Merge pull request #139 from rigdenlab/minor_fixes

Minor fixes

CHANGELOG.rst

@@ -1,3 +1,14 @@
+Changelog
+=========
+
+0.2.6
+-----
+
+Changed
+~~~~~~~
+- Lots of minor bug fixes including issue with amore rotation search
+- Added back in user defined MTZ column labels after changes to the MTZ parser meant this was lost
+
 
 Changelog
 =========

README.rst

@@ -10,7 +10,7 @@ Sequence Independent Molecular Replacement Based on Available Database
    :target: https://travis-ci.com/rigdenlab/SIMBAD
    :alt: CI Status
 
-.. image:: https://img.shields.io/badge/solution%20count-9-blue.svg?style=flat
+.. image:: https://img.shields.io/badge/solution%20count-8-blue.svg?style=flat
    :alt: Solution count
 
 .. image:: https://img.shields.io/badge/DOI-10.1107/S2059798318005752-blue.svg

scripts/stats.py

@@ -14,7 +14,7 @@
 import requests
 
 LOG = logging.getLogger(__name__)
-URL = 'https://search.rcsb.org/rcsbsearch/v1/query?json={"query":{"type":"terminal","service":"text","parameters":{"value":"simbad"}},"return_type":"entry"}'
+URL = 'https://search.rcsb.org/rcsbsearch/v1/query?json={"query":{"type":"terminal","service":"full_text","parameters":{"value":"simbad"}},"return_type":"entry"}'
 
 
 def update_readme(n_sols):

simbad/command_line/__init__.py

@@ -262,6 +262,12 @@ def _simbad_contaminant_search(args):
         skip_mr=args.skip_mr,
         process_all=args.process_all,
     )
+
+    # If user defined, set columns
+    if args.F and args.SIGF:
+        rotation_search.mtz_obj.f = args.F
+        rotation_search.mtz_obj.sigf = args.SIGF
+
     rotation_search.run(
         os.path.abspath(args.cont_db),
         nproc=args.nproc,
@@ -348,6 +354,12 @@ def _simbad_morda_search(args):
         skip_mr=args.skip_mr,
         process_all=args.process_all,
     )
+
+    # If user defined, set columns
+    if args.F and args.SIGF:
+        rotation_search.mtz_obj.f = args.F
+        rotation_search.mtz_obj.sigf = args.SIGF
+
     rotation_search.run(
         args.morda_db,
         nproc=args.nproc,
@@ -418,6 +430,7 @@ def _simbad_lattice_search(args):
         temp_mtz = os.path.join(args.work_dir, "input.mtz")
         simbad.util.mtz_util.ctruncate(args.mtz, temp_mtz)
         mp = MtzParser(temp_mtz)
+
         if isinstance(mp.spacegroup_symbol, str):
             space_group = "".join(mp.spacegroup_symbol.split())
         elif isinstance(mp.spacegroup_symbol, unicode):
@@ -650,6 +663,17 @@ def submit_mr_jobs(mtz, mr_dir, search_results, refine_type, refine_cycles, args
         tmp_dir=args.tmp_dir,
         timeout=args.phaser_kill,
     )
+
+    # If user defined, set columns
+    if args.F and args.SIGF:
+        molecular_replacement._mtz_obj.f = args.F
+        molecular_replacement._mtz_obj.sigf = args.SIGF
+    if args.FREE:
+        molecular_replacement._mtz_obj.free = args.FREE
+    if args.DANO and args.SIGDANO:
+        molecular_replacement._mtz_obj.dp = args.DANO
+        molecular_replacement._mtz_obj.sigdp = args.SIGDANO
+
     molecular_replacement.submit_jobs(
         search_results,
         nproc=args.nproc,

simbad/command_line/simbad_database.py

@@ -238,7 +238,7 @@ def create_contaminant_db(database, add_morda_domains, nproc=2, submit_qtype=Non
         msg = "Windows is currently not supported"
         raise RuntimeError(msg)
 
-    if StrictVersion(dimple.main.__version__) < StrictVersion('2.6.2'):
+    if StrictVersion(dimple.main.__version__) < StrictVersion('2.6.1'):
         msg = "Downloading latest Contaminant database from GitHub repo"
         logger.info(msg)
         cmd = ['svn', 'export', 'https://github.com/rigdenlab/SIMBAD/trunk/static/contaminants']

simbad/mr/__init__.py

@@ -278,7 +278,7 @@ def submit_jobs(self, results, nproc=1, process_all=False, submit_qtype=None, su
         else:
             input_arguments.append(mr_succeeded_log)
 
-        submit_chunk(*input_arguments)
+        submit_chunk(*input_arguments, timeout=self.timeout)
 
         mr_results = []
         mr_pdbouts, mr_logfiles, ref_logfiles = zip(*run_files)

simbad/rotsearch/amore_search.py

@@ -164,7 +164,6 @@ def run(
 
         i = InputMR_DAT()
         i.setHKLI(self.mtz)
-        i.setLABI_F_SIGF(str(self.mtz_obj.f), str(self.mtz_obj.sigf))
         i.setMUTE(True)
         run_mr_data = runMR_DAT(i)
 

simbad/rotsearch/phaser_search.py

@@ -112,7 +112,6 @@ def run(
 
         i = InputMR_DAT()
         i.setHKLI(self.mtz)
-        i.setLABI_F_SIGF(str(self.mtz_obj.f), str(self.mtz_obj.sigf))
         i.setMUTE(True)
         run_mr_data = runMR_DAT(i)
 

simbad/util/__init__.py

@@ -157,7 +157,8 @@ def source_ccp4():
     return "source {}".format(os.path.join(os.environ["CCP4"], "bin", "ccp4.setup-sh"))
 
 
-def submit_chunk(collector, run_dir, nproc, job_name, submit_qtype, submit_queue, permit_nonzero, monitor, success_func):
+def submit_chunk(collector, run_dir, nproc, job_name, submit_qtype, submit_queue, permit_nonzero, monitor, success_func,
+                 timeout=30):
     """Submit jobs in small chunks to avoid using too much disk space
 
     Parameters
@@ -197,6 +198,7 @@ def submit_chunk(collector, run_dir, nproc, job_name, submit_qtype, submit_queue
         permit_nonzero=permit_nonzero,
         shell="/bin/bash",
         priority=-10,
+        runtime=timeout,
         cleanup=True,
     ) as task:
         task.run()

simbad/version.py

@@ -2,7 +2,7 @@
 
 # Maintain sematantic versioning. Further information can
 # be found here [http://semver.org/]
-__version_info__ = (0, 2, 5)
+__version_info__ = (0, 2, 6)
 
 # ======================================================
 # Do __NOT__ change anything below here