User Guide

Installation

On Mac OS and Linux you can install from PyPI using Conda.

pip install --upgrade syndirella

Attention

Installation and usage have not been tested on Windows OS.

Setting Up

Once you have installed Syndirella, follow these steps to set it up:

1. Manifold API Key:

Syndirella uses Postera’s Manifold API to perform retrosynthesis searches of input scaffolds and superstructure searches of reactants. You can find more information on Manifold API access here.

Attention

A Manifold Pro account is required for API access.

Set the Manifold API key as an environment variable.

export MANIFOLD_API_KEY=[API_KEY]

2. Configuration of reaction constants (optional):

All reactions and alternative reaction/reactant specifications are formatted with SMIRKS or SMARTS. If you’d like to edit or add to the libraries, please feel free to add directly to the following files or open an issue and I can help in formatting SMARTS/SMIRKS strings to your needs as they can be quite finicky.

Reactions: Syndirella has >20 encoded reactions which you can find in RXN_SMIRKS_CONSTANTS.json.

Alternative Reactions: You can provide alternatives for reactions based on preference. Add them in ADDITIONAL_RXN_OPTIONS.json.

Alternative Reactants: If there are reactants for certain reactions that you prefer to use, you can add them in REACTANT_FILTER_CONSTANTS.json.

Please find more details and specification on editing these files in Reaction Constants.

Basic Usage

Elaborate a set of scaffolds using these steps:

1. Setup fragments and protein templates

Download the fragment hits from Fragalysis. In the download folder the important files are:

metadata.csv # contains short and long codes
target_name_combined.sdf # fragment poses with long code names
/aligned_files/fragment_name/fragment_name_apo-desolv.pdb # apo pdb used for placement

2. Create input csv

Syndirella can be run either in automatic or manual mode.

Automatic:

Scaffolds can be elaborated by routes automatically proposed by Manifold. An example template is at syndirella/syndirella_input_template.csv.

Required headers:

smiles:

smiles string of scaffold.

hit1:

string of short code (or any substring of short code found in the metadata.csv) of 1 fragment inspiring hit.

template:

path to apo protein template to use for placement.

compound_set:

string or int identifier.

Not required headers:

hitX:

string of short code of additional fragment inspiring hit.

Note

Any number of fragment inspirations can be used. You just need to specify in a seperate header. Ex. hit1, hit2, hit3, hit4, hit5.

Manual:

You can set the exact route to elaborate the scaffold with the reaction names, exact reactants, and number of steps in the route. An example template is at syndirella/syndirella_input_template_manual.csv.

Required headers:

smiles:

smiles string of scaffold.

hit1:

string of short code (or any substring of short code found in the metadata.csv) of 1 fragment inspiring hit.

template:

path to apo protein template to use for placement.

compound_set:

string or int identifier.

reaction_name_step1:

string of reaction name.

reactant_step1:

smiles string of reactant.

Not required headers:

reactant2_step1:

smiles string of second reactant in reaction step 1.

product_stepX:

smiles string of product of step X. Only required for internal or first step to specify reactant for next step. Not required if step is final step of route (as the scaffold is the final product).

reaction_name_stepX:

string of reaction name of step X.

reactant_stepX:

smiles string of reactant that is not a product of previous step.

hitX:

string of short code of additional fragment inspiring hit. Any number of hits can be used.

3. Run!

Run pipeline in automatic mode:

syndirella --input [path_to_automatic.csv] --output [path_to_output_dir] --templates [path_to_templates_dir]
--hits_path [path_to_fragments.sdf] --metadata [path_to_metadata.csv]
Run pipeline in manual mode:

Add --manual flag.

4. Outputs

Output directory structure:

🔑🔑🔑: Inchi key of scaffold. Example: ZJENMQHSGLZNHL-UHFFFAOYSA-N

output_dir
├── 🔑🔑🔑-scaffold-check # scaffold check directory per scaffold
│   └── scaffold-check
│       ├── scaffold-check.holo_minimised.pdb
│       ├── scaffold-check.minimised.json
│       └── scaffold-check.minimised.mol
├── 🔑🔑🔑 # directory per scaffold
│   ├── extra
│   │   ├── 🔑🔑🔑_[route_uuid]_[rxn_name]_r[reactant_num]_[step_num]of[total_steps].pkl.gz # reactants for step
│   │   └── continued for all steps...
│   ├── output
│   │   ├── 🔑🔑🔑_[route_uuid]_[num]-[stereoisomer]
│   │   │   ├── 🔑🔑🔑_[route_uuid]_[num]-[stereoisomer].mol
│   │   │   ├── 🔑🔑🔑_[route_uuid]_[num]-[stereoisomer].json # energy values
│   │   └── continued for all products...
│   ├── 🔑🔑🔑_[route_uuid]_[rxn_name]_products_[last_step]of[total_steps].pkl.gz & .csv # final products
│   ├── 🔑🔑🔑_[route_uuid]_[rxn_name]_products_[last_step]of[total_steps]_placements.pkl.gz & .csv # merged placements with products info
│   ├── 🔑🔑🔑_[route_uuid]_fragmenstein_placements.pkl.gz & .csv # fragmenstein output
│   └── 🔑🔑🔑_[route_uuid]_to_hippo.pkl.gz # full routes and placements
├── continued for all scaffolds...
└── [input_csv]_output_YYYYMMDD_HHMM.csv # summary stats of all scaffolds

Important output files:

[input_csv]_output_YYYYMMDD_HHMM.csv:

Summary stats of all scaffolds. Most columns are self-explanatory. The following columns might need clarification:

total_num_products_enumstereo:

Total number of products enumerated with stereochemistry in the final step. This is counting the number of unique products with stereochemistry, so if a product with same stereochemistry is generated multiple times via different routes it will only be counted once.

total_num_unique_products:

Total number of unique products without stereochemistry in the final step. If a product is generated multiple times by different routes it will only be counted once.

