diff --git a/README.rst b/README.rst index b5483bf..a996a0d 100644 --- a/README.rst +++ b/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 diff --git a/bin/simbad-contaminant.bat b/bin/simbad-contaminant.bat index 4d3b946..c9d9f9b 100755 --- a/bin/simbad-contaminant.bat +++ b/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 %* diff --git a/bin/simbad-database.bat b/bin/simbad-database.bat index 9e99cc4..d811a19 100755 --- a/bin/simbad-database.bat +++ b/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 %* diff --git a/bin/simbad-full.bat b/bin/simbad-full.bat index f71fe79..2ff52a5 100755 --- a/bin/simbad-full.bat +++ b/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 %* diff --git a/bin/simbad-lattice.bat b/bin/simbad-lattice.bat index 411430f..6b5feb5 100755 --- a/bin/simbad-lattice.bat +++ b/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 %* diff --git a/bin/simbad-morda.bat b/bin/simbad-morda.bat index a9b5dc0..694eee8 100755 --- a/bin/simbad-morda.bat +++ b/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 %* diff --git a/bin/simbad.bat b/bin/simbad.bat index a4f1a3e..ac0b727 100755 --- a/bin/simbad.bat +++ b/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 %* diff --git a/scripts/stats.py b/scripts/stats.py index 046ff61..9969e10 100755 --- a/scripts/stats.py +++ b/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): diff --git a/simbad/mr/__init__.py b/simbad/mr/__init__.py index 609d780..e4e0f1d 100644 --- a/simbad/mr/__init__.py +++ b/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 diff --git a/simbad/parsers/phaser_parser.py b/simbad/parsers/phaser_parser.py index f5ed927..aeba612 100644 --- a/simbad/parsers/phaser_parser.py +++ b/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