ion_charge · ion_register · ion_style

Ions

ion_style()

Python

Syntax:

oldstyle = n.ion_style("name_ion", c_style, e_style, einit, eadvance, cinit, sec=section)
oldstyle = n.ion_style("name_ion", sec=section)

Description:

In the section, force the named ion (eg. na_ion, k_ion, ca_ion, etc) to handle reversal potential and concentrations according to the indicated styles. You will not often need this function since the style chosen automatically on a per section basis should be appropriate to the set of mechanisms inserted in each section.

The oldstyle value is the previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. Additionally the two internal bit values of 128*ciwrite and 256*cowrite are present and set (not setable by user) only if the section has mechanisms that USEION WRITE the internal or external ion concentration, e.g. nai or nao. That is, to get the parameter values from oldstyle, use

c_style = oldstyle % 4
cinit = (oldstyle // 4) % 2
e_style = (oldstyle // 8) % 4
einit = (oldstyle // 32) % 2
eadvance = (oldstyle // 64) % 2
ci_is_written = (oldstyle // 128) % 2
co_is_written = (oldsytle // 256) % 2

c_style: 0, 1, 2, 3.

Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables. Determines which panel (if any) will show the concentrations.

e_style: 0, 1, 2, 3.

Reversal potential respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variable.

einit: 0 or 1.

If 1 then reversal potential computed by Nernst equation on call to finitialize() using values of concentrations.

eadvance: 0 or 1.

If 1 then reversal potential computed every call to fadvance() using the values of the concentrations.

cinit: 0 or 1.

If 1 then a call to finitialize() sets the concentrations to the values of the global initial concentrations. eg. nai set to n.nai0_na_ion and nao set to n.nao0_na_ion.

The automatic style is chosen based on how the set of mechanisms that have been inserted in a section use the ion. Note that the precedence is WRITE > READ > unused in the USEION statement; so if one mechanism READ’s cai/cao and another mechanism WRITE’s them then WRITE takes precedence in the following table. For compactness, the table assumes the ca ion. Each table entry identifies the equivalent parameters to the ion_style function.

cai/cao ->	unused	read	write
eca unused	0,0,0,0,0	1,0,0,0,0	3,0,0,0,1
eca read	0,1,0,0,0	1,2,1,0,0	3,2,1,1,1
eca write	0,2,0,0,0	1,2,0,0,0	3,2,0,0,1

For example suppose one has inserted a mechanism that READ’s eca, a mechanism that READ’s cai, cao and a mechanism that WRITE’s cai, cao Then, since WRITE takes precedence over READ in the above table, cai/cao would appear in the STATE variable panel (first arg is 3), eca would appear in the ASSIGNED variable panel (second arg is 2), eca would be calculated on a call to finitialize (third arg is 1), eca would be calculated on every call to fadvance (fourth arg is 1), cai/cao would be initialized (on finitialize) to the global variables cai0_ca_ion and cao0_ca_ion respectively. (note that this takes place just before the calculation of eca).

Warning

If other mechanisms are inserted subsequent to a call of this function, the style will be “promoted” according to the rules associated with adding the used ions to the style previously in effect.

Warning

If section is not specified, the style is set for the currently accessed section only (the section returned by n.cas()). In particular, this does not change the style for all sections. If you need to change for all sections, loop over the sections, e.g.,

for sec in n.allsec():
    n.ion_style("ca_ion", 3, 2, 1, 1, 1, sec=sec)

HOC

Syntax:

section {oldstyle = ion_style("name_ion", c_style, e_style, einit, eadvance, cinit)}
section {oldstyle = ion_style("name_ion")}

Description:

In the section, force the named ion (eg. na_ion, k_ion, ca_ion, etc) to handle reversal potential and concentrations according to the indicated styles. You will not often need this function since the style chosen automatically on a per section basis should be appropriate to the set of mechanisms inserted in each section.

