val))
-        alphas.append(numpy.array(ratios) / sum(ratios))
+        alphas.append(numpy.array(ratios) / numpy.nansum(ratios))
     alphas = numpy.maximum(0, numpy.mean(alphas, axis=0))
-    alphas /= numpy.sum(alphas)
+    alphas /= numpy.nansum(alphas)
     ccs = numpy.array(ccs)
     nums = numpy.array(nums)
     tmp = [{"Operator": gemmi.Op().triplet(),
@@ -54,7 +57,10 @@ def find_twin_domains_from_data(hkldata, max_oblique=5, min_alpha=0.05):
     for i_op, op in enumerate(ops):
         ii = numpy.array(twin_data.pairs(i_op))
         val = numpy.all(numpy.isfinite(Io[ii]), axis=1)
-        r_obs = numpy.sum(numpy.abs(Io[ii][val, 0] - Io[ii][val, 1])) / numpy.sum(Io[ii][val])
+        if numpy.sum(val) == 0:
+            r_obs = numpy.nan
+        else:
+            r_obs = numpy.sum(numpy.abs(Io[ii][val, 0] - Io[ii][val, 1])) / numpy.sum(Io[ii][val])
         tmp.append({"Operator": op.triplet(),
                     "CC_mean": numpy.sum(nums[:,i_op] * ccs[:,i_op]) / numpy.sum(nums[:,i_op]),
                     "R_twin_obs": r_obs,
@@ -77,7 +83,7 @@ def find_twin_domains_from_data(hkldata, max_oblique=5, min_alpha=0.05):
                                "Alpha": alphas})
         logger.writeln(df.to_string(float_format="%.2f"))
         twin_data = ext.TwinData()
-        twin_data.setup(hkldata.miller_array().to_numpy(), hkldata.df.bin, hkldata.sg, hkldata.cell, ops)
+        twin_data.setup(hkldata.miller_array(), hkldata.df.bin, hkldata.sg, hkldata.cell, ops)
     twin_data.alphas = alphas
     if "I" not in hkldata.df:
         logger.writeln('Generating "observed" intensities for twin refinement: Io = Fo**2, SigIo = 2*F*SigFo')

{servalcat-0.4.88.dist-info → servalcat-0.4.99.dist-info}/METADATA

@@ -1,16 +1,16 @@
 Metadata-Version: 2.1
 Name: servalcat
-Version: 0.4.88
+Version: 0.4.99
 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
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Requires-Dist: packaging
 Requires-Dist: numpy>=1.15
 Requires-Dist: scipy
 Requires-Dist: pandas>=1.1.0
-Requires-Dist: gemmi==0.6.7
+Requires-Dist: gemmi==0.7.0
 Description-Content-Type: text/markdown
 
 # Servalcat
@@ -40,7 +40,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.6.7](https://github.com/project-gemmi/gemmi/releases/tag/v0.6.7). 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 [v0.7.0](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.
 
