parmed.amber.titratable_residues module

This module contains all of the information for the titratable residues, including reference energies, model compound pKas, and charge vectors for every titratable residue treated.

class parmed.amber.titratable_residues.TitratableResidue(resname, atom_list, typ, pka=None, eo=None)

Bases: object

A residue with different protonation states defined for Amber for use in the Constant pH MD method implemented in sander

Methods

add_state(charges, refene[, refene_old, …])	Add a single titratable state for this titratable residue
add_states(charges, refenes[, refenes_old, …])	Add multiple titratable states for this titratable residue
check()	Checks that the charges are consistent w/ the protonation states
cpin_pointers(first_atom)	Sets and returns the cpin info
reset()	Resets the pointers
set_first_charge(index)	Sets the first charge index
set_first_state(index)	Sets the first state index

add_state(charges, refene, refene_old=None, protcnt=None, pka_corr=None, eleccnt=None, eo_corr=None)

Add a single titratable state for this titratable residue

add_states(charges, refenes, refenes_old=None, protcnts=None, pka_corrs=None, eleccnts=None, eo_corrs=None)

Add multiple titratable states for this titratable residue

check()

Checks that the charges are consistent w/ the protonation states

cpin_pointers(first_atom)

Sets and returns the cpin info

reset()

Resets the pointers

set_first_charge(index)

Sets the first charge index

set_first_state(index)

Sets the first state index

class parmed.amber.titratable_residues.TitratableResidueList(system_name='Unknown', solvated=False, first_solvent=0)

Bases: list

List of all titratable residues

Methods

add_residue(residue, resnum, first_atom[, state])	Adds a residue to the list
append(object, /)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(iterable, /)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
set_states(statelist)	Sets the initial protonation states from a list – make sure there are enough states in the list to set every residue, or emit a warning
sort()	Sorts by residue number
write_cpin(output[, igb, intdiel, oldfmt, …])	Writes the CPIN file based on the titrated residues

add_residue(residue, resnum, first_atom, state=0)

Adds a residue to the list

set_states(statelist)

Sets the initial protonation states from a list – make sure there are enough states in the list to set every residue, or emit a warning

sort()

Sorts by residue number

write_cpin(output, igb=2, intdiel=1.0, oldfmt=False, typ='ph', coions=False)

Writes the CPIN file based on the titrated residues