Merge pull request #122 from rigdenlab/uglymol_change

Removed generation of map files following uglymol update

simbad/command_line/__init__.py

@@ -603,8 +603,6 @@ def make_output_dir(run_dir, output_dir, csv, mr_program):
                 os.path.join(mr_workdir, "refine", "{0}_refinement_output.pdb".format(pdb_code)),
                 os.path.join(mr_workdir, "refine", "{0}_refinement_output.mtz".format(pdb_code)),
                 os.path.join(mr_workdir, "refine", "{0}_ref.log".format(pdb_code)),
-                os.path.join(mr_workdir, "refine", "{0}_refmac_2fofcwt.map".format(pdb_code)),
-                os.path.join(mr_workdir, "refine", "{0}_refmac_fofcwt.map".format(pdb_code)),
             ]
             for f in files_to_copy:
                 shutil.copy(f, pdb_output_path)

simbad/mr/__init__.py

@@ -383,9 +383,6 @@ def generate_script(self, result):
         ref_logfile = os.path.join(ref_workdir, "{0}_ref.log".format(result.pdb_code))
         ref_pdbout = os.path.join(ref_workdir, "{0}_refinement_output.pdb".format(result.pdb_code))
 
-        diff_mapout1 = os.path.join(ref_workdir, "{0}_refmac_2fofcwt.map".format(result.pdb_code))
-        diff_mapout2 = os.path.join(ref_workdir, "{0}_refmac_fofcwt.map".format(result.pdb_code))
-
         if isinstance(result, (AmoreRotationScore, PhaserRotationScore)):
             pdb_struct = PdbStructure.from_file(result.dat_path)
             mr_pdbin = os.path.join(self.output_dir, result.pdb_code + ".pdb")
@@ -478,22 +475,13 @@ def generate_script(self, result):
 
         if self.refine_program == "refmac5":
             ref_cmd += ["-refinement_type", self.refine_type]
+
         # ====
         # Create a run script - prefix __needs__ to contain mr_program so we can find log
         # Leave order of this as SGE does not like scripts with numbers as first char
         # ====
         prefix, stem = self.mr_program + "_", result.pdb_code
 
-        fft_cmd1, fft_stdin1 = self.fft(ref_hklout, diff_mapout1, "2mfo-dfc")
-        run_stdin_1 = tmp_file(directory=self.output_dir, prefix=prefix, stem=stem, suffix="_1.stdin")
-        with open(run_stdin_1, "w") as f_out:
-            f_out.write(fft_stdin1)
-
-        fft_cmd2, fft_stdin2 = self.fft(ref_hklout, diff_mapout2, "mfo-dfc")
-        run_stdin_2 = tmp_file(directory=self.output_dir, prefix=prefix, stem=stem, suffix="_2.stdin")
-        with open(run_stdin_2, "w") as f_out:
-            f_out.write(fft_stdin2)
-
         ccp4_scr = os.environ["CCP4_SCR"]
         if self.tmp_dir:
             tmp_dir = os.path.join(self.tmp_dir)
@@ -507,8 +495,6 @@ def generate_script(self, result):
             [EXPORT, "CCP4_SCR=" + tmp_dir],
             mr_cmd + [os.linesep],
             ref_cmd + [os.linesep],
-            fft_cmd1 + ["<", run_stdin_1, os.linesep],
-            fft_cmd2 + ["<", run_stdin_2, os.linesep],
             [EXPORT, "CCP4_SCR=" + ccp4_scr],
         ]
         run_script = Script(directory=self.output_dir, prefix=prefix, stem=stem)
@@ -576,57 +562,6 @@ def anomalous_data_present(self):
         else:
             return False
 
-    @staticmethod
-    def fft(hklin, mapout, map_type):
-        """Function to run fft to generate difference maps for uglymol
-
-        Parameters
-        ----------
-        hklin : str
-           Path to input HKL file
-        mapout : str
-           Path to output MAP file
-        map_type : str
-           Define type of run, either mfo-dfc or 2mfo-dfc
-
-        Returns
-        -------
-        list
-           cmd
-        str
-           stdin
-
-        Raises
-        ------
-        ValueError
-           Unknown map type
-
-        """
-
-        cmd = [CMD_PREFIX, "fft", "hklin", hklin, "mapout", mapout]
-        if map_type == "2mfo-dfc":
-            stdin = (
-                "title Sigmaa style 2mfo-dfc map calculated with refmac coefficients"
-                + os.linesep
-                + "labi F1=FWT PHI=PHWT"
-                + os.linesep
-                + "end"
-                + os.linesep
-            )
-        elif map_type == "mfo-dfc":
-            stdin = (
-                "title Sigmaa style mfo-dfc map calculated with refmac coefficients"
-                + os.linesep
-                + "labi F1=DELFWT PHI=PHDELWT"
-                + os.linesep
-                + "end"
-                + os.linesep
-            )
-        else:
-            msg = "Unknown map type!"
-            raise ValueError(msg)
-        return cmd, stdin
-
     def summarize(self, csv_file):
         """Summarize the search results
 

