Adding Structures to your AaronTools Library#
AaronTools is packaged with a number of rings, ligands, and substituents in its built-in library. Here, you’ll find information about adding more items to your personal AaronTools library. These structures can be added manually, using the file formats outlined below. AaronTools also includes several commands line scripts for ripping these fragments from existing structure. SEQCROW’s “Add to Personal Library” tool is another alternative, though it will not be covered in detail here.
Ligands#
Adding Ligands to Your Personal Library#
A ligand can be added to your personal library with the libaddLigand command line script:
libaddLigand.py -n NAME input_file
Where NAME is the name of the ligand in the input file. The input file should contain a full catalyst system. Ligands coordinating transition metals in the input file are detected automatically. For organic catalyst systems, the input file’s comments need to specify more information about the catalyst. If multiple ligands are detected, the script will print the structures of each and ask which one to add.
As an example, we’ll use libaddLigand.py to add BIBOP to the ligand library.
Catalyst structures with BIBOP can be found in AARON’s enamide hydrogenation TS library.
To add BIBOP, run
libaddLigand.py -n BIBOP tsa1.xyz
In this case, AaronTools identifies just one ligand, so we are not be prompted to select which one it BIBOP.
Format of Ligand XYZ File#
The comment line of ligand XYZ files lists the indices of atoms on the ligand that should coordinate the catalytic center.
The BIBOP ligand from the example is
54
K:1,5
P 0.41498 -1.11215 -1.18749
C 1.79693 -0.41865 -2.27788
O 2.76389 -1.46670 -2.48890
H 1.40342 -0.13917 -3.26115
P 2.18693 1.15538 0.10888
C 2.50554 0.80418 -1.70926
O 2.04910 1.96131 -2.43228
H 3.58432 0.68998 -1.88908
C 2.08383 2.91265 -0.26432
C 1.99848 3.08127 -1.65069
C 1.82402 4.33766 -2.22289
H 1.76242 4.44221 -3.30097
C 1.96879 4.02337 0.57319
C 1.80790 5.28912 0.01494
H 1.73366 6.15937 0.65904
C 1.73362 5.43723 -1.37359
H 1.60088 6.42585 -1.80281
H 2.00250 3.90201 1.65322
C 1.36202 -2.62422 -0.97634
C 2.52739 -2.58666 -1.74596
C 3.43257 -3.64499 -1.74636
C 1.10758 -3.72469 -0.15532
C 2.00301 -4.78869 -0.14064
H 1.81312 -5.65075 0.49082
C 3.15305 -4.74318 -0.93716
H 4.33027 -3.59791 -2.35403
H 3.85106 -5.57532 -0.92001
H 0.22092 -3.73487 0.47349
C -0.99587 -1.52381 -2.35446
C -0.48415 -2.10862 -3.66912
C -1.77820 -0.23319 -2.59278
C -1.86266 -2.56173 -1.64071
H -1.34087 -2.43971 -4.26651
H 0.15914 -2.98008 -3.50649
H 0.06343 -1.37980 -4.27397
H -2.16296 0.18215 -1.65476
H -1.16435 0.53538 -3.07823
H -2.63127 -0.43779 -3.24990
H -1.35653 -3.53026 -1.57489
H -2.79206 -2.70734 -2.20309
H -2.13993 -2.24317 -0.63141
C 3.78735 0.78640 1.01020
C 4.92593 1.65939 0.48760
C 3.55268 1.06319 2.49603
C 4.09027 -0.69731 0.78584
H 5.12733 1.49574 -0.57608
H 4.72578 2.72479 0.63671
H 5.84324 1.41016 1.03247
H 4.45481 0.80173 3.05963
H 2.72160 0.47036 2.89051
H 3.34118 2.12071 2.68718
H 3.26858 -1.33779 1.12624
H 4.98818 -0.97219 1.35028
H 4.29203 -0.91719 -0.26916
Substituents#
Adding Substituents to Your Personal Library#
Note: for simple structure modification features (e.g., substitute.py), it might be more convenient to fetch the substituent from RDKit or a web API, which allow you to utilize substituents without adding them to your library.
Typically, this is done by prefixing a substituent name or SMILES with iupac: or smiles:.
See the --help page for the relevant command line script for more details.
