From 7bfef18e0158235b3779a3c9ba6064e52436b918 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 11 Oct 2024 09:51:01 -0500 Subject: [PATCH 1/6] Update getting started guide, example script --- README.md | 148 ++++++++++++++++++++++++++++++++++++++++++++---------- run.py | 17 ++++--- 2 files changed, 131 insertions(+), 34 deletions(-) diff --git a/README.md b/README.md index 3196adb..5f0b0ca 100644 --- a/README.md +++ b/README.md @@ -1,63 +1,157 @@ -YAMMBS -====== +# YAMMBS Yet Another Molecular Mechanics Benchmarking Suite (YAMMBS, pronounced like "yams") is a tool for benchmarking force fields. -YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results. - -# Getting started +YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results. Feed back and contributions are welcome [on GitHub](https://github.com/openforcefield/yammbs) ## Installation Use the file `./devtools/conda-envs/dev.yaml` and also install `yammbs` with something like `python -m pip install -e .`. -## Data sources +## Getting started + +See the file `run.py` for a start-to-finish example. Note that the pattern in the script + +```python +from multiprocessing import freeze_support + +def main(): + # Your code here + +if __name__ == "__main__": + freeze_support() + main() +``` + +must be used for Python's `multiprocessing` module to behave well. + + +### Data sources + +It is assumed that the input molecules are stored in a `openff-qcsubmit` model like `OptimizationResultCollection` or YAMMBS's own input models. -It is assumed that the input molecules are stored in a `openff-qcsubmit` model like `OptimizationResultCollection`. +### Preparing an input dataset -## Key API points +YAMMBS relies on QCSumbit to provide datasets from QCArchive. See [their docs](https://docs.openforcefield.org/projects/qcsubmit/en/stable/), particularly the [dataset retrieval example](https://docs.openforcefield.org/projects/qcsubmit/en/stable/examples/retrieving-results.html), for more. -See the file `run.py` for a start-to-finish example. +Currently only optimization datasets (`OptimizationResultCollection` in QCSubmit) are supported. -Load a molecule dataset into the used representation: +First, retrieve a dataset from QCArchive: ```python -from yammbs import MoleculeStore +from qcportal import PortalClient + +from openff.qcsubmit.results import OptimizationResultCollection + -store = MoleculeStore.from_qcsubmit_collection( - collection=my_collection, - database_name="my_database.sqlite", +client = PortalClient("https://api.qcarchive.molssi.org:443", cache_dir=".") + +season1_dataset = OptimizationResultCollection.from_server( + client=client, + datasets="OpenFF Industry Benchmark Season 1 v1.1", + spec_name="default", ) + ``` -Run MM optimizations of all molecules using a particular force field +After retrieving it, probably after applying some filters, you can dump it to disk with `season1_dataset.json("qcsubmit.json")` to avoid pulling down all of the data from the server again. + +Once a `OptimizationResultCollection` is in memory, either by pulling it down from QCArchive or loading it from disk, convert it to a "YAMMBS input" model using the API: ```python -store.optimize_mm(force_field="openff-2.1.0.offxml") +from yammbs.inputs import QCArchiveDataset + + +season1_dataset = OptimizationResultCollection.parse_raw("qcsubmit.json") + +dataset = QCArchiveDataset.from_qcsubmit_collection(season1_dataset) + +dataset.model_dump_json("input.json") ``` -Run DDE (or RMSD, TFD, etc.) analyses and save to results disk: +This input model (`QCArchiveDataset`) stores a miniimum amount of information to use these QM geometries as reference structures. The dataset has fields for tagging the name and model version, but mostly stores a list of structures. Each QM-optimized structure is stored as a `QCArchiveMolecule` object which stores: + +* (Mapped) SMILES which can be used to regenerate the `openff.toolkit.Molecule` and similar objects +* QM-optimized geometry +* Final energy from QM optimization +* An ID uniquely defining this structure within the datasets + +Note: This JSON file ("input.json") is from a different model that the JSON file written from QCSUbmit - they are not interchangeable. + +Note: Both QCSubmit and YAMMBS rely on Pydantic for model validation and serialization. Even though both use V2 in packaging, YAMMBS uses the V2 API and (as of October 2024) QCSubmit still uses the V1 API. Usage like above should work fine; only esoteric use cases (in particular, defining a new model that has both YAMMBS and QCSubmit models as fields) should be unsupported. + +### Run a benchmark + +With the input prepared, create a `MoleculeStore` object: ```python -ddes = store.get_dde(force_field="openff-2.1.0.offxml") -ddes.to_csv(f"{force_field}-dde.csv") +from yammbs import MoleculeStore + +store = MoleculeStore.from_qcarchive_dataset(dataset) ``` -Note that the pattern in the script +This object is the focal point of running benchmarks; it stores the inputs (QM structures), runs minimizations with force field(s) of interest, stores the results (MM structures), and provides helper methods for use in analysis. + +Run MM optimizations of all molecules using a particular force field(s) using `optimize_mm`: ```python -from multiprocessing import freeze_support +store.optimize_mm(force_field="openff-2.1.0.offxml") -def main(): - # Your code here +# can also iterate over multiple force fields, and use more processors +for force_field in [ + "openff-1.0.0.offxml", + "openff-1.3.0.offxml", + "openff-2.0.0.offxml", + "openff-2.1.0.offxml", + "openff-2.2.1.offxml", + "gaff-2.11", + "de-force-1.0.1.offxml", +]: + store.optimize_mm(force_field=force_field, n_processes=16) +``` -if __name__ == "__main__": - freeze_support() - main() +This method short-circuits (i.e. does not run minimizations) if a force field's results are already stored. i.e. the Sage 2.1 optimizations in the loop will be skipped. + +There are "output" models that mirroring the input models, basically storing MM-minimized geometries without needing to re-load or re-optimize the QM geometries. This can again be saved out to disk as JSON: + +```python +store.get_outputs().model_dump_json("output.json") ``` -must be used for Python's `multiprocessing` module to behave well. +Summary metrics (including DDE, RMSD, TFD, and internal coordinate RMSDs) are available separately (in order to reduce file size when only summary statistics, and not whole molecular descriptions and geometries, are sought): + +```python +store.get_metrics().model_dump_json("metrics.json") +``` + +The basic structure of the metrics is a hierarchical dictionary. It is keyed by force field tag (i.e. "openff-2.2.1") mapping on to a dict of per-molecule summary metrics. Each of these dicts are keyed by QCArchvie ID (the same ID used to distinguish structures in the input and output models) mapping onto a dict of string-float keys that store the actual metrics (i.e. the DDE, RMSD, etc. of this particular structure optimized with the force field used as its high-level key). Access to these data is similar in memory (on the Pydantic models) and on disk (in JSON). Visually: + +```json +{ + "metrics": { + "openff-1.0.0": { + "37016854": { + "dde": 0.5890449032115157, + "rmsd": 0.011969891530473157, + "tfd": 0.001592046369769131, + "icrmsd": { + "Bond": 0.0033974261816308144, + "Angle": 0.9483605366613115, + "Dihedral": 1.353163675708829, + "Improper": 0.2922040744956022, + }, + }, + "37016855": {"this molecule's metrics ..."}, + }, + "openff-2.0.0": { + "37016855": {"this force field's molecules ..."}, + } + } +} +``` + +This data can be transformed for plotting, summary statistics, etc. which compare the metrics of each force field (for this molecule dataset). ### License diff --git a/run.py b/run.py index 6280435..a94ec2f 100644 --- a/run.py +++ b/run.py @@ -22,16 +22,19 @@ def main(): "de-force-1.0.1.offxml", ] - data = "ch" + # pre-processed data is stored in the repository, just a larger dataset + # filtered by elements, takes values of "ch" (~40) and "cho" (~1600 molecules) + data_key = "ch" - dataset = QCArchiveDataset.parse_file(f"yammbs/_tests/data/yammbs/01-processed-qm-{data}.json") + dataset = QCArchiveDataset.model_validate_json(f"yammbs/_tests/data/yammbs/01-processed-qm-{data_key}.json") - if pathlib.Path(f"{data}.sqlite").exists(): - store = MoleculeStore(f"{data}.sqlite") + # This file is also store at f"yammbs/_tests/data/yammbs/01-processed-qm-{data_key}.json" + if pathlib.Path(f"{data_key}.sqlite").exists(): + store = MoleculeStore(f"{data_key}.sqlite") else: store = MoleculeStore.from_qm_dataset( dataset, - database_name=f"{data}.sqlite", + database_name=f"{data_key}.sqlite", ) for force_field in force_fields: @@ -40,10 +43,10 @@ def main(): store.optimize_mm(force_field=force_field, n_processes=10) with open("minimized.json", "w") as f: - f.write(store.get_outputs().json()) + f.write(store.get_outputs().model_dump_json()) with open("metrics.json", "w") as f: - f.write(store.get_metrics().json()) + f.write(store.get_metrics().model_dump_json()) plot(force_fields) From 9926923a58db40380f644fe38d41f19f91fd7c52 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 11 Oct 2024 11:29:54 -0500 Subject: [PATCH 2/6] Update quickstart guide, add example notebook Co-authored-by: Lexie McIsaac --- README.md | 6 + examples.ipynb | 5238 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 5244 insertions(+) create mode 100644 examples.ipynb diff --git a/README.md b/README.md index 5f0b0ca..1f797a1 100644 --- a/README.md +++ b/README.md @@ -77,6 +77,8 @@ This input model (`QCArchiveDataset`) stores a miniimum amount of information to * Final energy from QM optimization * An ID uniquely defining this structure within the datasets +If running many benchmarks, we recommend using this file as a starting point. + Note: This JSON file ("input.json") is from a different model that the JSON file written from QCSUbmit - they are not interchangeable. Note: Both QCSubmit and YAMMBS rely on Pydantic for model validation and serialization. Even though both use V2 in packaging, YAMMBS uses the V2 API and (as of October 2024) QCSubmit still uses the V1 API. Usage like above should work fine; only esoteric use cases (in particular, defining a new model that has both YAMMBS and QCSubmit models as fields) should be unsupported. @@ -153,6 +155,10 @@ The basic structure of the metrics is a hierarchical dictionary. It is keyed by This data can be transformed for plotting, summary statistics, etc. which compare the metrics of each force field (for this molecule dataset). +## Custom analyses + +See `examples.ipynb` for some examples of interacting with benchmarking results and a starting point for custom analyses. + ### License YAMMBS is open-source software distrubuted under the MIT license (see LICENSE). It derives from diff --git a/examples.ipynb b/examples.ipynb new file mode 100644 index 0000000..06c43ab --- /dev/null +++ b/examples.ipynb @@ -0,0 +1,5238 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "d3fbabbd-f14a-4906-8925-a46b3e9b7a94", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:13:43.626103Z", + "iopub.status.busy": "2024-10-11T01:13:43.624657Z", + "iopub.status.idle": "2024-10-11T01:13:58.278389Z", + "shell.execute_reply": "2024-10-11T01:13:58.277869Z", + "shell.execute_reply.started": "2024-10-11T01:13:43.626046Z" + } + }, + "source": [ + "# YAMMBS Examples\n", + "\n", + "This notebook contains demonstrates some usage of the YAMMBS API." + ] + }, + { + "cell_type": "markdown", + "id": "0ca9fe29", + "metadata": {}, + "source": [ + "Download an existing database, complete with MM optimizations, from this url:\n", + "\n", + "https://zenodo.org/records/13920527/files/sample-store.sqlite" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "fbec333c-f6e4-48e0-acd7-32385fb804fc", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:13:58.280482Z", + "iopub.status.busy": "2024-10-11T01:13:58.279450Z", + "iopub.status.idle": "2024-10-11T01:13:58.302292Z", + "shell.execute_reply": "2024-10-11T01:13:58.301793Z", + "shell.execute_reply.started": "2024-10-11T01:13:58.280466Z" + } + }, + "outputs": [], + "source": [ + "from yammbs import MoleculeStore\n", + "\n", + "store = MoleculeStore(\"sample-store.sqlite\")" + ] + }, + { + "cell_type": "markdown", + "id": "96ad5884-5234-4e11-ab7f-3287b2aa9438", + "metadata": {}, + "source": [ + "From the `store` object, we can see which forcefield(s) were benchmarked:" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "35fbc3d2-b5d6-41d8-8c4d-7c6a6fb3ec2c", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:16:16.419661Z", + "iopub.status.busy": "2024-10-11T01:16:16.408214Z", + "iopub.status.idle": "2024-10-11T01:16:16.612084Z", + "shell.execute_reply": "2024-10-11T01:16:16.611602Z", + "shell.execute_reply.started": "2024-10-11T01:16:16.419594Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "['openff_unconstrained-2.2.0-rc1.offxml']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_force_fields()" + ] + }, + { + "cell_type": "markdown", + "id": "ff1c0e73", + "metadata": {}, + "source": [ + "More force fields could be benchmarked (but this takes hours on HPC, so it may not be wise to do locally!)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "865b5a66", + "metadata": {}, + "outputs": [], + "source": [ + "run_more = False\n", + "\n", + "if run_more:\n", + " for force_field in [\n", + " \"openff-1.0.0.offxml\",\n", + " \"openff-2.0.0.offxml\",\n", + " \"openff-2.1.0.offxml\",\n", + " \"openff-2.3.0.offxml\",\n", + " ]:\n", + " store.optimize_mm(\n", + " force_field=force_field,\n", + " n_processes=16,\n", + " )" + ] + }, + { + "cell_type": "markdown", + "id": "3daeabe0-d603-4ac2-a503-c6163e37953a", + "metadata": {}, + "source": [ + "## Searching for molecules and interconverting molecular identifiers" + ] + }, + { + "cell_type": "markdown", + "id": "eb81ace5-1aae-487f-b1a5-70a52bff116d", + "metadata": {}, + "source": [ + "Multi-conformer molecules are stored and labeled by a `molecule_id` specific to this database/`MoleculeStore` representation. Conformers, both QM- and MM-optimized, are stored separately.\n", + "\n", + "Get the molecule IDs:" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "50f89868-e61d-4a2b-9313-0db07a0f70a9", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:16:23.658963Z", + "iopub.status.busy": "2024-10-11T01:16:23.658217Z", + "iopub.status.idle": "2024-10-11T01:16:23.708118Z", + "shell.execute_reply": "2024-10-11T01:16:23.707579Z", + "shell.execute_reply.started": "2024-10-11T01:16:23.658909Z" + }, + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/plain": [ + "[1,\n", + " 2,\n", + " 3,\n", + " 4,\n", + " 5,\n", + " 6,\n", + " 7,\n", + " 8,\n", + " 9,\n", + " 10,\n", + " 11,\n", + " 12,\n", + " 13,\n", + " 14,\n", + " 15,\n", + " 16,\n", + " 17,\n", + " 18,\n", + " 19,\n", + " 20,\n", + " 21,\n", + " 22,\n", + " 23,\n", + " 24,\n", + " 25,\n", + " 26,\n", + " 27,\n", + " 28,\n", + " 29,\n", + " 30,\n", + " 31,\n", + " 32,\n", + " 33,\n", + " 34,\n", 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+ " 964,\n", + " 965,\n", + " 966,\n", + " 967,\n", + " 968,\n", + " 969,\n", + " 970,\n", + " 971,\n", + " 972,\n", + " 973,\n", + " 974,\n", + " 975,\n", + " 976,\n", + " 977,\n", + " 978,\n", + " 979,\n", + " 980,\n", + " 981,\n", + " 982,\n", + " 983,\n", + " 984,\n", + " 985,\n", + " 986,\n", + " 987,\n", + " 988,\n", + " 989,\n", + " 990,\n", + " 991,\n", + " 992,\n", + " 993,\n", + " 994,\n", + " 995,\n", + " 996,\n", + " 997,\n", + " 998,\n", + " 999,\n", + " 1000,\n", + " ...]