From 5a7b7cad0f8492daf3118111efd710627064e17b Mon Sep 17 00:00:00 2001 From: alongd Date: Sun, 21 Jul 2024 13:43:34 +0000 Subject: [PATCH] deploy: 08e7e93a069964c1898548795b26624cfa9a9bdb --- _modules/arc/species/conformers.html | 55 +++++++++++++++++++++++++-- api/conformers.html | 25 +++++++++++- genindex.html | 2 + objects.inv | Bin 6949 -> 6968 bytes searchindex.js | 2 +- 5 files changed, 78 insertions(+), 6 deletions(-) diff --git a/_modules/arc/species/conformers.html b/_modules/arc/species/conformers.html index a41ade8a21..393cb099dd 100644 --- a/_modules/arc/species/conformers.html +++ b/_modules/arc/species/conformers.html @@ -499,7 +499,7 @@

Source code for arc.species.conformers

     smeared_scan_res = smeared_scan_res or SMEARED_SCAN_RESOLUTIONS
     if not any(['torsion_dihedrals' in conformer for conformer in conformers]):
         conformers = determine_dihedrals(conformers, torsions)
-    torsion_angles = get_torsion_angles(label, conformers, torsions)  # get all wells per torsion
+    torsion_angles = get_torsion_angles(label, conformers, torsions, mol_list, tops)  # get all wells per torsion
     mol = mol_list[0]
 
     symmetries = dict()
@@ -1060,6 +1060,8 @@ 
Source code for arc.species.conformers
     smeared_scan_res = smeared_scan_res or SMEARED_SCAN_RESOLUTIONS
     sampling_points = list()
     wells = get_wells(label, torsion_angles, blank=WELL_GAP)
+    if symmetry % len(wells) == 0:
+        symmetry = len(wells)
     for i, well in enumerate(wells):
         width = abs(well['end_angle'] - well['start_angle'])
         mean = sum(well['angles']) / len(well['angles'])
@@ -1096,9 +1098,10 @@ 
Source code for arc.species.conformers
     mol = mol_list[0]
     top2 = [i + 1 for i in range(len(mol.atoms)) if i + 1 not in top1]
     for j, top in enumerate([top1, top2]):
-        # A quick bypass for methyl rotors which are too common:
+        # A quick bypass for carbon rotors that have three equal elements with only one bond that is connected to the carbon atom
         if len(top) == 4 and mol.atoms[top[0] - 1].is_carbon() \
-                and all([mol.atoms[top[i] - 1].is_hydrogen() for i in range(1, 4)]):
+                and all(mol.atoms[top[1] - 1].symbol == mol.atoms[top[i] - 1].symbol for i in range(2, 4)) \
+                    and all(len(mol.atoms[top[i] - 1].bonds) == 1 for i in range(1, 4)):
             symmetry *= 3
             check_tops[j] = 0
         # A quick bypass for methylene radicals:
@@ -1162,6 +1165,45 @@ 
Source code for arc.species.conformers
     return symmetry

 
 
+
[docs]def add_missing_symmetric_torsion_values(top1, mol_list, torsion_scan):
+    """
+    Add symmetry to a torsion scan in the rotor for efficient conformer generation.
+
+    Args:
+        top1 (list): A list of atom indices on one side of the torsion, including the pivotal atom.
+        mol_list (list): A list of molecules.
+        torsion_scan (list): The angles corresponding to this torsion from all conformers.
+
+    Returns:
+        torsion_scan (list): The modified torsion_scan with added symmetric angles.
+    """
+    mol = mol_list[0]
+    top2 = [i + 1 for i in range(len(mol.atoms)) if i + 1 not in top1]
+    for j, top in enumerate([top1, top2]):
+        # A quick bypass for carbon rotors that have three equal elements (e.g., CH3 or CF3) with only one bond that is connected to the carbon atom
+        # For such rotors, if a torsion angle difference of 60 degrees is found during the sampling, we would like to manually add this gap for the existing symmetries
+        if len(top) == 4 and mol.atoms[top[0] - 1].is_carbon() \
+                and all(mol.atoms[top[1] - 1].symbol == mol.atoms[top[i] - 1].symbol for i in range(2, 4)) \
+                    and all(len(mol.atoms[top[i] - 1].bonds) == 1 for i in range(1, 4)):
+
+            new_angles = []
+            for angle in torsion_scan:
+                test_angle = (angle + 60) % 360
+                if any((test_angle - 5) % 360 <= existing_angle <= (test_angle + 5) % 360 for existing_angle in torsion_scan):
+                    for angle_tba in torsion_scan:
+                        new_angle = (angle_tba + 60) % 360  # Calculate new angle and ensure it wraps around at 360
+                        # Check if the new angle, adjusted by ±30 degrees, overlaps with any existing angles
+                        if not any((new_angle - 30) % 360 <= existing_angle <= (new_angle + 30) % 360 for existing_angle in torsion_scan + new_angles):
+                            new_angles.append(new_angle)
+                            break
+    
+            # Extend the original list with non-overlapping new angles
+            torsion_scan.extend(new_angles)
+            torsion_scan.sort()  # Sort the list to maintain order
+
+    return torsion_scan

+
+
 
[docs]def determine_well_width_tolerance(mean_width):
     """
     Determine the tolerance by which well widths are determined to be nearly equal.
@@ -1241,7 +1283,7 @@ 
Source code for arc.species.conformers
     return lowest_confs

 
 
-
[docs]def get_torsion_angles(label, conformers, torsions):
+
[docs]def get_torsion_angles(label, conformers, torsions, mol_list=None, tops=None):
     """
     Populate each torsion pivots with all available angles from the generated conformers.
 
