6.3. ligandparam.multiresp.residueresp

This module is used to perform resp fitting for a molecule, based on multiple gaussian output files.

This was initially developed by Prof. Timothy Giese at Rutgers University, and was reproduced more or less in its entirety here (with modifications to the code for readibility and documentation). This code was initially meant for more options than are currently used by the ligand-param project, so some of the code may be redundant or not used.

class ligandparam.multiresp.residueresp.ResidueResp(comp, ires, theory='PBE0', basis='6-31G*', maxgrad=1e-06, etol=0.0001, fitgasphase=False)

Bases: object

This class is used to perform a residue-based resp fit.

Methods

add_state(prefix, parmfile, rstfiles[, qmmask])	Add a state to the residue resp object
apply_backbone_restraint([value])	Apply the backbone restraint to each state
apply_equiv_hydrogens([value])	Apply the equivalent hydrogens to each state
apply_equiv_nonbridge([value])	Apply the equivalent nonbridge to each state
apply_nucleobase_restraint([value])	Apply the nucleobase restraint to each state
apply_sugar_restraint([value])	Apply the sugar restraint to each state
clear_charge_data()	Clear the charge data from the states
multimolecule_fit([value])	Perform a multi-molecule fit
perform_fit([equiv_mask, unique_residues])	Perform the fit for each state
preserve_mm_charges_by_shifting(mm_mask)	Preserve the mm charges by shifting for each state
preserve_residue_charges_by_shifting()	Preserve the residue charges by shifting for each state
print_resp([fh])	Print the resp file for each state
read_respfile()	Read the resp file
write_mdin()	Write the mdin file

Initialize the ResidueResp object

Parameters:

• comp (BASH) – The computer object

• ires (int) – The residue number

• 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_state(prefix, parmfile, rstfiles[, qmmask])	Add a state to the residue resp object
apply_backbone_restraint([value])	Apply the backbone restraint to each state
apply_equiv_hydrogens([value])	Apply the equivalent hydrogens to each state
apply_equiv_nonbridge([value])	Apply the equivalent nonbridge to each state
apply_nucleobase_restraint([value])	Apply the nucleobase restraint to each state
apply_sugar_restraint([value])	Apply the sugar restraint to each state
clear_charge_data()	Clear the charge data from the states
multimolecule_fit([value])	Perform a multi-molecule fit
perform_fit([equiv_mask, unique_residues])	Perform the fit for each state
preserve_mm_charges_by_shifting(mm_mask)	Preserve the mm charges by shifting for each state
preserve_residue_charges_by_shifting()	Preserve the residue charges by shifting for each state
print_resp([fh])	Print the resp file for each state
read_respfile()	Read the resp file
write_mdin()	Write the mdin file

add_state(prefix, parmfile, rstfiles, qmmask=None)

Add a state to the residue resp object

TODO: Confirm meaning with TIM

Parameters:

• prefix (str) – The prefix of the state (e.g. the residue name)

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

• rstfiles (list of str) – A list of files (could be rst or gaussian log files)

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

apply_backbone_restraint(value=True)

Apply the backbone restraint to each state

Parameters:

value (bool, optional) – If True, apply the backbone restraint. Default is True

apply_equiv_hydrogens(value=True)

Apply the equivalent hydrogens to each state

Parameters:

value (bool, optional) – If True, apply the equivalent hydrogens. Default is True

apply_equiv_nonbridge(value=True)

Apply the equivalent nonbridge to each state

Parameters:

value (bool, optional) – If True, apply the equivalent nonbridge. Default is True

apply_nucleobase_restraint(value=True)

Apply the nucleobase restraint to each state

Parameters:

value (bool, optional) – If True, apply the nucleobase restraint. Default is True

apply_sugar_restraint(value=True)

Apply the sugar restraint to each state

Parameters:

value (bool, optional) – If True, apply the sugar restraint. Default is True

clear_charge_data()

Clear the charge data from the states

multimolecule_fit(value=True)

Perform a multi-molecule fit

Parameters:

value (bool, optional) – If True, perform a multi-molecule fit. Default is True

perform_fit(equiv_mask="@P,OP*,*'", unique_residues=True)

Perform the fit for each state

Parameters:

• equiv_mask (str, optional) – The equivalent mask. Default is “@P,OP*,*’”

• 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 for each state

preserve_residue_charges_by_shifting()

Preserve the residue charges by shifting for each state

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

Print the resp file for each state

read_respfile()

Read the resp file

write_mdin()

Write the mdin file