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_molecule_ids()" + ] + }, + { + "cell_type": "markdown", + "id": "06cf4089", + "metadata": {}, + "source": [ + "Molecules' SMILES and InChI keys are also stored and can be retrieved:" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "497fa14b-bc22-4ba7-9e70-f44512b71399", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:17:07.386955Z", + 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'[H:47][c:21]1[c:20]([c:17]([c:16]([c:15]2[c:14]1[N:12]([C:10](=[O:11])[N:9]([C:22]2=[O:23])[C:8]([H:37])([H:38])[C:7]([H:35])([H:36])[C:6]([H:33])([H:34])[O:5][C:4]([H:31])([H:32])[C:3]([H:29])([H:30])[C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[C:13]([H:39])([H:40])[H:41])[H:42])[O:18][C:19]([H:43])([H:44])[H:45])[H:46]',\n", + " '[H:64][c:34]1[c:35]([c:36]([n:37][c:32]([c:33]1[H:63])[c:29]2[c:28]([c:27]([c:26]([c:31]([c:30]2[H:61])[H:62])[c:23]3[c:22]([c:21]([c:20]([c:25]([c:24]3[H:57])[H:58])[N:19]([H:54])[C:17](=[O:18])[C:16]([H:52])([H:53])[C:15]([H:50])([H:51])[N:14]([H:49])[S:11](=[O:12])(=[O:13])[c:7]4[c:5]([c:4]([c:3]([c:10]([c:8]4[C:9]([H:45])([H:46])[H:47])[H:48])[O:2][C:1]([H:38])([H:39])[H:40])[H:41])[C:6]([H:42])([H:43])[H:44])[H:55])[H:56])[H:59])[H:60])[H:66])[H:65]',\n", + " '[H:47][c:25]1[c:24]([c:23]([c:22]([c:27]([c:26]1[H:48])[H:49])[c:19]2[c:18]([c:17]([c:16]([c:21]([c:20]2[H:43])[H:44])[C:14](=[O:15])[N:11]3[C:10]([C:9]([C:8]([C:13]([C:12]3([H:37])[H:38])([H:39])[H:40])([H:32])[c:5]4[c:6]([c:7]([c:2]([n:3][n:4]4)[N:1]([H:28])[H:29])[H:31])[H:30])([H:33])[H:34])([H:35])[H:36])[H:41])[H:42])[H:45])[H:46]',\n", + " '[H:44][c:16]1[c:17]([c:18]([n:19][c:20]([c:15]1[C@:4]([C:6]2=[N:7][O:8][C:9](=[N:14]2)[N:10]([H:38])[C:11]([H:39])([H:40])[C:12]([H:41])([H:42])[O:13][H:43])([C:5]([H:35])([H:36])[H:37])[C:2]([H:31])([C:1]([H:28])([H:29])[H:30])[C:3]([H:32])([H:33])[H:34])[H:46])[c:21]3[c:22]([n:23][c:24]([n:26][c:27]3[H:50])[N:25]([H:48])[H:49])[H:47])[H:45]',\n", + " '[H:43][c:19]1[c:18]([c:17]2[c:22]([c:23]([c:9]([n:10][c:11]2[N:12]([H:33])[C:13]([H:34])([H:35])[C:14]([H:36])([H:37])[C:15]([H:38])([H:39])[N:16]([H:40])[H:41])[c:5]3[c:4]([c:3]([c:2]([c:7]([c:6]3[H:29])[C:8]([H:30])([H:31])[H:32])[C:1]([H:24])([H:25])[H:26])[H:27])[H:28])[H:45])[n:21][c:20]1[H:44])[H:42]',\n", + " '[H:30][c:4]1[c:3]([c:2]([c:27]([c:26]([c:5]1[N:6]([H:31])[C:7]([H:32])([H:33])[O:8][c:9]2[c:10]([c:11]3[c:16]([c:17]([c:18]2[O:19][C@:20]4([C:21]([C:22]([C:23]([O:24][C:25]4([H:45])[H:46])([H:43])[H:44])([H:41])[H:42])([H:39])[H:40])[H:38])[H:37])[c:15]([n:14][c:13]([n:12]3)[H:35])[H:36])[H:34])[H:47])[Cl:28])[F:1])[H:29]',\n", + " '[H:29][c:8]1[c:9]([c:4]([c:5]([c:6]2[c:7]1[c:10]([c:11]([c:24]([c:25]2[H:37])[H:36])[N:12]([H:32])[S:13](=[O:14])(=[O:15])[c:16]3[c:17]([c:18]([c:20]([c:21]([c:23]3[H:35])[Cl:22])[H:34])[Cl:19])[H:33])[H:31])[H:28])[C:2](=[O:3])[N:1]([H:26])[H:27])[H:30]',\n", + " '[H:27][C:8]1=[C:7]([C:12]([C:11]([C:10]([C:9]1([H:28])[H:29])([H:30])[H:31])([H:32])[H:33])([H:34])[H:35])[C:6]([H:25])([H:26])[N:5]2[C:4]3=[C:3]([N:15]=[C:13]2[Cl:14])[N:2]([C:20](=[O:21])[N:18]([C:16]3=[O:17])[C:19]([H:36])([H:37])[H:38])[C:1]([H:22])([H:23])[H:24]',\n", + " '[H:34][c:10]1[c:9]([c:8]([c:22]([c:21]([c:11]1[C:12]([H:35])([H:36])[N:13]([H:37])[C:14](=[O:15])[C@@:16]([C:17]([H:38])([H:39])[H:40])([C:19]([H:43])([H:44])[O:20][H:45])[N:18]([H:41])[H:42])[H:46])[H:47])[O:7][c:6]2[c:23]([c:24]([c:3]([c:4]([c:5]2[C:25]([F:26])([F:27])[F:28])[H:32])[O:2][C:1]([H:29])([H:30])[H:31])[H:49])[H:48])[H:33]',\n", + " '[H:34][c:11]1[c:12]([c:14]([n:15][c:16]2[c:10]1[O:9][C:8](=[C:7]2[N:6]([H:33])[C:4](=[O:5])[O:3][C:2]([H:31])([H:32])[C:1]([H:28])([H:29])[H:30])[C:23](=[O:24])[O:25][C:26]([H:43])([H:44])[C:27]([H:45])([H:46])[H:47])[C:17]3=[C:18]([N:19]([N:21]=[C:22]3[H:42])[C:20]([H:39])([H:40])[H:41])[H:38])[C:13]([H:35])([H:36])[H:37]',\n", + " 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'[H:37][c:17]1[c:16]([c:15]([c:14]([c:19]([c:18]1[H:38])[H:39])[C@@:11]([H:12])([C:13]([H:32])([H:33])[H:34])[N:10]([H:31])[c:9]2[c:20]3[c:21]([c:22]([c:3]([c:4]([c:5]3[n:6][c:7]([n:8]2)[H:30])[H:29])[O:2][C:1]([H:26])([H:27])[H:28])[N+:23](=[O:25])[O-:24])[H:40])[H:35])[H:36]',\n", + " '[H:50][c:23]1[c:24]([c:25]([c:27]([c:28]([c:22]1[C:21]([H:48])([H:49])[N:20]([H:47])[C:18](=[O:19])[C:15]2([C:14]([C:13]([N:12]([C:17]([C:16]2([H:43])[H:44])([H:45])[H:46])[S:9](=[O:10])(=[O:11])[c:4]3[c:3]([c:2]([c:8]([c:6]([c:5]3[H:33])[C:7]([H:34])([H:35])[H:36])[H:37])[C:1]([H:29])([H:30])[H:31])[H:32])([H:38])[H:39])([H:40])[H:41])[H:42])[H:53])[H:52])[F:26])[H:51]',\n", + " 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'[H:35][c:22]1[c:21]([c:20]([c:19]([c:24]([c:23]1[H:36])[H:37])[C:16]2=[N:17][N:18]([C:14]3=[C:15]2[C@:10]([N:11]([C:12]3=[O:13])[H:31])([H:30])[c:6]4[c:7]([c:8]([c:9]([c:4]([c:5]4[H:26])[C:2](=[O:3])[O:1][H:25])[H:29])[H:28])[H:27])[H:32])[H:33])[H:34]',\n", + " '[H:42][c:20]1[c:19]([c:18]([c:17]([c:16]2[c:15]1[C:14](=[C:13]3[N:12]2[C:11]([C@@:6]4([C:9](=[O:10])[C:8]([C:7]4([H:33])[H:34])([H:35])[H:36])[C:5]([N:4]([C@:3]3([H:29])[C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[H:30])([H:31])[H:32])([H:37])[H:38])[H:39])[H:40])[C:21](=[O:23])[O:22][H:43])[H:41]',\n", + " '[H:35][c:6]1[c:7]([c:2]([c:3]([c:4]([c:5]1[C@@:8]2([C@:10]3([C:9]2([H:38])[H:39])[c:15]4[c:16]([c:17]([c:18]([c:20]([c:14]4[N:13]([C:11]3=[O:12])[H:40])[H:42])[Cl:19])[S:21](=[O:22])(=[O:23])[N:24]([H:43])[C:25]5([C:26]([C:27]5([H:47])[H:48])([H:45])[H:46])[H:44])[H:41])[H:37])[H:34])[C:28](=[O:30])[O:29][H:49])[C:1]([H:31])([H:32])[H:33])[H:36]',\n", + " 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'[H:44][c:14]1[c:15]([c:9]([n:10][c:11]([c:13]1[c:16]2[c:17]([c:18]([c:19]3[c:27]([n:28]2)[C:22]4([C:23]([C:24]([C:25]([C:26]4([H:57])[H:58])([H:55])[H:56])([H:53])[H:54])([H:51])[H:52])[C:21]([N:20]3[H:48])([H:49])[H:50])[H:47])[H:46])[C:12]([H:41])([H:42])[H:43])[N:7]5[C:8]([C@@:3]([C:4]([C:5]([C:6]5([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:32])[O:2][C:1]([H:29])([H:30])[H:31])([H:39])[H:40])[H:45]',\n", + " '[H:40][c:22]1[c:21]([c:20]([c:18]([c:17]([c:23]1[H:41])[C:14]2=[C:15]([S:16][C:12](=[N:13]2)[N:9]3[C:10]([C@:11]4([C@@:7]([C:8]3([H:31])[H:32])([C:6]4([H:29])[C:4](=[O:5])[O:3][C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[H:30])[H:35])([H:33])[H:34])[H:36])[O:19][H:37])[H:38])[H:39]',\n", + " 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'[H:47][c:17]1[c:18]([c:19]([c:20]([c:21]([c:16]1[C:15]([H:45])([H:46])[C@:13]([H:14])([C:28](=[O:29])[N:30]([C:31]([H:59])([H:60])[H:61])[C:32]([H:62])([H:63])[H:64])[O:12][C:10](=[O:11])[C@:3]([H:4])([C:5]([H:37])([H:38])[C:6]([C:7]([H:39])([H:40])[H:41])([C:8]([H:42])([H:43])[H:44])[F:9])[N:2]([H:36])[C:1]([H:33])([H:34])[H:35])[H:50])[H:49])[N:22]2[C:23]([C:24]([O:25][C:26]([C:27]2([H:57])[H:58])([H:55])[H:56])([H:53])[H:54])([H:51])[H:52])[H:48]',\n", + " '[H:38][c:15]1[c:16]([c:17]([c:18]2[c:13]([c:14]1[H:37])[c:12]([c:11]([c:10]([c:9]2[C:8]([H:32])([H:33])[N:7]3[c:19]4[c:20]([c:21]([c:22]([c:23]([c:24]4[N:4]([C:5]3=[O:6])[C:3]([H:30])([H:31])[C:2]([H:28])([H:29])[C:1]([H:25])([H:26])[H:27])[H:44])[H:43])[H:42])[H:41])[H:34])[H:35])[H:36])[H:40])[H:39]',\n", + " '[H:33][c:5]1[c:6]([c:7]([c:25]([c:27]([c:4]1[C@:2]([H:31])([C:1]([H:28])([H:29])[H:30])[O:3][H:32])[H:54])[Cl:26])[O:8][c:9]2[c:10]([c:11]([c:12]([c:23]([c:24]2[H:53])[H:52])[C:13]([H:37])([H:38])[N:14]([H:39])[C:15](=[O:16])[C@@:17]([H:40])([C:18]([H:41])([H:42])[H:43])[C:19]([H:44])([H:45])[C:20]([H:46])([H:47])[C:21]([H:48])([H:49])[N:22]([H:50])[H:51])[H:36])[H:35])[H:34]',\n", + " '[H:35][c:13]1[c:12]([c:11]2[c:10]([c:9]([c:8]1[C:7]([H:31])([H:32])[N:6]3[C:5](=[N:4][C:3](=[C:2]3[C:1]([H:26])([H:27])[H:28])[H:29])[H:30])[H:33])[C:16]([C:15]([N:14]2[C:19](=[O:20])[O:21][C:22]([C:23]([H:44])([H:45])[H:46])([C:24]([H:47])([H:48])[H:49])[C:25]([H:50])([H:51])[H:52])([H:36])[H:37])([C:17]([H:38])([H:39])[H:40])[C:18]([H:41])([H:42])[H:43])[H:34]',\n", + " '[H:44][c:17]1[c:16]([c:15]([c:20]([c:19]([c:18]1[C:21]2=[C:22]([C:23](=[N:24][N:25]2[H:49])[H:48])[H:47])[H:45])[H:46])[O:14][C:13]3=[C:12]([N:11]4[C:10](=[C:9]([N:29]=[C:28]4[C:27](=[C:26]3[H:50])[H:51])[C:8]([H:39])([H:40])[N:7]5[C:6]([C:5]([N:4]([C:31]([C:30]5([H:52])[H:53])([H:54])[H:55])[C:2](=[O:3])[C:1]([H:32])([H:33])[H:34])([H:35])[H:36])([H:37])[H:38])[H:41])[H:42])[H:43]',\n", + " '[H:43][c:24]1[c:23]([c:22]([c:20]([c:19]([c:25]1[H:44])[O:18][c:17]2[c:16]([c:15]([c:14]([c:27]([c:26]2[H:45])[H:46])[C:13]([H:37])([H:38])[N:12]([H:36])[C:10](=[O:11])[C@:5]3([C:6]([C:7]([O:8][C:9]3([H:34])[H:35])([H:32])[H:33])([H:30])[H:31])[N:4]([H:29])[C:2](=[O:3])[O:1][H:28])[H:39])[H:40])[Cl:21])[H:41])[H:42]',\n", + " '[H:42][c:21]1[c:22]2[c:26]([c:27]([c:5]([c:6]1[N:7]([H:35])[C:8]3=[N:9][C:10](=[N:11][N:12]4[C:20]3=[C:18]([C:14](=[C:13]4[H:37])[C:15](=[O:17])[O:16][H:38])[C:19]([H:39])([H:40])[H:41])[H:36])[O:4][C:2]([H:31])([C:1]([H:28])([H:29])[H:30])[C:3]([H:32])([H:33])[H:34])[H:45])[N:25]([N:24]=[C:23]2[H:43])[H:44]',\n", + " '[H:42][c:9]1[c:10]([c:11]([c:33]2[c:7]([c:8]1[H:41])[N:6]([C:4](=[O:5])[C:2]2([C:1]([H:34])([H:35])[H:36])[C:3]([H:37])([H:38])[H:39])[H:40])[C:12]([H:44])([H:45])[N:13]([H:46])[c:14]3[c:15]([c:17]([n:18][c:19]([n:32]3)[N:20]([H:48])[C@:21]4([C:25](=[N:24][N:23]([C:22]4([H:50])[H:51])[C:26]5([C:27]([C:28]([N:29]([C:30]([C:31]5([H:61])[H:62])([H:59])[H:60])[H:58])([H:56])[H:57])([H:54])[H:55])[H:53])[H:52])[H:49])[H:47])[Cl:16])[H:43]',\n", + " '[H:35][c:13]1[c:12]([c:11]([c:10]2[c:15]([c:14]1[H:36])[C@:16]3([C:21](=[O:22])[N:20]([C:18](=[O:19])[N:17]3[H:37])[H:38])[C:8]4([C:9]2([H:31])[H:32])[C:7]([C:6]([C:5]([C:24]([C:23]4([H:39])[H:40])([H:41])[H:42])([H:26])[O:4][C:2]([H:25])([F:1])[F:3])([H:27])[H:28])([H:29])[H:30])[H:33])[H:34]',\n", + " '[H:64][c:31]1[c:32]([c:21]([c:22]([c:23]2[c:24]1[C:25]([C:26]([N:27]([C:29]([C:30]2([H:62])[H:63])([H:60])[H:61])[C:28]([H:57])([H:58])[H:59])([H:55])[H:56])([H:53])[H:54])[H:52])[N:20]([H:51])[C:18](=[O:19])[C:17]([H:49])([H:50])[C:16]([H:47])([H:48])[N:14]([C:15]([H:44])([H:45])[H:46])[S:11](=[O:12])(=[O:13])[c:7]3[c:5]([c:4]([c:3]([c:10]([c:8]3[C:9]([H:40])([H:41])[H:42])[H:43])[O:2][C:1]([H:33])([H:34])[H:35])[H:36])[C:6]([H:37])([H:38])[H:39])[H:65]',\n", + " '[H:42][c:22]1[c:21]([c:20]([n:19][c:18]([c:17]1[C:14]2=[N:15][O:16][C:12](=[N:13]2)[C:9]3=[C:8]([N:7]([N:11]=[C:10]3[H:39])[C:6]([H:36])([H:37])[C:4](=[O:5])[N:3]([H:35])[C:2]([H:33])([H:34])[C:1]([H:30])([H:31])[H:32])[H:38])[H:40])[c:23]4[c:24]([n:25][c:26]([n:28][c:29]4[H:46])[N:27]([H:44])[H:45])[H:43])[H:41]',\n", + " '[H:44][c:21]1[c:22]([c:23]([n:24][c:18]([c:19]1[Cl:20])[N:17]2[C@:13]([C:15]([C:16]2([H:42])[H:43])([H:40])[H:41])([H:14])[C:11](=[O:12])[N:10]([H:39])[C:9]3=[C:29]([C:6](=[N:7][O:8]3)[C:2]([C:1]([H:30])([H:31])[H:32])([C:3]([H:33])([H:34])[H:35])[C:4]([H:36])([H:37])[O:5][H:38])[H:46])[H:45])[C:25]([F:26])([F:27])[F:28]',\n", + " '[H:47][c:24]1[c:18]2[c:19]([n:20][c:21]([c:22]1[C:23]([H:44])([H:45])[H:46])[H:43])[N:2]([C:3](=[O:4])[N:5]([C:16]2=[O:17])[C:6]([H:28])([H:29])[C:7]([H:30])([H:31])[C:8]([H:32])([H:33])[O:9][C@:10]3([C:11]([C:12]([C:13]([C:14]([O:15]3)([H:41])[H:42])([H:39])[H:40])([H:37])[H:38])([H:35])[H:36])[H:34])[C:1]([H:25])([H:26])[H:27]',\n", + 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'[H:32][c:9]1[c:10]([c:11]([c:12]([c:13]([c:8]1[c:5]2[c:4]([n:3][c:2]([n:7][c:6]2[H:31])[N:1]([H:28])[H:29])[H:30])[H:35])[H:34])[C:14]3([C:15]([C:16]([C:17]3([H:40])[H:41])([H:38])[H:39])([H:36])[H:37])[C:18]4=[N:19][O:20][C:21](=[N:22]4)[C:23]5=[C:24]([N:25]([N:26]=[C:27]5[H:44])[H:43])[H:42])[H:33]',\n", + " '[H:62][c:22]1[c:21]([c:20]([c:25]([c:24]([c:23]1[c:26]2[c:27]([c:28]([c:29]([n:30][c:31]2[H:67])[C:32]3([C:33]([C:34]3([H:70])[H:71])([H:68])[H:69])[C:35](=[O:37])[N:36]([H:72])[H:73])[H:66])[H:65])[H:63])[H:64])[C@:2]([H:3])([C:1]([H:38])([H:39])[H:40])[N:4]4[C:18](=[O:19])[O:17][C@:7]([C:6]([C:5]4([H:41])[H:42])([H:43])[H:44])([C:8]([H:45])([H:46])[C:9]5([C:10]([C:11]5([H:50])[H:51])([H:48])[H:49])[H:47])[C:12]([H:52])([H:53])[C:13]([C:14]([H:54])([H:55])[H:56])([C:15]([H:57])([H:58])[H:59])[O:16][H:60])[H:61]',\n", + " 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'[H:31][c:9]1[c:8]([c:7]([n:12][c:11]([c:10]1[C:13](=[O:14])[N:15]([C:16]2([C:17]([C:18]2([H:36])[H:37])([H:34])[H:35])[H:33])[C:19]3([C:20]([C:21]([N:22]([C:23]([C:24]3([H:46])[H:47])([H:44])[H:45])[H:43])([H:41])[H:42])([H:39])[H:40])[H:38])[H:32])[N:6]4[C:5](=[C:4]([N:3]=[C:2]4[C:1]([H:25])([H:26])[H:27])[H:28])[H:29])[H:30]',\n", + " '[H:35][c:17]1[c:16]([c:15]([c:21]([c:19]([c:18]1[H:36])[Cl:20])[H:37])[N:12]2[C:13](=[N:14][C:10](=[N:11]2)[C:8](=[O:9])[N:7]3[C@:2]([C:3]([N:4]([C:5]([C:6]3([H:31])[H:32])([H:29])[H:30])[H:28])([H:26])[H:27])([H:25])[C:1]([H:22])([H:23])[H:24])[H:33])[H:34]',\n", + " '[H:28][c:9]1[c:10]([c:11]([c:20]([c:21]([c:8]1[C:7]([H:26])([H:27])[N:6]2[C:5](=[C:4]([N:23]=[N:22]2)[C:2](=[O:3])[O:1][H:24])[H:25])[H:39])[H:38])[C:12]([H:30])([H:31])[N:13]3[C:18](=[O:19])[C@@:17]4([C@@:15]([C:16]4([H:35])[H:36])([C:14]3([H:32])[H:33])[H:34])[H:37])[H:29]',\n", + " 