From 0ff829a1fca6a81e79ccbe39af6bb000273cddae Mon Sep 17 00:00:00 2001
From: Alon Grinberg Dana <alon@technion.ac.il>
Date: Sun, 18 Aug 2024 10:08:39 +0300
Subject: [PATCH 1/2] Organised imports in job trsh

---
 arc/job/trsh.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/arc/job/trsh.py b/arc/job/trsh.py
index df27442b5c..ade06a3675 100644
--- a/arc/job/trsh.py
+++ b/arc/job/trsh.py
@@ -4,11 +4,11 @@
 
 import math
 import os
+import re
 from typing import List, Optional, Tuple, Union
 
 import numpy as np
 import pandas as pd
-import re
 
 from arc.common import (check_torsion_change,
                         convert_to_hours,
@@ -18,18 +18,19 @@
                         get_number_with_ordinal_indicator,
                         is_same_pivot,
                         is_same_sequence_sublist,
-                        is_str_float
+                        is_str_float,
                         )
 from arc.exceptions import InputError, SpeciesError, TrshError
 from arc.imports import settings
-from arc.level import Level
 from arc.job.local import execute_command
 from arc.job.ssh import SSHClient
+from arc.level import Level
 from arc.species import ARCSpecies
 from arc.species.conformers import determine_smallest_atom_index_in_scan
-from arc.species.converter import (displace_xyz, ics_to_scan_constraints)
+from arc.species.converter import displace_xyz, ics_to_scan_constraints
 from arc.species.species import determine_rotor_symmetry
 from arc.species.vectors import calculate_dihedral_angle, calculate_distance
+
 from arc.parser import (parse_1d_scan_coords,
                         parse_normal_mode_displacement,
                         parse_scan_args,
@@ -37,7 +38,6 @@
                         parse_xyz_from_file,
                         )
 
-
 logger = get_logger()
 
 

From 82f6c480e29fbc51bc2a8b522a65bfc37cca5fb3 Mon Sep 17 00:00:00 2001
From: Alon Grinberg Dana <alon@technion.ac.il>
Date: Sun, 18 Aug 2024 10:10:17 +0300
Subject: [PATCH 2/2] BugFix: Only call conf_xyzs[min_index] if the length
 makes sense

---
 arc/job/trsh.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/arc/job/trsh.py b/arc/job/trsh.py
index ade06a3675..815296b93b 100644
--- a/arc/job/trsh.py
+++ b/arc/job/trsh.py
@@ -1537,8 +1537,9 @@ def scan_quality_check(label: str,
             # Find the dihedrals in degrees of the lowest conformer:
             min_index = np.argmin(energies)
             conf_xyzs = parse_1d_scan_coords(log_file)
-            actions = {'change conformer': conf_xyzs[min_index]}
-            return invalidate, invalidation_reason, message, actions
+            if len(conf_xyzs) > min_index:
+                actions = {'change conformer': conf_xyzs[min_index]}
+                return invalidate, invalidation_reason, message, actions
 
         # 1.3 Check consistency
         if 0 in changed_ic_dict.keys() and len(changed_ic_dict) == 1: