From 558ff9ee98c6e0905a654aa78e3c8099376d5186 Mon Sep 17 00:00:00 2001 From: clami66 Date: Tue, 27 Aug 2024 10:07:06 +0200 Subject: [PATCH 1/2] increased heuristic distance cutoff --- src/DockQ/operations.pyx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/DockQ/operations.pyx b/src/DockQ/operations.pyx index 7ac0fcd..282d8a9 100644 --- a/src/DockQ/operations.pyx +++ b/src/DockQ/operations.pyx @@ -27,9 +27,9 @@ def residue_distances(float [:,:] atom_coordinates1, float [:,:] atom_coordinate this_d = (atom_coordinates1[x][0] - atom_coordinates2[y][0])**2 + (atom_coordinates1[x][1] - atom_coordinates2[y][1])**2 + (atom_coordinates1[x][2] - atom_coordinates2[y][2])**2 if this_d < min_d: min_d = this_d - if min_d > 400.0: + if min_d > 1000.0: break - if min_d > 400.0: + if min_d > 1000.0: break res_distances[i, j] = min_d cum_j_atoms = cum_j_atoms + j_atoms From 622824f9d9fd7d34c9f1999421fe308bfaa9e35a Mon Sep 17 00:00:00 2001 From: clami66 Date: Tue, 27 Aug 2024 10:14:50 +0200 Subject: [PATCH 2/2] fix conversion of nucleic acids names --- src/DockQ/parsers.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/DockQ/parsers.py b/src/DockQ/parsers.py index 7135422..d63db71 100644 --- a/src/DockQ/parsers.py +++ b/src/DockQ/parsers.py @@ -208,7 +208,7 @@ def _build_structure(self, structure_id, chains, parse_hetatms): resname1 = ( seq1(current_resname, custom_map=custom_map) if len(current_resname) == 3 - else current_resname[:-1] + else current_resname[-1] if (len(current_resname) == 2) else current_resname ) @@ -432,7 +432,7 @@ def _parse_coordinates(self, coords_trailer, chains=[], parse_hetatms=False): resname1 = ( seq1(current_resname, custom_map=custom_map) if len(current_resname) == 3 - else current_resname[:-1] + else current_resname[-1] if (len(current_resname) == 2) else current_resname ) @@ -453,7 +453,7 @@ def _parse_coordinates(self, coords_trailer, chains=[], parse_hetatms=False): resname1 = ( seq1(current_resname, custom_map=custom_map) if len(current_resname) == 3 - else current_resname[:-1] + else current_resname[-1] if (len(current_resname) == 2) else current_resname )