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'[H:43][c:27]1[c:28]([c:21]([c:22]([c:24]([c:26]1[H:42])[Cl:25])[C:23]([H:39])([H:40])[H:41])[C:4]2=[C:3]([N:2]([C:6](=[N:5]2)[c:7]3[c:20]([c:19]([c:10]([n:9][c:8]3[H:33])[N:11]([H:34])[C:12](=[O:13])[C:14]4=[C:15]([S:16][C:17](=[N:18]4)[H:36])[H:35])[H:37])[H:38])[C:1]([H:29])([H:30])[H:31])[H:32])[H:44]',\n", + " '[H:32][c:10]1[c:9]([c:8]2[c:7]([c:12]([c:11]1[c:13]3[c:14]([c:15]4[c:16]([c:21]([c:22]3[Cl:23])[H:38])[N:17]([C:18](=[O:19])[C:20]4([H:36])[H:37])[H:35])[H:34])[H:33])[C:6](=[C:5]([N:4]2[C:3]([H:27])([H:28])[C:2]([H:25])([H:26])[O:1][H:24])[H:29])[H:30])[H:31]',\n", + " '[H:32][c:6]1[c:5]([c:4]([c:29]([c:8]([c:7]1[H:33])[N:9]([H:34])[c:10]2[n:25][c:24]([c:23]([c:12]([n:11]2)[N:13]([H:35])[C:14]([H:36])([H:37])[C:15]([H:38])([H:39])[c:16]3[c:22]([c:21]([c:20]([c:18]([c:17]3[H:40])[O:19][H:41])[H:42])[H:43])[H:44])[N+:26](=[O:28])[O-:27])[H:45])[H:46])[C:2](=[O:3])[O:1][H:30])[H:31]',\n", + " '[H:41][c:17]1[c:18]([c:19]2[c:14]([c:15]([c:16]1[c:25]3[c:26]([n:27][c:28]([n:30][c:31]3[H:55])[N:29]([H:53])[H:54])[H:52])[H:40])[N:13]=[C:12]([N:20]2[C:21]([C:22]([H:43])([H:44])[H:45])([C:23]([H:46])([H:47])[H:48])[C:24]([H:49])([H:50])[H:51])[c:11]4[c:5]([c:6]([c:7]([c:8]([n:10]4)[N:9]([H:38])[H:39])[H:37])[H:36])[C:3](=[O:4])[N:2]([H:35])[C:1]([H:32])([H:33])[H:34])[H:42]',\n", + " '[H:29][c:6]1[c:5]([c:4]([c:3]([c:2]([c:7]1[H:30])[Cl:1])[H:27])[C:8]2=[N:9][N:10]=[C:11]([N:12]2[H:31])[c:13]3[c:14]([c:15]([c:16]([c:25]([c:26]3[H:37])[H:36])[N:17]([H:34])[C:18](=[O:19])[C:20]4=[C:21]([S:22][N:23]=[N:24]4)[H:35])[H:33])[H:32])[H:28]',\n", + " '[H:31][c:13]1[c:12]([c:11]([c:17]([c:15]([c:14]1[H:32])[Cl:16])[H:33])[N:10]([H:29])[c:9]2[c:18]3[c:19]([c:20]([c:3]([c:4]([c:5]3[n:6][c:7]([n:8]2)[H:28])[H:27])[O:2][C:1]([H:24])([H:25])[H:26])[N+:21](=[O:23])[O-:22])[H:34])[H:30]',\n", + " '[H:42][c:18]1[c:17]([c:16]([c:15]([c:14]2[c:13]1[C:10]([C:9]([N:8]2[C:6](=[O:7])[O:5][C:2]([C:1]([H:23])([H:24])[H:25])([C:3]([H:26])([H:27])[H:28])[C:4]([H:29])([H:30])[H:31])([H:32])[H:33])([C:11]([H:34])([H:35])[H:36])[C:12]([H:37])([H:38])[H:39])[H:40])[C:19]([F:20])([F:21])[F:22])[H:41]',\n", + " '[H:45][c:23]1[c:22]([c:21]([c:20]([c:25]([c:24]1[H:46])[H:47])[C:19]([H:41])([H:42])[O:18][C:16](=[O:17])[C@:6]([H:7])([C:5]([H:29])([H:30])[C:3](=[O:4])[O:2][C:1]([H:26])([H:27])[H:28])[N:8]([H:31])[C:9](=[O:10])[O:11][C:12]([C:13]([H:32])([H:33])[H:34])([C:14]([H:35])([H:36])[H:37])[C:15]([H:38])([H:39])[H:40])[H:43])[H:44]',\n", + " '[H:28][C:4]1=[C:5]([N:6]2[C:7](=[C:8]([N:9]=[C:10]2[C:11]3([C:12]([C:13]3([H:33])[H:34])([H:31])[H:32])[N:14]([H:35])[C:15](=[O:16])[C@@:17]4([C:19]([N:20]([C:21]([C:22]([O:23]4)([H:41])[H:42])([H:39])[H:40])[H:38])([H:36])[H:37])[H:18])[H:30])[C:2](=[C:3]1[H:27])[C:1]([H:24])([H:25])[H:26])[H:29]',\n", + " 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'[H:51][c:22]1[c:21]([c:20]([c:25]([c:24]([c:23]1[C:26]2=[C:27]([S:28][C:29](=[N:31]2)[C:30]([H:55])([H:56])[H:57])[H:54])[H:52])[H:53])[N:19]([H:49])[C:17](=[O:18])[C:13](=[C:14]([C:15]([H:43])([H:44])[H:45])[C:16]([H:46])([H:47])[H:48])[c:10]3[c:9]([c:8]([c:7]([c:12]([c:11]3[H:41])[H:42])[C@:4]4([C:5](=[N:6][N:2]([C:3]4([H:35])[H:36])[C:1]([H:32])([H:33])[H:34])[H:38])[H:37])[H:39])[H:40])[H:50]',\n", + " '[H:56][c:24]1[c:23]([c:22]([c:21]([c:26]([c:25]1[H:57])[H:58])[C@:2]([H:3])([C:1]([H:27])([H:28])[H:29])[N:4]([H:30])[C:5]([H:31])([H:32])[C:6]([H:33])([H:34])[C:7]2([C:9]([C:10]([C:11]3([C:12]([C:13]2([H:42])[H:43])([H:40])[H:41])[O:14][C:15]([C:16]([C:19]([O:20]3)([H:52])[H:53])([C:17]([H:46])([H:47])[H:48])[C:18]([H:49])([H:50])[H:51])([H:44])[H:45])([H:38])[H:39])([H:36])[H:37])[O:8][H:35])[H:54])[H:55]',\n", + " '[H:32][c:17]1[c:16]([c:10]([c:9]([c:8]2[c:7]1[C:6]([C:5]3([C:18]2=[O:19])[C:4]([C:3]([C:2]([C:21]([C:20]3([H:33])[H:34])([H:35])[H:36])([H:23])[O:1][H:22])([H:24])[H:25])([H:26])[H:27])([H:28])[H:29])[H:30])[O:11][C:12]([F:13])([F:14])[F:15])[H:31]',\n", + " '[H:13][C@:12]1([C:14]([C:15]([C:16]([N:17]1[C:18]2([C:19]([C:20]([C:21]2([H:44])[H:45])([H:42])[H:43])([H:40])[H:41])[H:39])([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])[C:10](=[O:11])[N:9]([H:32])[C:8]3=[N:7][N:6]=[C:5]([S:22]3)[C:2]([C:1]([H:23])([H:24])[H:25])([C:3]([H:26])([H:27])[H:28])[C:4]([H:29])([H:30])[H:31]',\n", + " '[H:38][c:20]1[c:18]([c:11]([n:10][c:9]2[c:21]1[O:22][C:6](=[C:7]2[N:8]([H:28])[H:29])[C:4](=[O:5])[O:3][C:2]([H:26])([H:27])[C:1]([H:23])([H:24])[H:25])[C:12]3=[C:13]([N:14]([N:16]=[C:17]3[H:34])[C:15]([H:31])([H:32])[H:33])[H:30])[C:19]([H:35])([H:36])[H:37]',\n", + " 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'[H:36][c:10]1[c:9]([c:8]([c:7]([c:12]([c:11]1[H:37])[H:38])[C@@:5]2([C@@:4]([C:3]([N:2]([C:6]2([H:32])[H:33])[C:1]([H:25])([H:26])[H:27])([H:28])[H:29])([H:30])[C:13]3=[C:14]([N:15]([N:16]=[C:17]3[C:18]([C:19]([H:40])([H:41])[H:42])([C:20]([H:43])([H:44])[H:45])[C:21]([H:46])([H:47])[H:48])[C:22]4([C:23]([C:24]4([H:52])[H:53])([H:50])[H:51])[H:49])[H:39])[H:31])[H:34])[H:35]',\n", + " '[H:30][C:8]1=[C:7]2[N:6]=[C:5]3[C:20](=[C:12]([N:11]2[N:10]=[C:9]1[H:31])[N:13]4[C:14]([C:15]([C:16]4([H:35])[H:36])([H:34])[C:17](=[O:19])[O:18][H:37])([H:32])[H:33])[C:21]([C:22]([N:2]([C:3]([C:4]3([H:28])[H:29])([H:26])[H:27])[C:1]([H:23])([H:24])[H:25])([H:40])[H:41])([H:38])[H:39]',\n", + " 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'[H:40][c:18]1[c:17]([c:16]([c:15]([c:20]([c:19]1[H:41])[H:42])[C:14]([H:36])([H:37])[O:13][C:12]2=[C:21]([C:22](=[O:23])[N:9]([C:10](=[N:11]2)[H:35])[C:8]([H:33])([H:34])[C:7]([H:31])([H:32])[c:6]3[c:5]([c:4]([c:3]([c:25]([c:24]3[H:44])[H:45])[C:2]([H:27])([H:28])[O:1][H:26])[H:29])[H:30])[H:43])[H:38])[H:39]',\n", + " '[H:45][c:24]1[c:18]2[c:19]([n:20][c:21]([c:22]1[O:23][H:44])[H:43])[N:2]([C:3](=[O:4])[N:5]([C:16]2=[O:17])[C:6]([H:28])([H:29])[C:7]([H:30])([H:31])[C:8]([H:32])([H:33])[O:9][C@:10]3([C:11]([C:12]([C:13]([C:14]([O:15]3)([H:41])[H:42])([H:39])[H:40])([H:37])[H:38])([H:35])[H:36])[H:34])[C:1]([H:25])([H:26])[H:27]',\n", + " 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'[H:26][c:4]1[c:5]([c:7]([c:8]([c:10]([c:3]1[O:2][C:1]([H:23])([H:24])[H:25])[H:33])[C:9]([H:30])([H:31])[H:32])[S:11](=[O:12])(=[O:13])[N:14]([C:15]([H:34])([H:35])[H:36])[C:16]([H:37])([H:38])[C:17](=[O:18])[N:19]([H:39])[C:20]([H:40])([H:41])[C:21]([H:42])([H:43])[N:22]([H:44])[H:45])[C:6]([H:27])([H:28])[H:29]',\n", + " '[H:41][c:21]1[c:22]([c:23]([c:25]([c:26]([c:20]1[C:19]2=[N:18][C:17](=[C:16]3[N:15]2[C:14](=[C:13]([C:12](=[C:11]3[C:9](=[O:10])[N:8]([H:36])[C:7]([H:34])([H:35])[c:6]4[c:5]([c:4]([c:3]([n:28][c:27]4[H:45])[S:2][C:1]([H:29])([H:30])[H:31])[H:32])[H:33])[H:37])[H:38])[H:39])[H:40])[H:44])[H:43])[F:24])[H:42]',\n", + " '[H:35][c:10]1[c:9]([c:8]2[c:13]([c:12]([c:11]1[C:16]#[C:17][C:18]([F:19])([F:20])[F:21])[H:36])[C:14](=[O:15])[C:6]3([C:7]2([H:32])[H:33])[C:5]([C:4]([C:3]([C:23]([C:22]3([H:37])[H:38])([H:39])[H:40])([H:27])[O:2][C:1]([H:24])([H:25])[H:26])([H:28])[H:29])([H:30])[H:31])[H:34]',\n", + " '[H:31][c:6]1[c:5]([c:15]([n:14][c:13]([c:7]1[N:8]([H:32])[S:9](=[O:11])(=[O:12])[C:10]([H:33])([H:34])[H:35])[H:36])[H:37])[C:4]([H:29])([H:30])[c:3]2[c:2]([n:19][c:18]([n:17][c:16]2[N:20]3[C:21]([C:22]([O:23][C:24]([C:25]3([H:45])[H:46])([H:43])[H:44])([H:41])[H:42])([H:39])[H:40])[H:38])[C:1]([H:26])([H:27])[H:28]',\n", + " '[H:35][c:16]1[c:15]([c:14]([c:19]([c:18]([c:17]1[H:36])[C:20]([H:38])([F:21])[F:22])[H:37])[C:11]2=[C:9]([N:8]([C:7](=[C:6]([C:12]2=[O:13])[C:4](=[O:5])[N:3]([H:28])[C:2]([H:26])([H:27])[C:1]([H:23])([H:24])[H:25])[H:29])[H:30])[C:10]([H:31])([H:32])[H:33])[H:34]',\n", + " '[H:45][c:23]1[c:22]([c:21]([c:26]([n:25][c:24]1[H:46])[H:47])[C@:4]([H:34])([C:3]([H:32])([H:33])[C:2]([H:30])([H:31])[C:1]([H:27])([H:28])[H:29])[N:5]([H:35])[C:6](=[O:7])[C:8]2=[C:9]([N:11]([N:12]=[C:13]2[H:39])[c:14]3[c:15]([c:16]([c:17]([c:19]([c:20]3[H:43])[H:42])[Cl:18])[H:41])[H:40])[C:10]([H:36])([H:37])[H:38])[H:44]',\n", + " 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'[H:39][c:9]1[c:8]([c:7]([c:6]([c:5]([c:10]1[H:40])[C:4]([H:35])([H:36])[N:3]([H:34])[C:2](=[O:1])[C:20]2=[C:21]([C:22](=[C:23]([N:24]([C:32]2=[O:33])[C:25]([H:49])([H:50])[c:26]3[c:31]([c:30]([c:29]([n:28][c:27]3[H:51])[H:52])[H:53])[H:54])[H:48])[H:47])[H:46])[H:37])[C:11]4=[C:12]([N:13]([c:14]5[c:15]4[c:16]([c:17]([c:18]([n:19]5)[H:45])[H:44])[H:43])[H:42])[H:41])[H:38]',\n", + " '[H:35][c:14]1[c:15]([c:16]([c:18]([c:20]([c:13]1[N:12]([H:34])[c:11]2[n:21][c:22]([c:23]([c:9]([n:10]2)[N:8]3[C@:4]([C:5]([S:6][C:7]3([H:32])[H:33])([H:30])[H:31])([H:29])[C:2](=[O:3])[O:1][H:28])[C:24]([F:25])([F:26])[F:27])[H:38])[H:37])[Cl:19])[Cl:17])[H:36]',\n", + " '[H:43][c:13]1[c:12]([c:11]([c:26]([c:25]([c:14]1[C:15]([H:44])([H:45])[C:16]([H:46])([H:47])[N:17]2[C:18](=[C:19]([C:20](=[C:22]([C:23]2=[O:24])[H:51])[O:21][H:50])[H:49])[H:48])[H:52])[H:53])[C:10]([H:40])([H:41])[N:9]3[C:8]([C:7]([C:6]([C:28]([C:27]3([H:54])[H:55])([H:56])[H:57])([H:35])[C:4](=[O:5])[N:2]([C:1]([H:29])([H:30])[H:31])[C:3]([H:32])([H:33])[H:34])([H:36])[H:37])([H:38])[H:39])[H:42]',\n", + " '[H:45][c:26]1[c:25]([c:24]([n:23][c:22]([c:27]1[H:46])[C:21]([H:41])([H:42])[N:20]([H:40])[C:18](=[O:19])[C:15]2([C:14]([C:13]([N:12]([C:17]([C:16]2([H:36])[H:37])([H:38])[H:39])[S:9](=[O:10])(=[O:11])[c:4]3[c:3]([c:2]([c:8]([c:6]([c:5]3[H:29])[Cl:7])[H:30])[Cl:1])[H:28])([H:31])[H:32])([H:33])[H:34])[H:35])[H:43])[H:44]',\n", + " 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'[H:27][C:4]1=[C:5]([N:6]2[C:7](=[C:8]([N:9]=[C:10]2[C:11]3([C:12]([C:13]([C:14]3([H:34])[H:35])([H:32])[H:33])([H:30])[H:31])[N:15]([H:36])[C:16](=[O:17])[O:18][C:19]([C:20]([H:37])([H:38])[H:39])([C:21]([H:40])([H:41])[H:42])[C:22]([H:43])([H:44])[H:45])[H:29])[C:2](=[C:3]1[H:26])[C:1]([H:23])([H:24])[H:25])[H:28]',\n", + " '[H:40][C:20]1=[C:19]([N:18]2[C:17](=[C:16]([N:15]=[C:14]2[C:2]([C:1]([H:24])([H:25])[H:26])([C:3]([H:27])([H:28])[H:29])[N:4]([H:30])[C:5](=[O:6])[C@@:7]3([C:9]([N:10]([C:11]([C:12]([O:13]3)([H:36])[H:37])([H:34])[H:35])[H:33])([H:31])[H:32])[H:8])[H:38])[C:22](=[C:21]1[H:41])[Cl:23])[H:39]',\n", + " '[H:44][c:21]1[c:20]([c:19]([c:18]([c:24]([c:22]1[C:23]([H:45])([H:46])[H:47])[H:48])[C:16](=[O:17])[N:3]([C@@:4]([H:5])([C:6]([H:35])([H:36])[H:37])[C:7]([H:38])([H:39])[N:8]([H:40])[c:9]2[n:10][c:11]([c:12]([c:14]([n:15]2)[H:42])[Cl:13])[H:41])[C:2]([H:33])([H:34])[C:1]([H:30])([H:31])[H:32])[N:25]3[N:26]=[C:27]([C:28](=[N:29]3)[H:50])[H:49])[H:43]',\n", + " 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'[H:26][c:5]1[c:4]([c:3]2[c:8]([c:9]([c:10]([n:11][c:2]2[O:1][H:24])[c:12]3[c:13]([c:14]([c:15]([c:16]([c:17]3[H:32])[H:31])[N:18]4[C:19]([C:20]([O:21][C:22]([C:23]4([H:39])[H:40])([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])[H:30])[H:29])[H:28])[n:7][c:6]1[H:27])[H:25]',\n", + " '[H:44][c:28]1[c:27]([c:26]([c:25]2[c:30]([c:29]1[H:45])[C@:20]([C:22](=[O:23])[N:24]2[H:41])([N:2]([c:3]3[c:4]([c:5]([n:6][c:7]([n:16]3)[N:8]([H:35])[c:9]4[c:10]([c:11]([c:12]([c:14]([c:15]4[H:39])[H:38])[Cl:13])[H:37])[H:36])[H:34])[N+:17](=[O:19])[O-:18])[C:1]([H:31])([H:32])[H:33])[O:21][H:40])[H:42])[H:43]',\n", + " '[H:26][c:4]1[c:3]([c:9]([c:8]([n:7][c:5]1[N:6]([H:27])[H:28])[H:29])[N:10]2[C:11]([C:12]([N:13]([C:14]([C:15]2([H:36])[H:37])([H:34])[H:35])[C:16](=[O:17])[O:18][C:19]([C:20]([H:38])([H:39])[H:40])([C:21]([H:41])([H:42])[H:43])[C:22]([H:44])([H:45])[H:46])([H:32])[H:33])([H:30])[H:31])[O:2][C:1]([H:23])([H:24])[H:25]',\n", + " 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'[H:29][C:11]1([c:10]2[c:20]([c:21]([c:6]([c:7]([n:9]2)[O:8][H:28])[C:4](=[O:5])[O:3][C:2]([H:26])([H:27])[C:1]([H:23])([H:24])[H:25])[O:22][H:41])[C:18](=[O:19])[C:17]([C:12]13[C:13]([C:14]([C:15]([C:16]3([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:31])[H:32])([H:39])[H:40])[H:30]',\n", + " '[H:42][c:13]1[c:14]([c:15]2[c:10]([c:11]([c:12]1[C:18]#[C:19][C:20]([H:45])([H:46])[N:21]([H:47])[C:22](=[O:23])[C:24]3=[C:25]([C:26](=[C:27]([N:28]([C:29]3=[O:30])[H:51])[H:50])[H:49])[H:48])[H:41])[c:9]4[c:8]([c:17]([n:16]2)[H:44])[N:7]=[C:5]([N:4]4[C:2]([H:34])([C:1]([H:31])([H:32])[H:33])[C:3]([H:35])([H:36])[H:37])[C:6]([H:38])([H:39])[H:40])[H:43]',\n", + " 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'[H:28][C:4]1=[C:5]([N:6]2[C:7](=[C:8]([N:9]=[C:10]2[C:2](=[C:3]1[H:27])[C:1]([H:24])([H:25])[H:26])[H:30])[C:11]([C:12]([H:31])([H:32])[H:33])([C:13]([H:34])([H:35])[H:36])[N:14]([H:37])[C:15](=[O:16])[C@@:17]3([C:19]([N:20]([C:21]([C:22]([O:23]3)([H:43])[H:44])([H:41])[H:42])[H:40])([H:38])[H:39])[H:18])[H:29]',\n", + " '[H:37][c:19]1[c:18]([c:16]([c:15]([c:13]([c:12]1[N:11]([H:33])[c:10]2[c:20]3[c:2]([c:3]([c:4]([c:5]([c:6]3[n:7][c:8]([n:9]2)[H:32])[H:31])[N:21]=[S:22]4(=[O:23])[C:24]([C:25]([C:26]4([H:42])[H:43])([H:40])[H:41])([H:38])[H:39])[H:30])[C:1]([H:27])([H:28])[H:29])[O:14][H:34])[H:35])[F:17])[H:36]',\n", + " '[H:26][c:6]1[c:7]([n:8][c:9]2[c:10]([c:5]1[C:3](=[O:4])[O:2][C:1]([H:23])([H:24])[H:25])[O:11][C:12]([C:13]([N:14]([C:15]2([H:32])[H:33])[C:16](=[O:17])[O:18][C:19]([C:20]([H:34])([H:35])[H:36])([C:21]([H:37])([H:38])[H:39])[C:22]([H:40])([H:41])[H:42])([H:30])[H:31])([H:28])[H:29])[H:27]',\n", + " '[H:33][c:18]1[c:17]([c:6]([c:5]([c:4]([c:3]1[O:2][C:1]([H:23])([H:24])[H:25])[H:26])[C:19]([F:20])([F:21])[F:22])[O:7][c:8]2[c:9]([n:10][c:11]([n:12][c:13]2[H:28])[C:14](=[O:16])[C:15]([H:29])([H:30])[H:31])[H:27])[H:32]',\n", + " '[H:30][c:9]1[c:10]([c:11]([c:6]2[c:7]([c:8]1[H:29])-[c:12]3[c:17]([c:16]([c:15]([c:14]([c:13]3[C:5]2([H:28])[C:4]([H:26])([H:27])[O:3][C:2](=[O:1])[N:18]4[C:24]([C@:23]5([C:22]([C:21]([C@@:20]([C:19]4([H:37])[H:38])([N:25]5[H:47])[H:39])([H:40])[H:41])([H:42])[H:43])[H:44])([H:45])[H:46])[H:33])[H:34])[H:35])[H:36])[H:32])[H:31]',\n", + " '[H:43][c:19]1[c:20]([c:21]([c:23]([c:16]2[c:17]1[C:18]([N:13]([C:14]([C:15]2([H:39])[H:40])([H:37])[H:38])[C:12]([H:35])([H:36])[c:11]3[c:10]([c:9]([c:8]([c:25]([c:24]3[H:47])[H:48])[C@:2]([H:3])([C:1]([H:26])([H:27])[H:28])[N:4]([H:29])[C:5](=[O:7])[C:6]([H:30])([H:31])[H:32])[H:33])[H:34])([H:41])[H:42])[H:46])[O:22][H:45])[H:44]',\n", + " '[H:39][c:18]1[c:17]([c:16]2[c:15]([c:20]([c:19]1[H:40])[Cl:21])[O:14][N:13]=[C:12]2[C:9]([C:10]([H:32])([H:33])[H:34])([C:11]([H:35])([H:36])[H:37])[N:8]([H:31])[C:6](=[O:7])[O:5][C:2]([C:1]([H:22])([H:23])[H:24])([C:3]([H:25])([H:26])[H:27])[C:4]([H:28])([H:29])[H:30])[H:38]',\n", + " '[H:41][c:18]1[c:19]([c:20]2[c:15]([c:16]([c:17]1[C:21]#[N:22])[H:40])[N:14]=[C:4]([N:3]2[C:2]([H:26])([H:27])[C:1]([H:23])([H:24])[H:25])[C:5]([H:28])([H:29])[N:6]([H:30])[C:7](=[O:8])[O:9][C:10]([C:11]([H:31])([H:32])[H:33])([C:12]([H:34])([H:35])[H:36])[C:13]([H:37])([H:38])[H:39])[H:42]',\n", + " '[H:39][c:16]1[c:15]([c:14]([n:13][c:12]([c:11]1[C:10]([H:35])([H:36])[C@@:9]([H:34])([C:21](=[O:23])[O:22][H:40])[N:8]([H:33])[C:6](=[O:7])[O:5][C:2]([C:1]([H:24])([H:25])[H:26])([C:3]([H:27])([H:28])[H:29])[C:4]([H:30])([H:31])[H:32])[H:37])[C:17]([F:18])([F:19])[F:20])[H:38]',\n", + " '[H:26][c:4]1[c:5]([c:6]([c:17]([c:18]([c:3]1[O:2][C:1]([H:23])([H:24])[H:25])[H:30])[C:19]([F:20])([F:21])[F:22])[O:7][c:8]2[c:16]([c:14]([c:11]([n:10][c:9]2[H:28])[C:12]#[N:13])[Cl:15])[H:29])[H:27]',\n", + " '[H:38][c:20]1[c:19]([c:18]([c:17]([c:22]([c:21]1[H:39])[H:40])[C:16]([H:34])([H:35])[N:15]2[C:14]([C:13](=[C:12]([C:24]([C:23]2([H:41])[H:42])([H:43])[H:44])[c:3]3[c:4]([c:5]4[c:6]([c:7]([c:8]([c:9]([c:10]4[n:11][c:2]3[O:1][H:25])[H:30])[H:29])[H:28])[H:27])[H:26])[H:31])([H:32])[H:33])[H:36])[H:37]',\n", + " '[H:29][c:10]1[c:11]([c:12]([c:6]2[c:7]([c:8]1[C:9]([H:26])([H:27])[H:28])[N:2]([C:3](=[O:4])[O:5]2)[C:1]([H:23])([H:24])[H:25])[H:30])[C:13](=[O:14])[c:15]3[c:16]([c:17]([c:19]([c:20]([c:22]3[H:33])[F:21])[H:32])[F:18])[H:31]',\n", + " '[H:36][c:22]1[c:23]([c:4]([c:5]([c:6]([c:21]1[H:35])[C:7]([H:27])([H:28])[C:8]2=[N:9][C:10](=[C:11]([N:12]2[H:30])[H:29])[c:13]3[c:14]([c:15]([c:16]([c:17]([c:18]3[H:34])[H:33])[C:19]#[N:20])[H:32])[H:31])[H:26])[C:2](=[O:3])[N:1]([H:24])[H:25])[H:37]',\n", + " '[H:10][C@:9]([C:12](=[O:14])[O:13][H:38])([C:11]([H:35])([H:36])[H:37])[O:8][C:7]([H:33])([H:34])[C@:5]([H:6])([C:4]([H:31])([H:32])[C:2]([H:27])([C:1]([H:24])([H:25])[H:26])[C:3]([H:28])([H:29])[H:30])[N:15]([C:17](=[O:18])[O:19][C:20]([C:21]([H:42])([H:43])[H:44])([C:22]([H:45])([H:46])[H:47])[C:23]([H:48])([H:49])[H:50])[C:16]([H:39])([H:40])[H:41]',\n", + " '[H:33][c:15]1[c:10]([n:11][c:12]([c:13]([n:14]1)[N:16]2[C:21]([C@@:20]3([C@@:18]([C:19]3([H:37])[H:38])([C:17]2([H:34])[H:35])[H:36])[H:39])([H:40])[H:41])[H:32])[C:9]([H:30])([H:31])[N:8]4[C:7](=[C:6]([C:23](=[N:22]4)[H:42])[C:4](=[O:5])[O:3][C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[H:29]',\n", + " 