Merge pull request #117 from rigdenlab/minor-updates

Minor updates

scripts/run_tests.py

@@ -8,6 +8,7 @@
 __date__ = "22 Mar 2016"
 __version__ = "1.0"
 
+import contextlib
 import glob
 import logging
 import os
@@ -70,7 +71,17 @@ def _load_suite(self, cases, pattern, directory):
         return suite
 
 
+@contextlib.contextmanager
+def mock_import_path():
+    """Patch CCP4 to ignore shipped SIMBAD."""
+    org_path = sys.path
+    sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
+    yield
+    sys.path = org_path
+
+
 if __name__ == "__main__":
     args = get_cli_args()
     m = SIMBADUnittestFramework()
-    m.run(buffer=args.buffer, cases=args.test_cases, verbosity=args.verbosity)
+    with mock_import_path():
+        m.run(buffer=args.buffer, cases=args.test_cases, verbosity=args.verbosity)

simbad/__init__.py

@@ -10,6 +10,7 @@
 
 from distutils.version import StrictVersion
 from simbad import version
+
 __version__ = version.__version__
 
 import os
@@ -18,11 +19,10 @@
 if "CCP4" not in os.environ:
     raise RuntimeError("Cannot find CCP4 root directory")
 
-if StrictVersion(pyjob.__version__) < StrictVersion('0.1.3'):
+if StrictVersion(pyjob.__version__) < StrictVersion("0.1.3"):
     raise RuntimeError("Please upgrade PyJOB")
 
-SIMBAD_SHARE_STATIC_DIR = os.path.join(os.environ["CCP4"], "share",
-                                       "simbad", "static")
+SIMBAD_SHARE_STATIC_DIR = os.path.join(os.environ["CCP4"], "share", "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')
+CONTAMINANT_MODELS = os.path.join(SIMBAD_SHARE_STATIC_DIR, "contaminants")
+MORDA_MODELS = os.path.join(SIMBAD_SHARE_STATIC_DIR, "morda")

simbad/command_line/simbad_contaminant.py

@@ -19,33 +19,29 @@
 
 def contaminant_argparse():
     """Create the argparse options"""
-    p = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    p = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     simbad.command_line._argparse_core_options(p)
     simbad.command_line._argparse_job_submission_options(p)
     simbad.command_line._argparse_contaminant_options(p)
     simbad.command_line._argparse_rot_options(p)
     simbad.command_line._argparse_mtz_options(p)
     simbad.command_line._argparse_mr_options(p)
-    p.add_argument('mtz', help="The path to the input mtz file")
+    p.add_argument("mtz", help="The path to the input mtz file")
     return p
 
 
 def main():
     """Main function to run SIMBAD's contaminant search"""
     args = contaminant_argparse().parse_args()
 
-    args.work_dir = simbad.command_line.get_work_dir(
-        args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml
-    )
+    args.work_dir = simbad.command_line.get_work_dir(args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml)
 
-    log_file = os.path.join(args.work_dir, 'simbad.log')
-    debug_log_file = os.path.join(args.work_dir, 'debug.log')
+    log_file = os.path.join(args.work_dir, "simbad.log")
+    debug_log_file = os.path.join(args.work_dir, "debug.log")
     log_class = simbad.command_line.LogController()
     log_class.add_console(level=args.debug_lvl)
     log_class.add_logfile(log_file, level="info", format="%(message)s")
-    log_class.add_logfile(debug_log_file, level="notset",
-                          format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
+    log_class.add_logfile(debug_log_file, level="notset", format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
     global logger
     logger = log_class.get_logger()
 
@@ -64,19 +60,17 @@ def main():
 
     solution_found = simbad.command_line._simbad_contaminant_search(args)
     if solution_found:
-        logger.info(
-            "Check you out, crystallizing contaminants! But don't worry, SIMBAD figured it out and found a solution.")
+        logger.info("Check you out, crystallizing contaminants! But don't worry, SIMBAD figured it out and found a solution.")
     else:
         logger.info("No results found - contaminant search was unsuccessful")
 
     if args.output_pdb and args.output_mtz:
-        csv = os.path.join(args.work_dir, 'cont', 'cont_mr.csv')
-        result = simbad.util.result_by_score_from_csv(csv, 'final_r_free', ascending=True)
+        csv = os.path.join(args.work_dir, "cont", "cont_mr.csv")
+        result = simbad.util.result_by_score_from_csv(csv, "final_r_free", ascending=True)
         simbad.util.output_files(args.work_dir, result, args.output_pdb, args.output_mtz)
 
     stopwatch.stop()
-    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds",
-                *stopwatch.time_pretty)
+    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds", *stopwatch.time_pretty)
 
     gui.display_results(True, args.results_to_display)
     if args.rvapi_document:
@@ -86,6 +80,7 @@ def main():
 
 if __name__ == "__main__":
     import logging
+
     logging.basicConfig(level=logging.NOTSET)
     try:
         main()

simbad/command_line/simbad_database.py

@@ -5,6 +5,7 @@
 __version__ = "1.0"
 
 import argparse
+import collections
 import datetime
 import glob
 import json
@@ -61,28 +62,7 @@
         os.environ["SSL_CERT_FILE"] = os.path.join(os.environ["CCP4"], 'etc', 'ssl', 'cacert.pem')
 
 
-class ContaminantSearchResult(object):
-    """A basic contabase storing class"""
-
-    __slots__ = ('pdb_code', 'space_group', 'uniprot_name', 'uniprot_mnemonic')
-
-    def __init__(self, pdb_code, space_group, uniprot_name, uniprot_mnemonic):
-        self.pdb_code = pdb_code
-        self.space_group = space_group
-        self.uniprot_name = uniprot_name
-        self.uniprot_mnemonic = uniprot_mnemonic
-
-    def __repr__(self):
-        template = "{name}(pdb_code={pdb_code} space_group={space_group} " \
-                   "uniprot_name={uniprot_name} uniprot_mnemonic={uniprot_mnemonic})"
-        return template.format(name=self.__class__.__name__, **{k: getattr(self, k) for k in self.__class__.__slots__})
-
-    def _as_dict(self):
-        """Convert the :obj: BlastSearchResult object to a dictionary"""
-        dictionary = {}
-        for k in self.__slots__:
-            dictionary[k] = getattr(self, k)
-        return dictionary
+ContaminantSearchResult = collections.namedtuple("ContaminantSearchResult", ["pdb_code", "space_group", "uniprot_name", "uniprot_mnemonic"])
 
 
 def is_valid_db_location(database):

simbad/command_line/simbad_lattice.py

@@ -20,43 +20,36 @@
 def lattice_argparse():
     """Create the argparse options"""
     prep = argparse.ArgumentParser(add_help=False)
-    prep.add_argument('-sg', dest="space_group", type=str, default=None,
-                      help='The space group to use')
-    prep.add_argument('-uc', dest="unit_cell", type=str, default=None,
-                      help="The unit cell, format 'a,b,c,alpha,beta,gamma'")
+    prep.add_argument("-sg", dest="space_group", type=str, default=None, help="The space group to use")
+    prep.add_argument("-uc", dest="unit_cell", type=str, default=None, help="The unit cell, format 'a,b,c,alpha,beta,gamma'")
     args, _ = prep.parse_known_args()
 
-    p = argparse.ArgumentParser(
-        parents=[prep], formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    p = argparse.ArgumentParser(parents=[prep], formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     simbad.command_line._argparse_core_options(p)
     simbad.command_line._argparse_job_submission_options(p)
     simbad.command_line._argparse_lattice_options(p)
     simbad.command_line._argparse_mtz_options(p)
     simbad.command_line._argparse_mr_options(p)
     if args.space_group and args.unit_cell:
         # Add to the namespace as we're looking for it later
-        p.add_argument('-mtz', dest="mtz", default=None,
-                       help=argparse.SUPPRESS)
+        p.add_argument("-mtz", dest="mtz", default=None, help=argparse.SUPPRESS)
     else:
-        p.add_argument('mtz', help="The path to the input mtz file")
+        p.add_argument("mtz", help="The path to the input mtz file")
     return p
 
 
 def main():
     """Main function to run SIMBAD's lattice search"""
     args = lattice_argparse().parse_args()
 