simbad/mr/anomalous_util.py

@@ -70,7 +70,7 @@ def work_dir(self, work_dir):
         self._work_dir = work_dir
 
     def run(self, input_model, cleanup=True):
-        """Function to run SFALL/CAD/FFT to create phased anomalous fourier map"""
+        """Function to run ANODE to create phased anomalous fourier map"""
         if not os.path.isdir(self.work_dir):
             os.mkdir(self.work_dir)
 

simbad/util/pyrvapi_results.py

@@ -362,13 +362,11 @@ def create_lattice_results_tab(self, lattice_results, lattice_mr_results, result
                     ref_pdb = os.path.join(mr_workdir, "{0}_refinement_output.pdb".format(pdb_code))
                     ref_mtz = os.path.join(mr_workdir, "{0}_refinement_output.mtz".format(pdb_code))
                     ref_log = os.path.join(mr_workdir, "{0}_ref.log".format(pdb_code))
-                    ref_map = os.path.join(mr_workdir, "{0}_refmac_2fofcwt.map".format(pdb_code))
-                    diff_map = os.path.join(mr_workdir, "{0}_refmac_fofcwt.map".format(pdb_code))
 
-                    pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
+                    pdb, mtz, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, mr_log, ref_log]))
 
-                    self.store_entry_in_rvapi_meta(i + 1, "latt", pdb_code, pdb, mtz, map_, dmap, False)
-                    self.output_result_files(download_sec, dmap, map_, mtz, pdb)
+                    self.store_entry_in_rvapi_meta(i + 1, "latt", pdb_code, pdb, mtz, False)
+                    self.output_result_files(download_sec, mtz, pdb)
                     self.output_log_files(logfile_sec, mr_log, ref_log)
 
                 except KeyError:
@@ -382,16 +380,14 @@ def create_lattice_results_tab(self, lattice_results, lattice_mr_results, result
                     ref_pdb = os.path.join(self.work_dir, "latt", "mr_search", "mr_models", "{}.pdb".format(pdb_code))
                     ref_mtz = None
                     ref_log = None
-                    ref_map = None
-                    diff_map = None
-                    pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
+                    pdb, mtz, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, mr_log, ref_log]))
 
                     if i == 0:
                         best = True
                     else:
                         best = False
 
-                    self.store_entry_in_rvapi_meta(i + 1, "latt", pdb_code, pdb, mtz, map_, dmap, best)
+                    self.store_entry_in_rvapi_meta(i + 1, "latt", pdb_code, pdb, mtz, best)
                 except KeyError:
                     logger.debug("No result found at position %s", (i + 1))
 
@@ -471,13 +467,11 @@ def create_contaminant_results_tab(self, contaminant_results, contaminant_mr_res
                     ref_pdb = os.path.join(mr_workdir, "{0}_refinement_output.pdb".format(pdb_code))
                     ref_mtz = os.path.join(mr_workdir, "{0}_refinement_output.mtz".format(pdb_code))
                     ref_log = os.path.join(mr_workdir, "{0}_ref.log".format(pdb_code))
-                    ref_map = os.path.join(mr_workdir, "{0}_refmac_2fofcwt.map".format(pdb_code))
-                    diff_map = os.path.join(mr_workdir, "{0}_refmac_fofcwt.map".format(pdb_code))
 
-                    pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
+                    pdb, mtz, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, mr_log, ref_log]))
 
-                    self.store_entry_in_rvapi_meta(i + 1, "cont", pdb_code, pdb, mtz, map_, dmap, False)
-                    self.output_result_files(download_sec, dmap, map_, mtz, pdb)
+                    self.store_entry_in_rvapi_meta(i + 1, "cont", pdb_code, pdb, mtz, False)
+                    self.output_result_files(download_sec, mtz, pdb)
                     self.output_log_files(logfile_sec, mr_log, ref_log)
 
                 except KeyError:
@@ -559,13 +553,11 @@ def create_morda_db_results_tab(self, morda_db_results, morda_db_mr_results, res
                     ref_pdb = os.path.join(mr_workdir, "{0}_refinement_output.pdb".format(pdb_code))
                     ref_mtz = os.path.join(mr_workdir, "{0}_refinement_output.mtz".format(pdb_code))
                     ref_log = os.path.join(mr_workdir, "{0}_ref.log".format(pdb_code))
-                    ref_map = os.path.join(mr_workdir, "{0}_refmac_2fofcwt.map".format(pdb_code))
-                    diff_map = os.path.join(mr_workdir, "{0}_refmac_fofcwt.map".format(pdb_code))
 
-                    pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
+                    pdb, mtz, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, mr_log, ref_log]))
 