 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-0.4.99.dist-info/RECORD

@@ -0,0 +1,45 @@
+servalcat/__init__.py,sha256=HJt3p1jXzt-hnlShh1LfxHF3WRNM7hyk1FY-B4EqExc,241
+servalcat/__main__.py,sha256=XUM193aDwZAEQY02VzvZasAzD6AYEM-_A4wqy93KDWE,4190
+servalcat/ext.cp311-win_amd64.pyd,sha256=np_8MkPh1MRhyQTE0KmWptpYz6RoE0OiM0s0P5TCdJY,1335296
+servalcat/refine/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+servalcat/refine/cgsolve.py,sha256=Xz7EwGI-mr4nnbfARyfFjAqbJbPWGH9qNWQ0GpltDuc,3172
+servalcat/refine/refine.py,sha256=P6epHQZLpz3Tl2fuGrdCp6WOxuzvik7YJJTBsd4zuHg,44941
+servalcat/refine/refine_geom.py,sha256=RMfhmBb-jlSFZoMhV3QONev9U2ZuHuPyjSslhECMYXo,11585
+servalcat/refine/refine_spa.py,sha256=BFoJPNhyLVUWl2U2aDufkRJheYmzhnP4iEdE9DZ5JWc,19528
+servalcat/refine/refine_xtal.py,sha256=kI6oqE2u8E82KUqk6zg4Y9JVLC2PIE9LG227rXWlYM8,15017
+servalcat/refine/spa.py,sha256=7aYSnSty0fSe46P_RQ79Bd_8RwD88k3uAaLHVsz6yHc,6616
+servalcat/refine/xtal.py,sha256=qusNpwRdBie9pnHol_NTDgou08reuiERWBujyhREFbc,14893
+servalcat/refmac/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+servalcat/refmac/exte.py,sha256=LRPej2yCZ4RoWJnEQldILEiUED6S_w1lgutWAdhu9_o,9201
+servalcat/refmac/refmac_keywords.py,sha256=WPLDQdk91i5yKZ0QcfaTQ6qL-_qBv7_91eUv4Is9j54,27288
+servalcat/refmac/refmac_wrapper.py,sha256=7FuYyWqN1UvSilFECWOSmWmYObXFLvO49PWkRbwBPHQ,18233
+servalcat/spa/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+servalcat/spa/fofc.py,sha256=DONPNvHPP9odKGNekpo781D_skjReUEytQ1wHBJxGwc,23592
+servalcat/spa/fsc.py,sha256=Rszx-zzJiX5iSY-Qp6q5uCrEhE3a5eyW-m_szT5itLA,17839
+servalcat/spa/localcc.py,sha256=FJMXiC0Po5eb1Le404mgNDj9VcxH5CRR9F5B7uDZn5w,8173
+servalcat/spa/realspcc_from_var.py,sha256=x3NaqGKpGmQyh3qp-SJ9kTA_hP2EvxBOIszYbV2EPKk,5403
+servalcat/spa/run_refmac.py,sha256=bHSj-8_RLdrfHTCyNWoMtXsrNT37AfpONZ8D3jR01ZE,50527
+servalcat/spa/shift_maps.py,sha256=G_EddBcdyncl2bhW7I-4YF0ZFtX9Q95a2SIJ9rpPeR4,13561
+servalcat/spa/shiftback.py,sha256=EtITj8Nllz-MWE6oJrxruDWeT0q7tS3RXCKtpWMuHNg,4801
+servalcat/spa/translate.py,sha256=PGf1vHh_b_mxDta_CAghY7QBRVPzHSaGLDhrnafqCdA,5228
+servalcat/utils/__init__.py,sha256=4umrD2fhG1QAQppDBQM95-6y8QYbtxr7Mi_-Nkc3XOA,1172
+servalcat/utils/commands.py,sha256=fEWF6HesIAuxnzbaKAPws_QaIPxJUQc6DVthHeex_Vk,72503
+servalcat/utils/fileio.py,sha256=3fyHTQ62sibP3cUYtX8D9G7cC6qelkfPKnbA47MqPOo,30246
+servalcat/utils/generate_operators.py,sha256=fCrcTcciRn-6fpFtHYvf1oPXAObjuqR3WQejz5d0RrA,10980
+servalcat/utils/hkl.py,sha256=sMaXJprnceVLDHWfwPSTWmbVbAJEPfj86tF3C0S2g_o,28776
+servalcat/utils/logger.py,sha256=VXSkn54Rp2dxnCQ-Smb5T0NZqysvw8GGb4bKyA8Vuig,4729
+servalcat/utils/maps.py,sha256=1Gm54nEvPj4peCuo0Rx-8_gvRD1pr2qECq7U9N6mrVw,13570
+servalcat/utils/model.py,sha256=YPqYNCPZrbtUPbtMROQUA1RowEC7zrBlUvAEFNfoW5k,30959
+servalcat/utils/refmac.py,sha256=dY92UZo2orgZJOEmPacCek8PMj-ydCp6-pR0rdsAVG8,31682
+servalcat/utils/restraints.py,sha256=hclAJ3CKzIqeyC-I0rH8TSwikwQN1k8dUtYWKC0OAnU,37741
+servalcat/utils/symmetry.py,sha256=PSSD-S_j_t1m4E9F8Fd9RJqTWyKf92zLCjSED7iXFkU,12164
+servalcat/xtal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+servalcat/xtal/french_wilson.py,sha256=u4wzHuotO8-avPkhuEylg9WmMZYdGHYz1IvG07uqW3M,12045
+servalcat/xtal/run_refmac_small.py,sha256=_Rw7wz7_yAlQgDqjJ_njeK6ZqN_r7KAakoor9WeNhxI,10634
+servalcat/xtal/sigmaa.py,sha256=uF552XnFyaBKfN36c8ajMOxFGrW_r3p9FFQ4T5nB1wg,76970
+servalcat/xtal/twin.py,sha256=gsDyyeC5jxsY8wepcB9lnNNPgVCvqlGVj9_kQZkkdWg,5021
+servalcat-0.4.99.dist-info/METADATA,sha256=OxT6LeODHswv4-Yg1Xtv6pjkvHjriRcZNFfq5asJObs,2741
+servalcat-0.4.99.dist-info/WHEEL,sha256=kXCl1J14PkmxQKXf5U_5vxmme_OmC3Ydcral7u0yA3M,106
+servalcat-0.4.99.dist-info/entry_points.txt,sha256=G1mDxhOCdF3umYz4k0kfwJbSdYSKqhvQdGCmrP8FRAY,111
+servalcat-0.4.99.dist-info/licenses/LICENSE,sha256=JoTeFzAOCkNGhvHsf4r2BFIHpLRXo_4EsrnOZV58XVA,17098
+servalcat-0.4.99.dist-info/RECORD,,

{servalcat-0.4.88.dist-info → servalcat-0.4.99.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.10.6
+Generator: scikit-build-core 0.10.7
 Root-Is-Purelib: false
 Tag: cp311-cp311-win_amd64
 

servalcat-0.4.88.dist-info/RECORD

@@ -1,45 +0,0 @@
-servalcat/__init__.py,sha256=J-eWO5IStrvYxM0WSIzvvyPYYjxss2eHwjvBI0SHvTc,241
-servalcat/__main__.py,sha256=XUM193aDwZAEQY02VzvZasAzD6AYEM-_A4wqy93KDWE,4190
-servalcat/ext.cp311-win_amd64.pyd,sha256=bbcmR2_siHbx1spn6lxF9qBeWPlbSDbqqbnUPI6hjvY,2034688
-servalcat/refine/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-servalcat/refine/cgsolve.py,sha256=Xz7EwGI-mr4nnbfARyfFjAqbJbPWGH9qNWQ0GpltDuc,3172
-servalcat/refine/refine.py,sha256=dnpIICEbhUehxuQXoJGuvYfvVGFAIAYp4pWZO5RT-Qs,39113
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