6.5. ligandparam.multiresp.intermolequiv

class ligandparam.multiresp.intermolequiv.IntermolEquiv(equiv_mask, unique_residues)

Bases: object

Class to handle the equivalent atoms between molecules

Methods

append(state, mdout)	Append a state to the IntermolEquiv class
get_unique_atoms([mask])	Get the unique atoms
get_unique_atoms_from_state(state[, mask])	Get the unique atoms from a state
print_equiv(fh)	Print the equivalent atoms

Initialize the IntermolEquiv class.

Parameters:

• equiv_mask (str) – The equivalent mask

• unique_residues (bool) – If True, use unique residues

Methods

append(state, mdout)	Append a state to the IntermolEquiv class
get_unique_atoms([mask])	Get the unique atoms
get_unique_atoms_from_state(state[, mask])	Get the unique atoms from a state
print_equiv(fh)	Print the equivalent atoms

append(state, mdout)

Append a state to the IntermolEquiv class

Parameters:

• state (str) – The state

• mdout (str) – The mdout file

get_unique_atoms(mask='@*')

Get the unique atoms

Parameters:

mask (str, optional) – The mask. Default is “@*”

Returns:

uatoms – The unique atoms

Return type:

list of int

get_unique_atoms_from_state(state, mask='@*')

Get the unique atoms from a state

Parameters:

• state (str) – The state

• mask (str, optional) – The mask. Default is “@*”

print_equiv(fh)

Print the equivalent atoms

Parameters:

fh (file) – The file handle

class ligandparam.multiresp.intermolequiv.RespMol(state, mdout, unique_residues)

Bases: object

Class to handle the RESP molecule

Methods

find_fitidx(name)	Find the fit index
get_selected_atoms(sele)	Get the selected atoms

Initialize the RespMol class

Parameters:

• state (str) – The state

• mdout (str) – The mdout file

• unique_residues (bool) – If True, use unique residues

Methods

find_fitidx(name)	Find the fit index
get_selected_atoms(sele)	Get the selected atoms

find_fitidx(name)

Find the fit index

Parameters:

name (str) – The name

Returns:

fitidx – The fit index

Return type:

int

get_selected_atoms(sele)

Get the selected atoms

Parameters:

sele (str) – The selection