New refs for software. Allow missing refs for software. Debug mode.

master/pyext/src/validation/__init__.py

@@ -30,6 +30,7 @@
 class IHMVAvailableModes(Enum):
     PRODUCTION = 0
     DEVELOPMENT = 1
+    DEBUG = 2
 
 
 def get_operational_mode() -> IHMVAvailableModes:
@@ -55,6 +56,10 @@ def get_operational_mode() -> IHMVAvailableModes:
 if IHMV_MODE == IHMVAvailableModes.DEVELOPMENT:
     __max_num_models = 20  # Cap number of structures for development purposes
 
+# Alter variables for the DEBUG mode
+if IHMV_MODE == IHMVAvailableModes.DEBUG:
+    logging.getLogger().setLevel(logging.DEBUG)
+
 # Setup final values for constants
 MAX_NUM_MODELS: Final = __max_num_models  # Set constant for maximum number of models in a file
 
@@ -349,12 +354,42 @@ def get_software_comp(self) -> dict:
         if len(lists) > 0:
             for software in lists:
                 software_comp['ID'].append(software._id)
+
+                # Get the name of software from mmCIF
                 ref_name = software.name.lower()
-                ref_tot = '<a href="' + \
-                    self.ref_link[ref_name]+'">'+software.name+"</a>"
-                ref_loc = '<a href="'+software.location+'">'+software.location+"</a>"
+
+                # Check if URL for sotware was defined in the mmCIF and parsed
+                # and parsed by ihm
+                if software.location is None:
+                    try:
+                        self.ref_link[ref_name]
+                    except KeyError:
+                        logging.warning(
+                            f'The URL for {software.name} is missing from '
+                                'from both mmCIF and references.csv'
+                            )
+                    else:
+                        logging.debug(
+                            f'Filling the url for {software.name} from '
+                            'references.csv'
+                            )
+
+                        software.location = self.ref_link[ref_name]
+
+                if software.location is None:
+                    ref_tot = f'{software.name}'
+                    ref_loc = f'Not available'
+
+                else:
+                    ref_tot = f'<a href="{software.location}">' \
+                                f'{software.name}</a>'
+
+                    ref_loc = f'<a href="{software.location}">' \
+                                f'{software.location}</a>'
+
                 software_comp['Software name'].append(ref_tot)
                 software_comp['Software location'].append(ref_loc)
+
                 if str(software.version) == ihm.unknown:
                     vers = 'Not available'
                 elif str(software.version) == '?':

templates/references.csv

@@ -62,3 +62,10 @@ QRNAS | http://genesilico.pl/software/stand-alone/qrnas | Stasiewicz J, Mukherje
 CRYSOL | https://www.embl-hamburg.de/biosaxs/crysol.html | Franke D, Petoukhov MV, Konarev PV, Panjkovich A, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh NR, Franklin JM, Jeffries CM, Svergun DI. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions.  J. Appl. Cryst. 2017;50(4), 1212-1225.
 Assembline | https://pubmed.ncbi.nlm.nih.gov/32879490/ | Allegretti M, Zimmerli CE, Rantos V, Wilfling F, Ronchi P, Fung HKH, Lee CW, Hagen W, Turoňová B, Karius K, Börmel M, Zhang X, Müller CW, Schwab Y, Mahamid J, Pfander B, Kosinski J, Beck M. In-cell architecture of the nuclear pore and snapshots of its turnover. Nature. 2020 Oct;586(7831):796-800.
 Naccess | http://www.bioinf.manchester.ac.uk/naccess/ | Hubbard S, Thornton J. Atomic Solvent Accessible Area Calculations
+FPS | https://github.com/Fluorescence-Tools/FPS | Kalinin, S., Peulen, T., Sindbert, S., Rothwell, P.J., Berger, S., Restle, T., Goody, R.S., Gohlke, H. and Seidel, C.A., 2012. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nature methods, 9(12), pp.1218-1225.
+Amber 14 | https://ambermd.org/ | D.A. Case, V. Babin, J.T. Berryman, R.M. Betz, Q. Cai, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, H. Gohlke, A.W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T.S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K.M. Merz, F. Paesani, D.R. Roe, A. Roitberg, C. Sagui, R. Salomon-Ferrer, G. Seabra, C.L. Simmerling, W. Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu and P.A. Kollman (2014), AMBER 14, University of California, San Francisco
+DeerAnalysis2006 | https://epr.ethz.ch/software/older-versions/old_deeranalysis.html | Jeschke, G., Chechik, V., Ionita, P. et al. DeerAnalysis2006—a comprehensive software package for analyzing pulsed ELDOR data. Appl. Magn. Reson. 30, 473–498 (2006).
+IMOD | https://bio3d.colorado.edu/imod/ | Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76.
+AlphaFold | https://www.deepmind.com/research/highlighted-research/alphafold | Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2
+foxsdock | https://modbase.compbio.ucsf.edu/foxsdock/ | Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2010
+phenix | https://phenix-online.org/ | D. Liebschner, P.V. Afonine, M.L. Baker, G. Bunkóczi, V.B. Chen, T.I. Croll, B. Hintze, L.W. Hung, S. Jain, A.J. McCoy, N.W. Moriarty, R.D. Oeffnner, B.K. Poon, M.G. Prisant, R.J. Read, J.S. Richardson, D.C. Richardson, M.D. Sammito, O.V. Sobolev, D.H. Stockwell, T.C. Terwilliger, A.G. Urzhumtsev, L.L. Videau, C.J. Williams, and P.D. Adams. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Cryst. D75, 861-877 (2019).