servalcat 0.4.88__tar.gz → 0.4.99__tar.gz

{servalcat-0.4.88 → servalcat-0.4.99}/CMakeLists.txt

@@ -8,11 +8,14 @@ string(REGEX REPLACE "__version__ = '(.+)'" "\\1" serval_version_str ${serval_ve
 project(servalcat LANGUAGES C CXX VERSION ${serval_version_str})
 message(STATUS "Servalcat version ${PROJECT_VERSION}")
 
+option(SEARCH_INSTALLED_GEMMI "Search for gemmi-config.cmake and use it if found" ON)
+option(INSTALL_GEMMI_IF_BUILT "Install also Python module gemmi, if it was built" OFF)
+
 include(GNUInstallDirs)
 
 if (DEFINED SKBUILD)  # building with scikit-build-core (pip install)
   set(PYTHON_INSTALL_DIR "${SKBUILD_PLATLIB_DIR}")
-  set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}")
+  #set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}")
 endif()
 
 set(CMAKE_CXX_EXTENSIONS OFF)
@@ -28,6 +31,7 @@ if (NOT CMAKE_BUILD_TYPE AND NOT USING_ENV_CXXFLAGS)
       FORCE)
 endif()
 
+
 # CMake >=3.18 has subcomponent Development.Module, scikit-build-core also has it
 if (${CMAKE_VERSION} VERSION_LESS 3.18 AND NOT SKBUILD)
   find_package(Python ${PYTHON_VERSION} REQUIRED COMPONENTS Interpreter Development)
@@ -35,13 +39,14 @@ else()
   find_package(Python ${PYTHON_VERSION} REQUIRED COMPONENTS Interpreter Development.Module)
 endif()
 
-# use pybind11-config (if available) to determine pybind11_DIR
-execute_process(COMMAND pybind11-config --cmakedir OUTPUT_VARIABLE pybind11_DIR)
-string(STRIP "${pybind11_DIR}" pybind11_DIR)
-find_package(pybind11 2.6 CONFIG REQUIRED)
-message(STATUS "Found pybind11 ${pybind11_VERSION}: ${pybind11_INCLUDE_DIRS}")
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+  OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE NB_DIR)
+list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+find_package(nanobind 2.2.0 CONFIG REQUIRED)
+message(STATUS "Found nanobind ${nanobind_VERSION}: ${NB_DIR}")
 
-pybind11_add_module(ext src/ext.cpp src/intensity.cpp src/amplitude.cpp src/refine.cpp src/twin.cpp)
+nanobind_add_module(ext src/ext.cpp src/intensity.cpp src/amplitude.cpp src/refine.cpp src/twin.cpp)
 
 if (EXISTS "${CMAKE_HOME_DIRECTORY}/eigen/Eigen")
   include_directories("${CMAKE_CURRENT_SOURCE_DIR}/eigen")
@@ -52,31 +57,46 @@ else()
   target_link_libraries(ext PRIVATE Eigen3::Eigen)
 endif()
 