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'[H:45][c:19]1[c:20]([c:21]([c:23]([c:25]([c:18]1[c:17]2[c:15]([c:13]([c:12]([c:28]([n+:26]2[O-:27])[C:29]([H:54])([H:55])[H:56])[C@@:5]([H:6])([C:3](=[O:4])[O:2][C:1]([H:30])([H:31])[H:32])[O:7][C:8]([C:9]([H:33])([H:34])[H:35])([C:10]([H:36])([H:37])[H:38])[C:11]([H:39])([H:40])[H:41])[Cl:14])[C:16]([H:42])([H:43])[H:44])[H:53])[C:24]([H:50])([H:51])[H:52])[C:22]([H:47])([H:48])[H:49])[H:46]',\n", + " '[H:35][c:17]1[c:16]([c:15]([n:14][c:13]([c:12]1[C@@:10]([H:29])([C:11]([H:30])([H:31])[H:32])[N:7]2[C:6](=[C:5]([C:9](=[N:8]2)[H:28])[C:3](=[O:4])[O:2][C:1]([H:24])([H:25])[H:26])[H:27])[H:33])[N:18]3[C:23]([C@@:22]4([C@@:20]([C:21]4([H:39])[H:40])([C:19]3([H:36])[H:37])[H:38])[H:41])([H:42])[H:43])[H:34]',\n", + " '[H:51][c:27]1[c:26]([c:25]2[c:24]([c:23]([c:22]1[C:21]#[C:20][C:19]([H:47])([H:48])[N:18]([H:46])[C:16](=[O:17])[C:15]3=[C:36]([N:2]([N:3]([C:13]3=[O:14])[C:4]([H:41])([H:42])[c:5]4[c:12]([c:11]([c:9]([c:7]([c:6]4[H:43])[F:8])[F:10])[H:44])[H:45])[C:1]([H:38])([H:39])[H:40])[C:37]([H:56])([H:57])[H:58])[H:49])[N:30]([N:29]=[C:28]2[C:31]5=[C:32]([C:33](=[C:34]([O:35]5)[H:55])[H:54])[H:53])[H:52])[H:50]',\n", + " '[H:56][c:25]1[c:24]([c:23]([n:22][c:21]([c:20]1[C:18](=[O:19])[N:14]([C:15]2([C:16]([C:17]2([H:52])[H:53])([H:50])[H:51])[H:49])[C:11]3([C:10]([C:9]([N:8]([C:13]([C:12]3([H:45])[H:46])([H:47])[H:48])[C:6](=[O:7])[O:5][C:2]([C:1]([H:31])([H:32])[H:33])([C:3]([H:34])([H:35])[H:36])[C:4]([H:37])([H:38])[H:39])([H:40])[H:41])([H:42])[H:43])[H:44])[H:54])[C:26]4=[C:27]([N:28]=[C:29]([O:30]4)[H:58])[H:57])[H:55]',\n", + " '[H:45][c:24]1[c:25]([c:26]([c:27]2[c:22]([c:23]1[H:44])[c:21]([c:20]([c:19]([c:18]2[N:12]([C:13]([H:37])([H:38])[P:14](=[O:17])([O:15][H:39])[O:16][H:40])[S:9](=[O:10])(=[O:11])[c:4]3[c:3]([c:2]([c:8]([c:6]([c:5]3[H:32])[C:7]([H:33])([H:34])[H:35])[H:36])[C:1]([H:28])([H:29])[H:30])[H:31])[H:41])[H:42])[H:43])[H:47])[H:46]',\n", + " '[H:33][c:11]1[c:12]([c:13]([c:14]([c:15]([c:10]1[c:7]2[c:6]([c:5]([c:4]([c:9]([c:8]2[H:31])[H:32])[O:3][C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[H:29])[H:30])[H:36])[H:35])[C@@:16]([H:37])([C:17]([H:38])([H:39])[H:40])[N:18]([H:41])[C:19](=[O:20])[N:21]([C:22]([H:42])([H:43])[H:44])[C:23]([H:45])([H:46])[H:47])[H:34]',\n", + " '[H:36][c:13]1[c:14]([c:9]([c:10]([n:11][c:12]1[H:35])[H:34])[C:7](=[O:8])[N:6]([c:15]2[c:16]([c:17]([c:18]([c:19]([c:20]2[H:41])[H:40])[N+:21](=[O:23])[O-:22])[H:39])[H:38])[C:5]([H:32])([H:33])[C:4]([H:30])([H:31])[N:2]([C:1]([H:24])([H:25])[H:26])[C:3]([H:27])([H:28])[H:29])[H:37]',\n", + " '[H:41][C:16]1=[C:15]([N:14]([C:18](=[N:17]1)[C:19]#[N:20])[C:13]([H:38])([H:39])[C:12]([H:36])([H:37])[C@@:10]([H:33])([C:8](=[O:9])[N:5]2[C:4]([C:3]([C:2]([C:7]([C:6]2([H:29])[H:30])([H:31])[H:32])([H:24])[C:1]([H:21])([H:22])[H:23])([H:25])[H:26])([H:27])[H:28])[N:11]([H:34])[H:35])[H:40]',\n", + " '[H:48][c:20]1[c:19]([c:18]([c:17]([c:22]([c:21]1[H:49])[c:23]2[c:24]([c:25]([c:26]([n:27][c:28]2[H:52])[C:29]#[N:30])[H:51])[H:50])[N:14]3[C:13]([C:12]([N:11]([C:16]([C:15]3([H:42])[H:43])([H:44])[H:45])[C:2](=[O:1])[C:3]([H:31])([H:32])[N:4]([H:33])[c:5]4[c:6]([c:7]([n:8][c:9]([c:10]4[H:37])[H:36])[H:35])[H:34])([H:38])[H:39])([H:40])[H:41])[H:46])[H:47]',\n", + " '[H:46][c:20]1[c:19]([c:18]([c:23]([c:22]([c:21]1[c:24]2[c:25]([n:26][c:27]([n:29][c:30]2[H:52])[N:28]([H:50])[H:51])[H:49])[H:47])[H:48])[C:14]3([C:15]([C:16]([C:17]3([H:43])[H:44])([H:41])[H:42])([H:39])[H:40])[C:11]4=[N:12][O:13][C:9](=[N:10]4)[C@:6]5([C:5]([N:4]=[C:3]([C:8](=[N:7]5)[H:38])[N:2]([H:34])[C:1]([H:31])([H:32])[H:33])([H:35])[H:36])[H:37])[H:45]',\n", + " '[H:39][c:5]1[c:6]([c:7]([c:31]([c:33]([c:4]1[C@:2]([H:37])([C:1]([H:34])([H:35])[H:36])[O:3][H:38])[H:57])[Cl:32])[O:8][c:9]2[c:10]([c:11]([c:12]([c:29]([c:30]2[H:56])[H:55])[C:13]([H:43])([H:44])[N:14]([H:45])[C:15](=[O:16])[C:17]([C:18]([H:46])([H:47])[H:48])([C:19]([H:49])([H:50])[H:51])[N:20]([H:52])[C:21](=[O:22])[C:23]3=[C:24]([C:25](=[C:26]([S:28]3)[Cl:27])[H:54])[H:53])[H:42])[H:41])[H:40]',\n", + " 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'[H:37][c:17]1[c:16]([c:15]([c:11]([c:10]([c:9]1[C:8]([H:32])([H:33])[N:7]([H:31])[C:5](=[O:6])[C:2]([C:1]([H:22])([H:23])[H:24])([C:3]([H:25])([H:26])[H:27])[C:4]([H:28])([H:29])[H:30])[H:34])[C:12](=[O:14])[O:13][H:35])[C:18]([F:19])([F:20])[F:21])[H:36]',\n", + " '[H:40][c:4]1[c:5]([c:6]([c:31]([c:32]([c:3]1[O:2][C:1]([H:37])([H:38])[H:39])[H:55])[C:33]([F:34])([F:35])[F:36])[O:7][c:8]2[c:9]([n:10][c:11]([c:29]([n:30]2)[H:54])[C:12]([H:43])([H:44])[N:13]([H:45])[C:14](=[O:15])[C:16]3([C:17]([C:18]3([H:48])[H:49])([H:46])[H:47])[N:19]([H:50])[C:20](=[O:21])[O:22][c:23]4[c:24]([n:25][c:26]([n:27][c:28]4[H:53])[H:52])[H:51])[H:42])[H:41]',\n", + " 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'[H:38][c:9]1[c:10]([c:11]([c:5]([c:6]([c:8]1[H:37])[Cl:7])[C:3](=[O:4])[O:2][C:1]([H:34])([H:35])[H:36])[N:12]2[C:13]([C:14]([C:15]([C:32]([C:33]2([H:60])[H:61])([H:58])[H:59])([H:44])[C:16]([H:45])([H:46])[N:17]([H:47])[C:18](=[O:19])[C:20]3([C:21]([C:22]3([H:50])[H:51])([H:48])[H:49])[N:23]([H:52])[C:24](=[O:25])[C:26]4=[C:27]([N:28]([C:30](=[N:31]4)[H:57])[C:29]([H:54])([H:55])[H:56])[H:53])([H:42])[H:43])([H:40])[H:41])[H:39]',\n", + " '[H:37][c:4]1[c:3]([c:8]([n:7][c:6]([n:5]1)[N:9]2[C:10]([C:11]([C:12]([C:13]([C:14]2([H:46])[H:47])([H:44])[H:45])([H:43])[N:15]([C:19](=[O:20])[c:21]3[c:26]([n:25][c:24]([c:23]([n:22]3)[H:53])[N:27]4[C:28](=[N:29][C:30](=[N:31]4)[H:56])[H:55])[H:54])[C:16]5([C:17]([C:18]5([H:51])[H:52])([H:49])[H:50])[H:48])([H:41])[H:42])([H:39])[H:40])[H:38])[C:2]([H:35])([H:36])[C:1]([H:32])([H:33])[H:34]',\n", + " '[H:39][c:16]1[c:15]([c:14]([c:20]([c:18]([c:17]1[H:40])[Cl:19])[H:41])[C@:12]([H:35])([N:13]([H:36])[H:37])[N:11]([H:34])[c:10]2[c:9]3[c:8]([c:7]([c:6]([c:5]([c:4]3[n:3][c:2]([n:21]2)[C:1]([H:28])([H:29])[H:30])[H:31])[H:32])[C:22]4=[C:23]([C:24]([N:25]([C:26]([C:27]4([H:48])[H:49])([H:46])[H:47])[H:45])([H:43])[H:44])[H:42])[H:33])[H:38]',\n", + " '[H:40][c:16]1[c:17]([c:18]([c:20]2[c:21]([c:15]1[c:11]3[c:9]([c:8]([c:7]([c:14]([c:12]3[C:13]([H:36])([H:37])[H:38])[H:39])[C:5]4=[N:6][N:2]([N:3]=[N:4]4)[C:1]([H:29])([H:30])[H:31])[H:32])[C:10]([H:33])([H:34])[H:35])[C:22]([C:23]([C@@:24]2([H:25])[N:26]=[N+:27]=[N-:28])([H:44])[H:45])([H:42])[H:43])[F:19])[H:41]',\n", + " '[H:41][C:17]1=[C:18]([N:14]([N:15]=[C:16]1[H:40])[C:13]([H:38])([H:39])[C:12]([H:36])([H:37])[C@@:10]([H:33])([C:8](=[O:9])[N:5]2[C:4]([C:3]([C:2]([C:7]([C:6]2([H:29])[H:30])([H:31])[H:32])([H:24])[C:1]([H:21])([H:22])[H:23])([H:25])[H:26])([H:27])[H:28])[N:11]([H:34])[H:35])[C:19]#[N:20]',\n", + " '[H:53][c:20]1[c:19]([c:18]([c:23]([c:22]([c:21]1[c:24]2[c:25]([n:26][c:27]([n:29][c:30]2[H:59])[N:28]([H:57])[H:58])[H:56])[H:54])[H:55])[C:12]3([C:13]([C:14]([C:15]([C:16]([C:17]3([H:50])[H:51])([H:48])[H:49])([H:46])[H:47])([H:44])[H:45])([H:42])[H:43])[C:10](=[O:11])[N:9]([H:41])[C:8]4=[N:31][C:5](=[N:6][O:7]4)[C:2]([C:1]([H:32])([H:33])[H:34])([C:3]([H:35])([H:36])[H:37])[C:4]([H:38])([H:39])[H:40])[H:52]',\n", + " '[H:45][c:26]1[c:25]([c:24]([c:22]2[c:21]([c:27]1[H:46])[N:20]=[C:19]([O:23]2)[c:16]3[c:15]([c:14]([c:13]([c:18]([c:17]3[H:41])[H:42])[N:2]([C:3](=[O:4])[C@:5]4([C:12]([C@@:9]([C:8]([C:7]4([H:31])[H:32])([H:33])[H:34])([H:10])[N:11]([H:35])[H:36])([H:37])[H:38])[H:6])[C:1]([H:28])([H:29])[H:30])[H:39])[H:40])[H:43])[H:44]',\n", + " '[H:38][c:17]1[c:16]([c:15]([c:14]([c:12]2[c:11]1[C:10]([C:9]([N:8]([C:13]2([H:34])[H:35])[c:7]3[c:2]([c:3]([c:4]([c:5]([n:6]3)[H:29])[H:28])[C:22](=[O:24])[O:23][H:39])[C:1]([H:25])([H:26])[H:27])([H:30])[H:31])([H:32])[H:33])[H:36])[C:18]([F:19])([F:20])[F:21])[H:37]',\n", + " '[H:41][c:22]1[c:21]([c:20]([c:18]([c:17]([c:23]1[H:42])[C:14]2=[C:15]([S:16][C:12](=[N:13]2)[C:9]3=[C:10]([C:11]([C@:6]([C:7]([C:8]3([H:32])[H:33])([H:30])[H:31])([H:29])[C:4](=[O:5])[O:3][C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])([H:35])[H:36])[H:34])[H:37])[O:19][H:38])[H:39])[H:40]',\n", + " '[H:50][c:21]1[c:22]([c:23]([c:26]([c:27]([c:20]1[C@:19]2([C:17](=[O:18])[N:10]([c:9]3[c:8]([c:7]([c:6]([c:5]([c:4]3[N:3]([C:28]2=[O:29])[C:2]([H:37])([H:38])[C:1]([H:34])([H:35])[H:36])[H:39])[H:40])[C:30]([F:31])([F:32])[F:33])[H:41])[C:11]4=[C:12]([C:13]([C:14]([C:15](=[C:16]4[H:48])[H:47])([H:45])[H:46])([H:43])[H:44])[H:42])[H:49])[H:56])[H:55])[C:24]([H:52])([H:53])[O:25][H:54])[H:51]',\n", + " '[H:54][c:22]1[c:23]([c:24]([c:25]([c:26]([c:21]1[C:19](=[O:20])[N:15]([C:16]2([C:17]([C:18]2([H:52])[H:53])([H:50])[H:51])[H:49])[C:12]3([C:11]([C:10]([N:9]([C:14]([C:13]3([H:45])[H:46])([H:47])[H:48])[c:6]4[n:5][c:4]([c:3]([c:8]([n:7]4)[H:39])[C:2]([H:36])([H:37])[C:1]([H:33])([H:34])[H:35])[H:38])([H:40])[H:41])([H:42])[H:43])[H:44])[H:57])[H:56])[N:27]5[C:28](=[C:29]([N:30]=[C:31]5[C:32]([H:60])([H:61])[H:62])[H:59])[H:58])[H:55]',\n", + " '[H:46][c:17]1[c:16]([c:15]([c:20]([c:19]([c:18]1[c:21]2[c:26]([c:25]([c:24]([n:23][c:22]2[H:49])[N:27]([C:28]([H:52])([H:53])[H:54])[C:29]([H:55])([H:56])[H:57])[H:50])[H:51])[H:47])[H:48])[C@:4]([C:6](=[O:7])[N:8]([H:40])[c:9]3[c:10]([c:11]([n:12][c:13]([c:14]3[H:44])[H:43])[H:42])[H:41])([C:5]([H:37])([H:38])[H:39])[C:2]([H:33])([C:1]([H:30])([H:31])[H:32])[C:3]([H:34])([H:35])[H:36])[H:45]',\n", + " '[H:59][c:28]1[c:27]([c:26]([c:25]([c:30]([c:29]1[H:60])[H:61])[C@:22]2([C:24]([C@@:17]([C:19]([C:20]([C:21]2([H:53])[H:54])([H:51])[H:52])([H:49])[H:50])([H:18])[C:16]([H:47])([H:48])[N:15]([H:46])[c:14]3[c:13]([n:12][n:11][c:10]([c:31]3[C:32]([H:62])([H:63])[H:64])[C:8](=[O:9])[N:5]4[C:4]([C:3]([C:2]([C:7]([C:6]4([H:41])[H:42])([H:43])[H:44])([H:36])[C:1]([H:33])([H:34])[H:35])([H:37])[H:38])([H:39])[H:40])[H:45])([H:55])[H:56])[H:23])[H:57])[H:58]',\n", + " '[H:29][c:4]1[c:5]([c:6]([c:7]([c:2]([c:3]1[H:28])[Cl:1])[H:31])[c:8]2[c:13]([c:12]([c:11]([c:10]([n:9]2)[c:14]3[c:15]([c:16]([c:17]([c:26]([c:27]3[H:41])[H:40])[N:18]([H:37])[C:19](=[O:20])[C:21]4=[C:22]([O:23][C:24](=[N:25]4)[H:39])[H:38])[H:36])[H:35])[H:32])[H:33])[H:34])[H:30]',\n", + " '[H:36][c:20]1[c:19]([c:18]([c:17]([c:22]([c:21]1[H:37])[H:38])[C@@:16]2([c:10]3[c:9]([c:8]([c:24]([c:23]([c:11]3[O:12][C:13](=[O:14])[N:15]2[H:32])[H:39])[H:40])[C:3]4=[C:2]([O:7][N:6]=[C:4]4[C:5]([H:28])([H:29])[H:30])[C:1]([H:25])([H:26])[H:27])[H:31])[H:33])[H:34])[H:35]',\n", + " '[H:39][c:14]1[c:13]([c:18]([n:17][c:16]([n:15]1)[N:19]2[C:20](=[C:21]([N:22]=[C:23]2[H:43])[H:42])[H:41])[H:40])[C:2](=[O:1])[N:3]([C:4]3([C:5]([C:6]3([H:27])[H:28])([H:25])[H:26])[H:24])[C:7]4([C:8]([C:9]([N:10]([C:11]([C:12]4([H:37])[H:38])([H:35])[H:36])[H:34])([H:32])[H:33])([H:30])[H:31])[H:29]',\n", + " '[H:42][c:16]1[c:17]([c:18]([c:28]([c:29]([c:15]1[O:14][c:13]2[c:30]([c:31]([c:10]([n:11][c:12]2[H:41])[C:9]3=[C:8]([C:7](=[N:6][N:5]3[C:4]([H:37])([H:38])[O:3][C:2]([H:35])([H:36])[C:1]([H:32])([H:33])[H:34])[H:39])[H:40])[H:54])[H:53])[H:52])[H:51])[O:19][C@@:20]4([C:22]([C:23]([C:24](=[O:25])[N:26]([C:27]4([H:49])[H:50])[H:48])([H:46])[H:47])([H:44])[H:45])[H:21])[H:43]',\n", + " '[H:45][c:21]1[c:20]([c:19]([c:18]([c:24]([c:22]1[C:23]([H:46])([H:47])[H:48])[H:49])[C:16](=[O:17])[N:14]([C@@:3]([H:4])([C:2]([H:33])([H:34])[C:1]([H:30])([H:31])[H:32])[C:5]([H:35])([H:36])[N:6]([H:37])[c:7]2[c:8]([c:9]([c:10]([c:12]([n:13]2)[H:40])[Cl:11])[H:39])[H:38])[C:15]([H:41])([H:42])[H:43])[N:25]3[N:26]=[C:27]([C:28](=[N:29]3)[H:51])[H:50])[H:44]',\n", + " '[H:64][c:25]1[c:24]([c:23]([c:28]([c:27]([c:26]1[c:29]2[c:30]([n:31][c:32]([n:34][c:35]2[H:70])[N:33]([H:68])[H:69])[H:67])[H:65])[H:66])[C:17]3([C:18]([C:19]([O:20][C:21]([C:22]3([H:61])[H:62])([H:59])[H:60])([H:57])[H:58])([H:55])[H:56])[C:15](=[O:16])[N:14]([H:54])[c:13]4[c:36]([c:37]([c:38]5[c:11]([c:12]4[H:53])[C:10]([C:9]([N:8]([C:39]5([H:73])[H:74])[C:6](=[O:7])[O:5][C:2]([C:1]([H:40])([H:41])[H:42])([C:3]([H:43])([H:44])[H:45])[C:4]([H:46])([H:47])[H:48])([H:49])[H:50])([H:51])[H:52])[H:72])[H:71])[H:63]',\n", + " '[H:43][c:25]1[c:24]([c:23]([c:19]2[c:18]([c:26]1[H:44])[C:17](=[C:16]([C:21](=[O:22])[N:20]2[H:40])[C:13]3([C:12]([C:11]([N:10]([C:15]([C:14]3([H:35])[H:36])([H:37])[H:38])[c:8]4[c:9]([c:4]([n:5][c:6]([n:7]4)[H:28])[C:2](=[O:3])[O:1][H:27])[H:29])([H:30])[H:31])([H:32])[H:33])[H:34])[H:39])[H:41])[H:42]',\n", + " '[H:29][c:11]1[c:12]([c:13]([c:14]([c:9]([c:10]1[H:28])[N:5]2[C:4]3=[C:3]([N:8]=[C:6]2[Cl:7])[N:2]([C:23](=[O:24])[N:21]([C:19]3=[O:20])[C:22]([H:32])([H:33])[H:34])[C:1]([H:25])([H:26])[H:27])[H:31])[C:15]([F:16])([F:17])[F:18])[H:30]',\n", + " '[H:31][c:7]1[c:6]([c:5]([c:10]([c:9]([c:8]1[c:11]2[n:12][c:13]([c:14]3[c:19]([n:20]2)[C:18]([C@@:16]([O:15]3)([H:17])[C:21]4([C:22]([C:23]([N:24]([C:25]([C:26]4([H:45])[H:46])([H:43])[H:44])[H:42])([H:40])[H:41])([H:38])[H:39])[H:37])([H:35])[H:36])[H:34])[H:32])[H:33])[S:2](=[O:3])(=[O:4])[C:1]([H:27])([H:28])[H:29])[H:30]',\n", + " '[H:34][c:7]1[c:6]([c:5]([c:4]([c:9]([c:8]1[H:35])[H:36])[C:3]([H:30])([H:31])[N:2]([C:10]2=[C:11]([C:12](=[O:13])[N:14]([C:25](=[C:26]2[H:50])[H:49])[C:15]([H:38])([H:39])[C:16]([H:40])([H:41])[c:17]3[c:18]([c:19]([c:20]([c:23]([c:24]3[H:48])[H:47])[C:21]([H:44])([H:45])[O:22][H:46])[H:43])[H:42])[H:37])[C:1]([H:27])([H:28])[H:29])[H:32])[H:33]',\n", + " '[H:34][c:15]1[c:16]([c:17]([c:18]([c:19]([c:14]1[C:13]([H:32])([H:33])[N:12]([H:31])[c:11]2[c:9]([c:5]([n:4][n:3][c:2]2[C:1]([H:24])([H:25])[H:26])[C:6](=[O:8])[O:7][H:27])[C:10]([H:28])([H:29])[H:30])[H:37])[H:36])[C:20]([C:21]([H:38])([H:39])[H:40])([C:22]([H:41])([H:42])[H:43])[C:23]([H:44])([H:45])[H:46])[H:35]',\n", + " '[H:53][c:26]1[c:25]([c:24]([c:29]([c:28]([c:27]1[C:30]2=[C:31]([N:32]=[C:33]([O:34]2)[H:57])[H:56])[H:54])[H:55])[C:2](=[O:1])[N:3]([C:4]3([C:5]([C:6]3([H:38])[H:39])([H:36])[H:37])[H:35])[C:7]4([C:8]([C:9]([N:10]([C:11]([C:12]4([H:47])[H:48])([H:45])[H:46])[C:13]5=[N:14][O:15][C:16](=[N:17]5)[c:18]6[c:19]([n:20][c:21]([c:22]([n:23]6)[H:51])[H:50])[H:49])([H:43])[H:44])([H:41])[H:42])[H:40])[H:52]',\n", + " '[H:32][c:5]1[c:6]([c:7]([c:24]([c:26]([c:4]1[C@:2]([H:30])([C:1]([H:27])([H:28])[H:29])[O:3][H:31])[H:50])[Cl:25])[O:8][c:9]2[c:10]([c:11]([c:12]([c:22]([c:23]2[H:49])[H:48])[C:13]([H:36])([H:37])[N:14]([H:38])[C:15](=[O:16])[C:17]([C:18]([H:39])([H:40])[H:41])([C:19]([H:42])([H:43])[H:44])[C:20]([H:45])([H:46])[O:21][H:47])[H:35])[H:34])[H:33]',\n", + " '[H:35][c:13]1[c:12]([c:11]2[c:10]([c:9]([c:8]1[C:5]3=[C:6]([C:7]([N:2]([C:3]([C:4]3([H:28])[H:29])([H:26])[H:27])[C:1]([H:23])([H:24])[H:25])([H:31])[H:32])[H:30])[H:33])[N:22]=[C:20]([N:14]2[C:15]([H:36])([H:37])[C:16]([C:17]([H:38])([H:39])[H:40])([C:18]([H:41])([H:42])[H:43])[O:19][H:44])[N:21]([H:45