-    args.work_dir = simbad.command_line.get_work_dir(
-        args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml
-    )
+    args.work_dir = simbad.command_line.get_work_dir(args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml)
 
-    log_file = os.path.join(args.work_dir, 'simbad.log')
-    debug_log_file = os.path.join(args.work_dir, 'debug.log')
+    log_file = os.path.join(args.work_dir, "simbad.log")
+    debug_log_file = os.path.join(args.work_dir, "debug.log")
     log_class = simbad.command_line.LogController()
     log_class.add_console(level=args.debug_lvl)
     log_class.add_logfile(log_file, level="info", format="%(message)s")
-    log_class.add_logfile(debug_log_file, level="notset",
-                          format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
+    log_class.add_logfile(debug_log_file, level="notset", format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
     global logger
     logger = log_class.get_logger()
 
@@ -74,22 +67,20 @@ def main():
     if args.space_group and args.unit_cell:
         display_summary = False
     elif solution_found:
-        logger.info(
-            "Lucky you! SIMBAD worked its charm and found a lattice match for you.")
+        logger.info("Lucky you! SIMBAD worked its charm and found a lattice match for you.")
         display_summary = True
     else:
         logger.info("No results found - lattice search was unsuccessful")
         display_summary = True
 
     if args.output_pdb and args.output_mtz:
-        csv = os.path.join(args.work_dir, 'latt', 'lattice_mr.csv')
+        csv = os.path.join(args.work_dir, "latt", "lattice_mr.csv")
         if os.path.exists(csv):
-            result = simbad.util.result_by_score_from_csv(csv, 'final_r_free', ascending=True)
+            result = simbad.util.result_by_score_from_csv(csv, "final_r_free", ascending=True)
             simbad.util.output_files(args.work_dir, result, args.output_pdb, args.output_mtz)
 
     stopwatch.stop()
-    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds",
-                *stopwatch.time_pretty)
+    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds", *stopwatch.time_pretty)
 
     gui.display_results(display_summary, args.results_to_display)
     if args.rvapi_document:
@@ -99,6 +90,7 @@ def main():
 
 if __name__ == "__main__":
     import logging
+
     logging.basicConfig(level=logging.NOTSET)
     try:
         main()

simbad/command_line/simbad_morda.py

@@ -20,33 +20,29 @@
 
 def morda_argparse():
     """Create the argparse options"""
-    p = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    p = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     simbad.command_line._argparse_core_options(p)
     simbad.command_line._argparse_job_submission_options(p)
     simbad.command_line._argparse_morda_options(p)
     simbad.command_line._argparse_rot_options(p)
     simbad.command_line._argparse_mtz_options(p)
     simbad.command_line._argparse_mr_options(p)
-    p.add_argument('mtz', help="The path to the input mtz file")
+    p.add_argument("mtz", help="The path to the input mtz file")
     return p
 
 
 def main():
     """Main function to run SIMBAD's MoRDa search"""
     args = morda_argparse().parse_args()
 
-    args.work_dir = simbad.command_line.get_work_dir(
-        args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml
-    )
+    args.work_dir = simbad.command_line.get_work_dir(args.run_dir, work_dir=args.work_dir, ccp4_jobid=args.ccp4_jobid, ccp4i2_xml=args.ccp4i2_xml)
 
-    log_file = os.path.join(args.work_dir, 'simbad.log')
-    debug_log_file = os.path.join(args.work_dir, 'debug.log')
+    log_file = os.path.join(args.work_dir, "simbad.log")
+    debug_log_file = os.path.join(args.work_dir, "debug.log")
     log_class = simbad.command_line.LogController()
     log_class.add_console(level=args.debug_lvl)
     log_class.add_logfile(log_file, level="info", format="%(message)s")
-    log_class.add_logfile(debug_log_file, level="notset",
-                          format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
+    log_class.add_logfile(debug_log_file, level="notset", format="%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s")
     global logger
     logger = log_class.get_logger()
 
