From 02b107fac251a7f1bfb367d5e3873cbae06b9835 Mon Sep 17 00:00:00 2001 From: Jerry Date: Tue, 25 Jul 2023 15:49:07 -0700 Subject: [PATCH] bug fixes to allow code to run --- src/mcsce/libs/libenergy.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/mcsce/libs/libenergy.py b/src/mcsce/libs/libenergy.py index 0999ec5..de01978 100644 --- a/src/mcsce/libs/libenergy.py +++ b/src/mcsce/libs/libenergy.py @@ -149,7 +149,7 @@ def prepare_energy_function( if clash_term: vdw_radii_sum = calc_vdw_radii_sum(atom_labels[new_indices], atom_labels[old_indices]) - vdw_radii_sum *= 0.65 # The clash check parameter as defined in the SI of the MCSCE paper + vdw_radii_sum *= 0.6 # The clash check parameter as defined in the SI of the MCSCE paper vdw_radii_sum[bonds_1_mask] = 0 vdw_radii_sum = vdw_radii_sum[None] else: @@ -190,6 +190,8 @@ def prepare_energy_function( new_indices, old_indices, forcefield.forcefield, + N_terminal_indicators, + C_terminal_indicators, ) if coulomb_term: @@ -489,14 +491,16 @@ def create_Coulomb_params_raw( new_indices, old_indices, force_field, + n_terminal_indicators, + c_terminal_indicators, ): """Borrowed from IDP Conformer Generator package (https://github.com/julie-forman-kay-lab/IDPConformerGenerator) developed by Joao M. C. Teixeira""" charges_i_new = extract_ff_params_for_seq( atom_labels[new_indices], residue_numbers[new_indices], residue_labels[new_indices], - min(residue_numbers), - max(residue_numbers), + n_terminal_indicators[new_indices], + c_terminal_indicators[new_indices], force_field, 'charge', ) @@ -505,8 +509,8 @@ def create_Coulomb_params_raw( atom_labels[old_indices], residue_numbers[old_indices], residue_labels[old_indices], - min(residue_numbers), - max(residue_numbers), + n_terminal_indicators[old_indices], + c_terminal_indicators[old_indices], force_field, 'charge', )