Fix citation, logging in libraries.py

KULL-Centre · Nov 5, 2024 · 7b6b5f4 · 7b6b5f4
1 parent d287968
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Showing 4 changed files with 48 additions and 47 deletions.
diff --git a/FRETpredict/FRET.py b/FRETpredict/FRET.py
@@ -153,9 +153,11 @@ def __init__(self, protein, residues, **kwargs):
 
         # Logging set up
         if self.verbose:
-            logging.basicConfig(filename=kwargs.get('log_file', 'log'), level=logging.INFO)
-        else:
             logging.basicConfig(filename=kwargs.get('log_file', 'log'), level=logging.DEBUG)
+            logging.root.setLevel(logging.DEBUG)
+        else:
+            logging.basicConfig(filename=kwargs.get('log_file', 'log'), level=logging.INFO)
+            logging.root.setLevel(logging.INFO)
 
         # Write the string for the placement residues selection
         for i in range(2):
@@ -167,7 +169,7 @@ def __init__(self, protein, residues, **kwargs):
                 residue_sel += " and segid {:s}".format(self.chains[i])
 
             # Logging information on the selected residues
-            logging.info('{:s} = {:s}'.format(residue_sel, self.protein.select_atoms(residue_sel).atoms.resnames[0]))
+            logging.debug('{:s} = {:s}'.format(residue_sel, self.protein.select_atoms(residue_sel).atoms.resnames[0]))
 
         # Raise error if the specified placement residues are different from two
         if len(residues) != 2:
@@ -337,7 +339,7 @@ def trajectoryAnalysis(self):
         """
 
         # Print info
-        logging.info("Starting rotamer distance analysis of trajectory {:s} with labeled residues "
+        logging.debug("Starting rotamer distance analysis of trajectory {:s} with labeled residues "
                      "{:d} and {:d}".format(self.protein.trajectory.filename, self.residues[0], self.residues[1]))
 
         # Create H5PY file
@@ -511,7 +513,7 @@ def save(self, **kwargs):
                 if self.weights.size != k2.size:
 
                     # Warning log
-                    logging.info('Weights array has size {} whereas the number of frames is {}'.
+                    logging.debug('Weights array has size {} whereas the number of frames is {}'.
                                  format(self.weights.size, k2.size))
 
                     # Raise error
@@ -534,7 +536,7 @@ def save(self, **kwargs):
                 if self.user_weights.size != k2.size:
 
                     # Warning log
-                    logging.info('User weights array has size {} whereas the number of frames is {}'.
+                    logging.debug('User weights array has size {} whereas the number of frames is {}'.
                                  format(self.user_weights.size, k2.size))
 
                     # Raise error
@@ -553,7 +555,7 @@ def save(self, **kwargs):
             else:
 
                 # Warning log
-                logging.info('User weights argument should be a numpy array')
+                logging.debug('User weights argument should be a numpy array')
 
                 # Raise error
                 raise ValueError('User weights argument should be a numpy array')
@@ -647,4 +649,4 @@ def run(self):
         # Calculate k2 distribution and k2, Static, Dynamic1, Dynamic2 averaging. Save data to file.
         self.save()
 
-        logging.info('Done')
+        logging.debug('Done')
diff --git a/FRETpredict/__init__.py b/FRETpredict/__init__.py
@@ -4,6 +4,6 @@
 from .lennardjones import lj_parameters
 from .libraries import *
 
-__version__ = '0.2.2'
+__version__ = '0.2.7'
 