The oldstyle value is the previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. That is, to get the parameter values from oldstyle, use c_style = oldstyle % 4, cinit = int(oldstyle / 4) % 2, e_style = int(oldstyle / 8) % 4, einit = int(oldstyle / 32) % 2, and eadvance = int(oldstyle / 64) % 2. Additionally the two internal bit values of 128*ciwrite and 256*cowrite are present and set (not setable by user) only if the section has mechanisms that USEION WRITE the internal or external ion concentration, e.g. nai or nao. That is, to get the parameter values from oldstyle, use c_style = oldstyle % 4, cinit = int(oldstyle / 4) % 2, e_style = int(oldstyle / 8) % 4, einit = int(oldstyle / 32) % 2, eadvance = int(oldstyle / 64) % 2, ciwrite = int(oldstyle / 128) % 2, and cowrite = int(oldstyle / 256) % 2.

c_style: 0, 1, 2, 3.

Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables. Determines which panel (if any) will show the concentrations.

e_style: 0, 1, 2, 3.

Reversal potential respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variable.

einit: 0 or 1.

If 1 then reversal potential computed by Nernst equation on call to finitialize() using values of concentrations.

eadvance: 0 or 1.

If 1 then reversal potential computed every call to fadvance() using the values of the concentrations.

cinit: 0 or 1.

If 1 then a call to finitialize() sets the concentrations to the values of the global initial concentrations. eg. nai set to nai0_na_ion and nao set to nao0_na_ion.

The automatic style is chosen based on how the set of mechanisms that have been inserted in a section use the ion. Note that the precedence is WRITE > READ > unused in the USEION statement; so if one mechanism READ’s cai/cao and another mechanism WRITE’s them then WRITE takes precedence in the following table. For compactness, the table assumes the ca ion. Each table entry identifies the equivalent parameters to the ion_style function.

cai/cao ->	unused	read	write
eca unused	0,0,0,0,0	1,0,0,0,0	3,0,0,0,1
eca read	0,1,0,0,0	1,2,1,0,0	3,2,1,1,1
eca write	0,2,0,0,0	1,2,0,0,0	3,2,0,0,1

For example suppose one has inserted a mechanism that READ’s eca, a mechanism that READ’s cai, cao and a mechanism that WRITE’s cai, cao Then, since WRITE takes precedence over READ in the above table, cai/cao would appear in the STATE variable panel (first arg is 3), eca would appear in the ASSIGNED variable panel (second arg is 2), eca would be calculated on a call to finitialize (third arg is 1), eca would be calculated on every call to fadvance (fourth arg is 1), cai/cao would be initialized (on finitialize) to the global variables cai0_ca_ion and cao0_ca_ion respectively. (note that this takes place just before the calculation of eca).

Warning

If other mechanisms are inserted subsequent to a call of this function, the style will be “promoted” according to the rules associated with adding the used ions to the style previously in effect.

Warning

If section is not specified, the style is set for the currently accessed section only. In particular, this does not change the style for all sections. If you need to change for all sections, loop over the sections, e.g.,

forall ion_style("ca_ion", 3, 2, 1, 1, 1)

MATLAB

Syntax:

oldstyle = n.ion_style("name_ion", c_style, e_style, einit, eadvance, cinit, section);
oldstyle = n.ion_style("name_ion", section);

Description:

In the section, force the named ion (eg. na_ion, k_ion, ca_ion, etc) to handle reversal potential and concentrations according to the indicated styles. You will not often need this function since the style chosen automatically on a per section basis should be appropriate to the set of mechanisms inserted in each section.

The oldstyle value is the previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. Additionally the two internal bit values of 128*ciwrite and 256*cowrite are present and set (not setable by user) only if the section has mechanisms that USEION WRITE the internal or external ion concentration, e.g. nai or nao. That is, to get the parameter values from oldstyle, use

] c_style = mod(oldstyle, 4);

cinit = mod(floor(oldstyle / 4), 2); e_style = mod(floor(oldstyle / 8), 4); einit = mod(floor(oldstyle / 32), 2); eadvance = mod(floor(oldstyle / 64), 2); ciwrite = mod(floor(oldstyle / 128) , 2); and cowrite = mod(floor(oldstyle / 256), 2);

c_style: 0, 1, 2, 3.

Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables. Determines which panel (if any) will show the concentrations.

e_style: 0, 1, 2, 3.

Reversal potential respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variable.

einit: 0 or 1.

If 1 then reversal potential computed by Nernst equation on call to finitialize() using values of concentrations.

eadvance: 0 or 1.

If 1 then reversal potential computed every call to fadvance() using the values of the concentrations.

cinit: 0 or 1.

If 1 then a call to finitialize() sets the concentrations to the values of the global initial concentrations. eg. nai set to n.nai0_na_ion and nao set to n.nao0_na_ion.

The automatic style is chosen based on how the set of mechanisms that have been inserted in a section use the ion. Note that the precedence is WRITE > READ > unused in the USEION statement; so if one mechanism READ’s cai/cao and another mechanism WRITE’s them then WRITE takes precedence in the following table. For compactness, the table assumes the ca ion. Each table entry identifies the equivalent parameters to the ion_style function.

cai/cao ->	unused	read	write
eca unused	0,0,0,0,0	1,0,0,0,0	3,0,0,0,1
eca read	0,1,0,0,0	1,2,1,0,0	3,2,1,1,1
eca write	0,2,0,0,0	1,2,0,0,0	3,2,0,0,1

For example suppose one has inserted a mechanism that READ’s eca, a mechanism that READ’s cai, cao and a mechanism that WRITE’s cai, cao Then, since WRITE takes precedence over READ in the above table, cai/cao would appear in the STATE variable panel (first arg is 3), eca would appear in the ASSIGNED variable panel (second arg is 2), eca would be calculated on a call to finitialize (third arg is 1), eca would be calculated on every call to fadvance (fourth arg is 1), cai/cao would be initialized (on finitialize) to the global variables cai0_ca_ion and cao0_ca_ion respectively. (note that this takes place just before the calculation of eca).

Warning

If other mechanisms are inserted subsequent to a call of this function, the style will be “promoted” according to the rules associated with adding the used ions to the style previously in effect.

Warning

If section is not specified, the style is set for the currently accessed section only (the section returned by n.cas()). In particular, this does not change the style for all sections. If you need to change for all sections, loop over the sections, e.g.,

for sec = n.allsec()
    n.ion_style("ca_ion", 3, 2, 1, 1, 1, sec);
end

---

ion_register()

Python

Syntax:

ion_type = n.ion_register("name", charge)

Description:

Create a new ion type with mechanism name, “name_ion”, and associated variables: iname, nameo, namei, ename, diname_dv. If any of these names already exists and name_ion is not already an ion, the function returns -1, otherwise it returns the mechanism type index. If name_ion is already an ion the charge is ignored but the type index is returned.

HOC

Syntax:

ion_type = ion_register("name", charge)

Description:

Create a new ion type with mechanism name, “name_ion”, and associated variables: iname, nameo, namei, ename, diname_dv. If any of these names already exists and name_ion is not already an ion, the function returns -1, otherwise it returns the mechanism type index. If name_ion is already an ion the charge is ignored but the type index is returned.

MATLAB

Syntax:

ion_type = n.ion_register("name", charge);

Description:

Create a new ion type with mechanism name, “name_ion”, and associated variables: iname, nameo, namei, ename, diname_dv. If any of these names already exists and name_ion is not already an ion, the function returns -1, otherwise it returns the mechanism type index. If name_ion is already an ion the charge is ignored but the type index is returned.

---

ion_charge()

Python

Syntax:

charge = n.ion_charge("name_ion")

Description:

Return the charge for the indicated ion mechanism. An error message is printed if name_ion is not an ion mechanism.

HOC

Syntax:

charge = ion_charge("name_ion")

Description:

Return the charge for the indicated ion mechanism. An error message is printed if name_ion is not an ion mechanism.

MATLAB

Syntax:

charge = n.ion_charge("name_ion");

Description:

Return the charge for the indicated ion mechanism. An error message is printed if name_ion is not an ion mechanism.