PEATDB/PE.py
def alanineScan(self):
        """Perform a full Alanine scan on all the selected proteins
        Add all mutant proteins to the DB"""
        if not self.get_selected_proteins():
            return
        #
        # Open information window
        #
        P=GUI_helper.progress_window(self.master,'Alanine scan')
        P.update_progress(0.0)
        #
        # Loop over all proteins
        #
        DBi=self.data['DBinstance']
        DB=DBi.DB
        count=0
        for protein in self.sel_prots:
            #minres=DBi[protein]['ORF_selected']['aastart_number']
            #maxres=minres+DBi[protein]['ORF_selected']['length']
            sequence=DB[protein]['aaseq'][:]
            for resnum,restyp in sequence:
                print resnum,restyp
                new_name=DBi.suggest_name(protein,resnum,'ALA',restyp)
                mutation=resnum+':'+restyp+'='+'ALA'
                DBi.file_mutation_data(parent_name=protein,mutation=mutation,protein_name=new_name)
                #self.update_display()
                count=count+1
                P.update_progress(float(count)/float(len(self.sel_prots)*len(sequence)))
        P.close()
        #
        # Save the database
        #
        DBi.checkDB()
        DBi.saveDB()
        #
        # Update everything
        #
        self.update_all()
        return
Perform a full Alanine scan on all the selected proteins
        Add all mutant proteins to the DB
Perform a full Alanine scan on all the selected proteins
Add all mutant proteins to the DB
Perform a full Alanine scan on all the selected proteins Add all mutant proteins to the DB
def alanineScan(self):
        if not self.get_selected_proteins():
            return
        P=GUI_helper.progress_window(self.master,'Alanine scan')
        P.update_progress(0.0)
        DBi=self.data['DBinstance']
        DB=DBi.DB
        count=0
        for protein in self.sel_prots:
            sequence=DB[protein]['aaseq'][:]
            for resnum,restyp in sequence:
                print resnum,restyp
                new_name=DBi.suggest_name(protein,resnum,'ALA',restyp)
                mutation=resnum+':'+restyp+'='+'ALA'
                DBi.file_mutation_data(parent_name=protein,mutation=mutation,protein_name=new_name)
                count=count+1
                P.update_progress(float(count)/float(len(self.sel_prots)*len(sequence)))
        P.close()
        DBi.checkDB()
        DBi.saveDB()
        self.update_all()
        return
def alanineScan ( self ) : if not self . get_selected_proteins ( ) : return P = GUI_helper . progress_window ( self . master , 'Alanine scan' ) P . update_progress ( 0.0 ) DBi = self . data [ 'DBinstance' ] DB = DBi . DB count = 0 for protein in self . sel_prots : sequence = DB [ protein ] [ 'aaseq' ] [ : ] for resnum , restyp in sequence : print resnum , restyp new_name = DBi . suggest_name ( protein , resnum , 'ALA' , restyp ) mutation = resnum + ':' + restyp + '=' + 'ALA' DBi . file_mutation_data ( parent_name = protein , mutation = mutation , protein_name = new_name ) count = count + 1 P . update_progress ( float ( count ) / float ( len ( self . sel_prots ) * len ( sequence ) ) ) P . close ( ) DBi . checkDB ( ) DBi . saveDB ( ) self . update_all ( ) return
Perform a full Alanine scan on all the selected proteins
Add all mutant proteins to the DB
Perform a full Alanine scan on all the selected proteins Add all mutant proteins to the DB
"""Perform a full Alanine scan on all the selected proteins
        Add all mutant proteins to the DB""" #
 # Open information window
 #
 #
 # Loop over all proteins
 #
 #minres=DBi[protein]['ORF_selected']['aastart_number']
 #maxres=minres+DBi[protein]['ORF_selected']['length']
 #self.update_display()
 #
 # Save the database
 #
 #
 # Update everything
 #

self