-if (DEFINED SKBUILD)
-  if (WIN32)
-    # Gemmi is installed in an overlay directory in virtualenv.
-    # For now, locate it relatively to pybind11.
-    get_filename_component(gemmi_ROOT "${pybind11_INCLUDE_DIR}/../../../.." ABSOLUTE)
+# We need either gemmi C++ development files (headers, library, cmake config)
+# or gemmi sources. If we have the former with a shared library, it may require
+# extra effort to make sure that the shared library is found at runtime.
+if (SEARCH_INSTALLED_GEMMI)
+  find_package(gemmi 0.7.0 CONFIG)
+endif()
+if (gemmi_FOUND)
+  message(STATUS "  based on config from ${gemmi_DIR}")
+  get_target_property(gemmi_TYPE gemmi::gemmi_cpp TYPE)
+  if (${gemmi_TYPE} STREQUAL "SHARED_LIBRARY")
+    message(STATUS "** Servalcat Python module will be linked with gemmi shared library.  **")
+    message(STATUS "** The module may require 'repairing' to find the library at runtime. **")
   endif()
-  find_package(gemmi 0.6.7 CONFIG REQUIRED)
 else()
   set(USE_PYTHON ON CACHE BOOL "" FORCE)
+  set(BUILD_GEMMI_PROGRAM OFF CACHE BOOL "" FORCE)
+  set(INSTALL_DEV_FILES OFF CACHE BOOL "" FORCE)
+  set(BUILD_SHARED_LIBS OFF CACHE BOOL "" FORCE)
   message(STATUS "")
   message(STATUS "Configuring GEMMI...")
+  if (INSTALL_GEMMI_IF_BUILT AND NOT gemmi_FOUND)
+    set(exclude_or_not)
+  else()
+    set(exclude_or_not EXCLUDE_FROM_ALL)
+  endif()
   if (EXISTS "${CMAKE_HOME_DIRECTORY}/gemmi/include/gemmi")
     message(STATUS "Using ${CMAKE_HOME_DIRECTORY}/gemmi (internal copy).")
-    add_subdirectory(gemmi EXCLUDE_FROM_ALL)
+    add_subdirectory(gemmi ${exclude_or_not})
   else()
+    message(STATUS "Using FetchContent...")
     include(FetchContent)
     FetchContent_Declare(
       gemmi
       GIT_REPOSITORY https://github.com/project-gemmi/gemmi.git
-      GIT_TAG        v0.6.7
+      GIT_TAG        v0.7.0
     )
     FetchContent_GetProperties(gemmi)
     if (NOT gemmi_POPULATED)
       FetchContent_Populate(gemmi)
-      add_subdirectory(${gemmi_SOURCE_DIR} ${gemmi_BINARY_DIR} EXCLUDE_FROM_ALL)
+      add_subdirectory(${gemmi_SOURCE_DIR} ${gemmi_BINARY_DIR} ${exclude_or_not})
     endif()
   endif()
   add_dependencies(ext gemmi_py)

{servalcat-0.4.88 → servalcat-0.4.99}/PKG-INFO

@@ -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-0.4.88 → servalcat-0.4.99}/README.md

@@ -25,7 +25,7 @@ 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-0.4.88 → servalcat-0.4.99}/pyproject.toml

@@ -1,16 +1,13 @@
 [build-system]
-requires = ["scikit-build-core~=0.10.5", "pybind11>=2.6.2",
-            "pybind11-stubgen~=2.5.1",
-            "gemmi @ git+https://github.com/project-gemmi/gemmi.git@v0.6.7",
-]
+requires = ["scikit-build-core~=0.10.7", "nanobind >=2.2"]
 build-backend = "scikit_build_core.build"
 
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 [project]
 name = "servalcat"
 dynamic = ["version"]
-requires-python = ">=3.7"
-dependencies = ['packaging', 'numpy>=1.15', 'scipy', 'pandas>=1.1.0', 'gemmi==0.6.7']
+requires-python = ">=3.8"
+dependencies = ['packaging', 'numpy>=1.15', 'scipy', 'pandas>=1.1.0', 'gemmi==0.7.0']
 description="Structure refinement and validation for crystallography and single particle analysis"
 readme = "README.md"
 authors = [
@@ -28,7 +25,7 @@ refmacat  = "servalcat.refmac.refmac_wrapper:command_line"
 #build-dir = "/tmp/gemmi_build2/{wheel_tag}"
 wheel.expand-macos-universal-tags = true  # not sure if this is useful
 cmake.build-type = "Release"
-cmake.verbose = true
+build.verbose = true
 sdist.include = ["eigen/Eigen", "eigen/README.md", "eigen/COPYING*"]
 sdist.exclude = [".*", "eigen/", "scripts/"]
 
