diff --git a/docs/tutorial.rst b/docs/tutorial.rst index bd150017b7c4080adc201900f130feea42366217..8272cb73d61f69692da6ff88e870721780de2b16 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -285,10 +285,11 @@ analysis pipeline. Contact map analysis -------------------- -To quickly see several plots and stats related to the reference structure -or/with the EC contact maps. We can use the ``maplot`` subcommand. The first -argument in this command will always be set as the reference map/pdb for the -contact map, ROC or precision-recall plots. +Aside ConKit_ :abbr:`Command Line Interface CLI)` tools, the +:ref:`maplot <./usage>` command line has been implemented to show statistics +between contact maps and the reference which can be a structure in PDB_ format. +The first argument in this command will always be set as the reference map/pdb +for the contact map, ROC or precision-recall plots. .. code-block:: console diff --git a/src/aria/conbox/protein.py b/src/aria/conbox/protein.py index 49e805a1a52d29aa440174baf1635dcaac4bf075..67b9636ad72d3d1dc2a9d2ff7634b61f2c2ed96b 100644 --- a/src/aria/conbox/protein.py +++ b/src/aria/conbox/protein.py @@ -51,6 +51,7 @@ class SsList(object): r'\s+(?P<h_conf>\d?\.?\d*)' r'\s+(?P<e_conf>\d?\.?\d*)' r'\s+(?P<c_conf>\d?\.?\d*)'), + 'ss': re.compile(r'^(?P<ss_pred>[HECBTG]+)'), } # psipred_reg = re.compile(r'^(?P<up_index>\d+)' # r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])' @@ -184,8 +185,18 @@ class SsList(object): filename, sstype) self.ssdict = reg_load(ssregex, filename) + + # Change the format of the ssdict if we have ss type format + if sstype == "ss": + tmpdict = {} + for sstridx in sorted(self.ssdict.keys()): + for ssidx, ss in enumerate(self.ssdict[sstridx]["ss_pred"]): + tmpdict[ssidx + 1] = {"ss_pred": ss} + self.ssdict = tmpdict + ss_index_dict = {'H': 1, 'C': 1, 'E': 1} for line_id in sorted(self.ssdict.keys()): + # Modif champ ss_pred # Si line_id if line_id != min(self.ssdict.keys()) and \