🔑🔑🔑_[route_uuid]_[rxn_name]_products_[last_step]of[total_steps]_placements.pkl.gz & .csv:

Merged placements with products info.

🔑🔑🔑_[route_uuid]_to_hippo.pkl.gz:

Full routes and placements.

Note

Placements of products are labeled succesful if:

  1. ΔΔG < 0.

  2. comRMSD < 2.0 Å.

  3. Pose of product passes PoseBusters intrageometry checks:

    • Bond lengths: The bond lengths in the input molecule are within 0.75 of the lower and 1.25 of the upper bounds determined by distance geometry.

    • Bond angles: The angles in the input molecule are within 0.75 of the lower and 1.25 of the upper bounds determined by distance geometry.

    • Planar aromatic rings: All atoms in aromatic rings with 5 or 6 members are within 0.25 Å of the closest shared plane.

    • Planar double bonds: The two carbons of aliphatic carbon–carbon double bonds and their four neighbours are within 0.25 Å of the closest shared plane.

    • Internal steric clash: The interatomic distance between pairs of non-covalently bound atoms is above 60% of the lower bound distance apart determined by distance geometry.

Usage Option: Only Place Scaffolds (or Specifically Don’t Place)

You can run Syndirella to only place scaffolds. It will not perform the full elaboration procedure.

syndirella --input [path_to_automatic.csv] --output [path_to_output_dir] --templates [path_to_templates_dir]
--hits_path [path_to_fragments.sdf] --metadata [path_to_metadata.csv] --scaffold_place

You can also specify to not place the scaffold (most likely you confirmed placement using another method).

syndirella --input [path_to_automatic.csv] --output [path_to_output_dir] --templates [path_to_templates_dir]
--hits_path [path_to_fragments.sdf] --metadata [path_to_metadata.csv] --no_scaffold_place

Usage Option: Only Get Retrosynthesis Routes of Scaffolds

You can run Syndirella to find the Top 5 retrosynthesis routes of the scaffolds. It will identify the routes that contains all reactions you have encoded in the RXN_SMIRKS_CONSTANTS.json file (a CAR route) and routes that don’t contain those reactions (non-CAR route).

syndirella --input [path_to_automatic.csv] --output [path_to_output_dir] --just_retro

Output file: [input_csv_name].pkl.gz

Note

You can read this file using pandas and reading it in as a pickle.

Structure of the important columns are:

routeX:

List of dictionaries of each step (X is an int) in the route with reaction names, reactants, and product.

routeX_names:

List of reaction names in the route.

routeX_CAR:

Boolean value if all reactions in route are in RXN_SMIRKS_CONSTANTS.json.

routeX_non_CAR:

List of reaction names that are not in RXN_SMIRKS_CONSTANTS.json. Or None if all reactions are in RXN_SMIRKS_CONSTANTS.json.

If there are NaN values for all above columns, it means that there are no routes found for the scaffold.

Command Line Interface

usage: syndirella [-h] -i INPUT -o OUTPUT [-t TEMPLATES] [--hits_path HITS_PATH] [--metadata METADATA] [--products PRODUCTS] [--batch_num BATCH_NUM] [--manual] [--scaffold_place] [--scaffold_place_num SCAFFOLD_PLACE_NUM]
                  [--profile] [--atom_diff_min ATOM_DIFF_MIN] [--atom_diff_max ATOM_DIFF_MAX] [--long_code_column LONG_CODE_COLUMN] [--just_retro]

Run the Syndirella pipeline with specified configurations.

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input .csv file path for the pipeline. (default: None)
  -o OUTPUT, --output OUTPUT
                        Output directory for the pipeline results. (default: None)
  -t TEMPLATES, --templates TEMPLATES
                        Absolute path to a directory containing the template(s). (default: None)
  --hits_path HITS_PATH
                        Absolute path to hits_path for placements (.sdf or .mol). (default: None)
  --metadata METADATA   Absolute path to metadata for placements. (default: None)
  --products PRODUCTS   Absolute path to products for placements. (default: None)
  --batch_num BATCH_NUM
                        Batch number for processing. (default: 10000)
  --manual              Use manual routes for processing. (default: False)
  --scaffold_place      Only place scaffolds. Do not continue to elaborate. (default: False)
  --scaffold_place_num SCAFFOLD_PLACE_NUM
                        Number of times to attempt scaffold placement. (default: 5)
  --profile             Run the pipeline with profiling. (default: False)
  --atom_diff_min ATOM_DIFF_MIN
                        Minimum atom difference between elaborations and scaffold to keep. (default: 0)
  --atom_diff_max ATOM_DIFF_MAX
                        Maximum atom difference between elaborations and scaffold to keep. (default: 10)
  --long_code_column LONG_CODE_COLUMN
                        Column name for long code in metadata csv to match to SDF name. The column can contain a substring for the SDF name. (default: Long code)
  --just_retro          Only run retrosynthesis querying of scaffolds. (default: False)
  --no_scaffold_place   Do not place scaffolds initially before elaborating, immediately start elaboration process. (default: False)

    Syndirella is installed at [path_to_installation]