@@ -39,9 +36,14 @@ input = "servalcat/__init__.py"
 [tool.cibuildwheel]
 # increase pip debugging output
 build-verbosity = 2
-test-command = "python {project}/tests/test_for_ci.py"
+test-command = "python {project}/tests/test_for_ci.py" # comment out to test with gemmi build
 [tool.cibuildwheel.environment]
-SKBUILD_CMAKE_ARGS = '-DBUILD_SHARED_LIBS=OFF;-DINSTALL_DEV_FILES=ON;-DGENERATE_STUBS=OFF'
+SKBUILD_CMAKE_ARGS = '-DGENERATE_STUBS=OFF' # -DINSTALL_GEMMI_IF_BUILT=1 to test with gemmi build
+
+# Needed for full C++17 support on macOS
+[tool.cibuildwheel.macos.environment]
+MACOSX_DEPLOYMENT_TARGET = "10.14"
+SKBUILD_CMAKE_ARGS = '-DGENERATE_STUBS=OFF' # -DINSTALL_GEMMI_IF_BUILT=1 to test with gemmi build
 
 [tool.codespell]
 skip = './eigen,./gemmi,*.pdb,*.crd,*.cif,*.mmcif,*.ent,*.log*,*.dic,tags,*.bak,*build*,*~'

{servalcat-0.4.88 → servalcat-0.4.99}/servalcat/__init__.py

@@ -6,5 +6,5 @@ This software is released under the
 Mozilla Public License, version 2.0; see LICENSE.
 """
 
-__version__ = '0.4.88'
-__date__ = '2024-09-13'
+__version__ = '0.4.99'
+__date__ = '2024-12-04'

{servalcat-0.4.88 → servalcat-0.4.99}/servalcat/refine/refine.py

@@ -28,7 +28,7 @@ b_to_u = utils.model.b_to_u
 #atexit.register(profile.print_stats)
 
 class Geom:
-    def __init__(self, st, topo, monlib, adpr_w=1, shake_rms=0,
+    def __init__(self, st, topo, monlib, adpr_w=1, occr_w=1, shake_rms=0,
                  params=None, unrestrained=False, use_nucleus=False,
                  ncslist=None, atom_pos=None):
         self.st = st
@@ -53,7 +53,7 @@ class Geom:
             n_sym = len(images) + 1
             self.geom.specials.append(ext.Geometry.Special(atom, matp, mata, n_sym))
         self.adpr_w = adpr_w
-        self.occr_w = 1.
+        self.occr_w = occr_w
         self.unrestrained = unrestrained
         if shake_rms > 0:
             numpy.random.seed(0)
@@ -225,6 +225,26 @@ def write_stats_json_safe(stats, json_out):
     logger.writeln(f"Refinement statistics saved: {json_out}")
 # write_stats_json_safe()
 
+def print_h_options(h_change, h_present, refine_h, hout, geom_only):
+    if not h_present:
+        h_change = gemmi.HydrogenChange.Remove
+    logger.writeln("Hydrogen related options")
+    logger.write(" use in refinement{}: hydrogen atoms ".format("" if geom_only else "/map calculation"))
+    logger.writeln({gemmi.HydrogenChange.ReAddButWater: "have been (re)generated",
+                    gemmi.HydrogenChange.ReAdd:         "(including water) have been (re)generated",
+                    gemmi.HydrogenChange.ReAddKnown:    "(except for rotatable) have been (re) generated",
+                    gemmi.HydrogenChange.NoChange:      "from the input model have been retained",
+                    gemmi.HydrogenChange.Remove:        "have either been removed or were not present"}[h_change])
+    if h_present:
+        logger.write(" target: hydrogen atoms will be ")
+        if geom_only or not refine_h:
+            logger.writeln("just optimized according to geometric restraints")
+        else:
+            logger.writeln("refined against experimental data")
+    logger.writeln(" in output model: " + ("written" if hout and h_present else "not written"))
+    logger.writeln("")
+# print_hydrogen_options()
+
 class GroupOccupancy:
     # TODO max may not be one. should check multiplicity
     def __init__(self, st, params):
@@ -293,6 +313,7 @@ class GroupOccupancy:
         vals = []
         for _, atoms in self.groups:
             occ = numpy.mean([a.occ for a in atoms])
+            occ = min(1, max(1e-3, occ))
             vals.append(occ)
         for is_comp, idxes in self.consts:
             sum_occ = sum(vals[i] for i in idxes)
@@ -311,6 +332,7 @@ class GroupOccupancy:
         for p, (_, atoms) in zip(x, self.groups):
             for a in atoms:
                 a.occ = p
+                #a.occ = max(1, min(1e-3, p))
 
