Merge pull request #93 from hlasimpk/master

A few small updates

simbad/__init__.py

@@ -25,3 +25,4 @@
                                        "simbad", "static")
 LATTICE_DB = os.path.join(SIMBAD_SHARE_STATIC_DIR, "niggli_database.npz")
 CONTAMINANT_MODELS = os.path.join(SIMBAD_SHARE_STATIC_DIR, 'contaminants')
+MORDA_MODELS = os.path.join(SIMBAD_SHARE_STATIC_DIR, 'morda')

simbad/command_line/__init__.py

@@ -246,7 +246,7 @@ def _argparse_contaminant_options(p):
 def _argparse_morda_options(p):
     """Morda search specific options"""
     sg = p.add_argument_group('Morda search specific options')
-    sg.add_argument('-morda_db', type=lambda x: is_valid_dir(sg, x),
+    sg.add_argument('-morda_db', type=lambda x: is_valid_dir(sg, x), default=simbad.MORDA_MODELS,
                     help='Path to local copy of the MoRDa database')
     sg.add_argument('-max_morda_results', type=int, default=200,
                     help="The maximum number of contaminant results to return")

simbad/command_line/simbad_database.py

@@ -752,7 +752,8 @@ def create_db_argparse():
         type=str,
         default='info',
         help='The console verbosity level < notset | info | debug | warning | error | critical > ')
-    pc.add_argument('simbad_db', type=str, help='Path to local copy of the SIMBAD database')
+    pc.add_argument('simbad_db', type=str, default=simbad.MORDA_MODELS,
+                    help='Path to local copy of the SIMBAD database')
 
     pd = sp.add_parser('ensemble', help='ensemble database')
     pd.set_defaults(which="ensemble")

simbad/mr/anomalous_util.py

@@ -141,5 +141,6 @@ def anode(self, input_model):
 
     def cleanup(self):
         for i in ["{0}_fa.hkl", "{0}_fa.ins", "{0}_fa.res", "{0}.hkl", "{0}.pha", "{0}.sca"]:
-            os.remove(os.path.join(self.work_dir, i.format(self.name)))
-
+            f = os.path.join(self.work_dir, i.format(self.name))
+            if os.path.isfile(f):
+                os.remove(f)

simbad/util/mtz_util.py

@@ -208,12 +208,16 @@ def run(self, mtz_file):
                 else:
                     msg = "Unexpected number of columns found in anomalous miller array"
                     logging.critical(msg)
-            elif m_a.is_xray_intensity_array():
+            elif m_a.is_xray_intensity_array() and len(m_a.info().labels) == 2:
                 if not self.i:
                     self.i, self.sigi = m_a.info().labels
-            elif m_a.is_xray_amplitude_array():
+            elif m_a.is_xray_amplitude_array() and len(m_a.info().labels) == 2:
                 if not self.f:
                     self.f, self.sigf = m_a.info().labels
+            # Catch for uncommon miller array that combines structure factors and DANO
+            elif len(m_a.info().labels) == 5:
+                if any(['DANO' in i.upper() for i in miller_arrays[1].info().labels]):
+                    self.f, self.sigf, self.dano, self.sigdano, isym = m_a.info().labels
             else:
                 pass
 

simbad/util/reference_manager.py

@@ -33,7 +33,7 @@ def setup_references(self):
         ref_fname = os.path.join(os.environ['CCP4'], "share", "simbad", "static", "simbad.bib")
         if not os.path.isfile(ref_fname):
             msg = "Cannot find BibTex file containing references. " \
-                  "Please determine them yourself and cite AMPLE."
+                  "Please determine them yourself and cite SIMBAD."
             return msg
         article = {}
         entry = False
@@ -99,15 +99,15 @@ def methods_as_html(self):
                "Numbers in superscript next to program/reference names refer to the number of the program reference in the overall list of references.</p>"
         for section in self.SECTIONS:
             if section == self.SECTIONS.GENERAL:
-                html += '<p>The first 2 references should be cited in all cases.</p>'
+                html += '<p>SIMBAD<sup>1</sup>, CCP4<sup>2</sup> and CCTBX<sup>3</sup> references should be cited in all cases.</p>'
             elif section == self.SECTIONS.ROTATION and len(self.section_labels[self.SECTIONS.ROTATION]):
                 standfirst = '<p>The rotation searches were carried out with the following programs:</p>'
                 html += self._methods_section_html(self.SECTIONS.ROTATION, standfirst)
             elif section == self.SECTIONS.MR and len(self.section_labels[self.SECTIONS.MR]):
                 standfirst = '<p>Molecular Replacement was carried out with the following programs:</p>'
                 html += self._methods_section_html(self.SECTIONS.MR, standfirst)
             elif section == self.SECTIONS.REFINEMENT and len(self.section_labels[self.SECTIONS.REFINEMENT]):
-                standfirst = '<p>Refinement of the MR solutions carried out with the following programs:</p>'
+                standfirst = '<p>Refinement of the MR solutions was carried out with the following programs:</p>'
                 html += self._methods_section_html(self.SECTIONS.REFINEMENT, standfirst)
         return html
 
@@ -136,7 +136,7 @@ def citations_as_html(self):
 
     @property
     def citations_as_text(self):
-        txt = """A number of programs and algorithms were used within the this run of AMPLE.
+        txt = """A number of programs and algorithms were used within the this run of SIMBAD.
     The following is a list of citations for this run:
     {0}
     """.format(self.citation_list_as_text)