])[H:46])[H:34]',\n", + " '[H:31][c:15]1[c:16]([c:17]([c:18]([c:13]([c:14]1[H:30])[N:10]2[C:9](=[C:8]([N:12]=[N:11]2)[C:7]3=[C:5]([N:4]=[C:3]([N:2]3[C:1]([H:22])([H:23])[H:24])[H:25])[C:6]([H:26])([H:27])[H:28])[H:29])[H:33])[C:19](=[O:21])[O:20][H:34])[H:32]',\n", + " '[H:30][C:9]1=[C:8]([N:7]([C:20](=[O:21])[C:19](=[C:10]1[N:11]([H:31])[C:12](=[O:13])[C:14]2=[C:15]([S:16][C:17](=[N:18]2)[H:33])[H:32])[H:34])[C:6]([H:27])([H:28])[C:4](=[O:5])[O:3][C:2]([H:25])([H:26])[C:1]([H:22])([H:23])[H:24])[H:29]',\n", + " '[H:30][c:8]1[c:7]([c:6]([c:5]([c:10]([c:9]1[H:31])[C:11](=[O:12])[C:13]([C:14]([H:32])([H:33])[H:34])([C:15]([H:35])([H:36])[H:37])[N:16]([H:38])[C:17](=[O:18])[O:19][C:20]([C:21]([H:39])([H:40])[H:41])([C:22]([H:42])([H:43])[H:44])[C:23]([H:45])([H:46])[H:47])[N:4]([H:27])[C:2](=[O:3])[C:1]([H:24])([H:25])[H:26])[H:28])[H:29]',\n", + " '[H:36][c:8]1[c:7]([c:6]([n:11][c:10]([c:9]1[C:12]([F:13])([F:14])[F:15])[H:37])[N:5]([H:34])[C:4]([H:32])([H:33])[C:2]([C:1]([H:26])([H:27])[H:28])([C:3]([H:29])([H:30])[H:31])[S:16](=[O:17])(=[O:18])[c:19]2[c:20]([c:21]([c:22]([c:24]([c:25]2[H:41])[H:40])[Cl:23])[H:39])[H:38])[H:35]',\n", + " '[H:47][c:19]1[c:18]([c:17]([c:16]([c:21]([c:20]1[H:48])[H:49])[C:15]([H:43])([H:44])[C:14]([H:41])([H:42])[C:11]2([C:10]([C:9]([N:8]([C:23]([C:22]2([H:50])[H:51])([H:52])[H:53])[C:6](=[O:7])[O:5][C:2]([C:1]([H:24])([H:25])[H:26])([C:3]([H:27])([H:28])[H:29])[C:4]([H:30])([H:31])[H:32])([H:33])[H:34])([H:35])[H:36])[C:12]([H:37])([H:38])[N:13]([H:39])[H:40])[H:45])[H:46]',\n", + " '[H:30][c:11]1[c:12]([c:13]([c:8]2[c:9]([c:10]1[H:29])[C:14](=[O:15])[N:5]([C:6]2=[O:7])[C:4]([H:27])([H:28])[C@:2]([H:3])([C:1]([H:24])([H:25])[H:26])[N:16]([H:33])[C:17](=[O:18])[O:19][C:20]([C:21]([H:34])([H:35])[H:36])([C:22]([H:37])([H:38])[H:39])[C:23]([H:40])([H:41])[H:42])[H:32])[H:31]',\n", + " '[H:44][c:24]1[c:25]([c:2]([c:3]([c:4]2[c:5]1[N:6]([C:7](=[N:23]2)[N:8]([H:28])[C:9](=[O:10])[C@@:11]3([C:13]([C:14]([C:15]([N:16]3[C:17]4([C:18]([C:19]([O:20][C:21]([C:22]4([H:42])[H:43])([H:40])[H:41])([H:38])[H:39])([H:36])[H:37])[H:35])([H:33])[H:34])([H:31])[H:32])([H:29])[H:30])[H:12])[H:27])[H:26])[Cl:1])[H:45]',\n", + " '[H:48][c:22]1[c:21]([c:20]([c:19]([c:24]([c:23]1[H:49])[H:50])[C@:17]2([C@:16]([C:15]([N:14]([C:18]2([H:44])[H:45])[C:12](=[O:13])[N:11]([H:39])[C:10]([H:37])([H:38])[c:9]3[c:8]([c:7]([c:6]([c:29]([c:28]3[H:52])[H:53])[S:3](=[O:4])(=[O:5])[C:2]([H:33])([H:34])[C:1]([H:30])([H:31])[H:32])[H:35])[H:36])([H:40])[H:41])([H:42])[C:25](=[O:27])[O:26][H:51])[H:43])[H:46])[H:47]',\n", + " 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'[H:25][C:3]1=[C:2]([N:6]=[C:5]([S:4]1)[N:7]2[C:8]([C:9]([C:10]([N:11]([C:12]([C:13]2([H:34])[H:35])([H:32])[H:33])[C:14](=[O:15])[C:16]3([C:17]([C:18]([O:19][C:20]([C:21]3([H:43])[H:44])([H:41])[H:42])([H:39])[H:40])([H:37])[H:38])[H:36])([H:30])[H:31])([H:28])[H:29])([H:26])[H:27])[C:1]([H:22])([H:23])[H:24]',\n", + " '[H:36][c:14]1[c:15]([c:7]([c:8]([c:9]2[c:10]1[C:11](=[N:12][N:13]2[H:35])[H:34])[H:33])[N:6]([H:32])[c:5]3[n:4][c:3]([c:2]([c:17]([n:16]3)[N:18]4[C:24]([C:23]([C:22]5=[C:21]([C:20]([C:19]4([H:38])[H:39])([H:40])[H:41])[N:27]([C:26](=[N:25]5)[H:46])[H:47])([H:42])[H:43])([H:44])[H:45])[C:1]([H:28])([H:29])[H:30])[H:31])[H:37]',\n", + " '[H:22][c:3]1[c:4]([c:5]([n:6][c:7]([c:2]1[F:1])[N:8]2[C:9]([C:10]([C:11]([C:12]([C:13]2([H:31])[H:32])([H:29])[H:30])([H:28])[N:14]([H:33])[C:15]3([C:16]([C:17]3([H:37])[H:38])([H:35])[H:36])[H:34])([H:26])[H:27])([H:24])[H:25])[H:23])[C:18]([F:19])([F:20])[F:21]',\n", + " '[H:47][c:25]1[c:24]([c:23]([c:22]([c:27]([c:26]1[H:48])[H:49])[c:19]2[c:18]([c:17]([c:16]([c:21]([c:20]2[H:43])[H:44])[N:2]([C:3](=[O:4])[C@:5]3([C:11]([C@@:9]([C:8]([C:7]3([H:31])[H:32])([H:33])[H:34])([H:10])[N:12]([H:37])[C:13](=[O:15])[C:14]([H:38])([H:39])[H:40])([H:35])[H:36])[H:6])[C:1]([H:28])([H:29])[H:30])[H:41])[H:42])[H:45])[H:46]',\n", + " '[H:28][c:6]1[c:7]([c:8]([n:9][c:4]([c:5]1[H:27])[C:2]([H:23])([C:1]([H:20])([H:21])[H:22])[C:3]([H:24])([H:25])[H:26])[C:10](=[O:11])[N:12]2[C:13]([C:14]([N:15]([C:16]([C:19]2([H:41])[H:42])([C:17]([H:35])([H:36])[H:37])[C:18]([H:38])([H:39])[H:40])[H:34])([H:32])[H:33])([H:30])[H:31])[H:29]',\n", + " '[H:37][c:14]1[c:13]([c:11]([c:10]([c:8]2[c:7]1[N:6]=[C:5]([O:9]2)[C:2]([C:1]([H:27])([H:28])[H:29])([C:3]([H:30])([H:31])[H:32])[C:4]([H:33])([H:34])[H:35])[S:15](=[O:16])(=[O:17])[N:18]3[C:26]([C@:25]4([C:24]([C:23]([C:22]([N:21]4[C:20]([C:19]3([H:38])[H:39])([H:40])[H:41])([H:42])[H:43])([H:44])[H:45])([H:46])[H:47])[H:48])([H:49])[H:50])[Cl:12])[H:36]',\n", + " '[H:33][c:13]1[c:14]([c:15]([c:23]([c:24]([c:12]1[C:11]#[C:10][C:6]2=[C:7]([C:8](=[O:9])[N:3]([C:4](=[C:5]2[H:31])[H:30])[C:2]([H:28])([H:29])[C:1]([H:25])([H:26])[H:27])[H:32])[H:46])[H:45])[C:16]([H:35])([H:36])[C@@:17]([H:37])([C:18]([H:38])([H:39])[H:40])[N:19]([H:41])[C:20](=[O:22])[C:21]([H:42])([H:43])[H:44])[H:34]',\n", + " '[H:32][c:14]1[c:15]([c:16]([c:11]2[c:12]([c:13]1[H:31])[C:6](=[N:7][N:8]([C:9]2=[O:10])[H:30])[C:5]([H:28])([H:29])[C:4]3=[C:3]([N:2]([c:18]4[c:17]3[c:22]([c:21]([c:20]([c:19]4[H:35])[H:36])[H:37])[C:23]([H:38])([H:39])[H:40])[C:1]([H:24])([H:25])[H:26])[H:27])[H:34])[H:33]',\n", + " 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'[H:36][c:9]1[c:10]([c:11]([c:12]([c:13]([c:8]1[N:7]([H:35])[c:6]2[n:5][c:4]([c:3]([c:21]([n:20]2)[N:22]([H:46])[C:23]([H:47])([H:48])[C:24]([H:49])([H:50])[N:25]([H:51])[C:26](=[O:28])[C:27]([H:52])([H:53])[H:54])[C:2]([H:32])([H:33])[C:1]([H:29])([H:30])[H:31])[H:34])[H:39])[H:38])[S:14](=[O:15])(=[O:16])[N:17]([C:18]([H:40])([H:41])[H:42])[C:19]([H:43])([H:44])[H:45])[H:37]',\n", + " '[H:42][c:24]1[c:23]([c:22]([c:21]([c:26]([c:25]1[H:43])[H:44])[C:20]([H:38])([H:39])[N:19]2[c:13]3[c:14]([c:15]([c:17]([c:18]([c:12]3[N:11]=[C:10]2[C:4]4=[C:3]([N:2]([C:8](=[O:9])[C:6](=[C:5]4[H:31])[C:7]([H:32])([H:33])[H:34])[C:1]([H:27])([H:28])[H:29])[H:30])[H:37])[H:36])[F:16])[H:35])[H:40])[H:41]',\n", + " '[H:47][c:26]1[c:25]([c:24]([c:23]([c:28]([c:27]1[H:48])[H:49])[c:22]2[c:21]([c:20]([c:19]([c:18]([c:17]2[C:15](=[O:16])[N:13]([C@@:2]([H:3])([C:1]([H:29])([H:30])[H:31])[C:4]([H:32])([H:33])[N:5]([H:34])[c:6]3[c:7]([c:8]([c:9]([c:11]([n:12]3)[H:37])[Cl:10])[H:36])[H:35])[C:14]([H:38])([H:39])[H:40])[H:41])[H:42])[H:43])[H:44])[H:45])[H:46]',\n", + " '[H:33][c:6]1[c:5]([c:4]([c:3]([c:2]([c:7]1[H:34])[Cl:1])[H:31])[C:8]2([C:9]([C:10]([C:11]2([H:39])[H:40])([H:37])[H:38])([H:35])[H:36])[C:12]3=[C:13]([N:14]=[C:15]([N:16]3[H:42])[c:17]4[c:18]([c:19]([c:20]([c:29]([n:30]4)[H:48])[N:21]([H:45])[C:22](=[O:23])[C:24]5=[C:25]([S:26][C:27](=[N:28]5)[H:47])[H:46])[H:44])[H:43])[H:41])[H:32]',\n", + " '[H:51][c:25]1[c:24]([c:23]([c:28]([c:27]([c:26]1[H:52])[C:29]([F:30])([F:31])[F:32])[H:53])[C@@:3]2([N:4]([C:5](=[C:7]([C@@:8]([N:2]2[C:1]([H:33])([H:34])[H:35])([H:41])[c:9]3[c:14]([c:13]([c:12]([c:11]([c:10]3[C:17](=[O:19])[N:18]([H:45])[H:46])[H:42])[C:15]#[N:16])[H:43])[H:44])[C:20](=[O:22])[C:21]([H:47])([H:48])[H:49])[C:6]([H:38])([H:39])[H:40])[H:37])[H:36])[H:50]',\n", + " '[H:46][c:23]1[c:22]([c:21]([c:27]([c:26]([c:24]1[F:25])[H:47])[H:48])[S:18](=[O:19])(=[O:20])[C:15]([C:13]2=[N:12][N:11]=[C:10]([N:14]2[H:38])[C:8]3=[C:9]([C:5](=[N:6][O:7]3)[C:2]([C:1]([H:28])([H:29])[H:30])([C:3]([H:31])([H:32])[H:33])[C:4]([H:34])([H:35])[H:36])[H:37])([C:16]([H:39])([H:40])[H:41])[C:17]([H:42])([H:43])[H:44])[H:45]',\n", + " 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'[H:41][c:10]1[c:3]([c:4]([c:5]([c:7]([c:8]1[Cl:9])[H:40])[Cl:6])[S:11](=[O:12])(=[O:13])[N:14]([C:15]([H:42])([H:43])[H:44])[C:16]([H:45])([H:46])[C:17]([H:47])([H:48])[O:18][C:19]([H:49])([H:50])[C:20](=[O:21])[N:22]([C@@:24]2([C:26]([C:27]([N:28]([C:29]2([H:58])[H:59])[C:30]3([C:31]([C:32]([N:33]([C:35]([C:36]3([H:70])[H:71])([H:68])[H:69])[C:34]([H:65])([H:66])[H:67])([H:63])[H:64])([H:61])[H:62])[H:60])([H:56])[H:57])([H:54])[H:55])[H:25])[C:23]([H:51])([H:52])[H:53])[O:2][C:1]([H:37])([H:38])[H:39]',\n", + " '[H:30][c:14]1[c:13]([c:12]([c:17]([c:16]([c:15]1[c:18]2[c:19]([c:20]([n:21][c:22]([c:23]2[H:36])[H:35])[H:34])[H:33])[H:31])[H:32])[c:11]3[c:10]([c:5]4[c:4]([c:3]([c:2]3[F:1])[H:24])[N:9]([C:7](=[O:8])[C:6]4([H:25])[H:26])[H:27])[H:28])[H:29]',\n", + " 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'[H:43][c:13]1[c:14]([c:9]([c:10]([n:11][c:12]1[H:42])[H:41])[N:8]([H:40])[C:6](=[O:7])[C@@:4]([c:15]2[c:16]([c:17]([c:18]([c:19]([c:20]2[H:48])[H:47])[c:21]3[c:22]([c:23]4[c:24]([n:28][c:29]3[H:53])[N:25]([C:26](=[C:27]4[H:52])[H:51])[H:50])[H:49])[H:46])[H:45])([C:5]([H:37])([H:38])[H:39])[C:2]([H:33])([C:1]([H:30])([H:31])[H:32])[C:3]([H:34])([H:35])[H:36])[H:44]',\n", + " '[H:34][c:15]1[c:14]([c:13]([c:12]([c:17]([c:16]1[H:35])[H:36])[N:11]2[c:18]3[c:24]([c:22]([c:21]([c:20]([c:19]3[N:3]([C:4]4=[C:5]([C:9]2=[O:10])[N:6]([C:7](=[N:8]4)[H:31])[H:30])[C:2]([H:28])([H:29])[C:1]([H:25])([H:26])[H:27])[H:37])[H:38])[Cl:23])[H:39])[H:32])[H:33]',\n", + " '[H:40][c:18]1[c:19]([c:20]([c:22]([c:23]([c:17]1[C@:2]([H:3])([C:1]([H:24])([H:25])[H:26])[N:4]2[C:15](=[O:16])[N:14]([C:7]3([C:8]([C:9]([C:10](=[O:11])[C:12]([C:13]3([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:31])[H:32])[C:6]([C:5]2([H:27])[H:28])([H:29])[H:30])[H:39])[H:43])[H:42])[Cl:21])[H:41]',\n", + " 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'[H:32][c:11]1[c:10]([n:9][c:8]([c:7]([n:12]1)[N:4]2[C:5](=[N:6][C@@:2]([N:3]2[H:29])([H:28])[C:1]([H:25])([H:26])[H:27])[H:30])[H:31])[C:13](=[O:14])[N:15]([C:16]3([C:17]([C:18]3([H:36])[H:37])([H:34])[H:35])[H:33])[C:19]4([C:20]([C:21]([N:22]([C:23]([C:24]4([H:46])[H:47])([H:44])[H:45])[H:43])([H:41])[H:42])([H:39])[H:40])[H:38]',\n", + " '[H:35][c:6]1[c:5]([c:4]([c:9]([c:8]([c:7]1[C:10]#[N:11])[H:36])[H:37])[C:3]([H:32])([H:33])[C@@:2]2([C:18](=[O:19])[N:17]([C:16]3=[N:15][C:14](=[C:13]([N:12]32)[H:38])[H:39])[c:20]4[c:21]([c:22]([c:24]([c:26]([c:28]4[H:41])[Cl:27])[F:25])[Cl:23])[H:40])[C:1]([H:29])([H:30])[H:31])[H:34]',\n", + " '[H:37][c:13]1[c:14]([c:15]([c:16]([c:17]([c:12]1[C:11]#[C:10][c:7]2[c:6]([c:5]([c:4]([c:9]([c:8]2[H:35])[H:36])[O:3][C:2]([H:31])([H:32])[C:1]([H:28])([H:29])[H:30])[H:33])[H:34])[H:40])[H:39])[C@:18]([H:41])([C:19]([H:42])([H:43])[H:44])[N:20]([H:45])[C:21](=[O:22])[C:23]3=[C:24]([N:25]=[C:26]([O:27]3)[H:47])[H:46])[H:38]',\n", + " '[H:39][c:13]1[c:14]([c:16]([c:17]([c:10]([c:11]1[C:12]([H:36])([H:37])[H:38])[S:7](=[O:8])(=[O:9])[N:6]([H:35])[C@:5]([H:34])([C@:3]([H:30])([C:4]([H:31])([H:32])[H:33])[C:2]([H:28])([H:29])[C:1]([H:25])([H:26])[H:27])[N:19]2[C:20]([C:21]([C:22]([C:23]([C:24]2([H:55])[H:56])([H:53])[H:54])([H:51])[H:52])([H:49])[H:50])([H:47])[H:48])[C:18]([H:44])([H:45])[H:46])[H:43])[C:15]([H:40])([H:41])[H:42]',\n", + " '[H:35][c:14]1[c:15]([c:16]([c:17]([c:18]([c:13]1[C:12]#[C:11][c:8]2[c:7]([c:6]([c:5]([c:10]([c:9]2[H:33])[H:34])[O:4][C:3]([H:29])([H:30])[C:2]([H:27])([H:28])[C:1]([H:24])([H:25])[H:26])[H:31])[H:32])[H:38])[H:37])[C@:19]([H:39])([C:21](=[O:23])[O:22][H:43])[C:20]([H:40])([H:41])[H:42])[H:36]',\n", + " '[H:47][c:24]1[c:23]([c:22]([c:21]([c:26]([c:25]1[H:48])[H:49])[C:20]([H:43])([H:44])[C:19]2([C:18]([C:17]([N:16]([C:28]([C:27]2([H:50])[H:51])([H:52])[H:53])[C:15]([H:36])([H:37])[C:14]([H:34])([H:35])[N:13]([H:33])[c:12]3[c:3]([c:4]([c:5]4[c:6]([n:7][c:8]([c:9]([c:10]4[n:11]3)[H:32])[H:31])[H:30])[H:29])[C:2]#[N:1])([H:38])[H:39])([H:40])[H:41])[H:42])[H:45])[H:46]',\n", + " '[H:31][C:5]1=[C:6]([N:2]([N:3]=[C:4]1[C:24]([C:25]([H:50])([H:51])[H:52])([C:26]([H:53])([H:54])[H:55])[C:27]([H:56])([H:57])[H:58])[C:1]([H:28])([H:29])[H:30])[C:7]2=[C:8]([N:9]=[C:10]([O:11]2)[C:12]([C:13]([H:33])([H:34])[H:35])([C:14]([H:36])([H:37])[H:38])[S:15](=[O:16])(=[O:17])[C:18]3([C:19]([C:20]([C:21]([C:22]([C:23]3([H:48])[H:49])([H:46])[H:47])([H:44])[H:45])([H:42])[H:43])([H:40])[H:41])[H:39])[H:32]',\n", + " 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'[H:34][c:6]1[c:5]([c:4]([c:9]([c:8]([c:7]1[C:10]#[C:11][c:12]2[c:13]([c:14]([c:15]([c:16]([c:17]2[H:40])[H:39])[N:18]3[C:19](=[C:20]([C:21](=[C:22]3[H:44])[H:43])[H:42])[H:41])[H:38])[H:37])[H:35])[H:36])[C:3]([H:31])([H:32])[C@@:2]([H:30])([C:1]([H:27])([H:28])[H:29])[N:23]([H:45])[C:24](=[O:26])[C:25]([H:46])([H:47])[H:48])[H:33]',\n", + " '[H:35][c:13]1[c:12]([c:11]([c:10]([c:15]([c:14]1[H:36])[H:37])[C:8](=[O:9])[C:7]([H:31])([H:32])[C:6]([H:29])([H:30])[N:5]([C:3](=[O:4])[O:2][C:1]([H:26])([H:27])[H:28])[C@:16]([H:17])([c:19]2[c:20]([c:21]([c:22]([c:24]([c:25]2[H:44])[H:43])[Cl:23])[H:42])[H:41])[C:18]([H:38])([H:39])[H:40])[H:33])[H:34]',\n", + " '[H:44][c:18]1[c:17]([c:7]([c:6]([c:5]([c:19]1[N+:20](=[O:22])[O-:21])[N:4]([H:30])[C:3]([H:28])([H:29])[C:2]([H:26])([H:27])[C:1]([H:23])([H:24])[H:25])[H:31])[O:8][C:9]([H:32])([H:33])[C:10](=[O:11])[O:12][C:13]([C:14]([H:34])([H:35])[H:36])([C:15]([H:37])([H:38])[H:39])[C:16]([H:40])([H:41])[H:42])[H:43]',\n", + " 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'[H:28][C:4]1=[C:5]([N:6]2[C:7](=[N:8][N:9]=[C:10]2[C:11]([C:12]([H:30])([H:31])[H:32])([C:13]([H:33])([H:34])[H:35])[N:14]([H:36])[C:15](=[O:16])[C@@:17]3([C:19]([N:20]([C:21]([C:22]([O:23]3)([H:42])[H:43])([H:40])[H:41])[H:39])([H:37])[H:38])[H:18])[C:2](=[C:3]1[H:27])[C:1]([H:24])([H:25])[H:26])[H:29]',\n", + " '[H:49][c:14]1[c:13]([c:12]([c:11]([c:16]([c:15]1[H:50])[H:51])[N:10]2[c:9]3[c:8]([c:7]([c:6]([c:5]([c:4]3[N:3]([C:33](=[O:34])[C@@:19]4([C:17]2=[O:18])[c:23]5[c:24]([c:25]([c:26]([c:27]([c:22]5[C:21]([C:20]4([H:52])[H:53])([H:54])[H:55])[H:58])[H:57])[C:28]6=[C:29]([C:30](=[N:31][N:32]6[H:61])[H:60])[H:59])[H:56])[C:2]([H:42])([H:43])[C:1]([H:39])([H:40])[H:41])[H:44])[H:45])[C:35]([F:36])([F:37])[F:38])[H:46])[H:47])[H:48]',\n", + " 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'[H:38][c:7]1[c:6]([c:5]([c:10]([c:9]([n:8]1)[H:39])[F:11])[C:3](=[O:4])[O:2][C:1]([H:35])([H:36])[H:37])[N:12]2[C:13]([C:14]([C:15]([C:33]([C:34]2([H:58])[H:59])([H:56])[H:57])([H:44])[C:16]([H:45])([H:46])[N:17]([H:47])[C:18](=[O:19])[C:20]3([C:21]([C:22]3([H:50])[H:51])([H:48])[H:49])[N:23]([H:52])[C:24](=[O:25])[O:26][c:27]4[c:28]([n:29][c:30]([n:31][c:32]4[H:55])[H:54])[H:53])([H:42])[H:43])([H:40])[H:41]',\n", + " '[H:36][c:19]1[c:20]([c:21]([c:22]([c:17]([c:18]1[H:35])[C:16]([H:33])([H:34])[N:15]([H:32])[C:13](=[O:14])[C:8]2=[C:7]([N:6]3[C:5](=[C:4]([C:12](=[C:11]([C:10]3=[N:9]2)[H:30])[H:31])[C:2](=[O:3])[N:1]([H:26])[H:27])[H:28])[H:29])[H:38])[C:23](=[O:25])[O:24][H:39])[H:37]',\n", + " '[H:34][c:18]1[c:19]([c:20]([c:22]([c:23]([c:17]1[C:5]2=[C:6]([N:2]([C:3](=[N:4]2)[H:27])[C:1]([H:24])([H:25])[H:26])[c:7]3[c:8]([c:9]([n:10][c:11]([c:16]3[H:33])[N:12]([H:30])[C:13](=[O:15])[N:14]([H:31])[H:32])[H:29])[H:28])[H:37])[H:36])[F:21])[H:35]',\n", + " 