-                    self.store_entry_in_rvapi_meta(i + 1, "full", pdb_code, pdb, mtz, map_, dmap, False)
-                    self.output_result_files(download_sec, dmap, map_, mtz, pdb)
+                    self.store_entry_in_rvapi_meta(i + 1, "full", pdb_code, pdb, mtz, False)
+                    self.output_result_files(download_sec, mtz, pdb)
                     self.output_log_files(logfile_sec, mr_log, ref_log)
 
                 except KeyError:
@@ -640,9 +632,7 @@ def display_summary_tab(self):
             mr_log = os.path.join(mr_workdir, "{0}_mr.log".format(pdb_code))
             ref_log = os.path.join(mr_workdir, "{0}_ref.log".format(pdb_code))
             ref_pdb = os.path.join(mr_workdir, "{0}_refinement_output.pdb".format(pdb_code))
-            ref_map = os.path.join(mr_workdir, "{0}_refmac_2fofcwt.map".format(pdb_code))
             ref_mtz = os.path.join(mr_workdir, "{0}_refinement_output.mtz".format(pdb_code))
-            diff_map = os.path.join(mr_workdir, "{0}_refmac_fofcwt.map".format(pdb_code))
 
             msg = "The best search model found by SIMBAD was {0}. \
                    This gave an R/Rfact of {1:.3f} and an R/Rfree of {2:.3f}. \
@@ -666,11 +656,11 @@ def display_summary_tab(self):
             logfile_sec = section_title.replace(" ", "_") + uid
             pyrvapi.rvapi_add_section(logfile_sec, section_title, tab, 0, 0, 1, 1, False)
 
-            pdb, mtz, map_, dmap, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, ref_map, diff_map, mr_log, ref_log]))
+            pdb, mtz, mr_log, ref_log = list(self.adjust_paths_of_files([ref_pdb, ref_mtz, mr_log, ref_log]))
             for e in self.rvapi_meta.results:
                 if e["name"] == pdb_code and e["source"] == source:
                     e["best"] = True
-            self.output_result_files(download_sec, dmap, map_, mtz, pdb)
+            self.output_result_files(download_sec, mtz, pdb)
             self.output_log_files(logfile_sec, mr_log, ref_log)
 
     def display_citation_tab(self):
@@ -701,17 +691,13 @@ def display_citation_tab(self):
             pyrvapi.rvapi_add_data("bibtex_file", "Citations as BIBTEX", self.fix_path(bibtex_file), "text", self.citation_tab_id, 2, 0, 1, 1, True)
 
     @staticmethod
-    def output_result_files(sec, diff_map, ref_map, ref_mtz, ref_pdb):
+    def output_result_files(sec, ref_mtz, ref_pdb):
         """Function to display the result files for the result
 
         Parameters
         ----------
         sec : str
             Section the output results files will be added to
-        diff_map : str
-            Path to the difference map
-        ref_map : str
-            Path to the refined map
         ref_mtz : str
             Path to the refined mtz
         ref_pdb : str
@@ -728,8 +714,6 @@ def output_result_files(sec, diff_map, ref_map, ref_mtz, ref_pdb):
 
         pyrvapi.rvapi_add_data1(os.path.join(sec, data), title, ref_pdb, "xyz", 2, 0, 1, 1, 1)
         pyrvapi.rvapi_append_to_data(data, ref_mtz, "hkl:map")
-        pyrvapi.rvapi_append_to_data(data, ref_map, "hkl:ccp4_map")
-        pyrvapi.rvapi_append_to_data(data, diff_map, "hkl:ccp4_dmap")
 
     @staticmethod
     def output_log_files(sec, mr_log, ref_log):
@@ -936,6 +920,6 @@ def adjust_paths_of_files(self, files):
             else:
                 yield ""
 
-    def store_entry_in_rvapi_meta(self, rank, source, name, pdb, mtz, map_, dmap, best):
-        entry = {"rank": rank, "source": source, "best": best, "name": name, "pdb": pdb, "mtz": mtz, "map": map_, "dmap": dmap}
+    def store_entry_in_rvapi_meta(self, rank, source, name, pdb, mtz, best):
+        entry = {"rank": rank, "source": source, "best": best, "name": name, "pdb": pdb, "mtz": mtz}
         self.rvapi_meta.add(entry)

simbad/util/simbad_results.py

@@ -27,8 +27,6 @@ def __init__(self):
         self.ref_pdb_annotation = None
         self.ref_mtz_annotation = None
         self.ref_log = None
-        self.ref_map = None
-        self.diff_map = None
 
 
 class SimbadResults(object):
@@ -113,8 +111,6 @@ def get_files(self, search_type, num_results=10):
                 fc.ref_mtz_annotation = 'MTZ #{0} from REFMAC-refined result of the {1} search'.format(
                     i + 1, ID2STR[search_type])
                 fc.ref_log = os.path.join(mr_workdir, 'refine', '{0}_ref.log'.format(pdb_code))
-                fc.ref_map = os.path.join(mr_workdir, 'refine', '{0}_refmac_2fofcwt.map'.format(pdb_code))
-                fc.diff_map = os.path.join(mr_workdir, 'refine', '{0}_refmac_fofcwt.map'.format(pdb_code))
                 results.append(fc)
             except KeyError:
                 logger.debug("No result found at position %s", (i + 1))