 
diff --git a/FRETpredict/lib/libraries.yml b/FRETpredict/lib/libraries.yml
@@ -1,6 +1,6 @@
 ATTO 390 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T39_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -12,7 +12,7 @@ ATTO 390 C2R:
   - C7 and resname T39
 ATTO 390 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T39_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -24,7 +24,7 @@ ATTO 390 L1R:
   - C7 and resname T39
 ATTO 425 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T42_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -36,7 +36,7 @@ ATTO 425 C2R:
   - C7 and resname T42
 ATTO 425 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T42_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -48,7 +48,7 @@ ATTO 425 L1R:
   - C7 and resname T42
 ATTO 465 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T46_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -63,7 +63,7 @@ ATTO 465 C2R:
   - N1 and resname T46
 ATTO 465 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T46_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -78,7 +78,7 @@ ATTO 465 L1R:
   - N1 and resname T46
 ATTO 488 C3R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T48_C3R_cutoff30
   licence: GPLv3
   mu:
@@ -94,7 +94,7 @@ ATTO 488 C3R:
   - C15 and resname T48
 ATTO 495 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T49_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -107,7 +107,7 @@ ATTO 495 C2R:
   - N1 and resname T49
 ATTO 495 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T49_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -120,7 +120,7 @@ ATTO 495 L1R:
   - N1 and resname T49
 ATTO 520 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T52_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -134,7 +134,7 @@ ATTO 520 C2R:
   - C7 and resname T52
 ATTO 520 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T52_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -148,7 +148,7 @@ ATTO 520 L1R:
   - C7 and resname T52
 ATTO 610 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T61_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -162,7 +162,7 @@ ATTO 610 C2R:
   - C8 and resname T61
 ATTO 610 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: T61_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -176,7 +176,7 @@ ATTO 610 L1R:
   - C8 and resname T61
 ATTO Thio12 C3R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: Tth_C3R_cutoff30
   licence: GPLv3
   mu:
@@ -190,7 +190,7 @@ ATTO Thio12 C3R:
   - C9 and resname Tth
 AlexaFluor 350 C1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A35_C1R_cutoff30
   licence: GPLv3
   mu:
@@ -204,7 +204,7 @@ AlexaFluor 350 C1R:
   - C5 and resname A35
 AlexaFluor 350 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A35_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -218,7 +218,7 @@ AlexaFluor 350 L1R:
   - C5 and resname A35
 AlexaFluor 488 B1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A48_B1R_cutoff30
   licence: GPLv3
   mu:
@@ -235,7 +235,7 @@ AlexaFluor 488 B1R:
   - C7 and resname A48
 AlexaFluor 488 C1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A48_C1R_cutoff30
   licence: GPLv3
   mu:
@@ -252,7 +252,7 @@ AlexaFluor 488 C1R:
   - C7 and resname A48
 AlexaFluor 488 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A48_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -269,7 +269,7 @@ AlexaFluor 488 L1R:
   - C7 and resname A48
 AlexaFluor 532 C1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A53_C1R_cutoff30
   licence: GPLv3
   mu:
@@ -285,7 +285,7 @@ AlexaFluor 532 C1R:
   - C7 and resname A53
 AlexaFluor 532 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A53_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -301,7 +301,7 @@ AlexaFluor 532 L1R:
   - C7 and resname A53
 AlexaFluor 568 C1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A56_C1R_cutoff30
   licence: GPLv3
   mu:
@@ -318,7 +318,7 @@ AlexaFluor 568 C1R:
   - C10 and resname A56
 AlexaFluor 568 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A56_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -335,7 +335,7 @@ AlexaFluor 568 L1R:
   - C10 and resname A56
 AlexaFluor 594 C1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A59_C1R_cutoff30
   licence: GPLv3
   mu:
@@ -352,7 +352,7 @@ AlexaFluor 594 C1R:
   - C10 and resname A59
 AlexaFluor 594 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A59_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -369,7 +369,7 @@ AlexaFluor 594 L1R:
   - C10 and resname A59
 AlexaFluor 647 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A64_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -387,7 +387,7 @@ AlexaFluor 647 C2R:
   - C29 and resname A64
 AlexaFluor 647 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: A64_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -466,7 +466,7 @@ Lumiprobe Cy5 C2R:
   - CX3
 Lumiprobe Cy5.5 C2R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: C55_C2R_cutoff30
   licence: GPLv3
   mu:
@@ -480,7 +480,7 @@ Lumiprobe Cy5.5 C2R:
   - C39 and resname C55
 Lumiprobe Cy5.5 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: C55_L1R_cutoff30
   licence: GPLv3
   mu:
@@ -494,7 +494,7 @@ Lumiprobe Cy5.5 L1R:
   - C39 and resname C55
 Lumiprobe Cy7.5 L1R:
   author: D Montepietra, G Tesei, JM Martins, MBA Kunze, RB Best, K Lindorff-Larsen
-  citation: TBD
+  citation: https://doi.org/10.1038/s42003-024-05910-6
   filename: C75_L1R_cutoff30
   licence: GPLv3
   mu:

diff --git a/FRETpredict/libraries.py b/FRETpredict/libraries.py
@@ -17,7 +17,9 @@
 import yaml
 
 # Create logger
-logger = logging.getLogger("MDAnalysis.app")
+#logger = logging.getLogger("MDAnalysis.app")
+#logger.setLevel(logging.DEBUG)
+#logger.root.setLevel(logging.DEBUG)
 
 #: Name of the directory in the package that contains the library data.
 LIBDIR = "lib"
@@ -107,17 +109,14 @@ def __init__(self, name):
             raise ValueError("No rotamer library with name {0} known: must be one of {1}".format(
                 name, list(LIBRARIES.keys())))
 
-        # Print logging information
-        logger.info("Using rotamer library '{0}' by {1[author]}".format(self.name, self.lib))
-        logger.info("Please cite: {0[citation]}".format(self.lib))
-
         # Obtain filename path
         self.lib['filename'] = find_file(self.lib['filename'][:-2] + name.split(' cutoff')[1])
 
         # Print logging information
-        logger.info("[rotamers] ensemble {:s} with topology {:s}.pdb".format(self.lib['filename'],
-                                                                              self.lib['filename'].split('_cutoff')[0]))
-        logger.info("[rotamers] populations {:s}".format(self.lib['filename'] + '_weights.txt'))
+        #logger.debug("Using rotamer library '{0}' by {1[author]}".format(self.name, self.lib))
+        #logger.debug("Please cite: {0[citation]}".format(self.lib))
+        #logger.debug("[rotamers] ensemble {:s} with topology {:s}.pdb".format(self.lib['filename'],self.lib['filename'].split('_cutoff')[0]))
+        #logger.debug("[rotamers] populations {:s}".format(self.lib['filename'] + '_weights.txt'))
 
         # If trajectory is not found
         if not os.path.isfile(self.lib['filename'] + '.dcd'):