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'[H:34][c:8]1[c:9]([c:4]([n:5][c:6]([c:7]1[c:10]2[n:11][c:12]([c:13]([c:14]([n:15]2)[H:37])[C:16](=[O:17])[N:18]([C:19]3([C:20]([C:21]3([H:41])[H:42])([H:39])[H:40])[H:38])[C:22]4([C:23]([C:24]([N:25]([C:26]([C:27]4([H:51])[H:52])([H:49])[H:50])[H:48])([H:46])[H:47])([H:44])[H:45])[H:43])[H:36])[H:33])[O:3][C:2]([H:31])([H:32])[C:1]([H:28])([H:29])[H:30])[H:35]',\n", + " '[H:43][c:20]1[c:19]([c:18]([c:23]([c:22]([c:21]1[C:24]#[N:25])[H:44])[H:45])[C:16]2=[C:17]([C:13](=[N:14][O:15]2)[C:2](=[O:1])[N:3]([C:4]3([C:5]([C:6]3([H:29])[H:30])([H:27])[H:28])[H:26])[C:7]4([C:8]([C:9]([N:10]([C:11]([C:12]4([H:39])[H:40])([H:37])[H:38])[H:36])([H:34])[H:35])([H:32])[H:33])[H:31])[H:41])[H:42]',\n", + " 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'[H:44][c:18]1[c:17]([c:16]([c:15]([c:20]([c:19]1[H:45])[H:46])[C:14]([H:40])([H:41])[O:13][C:12]([H:38])([H:39])[C:11]2([C:10]([C:9]([N:8]([C:22]([C:21]2([H:47])[H:48])([H:49])[H:50])[C:6](=[O:7])[O:5][C:2]([C:1]([H:25])([H:26])[H:27])([C:3]([H:28])([H:29])[H:30])[C:4]([H:31])([H:32])[H:33])([H:34])[H:35])([H:36])[H:37])[C:23]#[N:24])[H:42])[H:43]',\n", + " '[H:37][c:13]1[c:14]([c:15]([c:21]([c:22]([c:12]1[C:10]2([C:9]([N:8]([C:11]2([H:35])[H:36])[C:6](=[O:7])[O:5][C:2]([C:1]([H:23])([H:24])[H:25])([C:3]([H:26])([H:27])[H:28])[C:4]([H:29])([H:30])[H:31])([H:32])[H:33])[H:34])[H:47])[H:46])[O:16][C:17]([H:39])([H:40])[C:18]3([C:19]([C:20]3([H:44])[H:45])([H:42])[H:43])[H:41])[H:38]',\n", + " 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'[H:22][c:8]1[c:7]([c:6]([c:5]([c:10]([c:9]1[H:23])[H:24])[C:4]([H:18])([H:19])[N:3]([H:17])[C:2](=[O:1])[C:11]2([C:12]([C:13]([N:14]([C:15]([C:16]2([H:33])[H:34])([H:31])[H:32])[H:30])([H:28])[H:29])([H:26])[H:27])[H:25])[H:20])[H:21]',\n", + " '[H:28][c:11]1[c:12]([c:13]([c:15]([c:16]([c:10]1[C:8](=[O:9])[C@@:7]([H:27])([C:17]2=[N:18][C:19](=[C:20]([N:21]2[H:34])[H:33])[H:32])[N:6]([H:26])[c:5]3[c:4]([c:3]([c:2]([c:23]([c:22]3[H:35])[H:36])[F:1])[H:24])[H:25])[H:31])[H:30])[F:14])[H:29]',\n", + " '[H:61][c:32]1[c:31]([c:30]([c:28]2[c:27]([c:33]1[H:62])[C:26](=[C:25]([N:29]2[H:58])[C:8]3=[N:7][N:6]4[C:5](=[N:4][N:3]=[C:2]4[C:1]([H:34])([H:35])[H:36])[C:10](=[C:9]3[H:37])[N:11]([H:38])[C:12]5([C:13]([C:14]([N:15]([C:16]([C:17]5([H:46])[H:47])([H:44])[H:45])[C:18](=[O:19])[O:20][C:21]([C:22]([H:48])([H:49])[H:50])([C:23]([H:51])([H:52])[H:53])[C:24]([H:54])([H:55])[H:56])([H:42])[H:43])([H:40])[H:41])[H:39])[H:57])[H:59])[H:60]',\n", + " 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'[H:37][c:9]1[c:10]([c:11]([n:12][c:13]([c:8]1[C@:4]([C:6]#[N:7])([C:5]([H:34])([H:35])[H:36])[C:2]([H:30])([C:1]([H:27])([H:28])[H:29])[C:3]([H:31])([H:32])[H:33])[H:39])[c:14]2[c:15]([n:16][c:17]([n:18][c:19]2[H:41])[N:20]3[C:21](=[C:23]([C:24](=[C:25]3[C:26]([H:47])([H:48])[H:49])[H:46])[H:45])[C:22]([H:42])([H:43])[H:44])[H:40])[H:38]',\n", + " '[H:43][c:17]1[c:16]([c:15]([c:14]([c:19]([c:18]1[H:44])[H:45])[C@:11]2([C:13]([C@@:6]([C:8]([C:9]([C:10]2([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:7])[C:5]([H:31])([H:32])[N:4]([H:30])[c:3]3[c:20]([n:21][n:22][c:23]([c:2]3[C:1]([H:27])([H:28])[H:29])[C:24](=[O:26])[O:25][H:47])[H:46])([H:39])[H:40])[H:12])[H:41])[H:42]',\n", + " '[H:40][c:20]1[c:21]([c:22]([c:23]([c:18]([c:19]1[H:39])[N:17]([H:38])[C:15](=[O:16])[C:13]2=[C:14]([C:7](=[C:8]([N:10]([C:11]2=[O:12])[H:36])[C:9]([H:33])([H:34])[H:35])[C:6]3=[C:5]([C:4](=[N:3][N:2]3[C:1]([H:28])([H:29])[H:30])[H:31])[H:32])[H:37])[H:42])[C:24]([F:25])([F:26])[F:27])[H:41]',\n", + " 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+ " 'InChI=1/C14H10N4O2/c1-18-7-9(5-16-18)8-2-3-11-10(4-8)13-12(20-11)6-15-14(19)17-13/h2-7H,1H3,(H,15,17,19)/f/h17H',\n", + " 'InChI=1/C14H10N4O2/c1-5-16-18(7-1)14-15-6-4-11(17-14)10-2-3-12-13(8-10)20-9-19-12/h1-8H,9H2',\n", + " 'InChI=1/C14H10N4OS/c1-20-14-18-17-13(19-14)11-6-9-8-4-2-3-5-10(8)16-12(9)7-15-11/h2-7,16H,1H3',\n", + " 'InChI=1/C14H10N4S/c1-2-7-17(6-1)12-4-9-19-14(12)11-10-13-15-5-3-8-18(13)16-11/h1-10H',\n", + " 'InChI=1/C14H10N6/c1-3-11(20-8-7-16-19-20)4-2-10(1)14-12-9-15-6-5-13(12)17-18-14/h1-9H,(H,17,18)/f/h17H',\n", + " 'InChI=1/C14H10N6/c15-14-17-5-3-11(19-14)12-7-10-6-9-2-1-4-16-13(9)20(10)8-18-12/h1-8H,(H2,15,17,19)/f/h15H2',\n", + " 'InChI=1/C14H10N6O/c1-21-10-5-9(6-15-7-10)13-17-8-12-19-18-11-3-2-4-16-14(11)20(12)13/h2-8H,1H3',\n", + " 'InChI=1/C14H10N6OS2/c21-11-10(8-3-1-2-4-9(8)17-11)18-14-20-19-12(23-14)7-5-15-13(22)16-6-7/h1-5H,6H2,(H2,15,16,22)(H,17,18,20,21)/f/h15-17H/b18-10-',\n", + " 'InChI=1/C14H10O2/c15-13(11-7-3-1-4-8-11)14(16)12-9-5-2-6-10-12/h1-10H',\n", + " 'InChI=1/C14H10O5/c15-11-7-3-1-5-9(11)14(18)19-12-8-4-2-6-10(12)13(16)17/h1-8,15H,(H,16,17)/p-1/fC14H9O5/q-1',\n", + " 'InChI=1/C14H10O6S/c15-13(16)9-1-5-11(6-2-9)21(19,20)12-7-3-10(4-8-12)14(17)18/h1-8H,(H,15,16)(H,17,18)/p-2/fC14H8O6S/q-2',\n", + " 'InChI=1/C14H11BrClNO/c15-11-5-2-6-12-14(11)18-8-13(17-12)9-3-1-4-10(16)7-9/h1-7,13,17H,8H2/t13-/m0/s1',\n", + " 'InChI=1/C14H11BrFN3O3/c1-14(8-4-7(15)2-3-9(8)16)5-19-6-17-10(13(21)22)11(19)12(20)18-14/h2-4,6H,5H2,1H3,(H,18,20)(H,21,22)/t14-/m0/s1/f/h18,21H',\n", + " 'InChI=1/C14H11BrN2O/c1-18-12-6-3-5-11(8-12)17-9-10-4-2-7-13(15)14(10)16-17/h2-9H,1H3',\n", + " 'InChI=1/C14H11BrN2O2/c15-13-6-7-17(14(18)12(13)10-16)8-9-19-11-4-2-1-3-5-11/h1-7H,8-9H2',\n", + " 'InChI=1/C14H11BrO3/c15-11-5-3-6-12(8-11)18-9-10-4-1-2-7-13(10)14(16)17/h1-8H,9H2,(H,16,17)/f/h16H',\n", + " 'InChI=1/C14H11Cl2F3N2/c15-10-5-9(14(17,18)19)6-11(16)13(10)21-7-8-3-1-2-4-12(8)20-21/h5-7H,1-4H2',\n", + " 'InChI=1/C14H11Cl2F3N2O/c1-3-7(4-2)13(22,14(17,18)19)12-20-10-5-8(15)9(16)6-11(10)21-12/h5-6,22H,1,4H2,2H3,(H,20,21)/t13-/m1/s1/f/h20H',\n", + " 'InChI=1/C14H11Cl2N3O/c1-19-12-10(3-2-6-17-12)14(20)18-13(19)9-5-4-8(15)7-11(9)16/h2-7,13H,1H3,(H,18,20)/t13-/m1/s1/f/h18H',\n", + " ...]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_inchi_keys()" + ] + }, + { + "cell_type": "markdown", + "id": "2033b59f-95f4-478b-8977-3901fd5ec970", + "metadata": {}, + "source": [ + "Molecule descriptors can be inter-converted in a number of ways:" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "b82aaf58-83ad-4bea-a0ee-5ab725d64fb1", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:19:41.153533Z", + "iopub.status.busy": "2024-10-11T01:19:41.152625Z", + "iopub.status.idle": "2024-10-11T01:19:41.168787Z", + "shell.execute_reply": "2024-10-11T01:19:41.164915Z", + "shell.execute_reply.started": "2024-10-11T01:19:41.153476Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'[H:26]/[C:2](=[C:3](/[H:27])\\\\[C:4]([H:28])([H:29])[N:5]1[C:9]2=[C:8]([N:7]=[C:6]1[N:17]3[C:18]([C:19]([N:20]([C:21]([C:22]3([H:41])[H:42])([H:39])[H:40])[H:38])([H:36])[H:37])([H:34])[H:35])[N:15]([C:13](=[O:14])[N:12]([C:10]2=[O:11])[H:30])[C:16]([H:31])([H:32])[H:33])/[C:1]([H:23])([H:24])[H:25]'" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "smiles_1 = store.get_smiles_by_molecule_id(1)\n", + "smiles_1" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "39bb7456-24f9-45de-8242-8bdcb1ddd975", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:19:52.744677Z", + "iopub.status.busy": "2024-10-11T01:19:52.743622Z", + "iopub.status.idle": "2024-10-11T01:19:52.778700Z", + "shell.execute_reply": "2024-10-11T01:19:52.778050Z", + "shell.execute_reply.started": "2024-10-11T01:19:52.744630Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "1" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_molecule_id_by_smiles(smiles_1)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "da78dd2a-0cce-47f7-b661-4843ce1a604d", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:20:20.445001Z", + "iopub.status.busy": "2024-10-11T01:20:20.443791Z", + "iopub.status.idle": "2024-10-11T01:20:20.463873Z", + "shell.execute_reply": "2024-10-11T01:20:20.462929Z", + "shell.execute_reply.started": "2024-10-11T01:20:20.444947Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'InChI=1/C14H20N6O2/c1-3-4-7-20-10-11(18(2)14(22)17-12(10)21)16-13(20)19-8-5-15-6-9-19/h3-4,15H,5-9H2,1-2H3,(H,17,21,22)/b4-3+/f/h17H'" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "inchi_1 = store.get_inchi_key_by_molecule_id(1)\n", + "inchi_1" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "9f7a67be-d00b-415b-98e8-310f4119b886", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:20:30.787478Z", + "iopub.status.busy": "2024-10-11T01:20:30.785934Z", + "iopub.status.idle": "2024-10-11T01:20:30.805214Z", + "shell.execute_reply": "2024-10-11T01:20:30.804066Z", + "shell.execute_reply.started": "2024-10-11T01:20:30.786930Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "1" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_molecule_id_by_inchi_key(inchi_1)" + ] + }, + { + "cell_type": "markdown", + "id": "78225560-1c2f-49c4-a67b-eb461528a3f4", + "metadata": {}, + "source": [ + "Additionally, if you have the `QCArchiveID` for a specific conformer record, you can find its molecule ID and other properties:" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "1c4b11f3-b089-411f-9b68-4486d4ae12f4", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:26:47.085938Z", + "iopub.status.busy": "2024-10-11T01:26:47.084992Z", + "iopub.status.idle": "2024-10-11T01:26:47.171850Z", + "shell.execute_reply": "2024-10-11T01:26:47.171319Z", + "shell.execute_reply.started": "2024-10-11T01:26:47.085865Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "1" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_molecule_id_by_qcarchive_id(36967435)" + ] + }, + { + "cell_type": "markdown", + "id": "1ea62a94-6423-49d5-a321-cac07f2398a8", + "metadata": {}, + "source": [ + "And vice versa, you can get the list of `QCArchiveIDs` for the conformers of a given `molecule_id` (these are the same IDs store in the QCArchive):" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "b31eec3c-0a72-4e27-862b-5e21b4f2955b", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:26:43.009801Z", + "iopub.status.busy": "2024-10-11T01:26:43.008100Z", + "iopub.status.idle": "2024-10-11T01:26:43.027421Z", + "shell.execute_reply": "2024-10-11T01:26:43.026901Z", + "shell.execute_reply.started": "2024-10-11T01:26:43.009735Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "[36967435,\n", + " 36967436,\n", + " 36967437,\n", + " 36967438,\n", + " 36967439,\n", + " 36967440,\n", + " 36967441,\n", + " 36967442]" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_qcarchive_ids_by_molecule_id(1)" + ] + }, + { + "cell_type": "markdown", + "id": "634c4fbe-a808-42e1-acf3-7158cffa6403", + "metadata": {}, + "source": [ + "# Accessing properties about molecules and conformers" + ] + }, + { + "cell_type": "markdown", + "id": "4d0cc51d-2128-489d-9cf9-8085ffb5e6e0", + "metadata": {}, + "source": [ + "The `MoleculeStore` contains a lot of information about the benchmarked molecules, including their QM and MM energies and optimized geometries. You can access this information a number of ways:" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "1e4e1bcf-de5b-4ab8-b8a2-2e0160534950", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:27:50.233788Z", + "iopub.status.busy": "2024-10-11T01:27:50.232456Z", + "iopub.status.idle": "2024-10-11T01:27:50.270254Z", + "shell.execute_reply": "2024-10-11T01:27:50.269596Z", + "shell.execute_reply.started": "2024-10-11T01:27:50.233703Z" + }, + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/plain": [ + "[array([[-3.18892695, 2.60763111, 6.87188422],\n", + " [-2.88924841, 1.40280254, 6.02692163],\n", + " [-2.71077659, 1.42183558, 4.70068234],\n", + " [-2.38388331, 0.19121941, 3.89547835],\n", + " [-0.97850369, 0.21129344, 3.43860423],\n", + " [-0.47168018, 0.90252113, 2.36508375],\n", + " [ 0.83790373, 1.17358682, 2.49300744],\n", + " [ 1.17629623, 0.65809546, 3.70946597],\n", + " [ 0.09622564, 0.05094055, 4.3248862 ],\n", + " [ 0.19286562, -0.6020484 , 5.59178979],\n", + " [-0.68319995, -1.19132308, 6.23092754],\n", + " [ 1.51003967, -0.49230752, 6.0959437 ],\n", + " [ 2.63705142, 0.09346444, 5.51911689],\n", + " [ 3.73185714, 0.08708018, 6.07360484],\n", + " [ 2.43443943, 0.68093195, 4.27393775],\n", + " [ 3.57705292, 1.30535657, 3.60602963],\n", + " [-1.26364851, 1.30271887, 1.30686296],\n", + " [-1.96866959, 0.25327916, 0.53924404],\n", + " [-1.08143146, -0.31801253, -0.57008774],\n", + " [-0.64275222, 0.77254986, -1.44583729],\n", + " [ 0.15957681, 1.75138459, -0.69722039],\n", + " [-0.70013957, 2.3395519 , 0.42325276],\n", + " [-2.41044127, 2.74850003, 7.63179852],\n", + " [-4.13601365, 2.48233597, 7.41096215],\n", + " [-3.25324353, 3.51990806, 6.27121871],\n", + " [-2.79146742, 0.44993833, 6.547565 ],\n", + " [-2.76374445, 2.3602938 , 4.14741773],\n", + " [-3.02414624, 0.12213738, 3.01609298],\n", + " [-2.51343629, -0.71026668, 4.49509414],\n", + " [ 1.67839365, -0.92792535, 6.99711983],\n", + " [ 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"output_type": "execute_result" + } + ], + "source": [ + "store.get_mm_conformer_by_qcarchive_id(36967435, \"openff_unconstrained-2.2.0-rc1.offxml\")" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "2865d8a3-e821-41cd-aca9-740566c43d7c", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:34:04.319082Z", + "iopub.status.busy": "2024-10-11T01:34:04.317786Z", + "iopub.status.idle": "2024-10-11T01:34:04.335886Z", + "shell.execute_reply": "2024-10-11T01:34:04.335179Z", + "shell.execute_reply.started": "2024-10-11T01:34:04.318728Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "[-170.17696446874925,\n", + " -166.98932560834777,\n", + " -165.86022393745745,\n", + " -168.55106225439113,\n", + " -166.41800584081335,\n", + " -166.12066373226307,\n", + " -166.10796495554544,\n", + " -166.17417040557143]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_mm_energies_by_molecule_id(1, \"openff_unconstrained-2.2.0-rc1.offxml\") # in kcal/mol" + ] + }, + { + "cell_type": "markdown", + "id": "09e67bb4-20f5-4eb4-9141-f24b7278d842", + "metadata": {}, + "source": [ + "# Example analysis " + ] + }, + { + "cell_type": "markdown", + "id": "9d0a38e6-6d4c-438d-ba58-fe2258400936", + "metadata": {}, + "source": [ + "## Examining the difference between the QM and MM structures\n", + "\n", + "If summary statistics like RMSD, TFD, or ICRMSD aren't enough, you can visually compare the structures, or do more in-depth analysis using the OpenFF Toolkit API." + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "233f7193-abe4-4666-9b97-b56a9d98c880", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:41:18.410880Z", + "iopub.status.busy": "2024-10-11T01:41:18.408284Z", + "iopub.status.idle": "2024-10-11T01:41:18.421393Z", + "shell.execute_reply": "2024-10-11T01:41:18.420342Z", + "shell.execute_reply.started": "2024-10-11T01:41:18.410766Z" + } + }, + "outputs": [], + "source": [ + "from openff.toolkit import Molecule, Quantity" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "cb1054f6-3aee-4a09-9e70-308bf66c2230", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:38:57.457227Z", + "iopub.status.busy": "2024-10-11T01:38:57.456216Z", + "iopub.status.idle": "2024-10-11T01:38:57.483499Z", + "shell.execute_reply": "2024-10-11T01:38:57.482904Z", + "shell.execute_reply.started": "2024-10-11T01:38:57.457179Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "1" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "qm_mol = Molecule.from_mapped_smiles(store.get_smiles_by_molecule_id(1))\n", + "qm_mol.add_conformer(\n", + " Quantity(\n", + " store.get_qm_conformers_by_molecule_id(1)[0],\n", + " \"angstrom\",\n", + " ),\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "a8541c27", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[array([[-3.18892695, 2.60763111, 6.87188422],\n", + " [-2.88924841, 1.40280254, 6.02692163],\n", + " [-2.71077659, 1.42183558, 4.70068234],\n", + " [-2.38388331, 0.19121941, 3.89547835],\n", + " [-0.97850369, 0.21129344, 3.43860423],\n", + " [-0.47168018, 0.90252113, 2.36508375],\n", + " [ 0.83790373, 1.17358682, 2.49300744],\n", + " [ 1.17629623, 0.65809546, 3.70946597],\n", + " [ 0.09622564, 0.05094055, 4.3248862 ],\n", + " [ 0.19286562, -0.6020484 , 5.59178979],\n", + " [-0.68319995, -1.19132308, 6.23092754],\n", + " [ 1.51003967, -0.49230752, 6.0959437 ],\n", + " [ 2.63705142, 0.09346444, 5.51911689],\n", + " [ 3.73185714, 0.08708018, 6.07360484],\n", + " [ 2.43443943, 0.68093195, 4.27393775],\n", + " [ 3.57705292, 1.30535657, 3.60602963],\n", + " [-1.26364851, 1.30271887, 1.30686296],\n", + " [-1.96866959, 0.25327916, 0.53924404],\n", + " [-1.08143146, -0.31801253, -0.57008774],\n", + " 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+ " [-5.70590668e+00, 1.26581937e+00, 5.21041339e+00],\n", + " [-5.35493302e+00, -1.30143374e-01, 4.19542028e+00],\n", + " [-3.97357952e+00, 1.89775844e+00, 3.41062107e+00],\n", + " [-2.25115724e+00, 7.46376629e-01, 5.68111372e+00],\n", + " [-1.67417462e+00, 2.59972999e+00, 3.25848848e+00],\n", + " [-1.04443341e+00, 2.85836717e+00, 4.89383066e+00],\n", + " [ 2.28416247e+00, 5.96561470e-01, 7.66202735e+00],\n", + " [ 4.42067599e+00, 3.17748768e-01, 2.96800038e+00],\n", + " [ 4.97368789e+00, -7.09665366e-01, 4.32463295e+00],\n", + " [ 3.78088066e+00, -1.33070437e+00, 3.14458073e+00],\n", + " [ 1.02079075e+00, 2.09421141e+00, 2.53414722e-01],\n", + " [ 1.04506949e+00, 3.25487937e-01, 1.42757992e-01],\n", + " [-3.96489475e-02, 1.72418574e+00, -1.82196661e+00],\n", + " [-8.39286152e-01, 2.41513525e-01, -1.29828519e+00],\n", + " [-2.26778604e+00, 2.30523811e+00, -1.46366105e+00],\n", + " [-3.06731439e+00, 2.23181666e+00, 9.69636880e-01],\n", + " [-3.36990164e+00, 8.15615722e-01, -5.63290579e-02],\n", + " [-1.61465857e+00, -4.48060811e-01, 8.70136480e-01],\n", + " [-2.20755892e+00, 4.36123799e-01, 2.26597370e+00]]) ,\n", + " array([[-3.70239718, -0.37597848, 6.24029798],\n", + " [-2.94517733, 0.8055422 , 5.70538573],\n", + " [-2.63609807, 1.00061475, 4.41769026],\n", + " [-1.84379507, 2.18782771, 3.93593914],\n", + " [-0.46499563, 1.79854764, 3.56521033],\n", + " [-0.08031479, 1.07671076, 2.45703014],\n", + " [ 1.05184141, 0.37766785, 2.65004761],\n", + " [ 1.38719403, 0.63390881, 3.9464194 ],\n", + " [ 0.49298438, 1.49809275, 4.54973427],\n", + " [ 0.62955564, 1.92213581, 5.9045319 ],\n", + " [-0.09179555, 2.67919925, 6.56169794],\n", + " [ 1.77407463, 1.32620791, 6.48774671],\n", + " [ 2.72195981, 0.4711378 , 5.92645515],\n", + " [ 3.67964241, 0.05728057, 6.57317915],\n", + " [ 2.49518056, 0.13159202, 4.59247483],\n", + " [ 3.42525242, -0.75204327, 3.89040078],\n", + " [-0.79240064, 1.04733188, 1.28840121],\n", + " [-0.3707295 , 0.04878737, 0.29180112],\n", + " [-1.35877911, 0.07867748, -0.87320061],\n", + " [-1.43288326, 1.39341344, -1.54353838],\n", + " [-0.94014914, 2.49751424, -0.70771695],\n", + " [-1.37482794, 2.29170073, 0.74163799],\n", + " [-4.61614516, -0.05510818, 6.75541187],\n", + " [-3.98285595, -1.07297764, 5.4448432 ],\n", + " [-3.09911263, -0.91896532, 6.97821172],\n", + " [-2.6126062 , 1.54623981, 6.43354828],\n", + " [-2.92172829, 0.26599827, 3.6635446 ],\n", + " [-2.3169789 , 2.65537482, 3.07279062],\n", + " [-1.75328624, 2.93564156, 4.72405903],\n", + " [ 1.95488243, 1.57109343, 7.45591802],\n", + " [ 2.90459405, -1.65275391, 3.55544276],\n", + " [ 4.22066915, -1.01488151, 4.58494593],\n", + " [ 3.83812831, -0.23931032, 3.01801504],\n", + " [-0.36739673, -0.93400876, 0.7694398 ],\n", + " [ 0.65305313, 0.24262812, -0.05485368],\n", + " [-2.35278164, -0.1914893 , -0.49528596],\n", + " [-1.07781936, -0.68607158, -1.60300952],\n", + " [-0.90798241, 1.37054109, -2.41234048],\n", + " [-1.36610389, 3.4406275 , -1.06814035],\n", + " [ 0.15688515, 2.60410036, -0.7266763 ],\n", + " [-1.0320265 , 3.13997345, 1.33830524],\n", + " [-2.4700304 , 2.25647888, 0.79030451]]) ,\n", + " array([[-2.11710818, 3.94194053, 5.62159187],\n", + " [-1.84208877, 2.62607871, 4.94861536],\n", + " [-2.73960645, 1.64952233, 4.78859304],\n", + " [-2.49434991, 0.30860414, 4.1405124 ],\n", + " [-1.12521055, 0.12868643, 3.64984836],\n", + " [-0.54210261, 0.75295516, 2.57142997],\n", + " [ 0.79948269, 0.80324597, 2.66240717],\n", + " [ 1.08353496, 0.21364714, 3.85896656],\n", + " [-0.06185573, -0.22078715, 4.50028415],\n", + " [-0.03759486, -0.9162283 , 5.74769874],\n", + " [-0.98002026, -1.37940718, 6.39439127],\n", + " [ 1.2937005 , -1.02792446, 6.2155129 ],\n", + " [ 2.48322552, -0.6183071 , 5.61400191],\n", + " [ 3.57861545, -0.81118969, 6.13211652],\n", + " [ 2.34356811, 0.02179229, 4.38516281],\n", + " [ 3.55452958, 0.46104142, 3.6907052 ],\n", + " [-1.2635995 , 1.29366501, 1.54007761],\n", + " [-2.31797631, 0.48712886, 0.89207987],\n", + " [-1.96234507, 0.2331659 , -0.59704292],\n", + " [-0.52483752, 0.0947235 , -0.81640013],\n", + " [ 0.18437347, 1.34483274, -0.48940667],\n", + " [-0.53750809, 2.16343466, 0.60882931],\n", + " [-1.92037898, 4.77966358, 4.94108949],\n", + " [-1.46233938, 4.07927275, 6.49084249],\n", + " [-3.15443518, 4.01382488, 5.96175314],\n", + " [-0.82697369, 2.48020631, 4.58139973],\n", + " [-3.7551763 , 1.78183359, 5.16440642],\n", + " [-2.67301357, -0.49060793, 4.8654819 ],\n", + " [-3.19573904, 0.15847492, 3.31673353],\n", + " [ 1.41400921, -1.50628126, 7.10268133],\n", + " [ 3.25154635, 0.93544493, 2.75871115],\n", + " [ 4.19999319, -0.39611595, 3.48525167],\n", + " [ 4.10603827, 1.16936234, 4.31297084],\n", + " [-2.37871781, -0.47385973, 1.40824854],\n", + " [-3.29370245, 0.98367385, 0.98263635],\n", + " [-2.32244593, 1.05631432, -1.2236147 ],\n", + " [-2.47867147, -0.66916795, -0.93954212],\n", + " [-0.16731259, -0.65415236, -0.22677503],\n", + " [ 0.27115526, 1.95938553, -1.39490689],\n", + " [ 1.19343504, 1.08998004, -0.15990979],\n", + " [-1.27689199, 2.83909286, 0.16574473],\n", + " [ 0.16959461, 2.77203437, 1.17272197]]) ]" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_qm_conformers_by_molecule_id(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "6c633d58-264e-4d7b-89b8-34b60da8e316", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:39:01.234352Z", + "iopub.status.busy": "2024-10-11T01:39:01.232815Z", + "iopub.status.idle": "2024-10-11T01:39:01.285833Z", + "shell.execute_reply": "2024-10-11T01:39:01.285348Z", + "shell.execute_reply.started": "2024-10-11T01:39:01.234264Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "23f98f0ab1f04b50b16be1c3204fec1f", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "156e033e655d4ecc99e872a0454a2aef", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget()" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "qm_mol" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "3a897778-8145-4de7-96da-8eafbcc7fe8a", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:42:23.438860Z", + "iopub.status.busy": "2024-10-11T01:42:23.437383Z", + "iopub.status.idle": "2024-10-11T01:42:23.462742Z", + "shell.execute_reply": "2024-10-11T01:42:23.462098Z", + "shell.execute_reply.started": "2024-10-11T01:42:23.438772Z" + } + }, + "outputs": [], + "source": [ + "mm_mol = Molecule.from_mapped_smiles(store.get_smiles_by_molecule_id(1))\n", + "mm_mol._conformers = [\n", + " Quantity(value=conf, units=\"angstrom\")\n", + " for conf in store.get_mm_conformers_by_molecule_id(\n", + " 1,\n", + " \"openff_unconstrained-2.2.0-rc1.offxml\",\n", + " )\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "c718f7be-a651-4fef-8c69-137d45865677", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:42:24.455985Z", + "iopub.status.busy": "2024-10-11T01:42:24.454489Z", + "iopub.status.idle": "2024-10-11T01:42:24.493042Z", + "shell.execute_reply": "2024-10-11T01:42:24.492653Z", + "shell.execute_reply.started": "2024-10-11T01:42:24.455942Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "7c56c475401e4672a45e664ebe087b3c", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget(max_frame=7)" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "mm_mol" + ] + }, + { + "cell_type": "markdown", + "id": "6aee2f6c-038d-42ed-b2ac-386985587b83", + "metadata": {}, + "source": [ + "If you want to easily compare two conformers, you can add the QM and MM structures to the same `Molecule` as distinct conformers. (The toolkit thinks they're just two conformers, so keep track of which is from QM and which is from MM.)" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "79e5affc-39d3-40ba-9096-f4430b6ef84f", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:43:41.288105Z", + "iopub.status.busy": "2024-10-11T01:43:41.287091Z", + "iopub.status.idle": "2024-10-11T01:43:41.312905Z", + "shell.execute_reply": "2024-10-11T01:43:41.312062Z", + "shell.execute_reply.started": "2024-10-11T01:43:41.288049Z" + } + }, + "outputs": [], + "source": [ + "conf_1_mol = Molecule.from_mapped_smiles(store.get_smiles_by_molecule_id(1))\n", + "conf_1_mol._conformers = [\n", + " store.get_qm_conformers_by_molecule_id(1)[0],\n", + " Quantity(\n", + " value=store.get_mm_conformers_by_molecule_id(1, \"openff_unconstrained-2.2.0-rc1.offxml\")[0],\n", + " units=\"angstrom\",\n", + " ),\n", + "]" + ] + }, + { + "cell_type": "markdown", + "id": "23a404f9", + "metadata": {}, + "source": [ + "`Molecule` visualization, when multiple conformers are stored, defaults to using `nglview` to view them like a trajectory. This isn't strictly a trajecotry, but it's a handy way to compare the structures side-by-side." + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "15e59d55-c594-4c90-9c51-54fc5997160e", + "metadata": { + "execution": { + "iopub.execute_input": "2024-10-11T01:43:46.808017Z", + "iopub.status.busy": "2024-10-11T01:43:46.806913Z", + "iopub.status.idle": "2024-10-11T01:43:46.845578Z", + "shell.execute_reply": "2024-10-11T01:43:46.845187Z", + "shell.execute_reply.started": "2024-10-11T01:43:46.807938Z" + } + }, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "fa79a53c7dd34174a3d0fbdb318de915", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "NGLWidget(max_frame=1)" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "conf_1_mol" + ] + }, + { + "cell_type": "markdown", + "id": "b00e2bd2", + "metadata": {}, + "source": [ + "## Compute DDEs" + ] + }, + { + "cell_type": "markdown", + "id": "e565104d", + "metadata": {}, + "source": [ + "QM energies, reported by QCArchive, and MM energies, reported by OpenMMM, are also stored and can be retrieved using the high-level API much in the same way we got conformers:" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "83f0be91", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([-170.17696447, -166.98932561, -165.86022394, -168.55106225,\n", + " -166.41800584, -166.12066373, -166.10796496, -166.17417041])" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import numpy\n", + "\n", + "mm_energies = numpy.array(\n", + " store.get_mm_energies_by_molecule_id(\n", + " 1,\n", + " \"openff_unconstrained-2.2.0-rc1.offxml\",\n", + " )\n", + ")\n", + "\n", + "mm_energies" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "bee503f5", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([-643021.68409096, -643016.59145923, -643016.15874375,\n", + " -643021.73164061, -643016.28048558, -643015.51702181,\n", + " -643016.32580181, -643016.86987724])" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "qm_energies = numpy.array(store.get_qm_energies_by_molecule_id(1))\n", + "\n", + "qm_energies" + ] + }, + { + "cell_type": "markdown", + "id": "3de0d137", + "metadata": {}, + "source": [ + "DDEs are conventionally computed by comparing the QM and MM energies of each structure to each other after subtracting out the minimum energy of all structures, using the structure with the lowest QM energy as a reference point. " + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "7c998784", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[(36967435, -1.6734518596581438),\n", + " (36967436, -3.5784447340478778),\n", + " (36967437, -2.882058544188311),\n", + " (36967438, nan),\n", + " (36967439, -3.318098614495341),\n", + " (36967440, -3.7842202757516077),\n", + " (36967441, -2.962741494181529),\n", + " (36967442, -2.484871522684216)]" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import numpy\n", + "\n", + "qm_minimum_index = qm_energies.argmin()\n", + "\n", + "mm_energies -= mm_energies[qm_minimum_index]\n", + "qm_energies -= qm_energies[qm_minimum_index]\n", + "\n", + "# The reference point has an artifically zero DDE, so we manually make it NaN.