projet_court/src/structure.py

class Turn:

    def __init__(self, turn_type, res_num):
        self.turn_type = turn_type
                        
class Bridge:

    def __init__(self, bridge_type, res_num):
        self.bridge_type = bridge_type
        self.res_num = res_num

class Helix:

    def __init__(self, residues):
        self.residues = residues
        
def get_turns(residues):
    turns = []
    for i,res in enumerate(residues):
        for j in range(3,6):
            if(i+j<len(residues)):
                if(res.h_bond(residues[i+j]<-0.5)):
                    turns.append(Turn(j,i))
    return(turns)

def get_bridges(residues):
    bridges = []
    bridge = {}
    strongest_bridge = {}
    for i in range(1,len(residues)-4):
        E_min = 0
        for j in range(i+2,len(residues)-1):
            # select triplet with the minimal energy 

            if(residues[i-1].h_bond(residues[j])<-0.5
               and residues[j].h_bond(residues[i+1])<-0.5):
                bridge = {'res1':residues[i-1].h_bond(residues[j]),
                          'res2':residues[j].h_bond(residues[i+1]),
                          'ipos':i,
                          'jpos':j,
                          'btype':"para"}
                # if(residues[i-1].h_bond(residues[j])+
                #    residues[j].h_bond(residues[i+1]))<E_min:
                #    E_min = residues[i-1].h_bond(residues[j])
                #    +residues[j].h_bond(residues[i+1])
                #    bridge_type = "para"
                   
            if(residues[j-1].h_bond(residues[i])<-0.5
               and residues[i].h_bond(residues[j+1])<-0.5):
                bridge = {'res1':residues[j-1].h_bond(residues[i]),
                          'res2':residues[i].h_bond(residues[j+1]),
                          'ipos':i,
                          'jpos':j,
                          'btype':"para"}
                # if(residues[j-1].h_bond(residues[i])+
                #    residues[i].h_bond(residues[j+1]))<E_min:
                #    E_min = residues[j-1].h_bond(residues[i])
                #    +residues[i].h_bond(residues[j+1])
                #    bridge_type = "para"

            if(residues[i].h_bond(residues[j])<-0.5
               and residues[j].h_bond(residues[i])<-0.5):
                bridge = {'res1':residues[i].h_bond(residues[j]),
                          'res2':residues[j].h_bond(residues[i]),
                          'ipos':i,
                          'jpos':j,
                          'btype':"anti"}
                # if(residues[i].h_bond(residues[j])+
                #    residues[j].h_bond(residues[i]))<E_min:
                #    E_min = residues[i].h_bond(residues[j])
                #    +residues[j].h_bond(residues[i])
                #    bridge_type = "anti"
                   
            if(residues[i-1].h_bond(residues[j+1])<-0.5
               and residues[j-1].h_bond(residues[i+1])<-0.5):
                bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
                          'res2':residues[j-1].h_bond(residues[i+1]),
                          'ipos':i,
                          'jpos':j,
                          'btype':"anti"}
                 # if(residues[i-1].h_bond(residues[j+1])+
                 #   residues[j-1].h_bond(residues[i+1]))<E_min:
                 #   E_min = residues[i-1].h_bond(residues[j+1])
                 #   +residues[j-1].h_bond(residues[i+1])
                 #   bridge_type = "anti"
            if(bridge):
                if(bridge['res1']+bridge['res2']<E_min):
                    E_min = bridge['res1']+bridge['res2']
                    strongest_bridge = bridge
                    bridge = {}
        # finally add the strongest bridge at i and j pos
        if(strongest_bridge):
            bridges.append(Bridge(strongest_bridge['btype'],
                                  strongest_bridge['ipos']))
            bridges.append(Bridge(strongest_bridge['btype'],
                                  strongest_bridge['jpos']))
    if(len(bridges)>0):
        return(bridges)
    else:
        return(False)

def get_helix(residues, turns):
    for i in range(residues):
        for j in range(i+1,i+5):
            if