@@ -1249,6 +1291,8 @@ 
Source code for arc.species.conformers
         label (str): The species' label.
         conformers (list): The conformers from which to extract the angles.
         torsions (list): The torsions to consider.
+        mol_list (list, optional): A list of Molecule objects.
+        tops (list, optional): A list of tops corresponding to torsions.
 
     Returns:
         dict: The torsion angles. Keys are torsion tuples, values are lists of all corresponding angles from conformers.
@@ -1265,6 +1309,9 @@ 
Source code for arc.species.conformers
                 torsion_angles[tuple(torsion)].append(conformer['torsion_dihedrals'][tuple(torsion)])
     for tor in torsion_angles.keys():
         torsion_angles[tor].sort()
+    if mol_list is not None and tops is not None:
+        for torsion, top in zip(torsions, tops):
+            torsion_angles[tuple(torsion)] = add_missing_symmetric_torsion_values(top, mol_list, torsion_angles[tuple(torsion)])
     return torsion_angles

 
 
diff --git a/api/conformers.html b/api/conformers.html
index 5b11600ce2..bc0f90d159 100644
--- a/api/conformers.html
+++ b/api/conformers.html
@@ -218,6 +218,27 @@
     get_lowest_confs
 

 

+

+

+arc.species.conformers.add_missing_symmetric_torsion_values(top1, mol_list, torsion_scan)[source]

+
Add symmetry to a torsion scan in the rotor for efficient conformer generation.

+

+
Parameters:

+
    
+
  • top1 (list) – A list of atom indices on one side of the torsion, including the pivotal atom.
    • 
+
  • mol_list (list) – A list of molecules.
    • 
+
  • torsion_scan (list) – The angles corresponding to this torsion from all conformers.
    • 
+

+

+
Returns:

+
The modified torsion_scan with added symmetric angles.

+

+
Return type:

+
torsion_scan (list)

+

+

+

+
 

 

 arc.species.conformers.change_dihedrals_and_force_field_it(label, mol, xyz, torsions, new_dihedrals, optimize=True, force_field='MMFF94s')[source]

@@ -959,7 +980,7 @@
 
 

 

-arc.species.conformers.get_torsion_angles(label, conformers, torsions)[source]

+arc.species.conformers.get_torsion_angles(label, conformers, torsions, mol_list=None, tops=None)[source]
 
Populate each torsion pivots with all available angles from the generated conformers.

 

 
Parameters:

@@ -967,6 +988,8 @@
 
  • label (str) – The species’ label.
    • 
 
  • conformers (list) – The conformers from which to extract the angles.
    • 
 
  • torsions (list) – The torsions to consider.
    • 
+
  • mol_list (list, optional) – A list of Molecule objects.
    • 
+
  • tops (list, optional) – A list of tops corresponding to torsions.
    • 
 
 
    
 
    Returns:
    
diff --git a/genindex.html b/genindex.html
index 1f984dd5c1..28673f9a15 100644
--- a/genindex.html
+++ b/genindex.html
@@ -224,6 +224,8 @@ 
    A
    
       
  • add_label_to_unique_species_labels() (arc.scheduler.Scheduler method)
 
    • 
       
  • add_lone_pairs_by_atom_valance() (in module arc.species.converter)
+
    • 
+      
  • add_missing_symmetric_torsion_values() (in module arc.species.conformers)
 
    • 
       
  • add_rads_by_atom_valance() (in module arc.species.converter)
 
    • 
diff --git a/objects.inv b/objects.inv
index 81ca12bd7ea64f6ba9cdc6ad97b68fa549a528b0..c154c8d1ed02edd261cc610a3d14b7f6b0971a0d 100644
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diff --git a/searchindex.js b/searchindex.js
index fe91fa1444..a0f7c0796b 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"running.rst", "tools.rst"], "titles": ["Advanced Features", "arc.common", "arc.species.conformers", "arc.species.converter", "ARC\u2019s API", "arc.job", "arc.level", "arc.job.local", "arc.main", "arc.parser", "arc.plotter", "arc.processor", "arc.reaction", "arc.rmgdb", "arc.utils.scale", "arc.scheduler", "arc.species.species", "arc.job.ssh", "arc.job.trsh", "arc.species.vectors", "arc.species.zmat", "How to cite ARC", "Contribute", "Credits", "Examples", "ARC - Automated Rate Calculator v1.1.0", "Installation instructions", "Licence", "Media", "Output", "Release notes", "Running ARC", "Standalone tools"], "terms": {"The": [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 32], "attribut": [0, 1, 2, 3, 6, 8, 10, 12, 13, 15, 16], "arcspeci": [0, 3, 8, 10, 11, 12, 15, 16, 18, 24, 30, 31], "object": [0, 1, 2, 3, 6, 8, 9, 10, 11, 12, 13, 15, 16, 20, 31], "whether": [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27], "ts": [0, 1, 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