\n", + "mm_energies[qm_minimum_index] = numpy.nan\n", + "qm_energies[qm_minimum_index] = numpy.nan\n", + "\n", + "ddes = mm_energies - qm_energies\n", + "\n", + "[(id, dde) for id, dde in zip(store.get_qcarchive_ids_by_molecule_id(1), ddes)]" + ] + }, + { + "cell_type": "markdown", + "id": "78765550", + "metadata": {}, + "source": [ + "`MoleculeStore` has a high-level API that does this (the numerical values below should be identical). Above is provided as an example of what internally happens in this methods, which can be taken apart or modified for custom analyses." + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "5dffa23f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[DDE(qcarchive_id=36967435, difference=-1.6734518596581438),\n", + " DDE(qcarchive_id=36967436, difference=-3.5784447340478778),\n", + " DDE(qcarchive_id=36967437, difference=-2.882058544188311),\n", + " DDE(qcarchive_id=36967438, difference=nan),\n", + " DDE(qcarchive_id=36967439, difference=-3.318098614495341),\n", + " DDE(qcarchive_id=36967440, difference=-3.7842202757516077),\n", + " DDE(qcarchive_id=36967441, difference=-2.962741494181529),\n", + " DDE(qcarchive_id=36967442, difference=-2.484871522684216)]" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "store.get_dde(force_field=\"openff_unconstrained-2.2.0-rc1.offxml\", molecule_ids=[1], skip_check=True)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 1b9be636de672c42e9286e149e5b5b8b1e983b97 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 11 Oct 2024 12:49:19 -0500 Subject: [PATCH 3/6] Fix bad API calls --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1f797a1..7289ab4 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,6 @@ if __name__ == "__main__": must be used for Python's `multiprocessing` module to behave well. - ### Data sources It is assumed that the input molecules are stored in a `openff-qcsubmit` model like `OptimizationResultCollection` or YAMMBS's own input models. @@ -55,7 +54,12 @@ season1_dataset = OptimizationResultCollection.from_server( ``` -After retrieving it, probably after applying some filters, you can dump it to disk with `season1_dataset.json("qcsubmit.json")` to avoid pulling down all of the data from the server again. +After retrieving it, probably after applying some filters, you can dump it to disk to avoid pulling down all of the data from the server again. + +```python +with open("qcsubmit.json", "w") as f: + f.write(season1_dataset.json()) +``` Once a `OptimizationResultCollection` is in memory, either by pulling it down from QCArchive or loading it from disk, convert it to a "YAMMBS input" model using the API: @@ -63,7 +67,7 @@ Once a `OptimizationResultCollection` is in memory, either by pulling it down fr from yammbs.inputs import QCArchiveDataset -season1_dataset = OptimizationResultCollection.parse_raw("qcsubmit.json") +season1_dataset = OptimizationResultCollection.parse_raw(open("qcsubmit.json").read()) dataset = QCArchiveDataset.from_qcsubmit_collection(season1_dataset) From 8b5f41fdc8468b1869b632ca96becd7a2a90a1ff Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 11 Oct 2024 14:01:15 -0500 Subject: [PATCH 4/6] Small fixes --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7289ab4..2f68f61 100644 --- a/README.md +++ b/README.md @@ -51,10 +51,9 @@ season1_dataset = OptimizationResultCollection.from_server( datasets="OpenFF Industry Benchmark Season 1 v1.1", spec_name="default", ) - ``` -After retrieving it, probably after applying some filters, you can dump it to disk to avoid pulling down all of the data from the server again. +After retrieving it - and after applying filters to remove problematic records - you can dump it to disk to avoid pulling down all of the data from the server again. ```python with open("qcsubmit.json", "w") as f: @@ -71,7 +70,8 @@ season1_dataset = OptimizationResultCollection.parse_raw(open("qcsubmit.json").r dataset = QCArchiveDataset.from_qcsubmit_collection(season1_dataset) -dataset.model_dump_json("input.json") +with open("input.json", "w") as f: + f.write(dataset.model_dump_json()) ``` This input model (`QCArchiveDataset`) stores a miniimum amount of information to use these QM geometries as reference structures. The dataset has fields for tagging the name and model version, but mostly stores a list of structures. Each QM-optimized structure is stored as a `QCArchiveMolecule` object which stores: From edf324a1e4dd3fb5179c7a809b42afebea0976f3 Mon Sep 17 00:00:00 2001 From: Matt Thompson Date: Thu, 17 Oct 2024 11:33:47 -0500 Subject: [PATCH 5/6] Apply suggestions from code review Co-authored-by: Brent Westbrook <36778786+ntBre@users.noreply.github.com> --- README.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 2f68f61..4d8917f 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Yet Another Molecular Mechanics Benchmarking Suite (YAMMBS, pronounced like "yams") is a tool for benchmarking force fields. -YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results. Feed back and contributions are welcome [on GitHub](https://github.com/openforcefield/yammbs) +YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results. Feedback and contributions are welcome [on GitHub](https://github.com/openforcefield/yammbs). ## Installation @@ -11,7 +11,7 @@ Use the file `./devtools/conda-envs/dev.yaml` and also install `yammbs` with som ## Getting started -See the file `run.py` for a start-to-finish example. Note that the pattern in the script +See the file [run.py](run.py) for a start-to-finish example. Note that the pattern in the script ```python from multiprocessing import freeze_support @@ -28,11 +28,11 @@ must be used for Python's `multiprocessing` module to behave well. ### Data sources -It is assumed that the input molecules are stored in a `openff-qcsubmit` model like `OptimizationResultCollection` or YAMMBS's own input models. +It is assumed that the input molecules are stored in an `openff-qcsubmit` model like `OptimizationResultCollection` or YAMMBS's own input models. ### Preparing an input dataset -YAMMBS relies on QCSumbit to provide datasets from QCArchive. See [their docs](https://docs.openforcefield.org/projects/qcsubmit/en/stable/), particularly the [dataset retrieval example](https://docs.openforcefield.org/projects/qcsubmit/en/stable/examples/retrieving-results.html), for more. +YAMMBS relies on QCSubmit to provide datasets from QCArchive. See [their docs](https://docs.openforcefield.org/projects/qcsubmit/en/stable/), particularly the [dataset retrieval example](https://docs.openforcefield.org/projects/qcsubmit/en/stable/examples/retrieving-results.html), for more. Currently only optimization datasets (`OptimizationResultCollection` in QCSubmit) are supported. @@ -60,13 +60,13 @@ with open("qcsubmit.json", "w") as f: f.write(season1_dataset.json()) ``` -Once a `OptimizationResultCollection` is in memory, either by pulling it down from QCArchive or loading it from disk, convert it to a "YAMMBS input" model using the API: +Once an `OptimizationResultCollection` is in memory, either by pulling it down from QCArchive or loading it from disk, convert it to a "YAMMBS input" model using the API: ```python from yammbs.inputs import QCArchiveDataset -season1_dataset = OptimizationResultCollection.parse_raw(open("qcsubmit.json").read()) +season1_dataset = OptimizationResultCollection.parse_file("qcsubmit.json") dataset = QCArchiveDataset.from_qcsubmit_collection(season1_dataset) @@ -74,7 +74,7 @@ with open("input.json", "w") as f: f.write(dataset.model_dump_json()) ``` -This input model (`QCArchiveDataset`) stores a miniimum amount of information to use these QM geometries as reference structures. The dataset has fields for tagging the name and model version, but mostly stores a list of structures. Each QM-optimized structure is stored as a `QCArchiveMolecule` object which stores: +This input model (`QCArchiveDataset`) stores a minimum amount of information to use these QM geometries as reference structures. The dataset has fields for tagging the name and model version, but mostly stores a list of structures. Each QM-optimized structure is stored as a `QCArchiveMolecule` object which stores: * (Mapped) SMILES which can be used to regenerate the `openff.toolkit.Molecule` and similar objects * QM-optimized geometry @@ -83,7 +83,7 @@ This input model (`QCArchiveDataset`) stores a miniimum amount of information to If running many benchmarks, we recommend using this file as a starting point. -Note: This JSON file ("input.json") is from a different model that the JSON file written from QCSUbmit - they are not interchangeable. +Note: This JSON file ("input.json") is from a different model than the JSON file written from QCSubmit - they are not interchangeable. Note: Both QCSubmit and YAMMBS rely on Pydantic for model validation and serialization. Even though both use V2 in packaging, YAMMBS uses the V2 API and (as of October 2024) QCSubmit still uses the V1 API. Usage like above should work fine; only esoteric use cases (in particular, defining a new model that has both YAMMBS and QCSubmit models as fields) should be unsupported. @@ -119,7 +119,7 @@ for force_field in [ This method short-circuits (i.e. does not run minimizations) if a force field's results are already stored. i.e. the Sage 2.1 optimizations in the loop will be skipped. -There are "output" models that mirroring the input models, basically storing MM-minimized geometries without needing to re-load or re-optimize the QM geometries. This can again be saved out to disk as JSON: +There are "output" models that mirror the input models, basically storing MM-minimized geometries without needing to re-load or re-optimize the QM geometries. This can again be saved out to disk as JSON: ```python store.get_outputs().model_dump_json("output.json") @@ -161,7 +161,7 @@ This data can be transformed for plotting, summary statistics, etc. which compar ## Custom analyses -See `examples.ipynb` for some examples of interacting with benchmarking results and a starting point for custom analyses. +See [examples.ipynb](examples.ipynb) for some examples of interacting with benchmarking results and a starting point for custom analyses. ### License From 2eb5cfe66d51d53053e7c572f95350e21bbdcf8d Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Thu, 17 Oct 2024 15:33:15 -0500 Subject: [PATCH 6/6] Fixes from code review, running script --- examples.ipynb | 67 ++++++++++++---------------------------------- run.py | 13 ++++++--- yammbs/analysis.py | 2 +- yammbs/outputs.py | 6 +++-- 4 files changed, 32 insertions(+), 56 deletions(-) diff --git a/examples.ipynb b/examples.ipynb index 06c43ab..c4fbfdc 100644 --- a/examples.ipynb +++ b/examples.ipynb @@ -15,7 +15,7 @@ "source": [ "# YAMMBS Examples\n", "\n", - "This notebook contains demonstrates some usage of the YAMMBS API." + "This notebook demonstrates some usage of the YAMMBS API." ] }, { @@ -3399,7 +3399,7 @@ "id": "1ea62a94-6423-49d5-a321-cac07f2398a8", "metadata": {}, "source": [ - "And vice versa, you can get the list of `QCArchiveIDs` for the conformers of a given `molecule_id` (these are the same IDs store in the QCArchive):" + "And vice versa, you can get the list of QCArchive IDs for the conformers of a given `molecule_id` (these are the same IDs stored in the QCArchive):" ] }, { @@ -4896,7 +4896,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "23f98f0ab1f04b50b16be1c3204fec1f", + "model_id": "391815959145449e846c19d6082200cb", "version_major": 2, "version_minor": 0 }, @@ -4908,7 +4908,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "156e033e655d4ecc99e872a0454a2aef", + "model_id": "79a18e68706d4543b2406df6996d7c32", "version_major": 2, "version_minor": 0 }, @@ -4949,39 +4949,6 @@ "]" ] }, - { - "cell_type": "code", - "execution_count": 24, - "id": "c718f7be-a651-4fef-8c69-137d45865677", - "metadata": { - "execution": { - "iopub.execute_input": "2024-10-11T01:42:24.455985Z", - "iopub.status.busy": "2024-10-11T01:42:24.454489Z", - "iopub.status.idle": "2024-10-11T01:42:24.493042Z", - "shell.execute_reply": "2024-10-11T01:42:24.492653Z", - "shell.execute_reply.started": "2024-10-11T01:42:24.455942Z" - } - }, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "7c56c475401e4672a45e664ebe087b3c", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "NGLWidget(max_frame=7)" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "mm_mol" - ] - }, { "cell_type": "markdown", "id": "6aee2f6c-038d-42ed-b2ac-386985587b83", @@ -4992,7 +4959,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 24, "id": "79e5affc-39d3-40ba-9096-f4430b6ef84f", "metadata": { "execution": { @@ -5025,7 +4992,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 25, "id": "15e59d55-c594-4c90-9c51-54fc5997160e", "metadata": { "execution": { @@ -5040,7 +5007,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "fa79a53c7dd34174a3d0fbdb318de915", + "model_id": "e86bb1ff141f4212983b5fcdee26b6f4", "version_major": 2, "version_minor": 0 }, @@ -5069,12 +5036,12 @@ "id": "e565104d", "metadata": {}, "source": [ - "QM energies, reported by QCArchive, and MM energies, reported by OpenMMM, are also stored and can be retrieved using the high-level API much in the same way we got conformers:" + "QM energies, reported by QCArchive, and MM energies, reported by OpenMM, are also stored and can be retrieved using the high-level API much in the same way we got conformers:" ] }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 26, "id": "83f0be91", "metadata": {}, "outputs": [ @@ -5085,7 +5052,7 @@ " -166.41800584, -166.12066373, -166.10796496, -166.17417041])" ] }, - "execution_count": 27, + "execution_count": 26, "metadata": {}, "output_type": "execute_result" } @@ -5105,7 +5072,7 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 27, "id": "bee503f5", "metadata": {}, "outputs": [ @@ -5117,7 +5084,7 @@ " -643016.32580181, -643016.86987724])" ] }, - "execution_count": 28, + "execution_count": 27, "metadata": {}, "output_type": "execute_result" } @@ -5138,7 +5105,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 28, "id": "7c998784", "metadata": {}, "outputs": [ @@ -5155,7 +5122,7 @@ " (36967442, -2.484871522684216)]" ] }, - "execution_count": 29, + "execution_count": 28, "metadata": {}, "output_type": "execute_result" } @@ -5182,12 +5149,12 @@ "id": "78765550", "metadata": {}, "source": [ - "`MoleculeStore` has a high-level API that does this (the numerical values below should be identical). Above is provided as an example of what internally happens in this methods, which can be taken apart or modified for custom analyses." + "`MoleculeStore` has a high-level API that does this (the numerical values below should be identical). Above is provided as an example of what internally happens in this method, which can be taken apart or modified for custom analyses." ] }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 29, "id": "5dffa23f", "metadata": {}, "outputs": [ @@ -5204,7 +5171,7 @@ " DDE(qcarchive_id=36967442, difference=-2.484871522684216)]" ] }, - "execution_count": 30, + "execution_count": 29, "metadata": {}, "output_type": "execute_result" } diff --git a/run.py b/run.py index a94ec2f..5ad1df6 100644 --- a/run.py +++ b/run.py @@ -24,9 +24,11 @@ def main(): # pre-processed data is stored in the repository, just a larger dataset # filtered by elements, takes values of "ch" (~40) and "cho" (~1600 molecules) - data_key = "ch" + data_key = "cho" - dataset = QCArchiveDataset.model_validate_json(f"yammbs/_tests/data/yammbs/01-processed-qm-{data_key}.json") + dataset = QCArchiveDataset.model_validate_json( + open(f"yammbs/_tests/data/yammbs/01-processed-qm-{data_key}.json").read(), + ) # This file is also store at f"yammbs/_tests/data/yammbs/01-processed-qm-{data_key}.json" if pathlib.Path(f"{data_key}.sqlite").exists(): @@ -90,8 +92,13 @@ def plot(force_fields: list[str]): for force_field in force_fields: if key == "dde": - counts, bins = numpy.histogram( + _data = numpy.array( [*data[key][force_field].values()], + dtype=float, + ) + + counts, bins = numpy.histogram( + _data[numpy.isfinite(_data)], bins=numpy.linspace(-15, 15, 31), ) diff --git a/yammbs/analysis.py b/yammbs/analysis.py index 4eddc36..03242d5 100644 --- a/yammbs/analysis.py +++ b/yammbs/analysis.py @@ -9,7 +9,7 @@ class DDE(ImmutableModel): qcarchive_id: int - difference: float + difference: float | None class DDECollection(list[DDE]): diff --git a/yammbs/outputs.py b/yammbs/outputs.py index e014560..9247a49 100644 --- a/yammbs/outputs.py +++ b/yammbs/outputs.py @@ -1,3 +1,5 @@ +from __future__ import annotations + from pydantic import Field from yammbs._base.array import Array @@ -35,10 +37,10 @@ class MinimizedQCArchiveDataset(MinimizedQMDataset): class Metric(ImmutableModel): - dde: float + dde: float | None rmsd: float tfd: float - icrmsd: dict[str, float] + icrmsd: dict[str, float | None] # This could maybe be NamedTuple for cleaner typing class MetricCollection(ImmutableModel):