     def target(self, x, ll, ls, u):
         self.set_x(x)
@@ -425,7 +447,7 @@ class Refine:
             self.geom.set_h_parents()
         if params and params.get("write_trajectory"):
             self.st_traj = self.st.clone()
-            self.st_traj[-1].name = "0"
+            self.st_traj[-1].num = 0
         assert self.geom.group_occ.groups or self.n_params() > 0
     # __init__()
     
@@ -442,6 +464,9 @@ class Refine:
                 logger.writeln("  sigmas: {}".format(" ".join("{:.2f}".format(x) for x in g.adpr_kl_sigs)))
             else:
                 raise LookupError("unknown adpr_mode")
+        if self.refine_occ:
+            logger.writeln(" Occupancy restraints")
+            logger.writeln("  weight: {}".format(self.geom.occr_w))
 
     def scale_shifts(self, dx, scale):
         n_atoms = self.geom.n_refine_atoms
@@ -525,7 +550,7 @@ class Refine:
             elif self.adp_mode == 2:
                 a = x[offset_b + 6 * j: offset_b + 6 * (j+1)]
                 a = gemmi.SMat33d(*a)
-                M = numpy.array(a.as_mat33())
+                M = a.as_mat33().array
                 v, Q = numpy.linalg.eigh(M) # eig() may return complex due to numerical precision?
                 v = numpy.maximum(v, 0.5) # avoid NPD with minimum B = 0.5
                 M2 = Q.dot(numpy.diag(v)).dot(Q.T)
@@ -736,7 +761,7 @@ class Refine:
                     weight /= 1.1
             if self.st_traj is not None:
                 self.st_traj.add_model(self.st[0])
-                self.st_traj[-1].name = str(len(self.st_traj))
+                self.st_traj[-1].num = len(self.st_traj)
             if stats_json_out:
                 write_stats_json_safe(stats, stats_json_out)
 
@@ -781,43 +806,101 @@ class Refine:
         lstr = utils.make_loggraph_str(df, "stats vs cycle", forplot,
                                        float_format="{:.4f}".format)
         logger.writeln(lstr)
-        self.update_meta(stats[-1])
         return stats
 