@@ -70,13 +66,12 @@ def main():
         logger.info("No results found - full search was unsuccessful")
 
     if args.output_pdb and args.output_mtz:
-        csv = os.path.join(args.work_dir, 'morda', 'morda_mr.csv')
-        result = simbad.util.result_by_score_from_csv(csv, 'final_r_free', ascending=True)
+        csv = os.path.join(args.work_dir, "morda", "morda_mr.csv")
+        result = simbad.util.result_by_score_from_csv(csv, "final_r_free", ascending=True)
         simbad.util.output_files(args.work_dir, result, args.output_pdb, args.output_mtz)
 
     stopwatch.stop()
-    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds",
-                *stopwatch.time_pretty)
+    logger.info("All processing completed in %d days, %d hours, %d minutes, and %d seconds", *stopwatch.time_pretty)
 
     gui.display_results(True, args.results_to_display)
     if args.rvapi_document:
@@ -86,6 +81,7 @@ def main():
 
 if __name__ == "__main__":
     import logging
+
     logging.basicConfig(level=logging.NOTSET)
     try:
         main()

simbad/core/__init__.py

@@ -1,15 +0,0 @@
-__author__ = "Adam Simpkin"
-__date__ = "16 April 2018"
-__version__ = "0.1"
-
-import abc
-
-
-class ScoreBase(object):
-    """Abstract class for storing scores"""
-    __metaclass__ = abc.ABCMeta
-
-    @abc.abstractmethod
-    def _as_dict(self):
-        """Convert the object to a dictionary"""
-        return

simbad/core/amore_score.py

@@ -4,40 +4,24 @@
 __date__ = "10 Oct 2017"
 __version__ = "0.1"
 
-from simbad.core import ScoreBase
-
-
-class AmoreRotationScore(ScoreBase):
-    """An amore rotation scoring class"""
-
-    __slots__ = ("pdb_code", "dat_path", "ALPHA", "BETA", "GAMMA", "CC_F", "RF_F", "CC_I", "CC_P", "Icp",
-                 "CC_F_Z_score", "CC_P_Z_score", "Number_of_rotation_searches_producing_peak")
-
-    def __init__(self, pdb_code, dat_path, ALPHA, BETA, GAMMA, CC_F, RF_F, CC_I, CC_P, Icp,
-                 CC_F_Z_score, CC_P_Z_score, Number_of_rotation_searches_producing_peak):
-        self.pdb_code = pdb_code
-        self.dat_path = dat_path
-        self.ALPHA = ALPHA
-        self.BETA = BETA
-        self.GAMMA = GAMMA
-        self.CC_F = CC_F
-        self.RF_F = RF_F
-        self.CC_I = CC_I
-        self.CC_P = CC_P
-        self.Icp = Icp
-        self.CC_F_Z_score = CC_F_Z_score
-        self.CC_P_Z_score = CC_P_Z_score
-        self.Number_of_rotation_searches_producing_peak = Number_of_rotation_searches_producing_peak
-
-    def __repr__(self):
-        string = "{name}(pdb_code={pdb_code} dat_path={dat_path} " \
-                 "ALPHA={ALPHA} BETA={BETA} GAMMA={GAMMA} " \
-                 "CC_F=CC_F RF_F={RF_F} CC_I={CC_I} CC_P={CC_P} Icp={Icp} " \
-                 "CC_F_Z_score={CC_F_Z_score} CC_P_Z_score={CC_P_Z_score} " \
-                 "Number_of_rotation_searches_producing_peak={Number_of_rotation_searches_producing_peak})"
-        return string.format(name=self.__class__.__name__, **{k: getattr(self, k) for k in self.__slots__})
-
-    def _as_dict(self):
-        """Convert the :obj:`AmoreRotationScore <simbad.score.amore_score.AmoreRotationScore>`
-        object to a dictionary"""
-        return {k: getattr(self, k) for k in self.__slots__}
+from collections import namedtuple
+
+
+AmoreRotationScore = namedtuple(
+    "AmoreRotationScore",
+    [
+        "pdb_code",
+        "dat_path",
+        "ALPHA",
+        "BETA",
+        "GAMMA",
+        "CC_F",
+        "RF_F",
+        "CC_I",
+        "CC_P",
+        "Icp",
+        "CC_F_Z_score",
+        "CC_P_Z_score",
+        "Number_of_rotation_searches_producing_peak",
+    ],
+)