6.4. ligandparam.multiresp.endstate

class ligandparam.multiresp.endstate.EndState(parmfile, rstfiles, comp, ires, qmmask=None, theory='PBE0', basis='6-31G*', maxgrad=1e-06, etol=0.0001, fitgasphase=False)

Bases: object

Class to handle the end state of a residue.

Methods

add_group_restraint(cmask[, q])	Add a group restraint to the residue.
append_esp(fh, mdout)	Append the ESP data to the file handle
append_esps(fh)	Append the ESP data to the file handle
apply_backbone_restraint([value])	Apply a backbone restraint to the residue.
apply_nucleobase_restraint([value])	Apply a nucleobase restraint to the residue.
apply_sugar_restraint([value])	Apply a sugar restraint to the residue.
clear_charge_data()	Clear the charge data for the residue.
get_mdouts()	Get the mdout files
get_resp_header()	Get the RESP header
multimolecule_fit([value])	Perform a multi-molecule fit
perform_fit([unique_residues])	Perform the fit
preserve_mm_charges_by_shifting(mm_mask)	Preserve the MM charges by shifting
preserve_residue_charges_by_shifting()	Preserve the residue charges by shifting
print_resp([prefix, fh])	Print the RESP charges
read_next_resp(fh)	Read the next set of RESP charges from the file handle
read_respfile()	Read the resp file
set_equiv_atoms(sele)	Set the equivalent atoms for the residue.
write_mdin()	Write the mdin files for the residue.

get_resp_body

Initialize the EndState object

Parameters:

• parmfile (str) – The name of the parameter file (either parm or mol2)

• rstfiles (list of str) – A list of files (could be rst or gaussian log files, specifically with .log or .rst7 extensions)

• comp (BASH) – The computer object

• ires (int) – The residue number

• qmmask (str, optional) – The quantum mask. Default is None

• theory (str) – The quantum theory used. Default is PBE0

• basis (str) – The basis set used. Default is 6-31G*

• maxgrad (float) – The maximum gradient. Default is 1.e-6

• etol (float) – The energy tolerance. Default is 0.0001

• fitgasphase (bool) – If True, fit the gas phase. Default is False

Methods

add_group_restraint(cmask[, q])	Add a group restraint to the residue.
append_esp(fh, mdout)	Append the ESP data to the file handle
append_esps(fh)	Append the ESP data to the file handle
apply_backbone_restraint([value])	Apply a backbone restraint to the residue.
apply_nucleobase_restraint([value])	Apply a nucleobase restraint to the residue.
apply_sugar_restraint([value])	Apply a sugar restraint to the residue.
clear_charge_data()	Clear the charge data for the residue.
get_mdouts()	Get the mdout files
get_resp_header()	Get the RESP header
multimolecule_fit([value])	Perform a multi-molecule fit
perform_fit([unique_residues])	Perform the fit
preserve_mm_charges_by_shifting(mm_mask)	Preserve the MM charges by shifting
preserve_residue_charges_by_shifting()	Preserve the residue charges by shifting
print_resp([prefix, fh])	Print the RESP charges
read_next_resp(fh)	Read the next set of RESP charges from the file handle
read_respfile()	Read the resp file
set_equiv_atoms(sele)	Set the equivalent atoms for the residue.
write_mdin()	Write the mdin files for the residue.

get_resp_body

add_group_restraint(cmask, q=None)

Add a group restraint to the residue.

Parameters:

• cmask (str) – The mask for the group

• q (float, optional) – The charge. Default is None

append_esp(fh, mdout)

Append the ESP data to the file handle

Parameters:

• fh (file handle) – The file handle to append the ESP data to

• mdout (str) – The mdout file

append_esps(fh)

Append the ESP data to the file handle

apply_backbone_restraint(value=True)

Apply a backbone restraint to the residue.

apply_nucleobase_restraint(value=True)

Apply a nucleobase restraint to the residue.

apply_sugar_restraint(value=True)

Apply a sugar restraint to the residue.

clear_charge_data()

Clear the charge data for the residue.

get_mdouts()

Get the mdout files

Returns:

mdouts – The list of mdout files

Return type:

list of str

get_resp_body()

get_resp_header()

Get the RESP header

multimolecule_fit(value=True)

Perform a multi-molecule fit

perform_fit(unique_residues=True)

Perform the fit

Parameters:

unique_residues (bool, optional) – If True, use unique residues. Default is True

preserve_mm_charges_by_shifting(mm_mask)

Preserve the MM charges by shifting

Parameters:

mm_mask (str) – The mask for the MM charges

preserve_residue_charges_by_shifting()

Preserve the residue charges by shifting

print_resp(prefix='', fh=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Print the RESP charges

Parameters:

• prefix (str, optional) – The prefix. Default is “”

• fh (file handle, optional) – The file handle. Default is sys.stdout

read_next_resp(fh)

Read the next set of RESP charges from the file handle

Parameters:

fh (file handle) – The file handle to read the charges from

read_respfile()

Read the resp file

set_equiv_atoms(sele)

Set the equivalent atoms for the residue.

write_mdin()

Write the mdin files for the residue.