-    def update_meta(self, stats):
-        # TODO write stats. probably geom.reporting.get_summary_table should return with _refine_ls_restr.type names
-        # should remove st.mod_residues?
-        self.st.helices.clear()
-        self.st.sheets.clear()
-        raw_remarks = [f'REMARK   3',
-                       f'REMARK   3 REFINEMENT.',
-                       f'REMARK   3   PROGRAM     : SERVALCAT {servalcat.__version__}',
-                       f'REMARK   3   AUTHORS     : YAMASHITA,MURSHUDOV',
-                       f'REMARK   3',
-                       ]
-        si = gemmi.SoftwareItem()
-        si.classification = gemmi.SoftwareItem.Classification.Refinement
-        si.name = "Servalcat"
-        si.version = servalcat.__version__
-        si.date = servalcat.__date__
-        self.st.meta.software = [si]
-
-        ri = gemmi.RefinementInfo()
-        if "geom" in stats:
-            restr_stats = []
-            raw_remarks.append("REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT")
-            for k, n, l, pl in (("r.m.s.d.", "Bond distances, non H", "s_bond_nonh_d", "BOND LENGTHS REFINED ATOMS        (A)"),
-                                ("r.m.s.d.", "Bond angles, non H", "s_angle_nonh_d", "BOND ANGLES REFINED ATOMS   (DEGREES)")):
-                if k in stats["geom"]["summary"] and n in stats["geom"]["summary"][k]:
-                    rr = gemmi.RefinementInfo.Restr(l)
-                    rr.dev_ideal = stats["geom"]["summary"][k].get(n)
-                    rr.count = stats["geom"]["summary"]["N restraints"].get(n)
-                    rr.weight = stats["geom"]["summary"]["Mn(sigma)"].get(n)
-                    restr_stats.append(rr)
-                    raw_remarks.append(f"REMARK   3   {pl}:{rr.count:6d} ;{rr.dev_ideal:6.3f} ;{rr.weight:6.3f}")
-            ri.restr_stats = restr_stats
-            raw_remarks.append("REMARK   3")
-        self.st.meta.refinement = [ri]
-        self.st.raw_remarks = raw_remarks
-
 # class Refine
+
+def update_meta(st, stats, ll=None):
+    # TODO write stats. probably geom.reporting.get_summary_table should return with _refine_ls_restr.type names
+    # should remove st.mod_residues?
+    st.helices.clear()
+    st.sheets.clear()
+    raw_remarks = [f'REMARK   3',
+                   f'REMARK   3 REFINEMENT.',
+                   f'REMARK   3   PROGRAM     : SERVALCAT {servalcat.__version__}',
+                   f'REMARK   3   AUTHORS     : YAMASHITA,MURSHUDOV',
+                   f'REMARK   3',
+                   ]
+    si = gemmi.SoftwareItem()
+    si.classification = gemmi.SoftwareItem.Classification.Refinement
+    si.name = "Servalcat"
+    si.version = servalcat.__version__
+    si.date = servalcat.__date__
+    st.meta.software = [si]
+
+    ri = gemmi.RefinementInfo()
+    if "geom" in stats:
+        restr_stats = []
+        raw_remarks.append("REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT")
+        for k, n, l, pl in (("r.m.s.d.", "Bond distances, non H", "s_bond_nonh_d",             "BOND LENGTHS REFINED ATOMS        (A)"),
+                            ("r.m.s.d.", "Bond angles, non H", "s_angle_nonh_deg",             "BOND ANGLES REFINED ATOMS   (DEGREES)"),
+                            ("r.m.s.d.", "Torsion angles, period 1", "s_dihedral_angle_1_deg", "TORSION ANGLES, PERIOD 1    (DEGREES)"),
+                            ("r.m.s.d.", "Torsion angles, period 2", "s_dihedral_angle_2_deg", "TORSION ANGLES, PERIOD 2    (DEGREES)"),
+                            ("r.m.s.d.", "Torsion angles, period 3", "s_dihedral_angle_3_deg", "TORSION ANGLES, PERIOD 3    (DEGREES)"),
+                            ("r.m.s.d.", "Torsion angles, period 6", "s_dihedral_angle_6_deg", "TORSION ANGLES, PERIOD 6    (DEGREES)"),
+                            ("r.m.s.d.", "Chiral centres", "s_chiral_restr",                   "CHIRAL-CENTER RESTRAINTS       (A**3)"),
+                            ("r.m.s.d.", "Planar groups", "s_planes",                          "GENERAL PLANES REFINED ATOMS      (A)"),
+                            ("r.m.s.d.", "VDW nonbonded", "s_nbd",                             ""),