New substituents can be added to your personal library with the libaddSubstituent.py command line script:
libaddSubstituent.py -n NAME -t TARGET -a AVOID -c CONFORMERS ANGLE input_file
When adding a new substituent, you should use a structure with the substituent connected to another atom.
The index of this atom should be used as AVOID for the libaddSubstituent.py script.
The substituent atom connected to the “avoid” atom is the TARGET.
The number of conformers for AARON’s hierarchical search and the angle between each conformer are CONFORMERS and ANGLE, respectively.
As an example, we’ll use libaddSubstituent.py to add a phenyl ring to our library starting from this toluene structure:
15
C -4.20339 -0.06691 -0.00131
C -4.19394 -1.46592 -0.00065
C -2.99654 0.64078 -0.00092
C -1.78023 -0.05054 0.00013
C -1.77078 -1.44955 0.00079
C -2.97763 -2.15724 0.00040
H -2.97032 -3.23955 0.00091
H -0.82981 -1.98437 0.00161
H -5.12759 -2.01341 -0.00096
H -5.14436 0.46792 -0.00213
H -3.00385 1.72310 -0.00143
C -0.45179 0.72846 0.00057
H -0.49330 1.54892 -0.74677
H 0.38697 0.04751 -0.25671
H -0.26821 1.16409 1.00552
The methyl group starts with atom 12 and connects to atom 4 of the phenyl ring. We’ll consider 2 conformers that are 90 degrees apart. To add this structure (from toluene.xyz), run
libaddSubstituent.py -n phenyl -t 4 -a 12 -c 2 90
Format of Substituent XYZ File#
The comment line of the XYZ file contains the conformer information. The first atom in the file is the atom that connects to the rest of the structure. The substituent is also oriented so that the bond to the molecule is along the x-axis. If this substituent is used with the Perl version of AARON/AaronTools, the distance from the origin to the first atom should be roughly the length of the carbon-X bond (X is the atom’s element).
The phenyl substituent from the example is
11
CF:2,90
C 1.49318 0.00000 -0.00000
C 2.15765 -1.20330 -0.28027
C 2.23789 1.15606 0.27517
C 4.28725 -0.09297 -0.01271
C 3.63039 1.10760 0.26979
C 3.54948 -1.24768 -0.28759
H 1.56687 -2.08812 -0.48996
H 4.06028 -2.18022 -0.50725
H 5.37268 -0.12853 -0.01823
H 4.20485 2.00355 0.48521
H 1.72026 2.08265 0.49524
Rings#
Adding Rings to Your Personal Library#
New rings can be added to your personal library with the libaddRing command line script:
libaddRing.py ring.xyz -n NAME -w WALK input_file
When adding a new ring, you should use a structure for a completed ring (e.g. for cyclohexane, your file should contain 18 atoms). You also need to decide which direction the ring should be traversed.
As an example, we’ll use libaddRing.py to add cyclohexane
(using the structure in Format of Ring Fragment XYZ File) to our personal library.
Let’s say we want AaronTools to go around the ring starting with atom 1 and going to atom 2. See the AaronTools library page for information on how AaronTools uses rings. We can add this to our personal library:
libaddRing.py cyclohexane.xyz -n my_cyclohexane -w 1,2
Format of Ring XYZ File#
When AaronTools finds a file with the appropriate name, it will then read the file’s comment for information about the direction to traverse the ring for when it’s attaching the ring fragment to another structure. An example cyclohexane ring fragment file is shown below:
18
E:1,2
C -3.39687 0.76221 0.28650
C -2.39066 -0.34691 -0.05366
C -0.97789 0.05976 0.39024
H -2.39597 -0.52733 -1.15140
H -2.68621 -1.28962 0.45473
C -2.98525 2.08048 -0.38512
H -3.43227 0.90413 1.38933
H -4.41088 0.46673 -0.05842
C -1.57248 2.48715 0.05878
H -3.70761 2.88019 -0.11466
H -3.00384 1.95424 -1.49026
C -0.56627 1.37802 -0.28139
H -0.25553 -0.73996 0.11977
H -0.95930 0.18600 1.49538
H -0.53087 1.23610 -1.38421
H 0.44774 1.67351 0.06354
H -1.56717 2.66757 1.15652
H -1.27693 3.42985 -0.44961
This is a six-membered ring. The atoms specified in the comment are used to determine which direction to “walk” around the ring. As shown below, AaronTools will start from atom 1 and go to atom 2:
