2_connections.hoc

// create the sections
create node[Nnode],mysaleft[Nmysa],mysaright[Nmysa],flut[Nflut],stin[Nstin],soma,mysaextra[NmysaSec]
// node - node = NODE
// mysa - myelin sheath attachment = PARA (paranode) - part that tapers
// flut - fluted region = JUXTA (juxtaparanode) - has potassium
// stin - stereotyped internode = INTER (internode)

// repeating pattern
// starts: soma - PARA - NODE
// then: NODE - PARA - JUXTA - INTER - JUXTA - PARA
// all NODE (x1), PARA (x10), JUXTA (x2), INTER (x1)

//connect the nodes
connect mysaextra[0](0), soma(1)
for l=0,NmysaSec-2 {
    connect mysaextra[l+1](0),mysaextra[l](1)
}
connect node[0](0),mysaextra[NmysaSec-1](1)
for k=0,Send {
    connect mysaleft[NmysaSec*k](0),node[k](1)  // NODE - PARA
    connect mysaleft[NmysaSec*k+1](0),mysaleft[NmysaSec*k](1)
    connect mysaleft[NmysaSec*k+2](0),mysaleft[NmysaSec*k+1](1)
    connect mysaleft[NmysaSec*k+3](0), mysaleft[NmysaSec*k+2](1)
    connect mysaleft[NmysaSec*k+4](0), mysaleft[NmysaSec*k+3](1)
    connect mysaleft[NmysaSec*k+5](0), mysaleft[NmysaSec*k+4](1)
    connect mysaleft[NmysaSec*k+6](0), mysaleft[NmysaSec*k+5](1)
    connect mysaleft[NmysaSec*k+7](0), mysaleft[NmysaSec*k+6](1)
    connect mysaleft[NmysaSec*k+8](0), mysaleft[NmysaSec*k+7](1)
    connect mysaleft[NmysaSec*k+9](0), mysaleft[NmysaSec*k+8](1)
    connect flut[2*k](0), mysaleft[NmysaSec*k+9](1)     // PARA - JUXTA
    connect stin[k](0), flut[2*k](1)                    // JUXTA - INTER
    connect flut[2*k+1](0), stin[k](1)                  // INTER - JUXTA
    connect mysaright[NmysaSec*k](0), flut[2*k+1](1)    // JUXTA - PARA
    connect mysaright[NmysaSec*k+1](0), mysaright[NmysaSec*k](1)
    connect mysaright[NmysaSec*k+2](0), mysaright[NmysaSec*k+1](1)
    connect mysaright[NmysaSec*k+3](0), mysaright[NmysaSec*k+2](1)
    connect mysaright[NmysaSec*k+4](0), mysaright[NmysaSec*k+3](1)
    connect mysaright[NmysaSec*k+5](0), mysaright[NmysaSec*k+4](1)
    connect mysaright[NmysaSec*k+6](0), mysaright[NmysaSec*k+5](1)
    connect mysaright[NmysaSec*k+7](0), mysaright[NmysaSec*k+6](1)
    connect mysaright[NmysaSec*k+8](0), mysaright[NmysaSec*k+7](1)
    connect mysaright[NmysaSec*k+9](0), mysaright[NmysaSec*k+8](1)
    connect node[k+1](0), mysaright[NmysaSec*k+9](1)    // PARA - NODE
}