objref apical_list, basal_list, dendrite_list, axon_list, myelin_list, node_list, soma_list, axonall_list
apical_list = new SectionList()
basal_list = new SectionList()
dendrite_list = new SectionList()
axon_list = new SectionList()
myelin_list = new SectionList()
node_list = new SectionList()
soma_list = new SectionList()
axonall_list = new SectionList()

forsec "a1_" basal_list.append()
forsec "a2_" basal_list.append()
forsec "a3_" basal_list.append()
forsec "a4_" basal_list.append()
forsec "a5_" basal_list.append()
forsec "a6_" basal_list.append()
forsec "a7_" basal_list.append()
forsec "a8_" basal_list.append()
forsec "a9_" basal_list.append()
forsec "a10_" basal_list.append()
forsec basal_list dendrite_list.append()

//commented out to try to speed up simulations
forsec "a11_" apical_list.append()
forsec apical_list dendrite_list.append()

forsec "soma" soma_list.append()

objref trunk_list
trunk_list = new SectionList()

//commented out to try to speed up simulations
a11_1 trunk_list.append()
a11_12 trunk_list.append()
a11_122 trunk_list.append()
a11_1222 trunk_list.append()
a11_12222 trunk_list.append()
a11_122222 trunk_list.append()
a11_1222222 trunk_list.append()
a11_12222222 trunk_list.append()
a11_12222221 trunk_list.append()
a11_122222211 trunk_list.append()
a11_122222212 trunk_list.append()


objref soma_prox_list, prox_dend_list
soma_prox_list = new SectionList()

a1_1 soma_prox_list.append()
a2_1 soma_prox_list.append()
a3_1 soma_prox_list.append()
a4_1 soma_prox_list.append()
a5_1 soma_prox_list.append()
a6_1 soma_prox_list.append()
a7_1 soma_prox_list.append()
a8_1 soma_prox_list.append()
a9_1 soma_prox_list.append()
a10_1 soma_prox_list.append()
// a11_1 is trunk; handle that separately.

prox_dend_list = new SectionList()
forsec soma_prox_list prox_dend_list.append()
a11_11 prox_dend_list.append()
a11_121 prox_dend_list.append()
a11_1221 prox_dend_list.append()
a11_12221 prox_dend_list.append()
a11_122221 prox_dend_list.append()
a11_1222221 prox_dend_list.append()
a11_122222222 prox_dend_list.append()
a11_122222221 prox_dend_list.append()
a11_1222222112 prox_dend_list.append()
a11_1222222111 prox_dend_list.append()
a11_1222222122 prox_dend_list.append()
a11_1222222121 prox_dend_list.append()

objref trunkInhibList
trunkInhibList = new SectionList()

a11_1 trunkInhibList.append()
a11_12 trunkInhibList.append()
a11_122 trunkInhibList.append()
a11_1222 trunkInhibList.append()
a11_12222 trunkInhibList.append()
a11_122222 trunkInhibList.append()


objref input_list		// needed by passive.hoc
input_list = new SectionList()
forsec soma_list input_list.append()
forsec trunkInhibList input_list.append()
forsec basal_list input_list.append()

objref spine_list
spine_list = new SectionList()

// leaf list
objref lsec, leaf_list, basal_leaves
leaf_list = new SectionList()
forsec dendrite_list {
    lsec = new SectionRef()
    if (!lsec.nchild) leaf_list.append()
}

//basal leaves
basal_leaves = new SectionList()
forsec leaf_list ifsec basal_list basal_leaves.append()