Merge pull request #145 from rigdenlab/fix_more_tests

Fix more tests

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-8-blue.svg?style=flat
+.. image:: https://img.shields.io/badge/solution%20count-12-blue.svg?style=flat
    :alt: Solution count
 
 .. image:: https://img.shields.io/badge/DOI-10.1107/S2059798318005752-blue.svg

bin/simbad-contaminant.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_contaminant.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_contaminant.py %*

bin/simbad-database.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_database.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_database.py %*

bin/simbad-full.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_full.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_full.py %*

bin/simbad-lattice.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_lattice.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_lattice.py %*

bin/simbad-morda.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_morda.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_morda.py %*

bin/simbad.bat

@@ -1 +1 @@
-@ccp4-python %CCP4%\Lib\site-packages\simbad\command_line\simbad_main.py %*
+@ccp4-python %CCP4%\Python39\Lib\site-packages\simbad\command_line\simbad_main.py %*

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":"full_text","parameters":{"value":"simbad"}},"return_type":"entry"}'
+URL = 'https://search.rcsb.org/rcsbsearch/v2/query?json={"query":{"type":"terminal","service":"full_text","parameters":{"value":"simbad"}},"return_type":"entry"}'
 
 
 def update_readme(n_sols):

simbad/mr/__init__.py

@@ -563,16 +563,22 @@ def summarize(self, csv_file):
 
 def _mr_job_succeeded(r_fact, r_free):
     """Check values for job success"""
+    if r_fact is None or r_free is None:
+        return False
     return r_fact < 0.45 and r_free < 0.45
 
 
 def _refinement_succeeded(r_fact, r_free):
     """Check values for job success"""
+    if r_fact is None or r_free is None:
+        return False
     return r_fact < 0.45 and r_free < 0.45
 
 
 def _phaser_succeeded(llg, tfz):
     """Check values for job success"""
+    if llg is None or tfz is None:
+        return False
     return llg > 120 and tfz > 8
 
 

simbad/parsers/phaser_parser.py

@@ -10,9 +10,9 @@
 class PhaserParser(simbad.parsers._Parser):
     def __init__(self, logfile):
         super(PhaserParser, self).__init__(logfile)
-        self.llg = None
-        self.tfz = None
-        self.rfz = None
+        self.llg = 0
+        self.tfz = 0
+        self.rfz = 0
         self.parse()
 
     def parse(self):
@@ -22,10 +22,10 @@ def parse(self):
                     llist = line.split()
                     llist.reverse()
                     for i in llist:
-                        if "TFZ==" in i and "*" not in i:
+                        if all(x not in i for x in ['*', '(', ')']) and "TFZ==" in i:
                             self.tfz = float(i.replace("TFZ==", ""))
                             break
-                        if "TFZ=" in i and "TFZ==" not in i and "*" not in i:
+                        if all(x not in i for x in ['*', '(', ')', 'TFZ==']) and "TFZ=" in i:
                             self.tfz = float(i.replace("TFZ=", ""))
                             break