+                            ("r.m.s.d.", "VDW torsion", "s_nbtor",                             ""),
+                            ("r.m.s.d.", "VDW hbond", "s_hbond_nbd",                           ""),
+                            ("r.m.s.d.", "VDW metal", "s_metal_ion",                           ""),
+                            ("r.m.s.d.", "VDW dummy", "s_dummy_nbd",                           ""),
+                            ("r.m.s.d.", "VDW nonbonded, symmetry", "s_symmetry_nbd",          ""),
+                            ("r.m.s.d.", "VDW torsion, symmetry", "s_symmetry_nbtor",          ""),
+                            ("r.m.s.d.", "VDW hbond, symmetry", "s_symmetry_hbond_nbd",        ""),
+                            ("r.m.s.d.", "VDW metal, symmetry", "s_symmetry_metal_ion",        ""),
+                            ("r.m.s.d.", "VDW dummy, symmetry", "s_symmetry_dummy_nbd",        "")):
+            if k in stats["geom"]["summary"] and n in stats["geom"]["summary"][k]:
+                rr = gemmi.RefinementInfo.Restr(l)
+                rr.dev_ideal = round(stats["geom"]["summary"][k].get(n), 4)
+                rr.count = stats["geom"]["summary"]["N restraints"].get(n)
+                rr.weight = round(stats["geom"]["summary"]["Mn(sigma)"].get(n), 4)
+                restr_stats.append(rr)
+                if pl:
+                    raw_remarks.append(f"REMARK   3   {pl}:{rr.count:6d} ;{rr.dev_ideal:6.3f} ;{rr.weight:6.3f}")
+        ri.restr_stats = restr_stats
+        raw_remarks.append("REMARK   3")
+    if ll is not None:
+        ri.id = ll.refine_id()
+        ri.mean_b = round(numpy.mean([cra.atom.b_iso for cra in st[0].all()]), 2)
+        if ll.b_aniso is not None:
+            ri.aniso_b = ll.b_aniso
+        for k, kd, nd in (("Rwork", "r_work", 4), ("Rfree", "r_free", 4), ("R", "r_all", 4),
+                          ("FSCaverage", "fsc_work", 4),
+                          ("FSCaverage_half1", "fsc_work", 4), ("FSCaverage_half2", "fsc_free", 4)):
+            if k in stats["data"]["summary"]:
+                setattr(ri, kd, round(stats["data"]["summary"][k], nd))
+        bins = []
+        n_all = 0
+        for b in stats["data"]["binned"]:
+            bri = gemmi.BasicRefinementInfo()
+            bri.resolution_high = round(b["d_min"], 3)
+            bri.resolution_low = round(b["d_max"], 3)
+            for k, kd, nd in (("Rwork", "r_work", 4), ("Rfree", "r_free", 4),
+                              ("R1work", "r_work", 4), ("R1free", "r_free", 4),
+                              ("R", "r_all", 4), ("R1", "r_all", 4),
+                              ("CCI", "cc_intensity_work", 4), ("CCF", "cc_fo_fc_work", 4),
+                              ("CCIwork", "cc_intensity_work", 4), ("CCIfree", "cc_intensity_free", 4),
+                              ("CCFwork", "cc_fo_fc_work", 4), ("CCFfree", "cc_fo_fc_free", 4),
+                              ("fsc_FC_full", "fsc_work", 4), ("fsc_model", "fsc_work", 4),
+                              ("fsc_model_half1", "fsc_work", 4), ("fsc_model_half2", "fsc_free", 4),
+                              ("n_work", "work_set_count", 0), ("n_free", "rfree_set_count", 0),
+                              ("n_obs", "reflection_count", 0), ("ncoeffs", "reflection_count", 0)):
+                if k in b: setattr(bri, kd, round(b[k], nd))
+            if "n_all" in b and "n_obs" in b:
+                bri.completeness = round(b["n_obs"] / b["n_all"] * 100, 2)
+                n_all += b["n_all"]
+            bins.append(bri)
+        ri.rfree_set_count = max(-1, sum(b.rfree_set_count for b in bins))
+        ri.work_set_count = max(-1, sum(b.work_set_count for b in bins))
+        ri.reflection_count = max(-1, sum(b.reflection_count for b in bins))
+        ri.resolution_high = round(min(b.resolution_high for b in bins), 3)
+        ri.resolution_low = round(max(b.resolution_low for b in bins), 3)
+        if ri.reflection_count > 0 and n_all > 0:
+            ri.completeness = round(ri.reflection_count / n_all * 100, 2)
+        ri.bins = bins
+        if ri.rfree_set_count > 0:
+            ri.cross_validation_method = "THROUGHOUT"
+    st.meta.refinement = [ri]
+    st.raw_remarks = raw_remarks
+# update_meta()

{servalcat-0.4.88 → servalcat-0.4.99}/servalcat/refine/refine_geom.py

@@ -14,7 +14,7 @@ import json
 import servalcat # for version
 from servalcat.utils import logger
 from servalcat import utils
-from servalcat.refine.refine import Geom, Refine, convert_stats_to_dicts
+from servalcat.refine.refine import Geom, Refine, convert_stats_to_dicts, update_meta, print_h_options
 from servalcat.refmac import refmac_keywords
 
 def add_arguments(parser):
@@ -93,9 +93,14 @@ def refine_and_update_dictionary(cif_in, monomer_dir, output_prefix, randomize=0
         if len(st) > 0: break
     else:
         raise SystemExit("No model in the cif file")
-    monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir, # monlib is needed for ener_lib
-                                                   cif_files=[cif_in],
-                                                   stop_for_unknowns=True)
+    for i in range(len(st)-1):
+        del st[1]
+    try:
+        monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir, # monlib is needed for ener_lib
+                                                       cif_files=[cif_in],
+                                                       stop_for_unknowns=True)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
     all_stats = []
     for i_macro in 0, 1:
         try:
@@ -121,16 +126,19 @@ def refine_and_update_dictionary(cif_in, monomer_dir, output_prefix, randomize=0
     for row in block.find("_chem_comp_atom.", ["atom_id", "?x", "?y", "?z",
                                                "?pdbx_model_Cartn_x_ideal",
                                                "?pdbx_model_Cartn_y_ideal",
-                                               "?pdbx_model_Cartn_z_ideal"]):
+                                               "?pdbx_model_Cartn_z_ideal",
+                                               "?model_Cartn_x", "?model_Cartn_y", "?model_Cartn_z"]):
         p = pos[row.str(0)]
         for i in range(3):
             if row.has(i+1):
                 row[i+1] = "{:.3f}".format(p[i])
             if row.has(i+4):
                 row[i+4] = "{:.3f}".format(p[i])
+            if row.has(i+7):
+                row[i+7] = "{:.3f}".format(p[i])
     # add description
     add_program_info_to_dictionary(block, st[0][0][0].name)
-    doc.write_file(output_prefix + "_updated.cif", style=gemmi.cif.Style.Aligned)
+    doc.write_file(output_prefix + "_updated.cif", options=gemmi.cif.Style.Aligned)
     logger.writeln("Updated dictionary saved: {}".format(output_prefix + "_updated.cif"))
     with open(output_prefix + "_stats.json", "w") as ofs:
         json.dump([convert_stats_to_dicts(x) for x in all_stats],
@@ -147,11 +155,13 @@ def refine_geom(model_in, monomer_dir, cif_files, h_change, ncycle, output_prefi
         logger.writeln("Take NCS constraints into account.")
         st2.expand_ncs(gemmi.HowToNameCopiedChain.Dup, merge_dist=0)
         utils.fileio.write_model(st2, file_name="input_expanded.pdb")
-
-    monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir,
-                                                   cif_files=cif_files,
-                                                   stop_for_unknowns=True,
-                                                   params=params)
+    try:
+        monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir,
+                                                       cif_files=cif_files,
+                                                       stop_for_unknowns=True,
+                                                       params=params)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
     utils.restraints.find_and_fix_links(st, monlib, find_metal_links=find_links,
                                         add_found=find_links) # should remove unknown id here?
     try:
@@ -161,6 +171,8 @@ def refine_geom(model_in, monomer_dir, cif_files, h_change, ncycle, output_prefi
     except RuntimeError as e:
         raise SystemExit("Error: {}".format(e))
 
+    print_h_options(h_change, st[0].has_hydrogen(), refine_h=True, hout=True, geom_only=True)
+        
     if use_ncsr:
         ncslist = utils.restraints.prepare_ncs_restraints(st)
     else:
@@ -169,6 +181,7 @@ def refine_geom(model_in, monomer_dir, cif_files, h_change, ncycle, output_prefi
     refiner = Refine(st, geom, params=params)
     stats = refiner.run_cycles(ncycle,
                                stats_json_out=output_prefix + "_stats.json")
+    update_meta(st, stats[-1])
     refiner.st.name = output_prefix
     utils.fileio.write_model(refiner.st, output_prefix, pdb=True, cif=True)
     if params["write_trajectory"]: