update to most recent DBs, add split without KRAS
Browse files- .gitattributes +19 -0
- README.md +16 -6
- binding_affinity.py +14 -22
- bindingdb.ipynb +140 -347
- biolip.ipynb +90 -48
- biolip.py +1 -1
- biolip.slurm +2 -2
- combine_dbs.ipynb +406 -301
- data/all.parquet +2 -2
- data/all_nokras.parquet +3 -0
- data/bindingdb.parquet +3 -0
- data/biolip.parquet +3 -0
- data/biolip_complex.parquet +3 -0
- data/moad.parquet +3 -0
- data/moad_complex.parquet +3 -0
- data/pdbbind.parquet +3 -0
- data/pdbbind_complex.parquet +3 -0
- data/scaling.json +1 -0
- moad.ipynb +96 -88
- pdbbind.ipynb +22 -29
- pdbbind.py +1 -1
- pdbbind.slurm +1 -1
.gitattributes
CHANGED
@@ -820,3 +820,22 @@ data/dcoid_rf2.parquet filter=lfs diff=lfs merge=lfs -text
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data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
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data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_predict.parquet filter=lfs diff=lfs merge=lfs -text
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data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
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data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_predict.parquet filter=lfs diff=lfs merge=lfs -text
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+
data/all_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/biolip_complex.parquet filter=lfs diff=lfs merge=lfs -text
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data/biolip_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/biolip.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_rf2_actives.parquet filter=lfs diff=lfs merge=lfs -text
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data/pdbbind.parquet filter=lfs diff=lfs merge=lfs -text
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data/bindingdb.parquet filter=lfs diff=lfs merge=lfs -text
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data/moad_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/moad.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_rf2_decoys.parquet filter=lfs diff=lfs merge=lfs -text
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data/all_nokras.parquet filter=lfs diff=lfs merge=lfs -text
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data/pdbbind_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/all_maccs_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/bindingdb_ic50.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_actives.parquet filter=lfs diff=lfs merge=lfs -text
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data/dcoid_decoys.parquet filter=lfs diff=lfs merge=lfs -text
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data/moad_complex.parquet filter=lfs diff=lfs merge=lfs -text
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data/pdbbind_complex.parquet filter=lfs diff=lfs merge=lfs -text
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data/all_maccs.parquet filter=lfs diff=lfs merge=lfs -text
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README.md
CHANGED
@@ -50,22 +50,32 @@ Go to <https://bindingmoad.org> and download the files `every.csv`
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(`nr_bind.zip`). Place and extract those files into `binding_moad`.
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Run the script `moad.py` in a compute job on an MPI-enabled cluster
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-
(e.g., `mpirun -n 64 moad.py).
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Perform the steps in the notebook `moad.ipynb`
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4. BioLIP
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Download from <https://zhanglab.ccmb.med.umich.edu/BioLiP/> the files
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-
-
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-
-
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-
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and extract them in `biolip/data`.
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Run the script `biolip.py` in a compute job on an MPI-enabled cluster
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(e.g., `mpirun -n 64 biolip.py).
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-
Perform
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5. Final concatenation and filtering
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(`nr_bind.zip`). Place and extract those files into `binding_moad`.
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Run the script `moad.py` in a compute job on an MPI-enabled cluster
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+
(e.g., `mpirun -n 64 moad.py`).
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Perform the steps in the notebook `moad.ipynb`
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4. BioLIP
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Download from <https://zhanglab.ccmb.med.umich.edu/BioLiP/> the files
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+
- receptor1.tar.bz2 (Receptor1, Non-redudant set)
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+
- ligand_2013-03-6.tar.bz2 (Ligands)
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- BioLiP.tar.bz2 (Annotations)
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and extract them in `biolip/data`.
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The following steps are **optional**, they **do not** result in additional binding affinity data.
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Download the script
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- download_all_sets.pl
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from the Weekly update subpage.
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Update the 2013 database to its current state
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`perl download_all-sets.pl`
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Run the script `biolip.py` in a compute job on an MPI-enabled cluster
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(e.g., `mpirun -n 64 biolip.py`).
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+
Perform the steps in the notebook `biolip.ipynb`
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5. Final concatenation and filtering
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binding_affinity.py
CHANGED
@@ -47,8 +47,10 @@ _LICENSE = "BSD two-clause"
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# TODO: Add link to the official dataset URLs here
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# The HuggingFace dataset library don't host the datasets but only point to the original files
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# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
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_URLs = {
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-
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}
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@@ -56,7 +58,7 @@ _URLs = {
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class BindingAffinity(datasets.ArrowBasedBuilder):
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"""List of protein sequences, ligand SMILES and binding affinities."""
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-
VERSION = datasets.Version("1.
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# If you don't want/need to define several sub-sets in your dataset,
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# just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
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@@ -121,33 +123,23 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
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# dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLs
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# It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
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# By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
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-
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-
files = dl_manager.download_and_extract(my_urls)
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return [
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datasets.SplitGenerator(
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name=datasets.Split.TRAIN,
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# These kwargs will be passed to _generate_examples
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gen_kwargs={
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-
"filepath": files[
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"split": "train",
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},
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),
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-
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# datasets.SplitGenerator(
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# name=datasets.Split.VALIDATION,
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# # These kwargs will be passed to _generate_examples
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# gen_kwargs={
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# "filepath": os.path.join(data_dir, "dev.parquet"),
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# "split": "dev",
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# },
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# ),
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]
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def _generate_examples(
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# TODO: Add link to the official dataset URLs here
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# The HuggingFace dataset library don't host the datasets but only point to the original files
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# This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
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+
_URL = "https://huggingface.co/datasets/jglaser/binding_affinity/resolve/main/data/"
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_URLs = {
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"default": [_URL + "all.parquet"],
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"no_kras": [_URL + "all_nokras.parquet"],
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}
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class BindingAffinity(datasets.ArrowBasedBuilder):
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"""List of protein sequences, ligand SMILES and binding affinities."""
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+
VERSION = datasets.Version("1.1.0")
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# If you don't want/need to define several sub-sets in your dataset,
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# just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
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# dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLs
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# It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
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# By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
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+
files = dl_manager.download_and_extract(_URLs)
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return [
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datasets.SplitGenerator(
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name=datasets.Split.TRAIN,
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# These kwargs will be passed to _generate_examples
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gen_kwargs={
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"filepath": files["default"],
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},
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),
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datasets.SplitGenerator(
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name=datasets.Split.TRAIN+"_no_kras",
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# These kwargs will be passed to _generate_examples
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gen_kwargs={
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"filepath": files["no_kras"],
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},
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),
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]
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def _generate_examples(
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bindingdb.ipynb
CHANGED
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"cells": [
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{
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"cell_type": "code",
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"execution_count":
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"id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "e9f76b32-e8f0-47ee-b592-a91a88f4f93e",
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"metadata": {},
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"outputs": [
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"source": [
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"for i in tqdm.notebook.tqdm(range(0,13)):\n",
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" mycol = 'BindingDB Target Chain Sequence.{}'.format(i)\n",
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "be79bbcf-0622-4d1e-8f08-a723a4167d8b",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "35ca09cb-6264-4526-b504-0d29236a03c1",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "ba518a9a-0d15-47be-977b-e2dfe2511529",
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"metadata": {},
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"outputs": [
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"4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
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]
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},
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"execution_count":
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "f504d7aa-dfc1-4346-a136-8814c4b5d979",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
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"metadata": {},
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"outputs": [],
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"source": [
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-
"ddf = dd.read_parquet('../
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]
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},
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{
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"cell_type": "code",
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-
"execution_count":
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"id": "b151868a-0cd6-405e-8401-f79918fb0b07",
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"metadata": {},
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"outputs": [
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" <th>seq</th>\n",
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" </tr>\n",
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" <tr>\n",
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-
" <th>npartitions=
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" <th></th>\n",
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" <th></th>\n",
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" <th></th>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>\n",
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-
"<div>Dask Name: read-parquet,
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],
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"text/plain": [
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"Dask DataFrame Structure:\n",
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" Ligand SMILES IC50 (nM) KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) seq\n",
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-
"npartitions=
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" object object object object object object object\n",
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" ... ... ... ... ... ... ...\n",
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"... ... ... ... ... ... ... ...\n",
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" ... ... ... ... ... ... ...\n",
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" ... ... ... ... ... ... ...\n",
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"Dask Name: read-parquet,
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]
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},
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"execution_count":
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"metadata": {},
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"output_type": "execute_result"
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}
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},
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{
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"cell_type": "code",
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"execution_count":
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"id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
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"metadata": {},
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"outputs": [
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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-
" <th>
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" <td>
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" <td>9.4</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>
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" </tr>\n",
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" <tr>\n",
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" <th>
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" <td>11</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>
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" </tr>\n",
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" <tr>\n",
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" <th>
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" <td>None</td>\n",
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" <td>None</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>
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" </tr>\n",
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" <tr>\n",
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" <th>
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" <td>
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" <td>76</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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" <td>None</td>\n",
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-
" <td>
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>"
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],
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"text/plain": [
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"\u001b[?25h Created wheel for pandarallel: filename=pandarallel-1.5.2-py3-none-any.whl size=18384 sha256=d611c0def59d5c3b807ccd787aeba685a821000f283d6082fce6b37d77b4d542\n",
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|
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@@ -780,242 +809,6 @@
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|
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|
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|
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|
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|
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800 |
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|
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|
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{
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"data": {
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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"<table border=\"1\" class=\"dataframe\">\n",
|
827 |
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" <thead>\n",
|
828 |
-
" <tr style=\"text-align: right;\">\n",
|
829 |
-
" <th></th>\n",
|
830 |
-
" <th>Ligand SMILES</th>\n",
|
831 |
-
" <th>IC50 (nM)</th>\n",
|
832 |
-
" <th>KEGG ID of Ligand</th>\n",
|
833 |
-
" <th>Ki (nM)</th>\n",
|
834 |
-
" <th>Kd (nM)</th>\n",
|
835 |
-
" <th>EC50 (nM)</th>\n",
|
836 |
-
" <th>seq</th>\n",
|
837 |
-
" <th>affinity_uM</th>\n",
|
838 |
-
" </tr>\n",
|
839 |
-
" </thead>\n",
|
840 |
-
" <tbody>\n",
|
841 |
-
" <tr>\n",
|
842 |
-
" <th>0</th>\n",
|
843 |
-
" <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
|
844 |
-
" <td>None</td>\n",
|
845 |
-
" <td>None</td>\n",
|
846 |
-
" <td>0.24</td>\n",
|
847 |
-
" <td>None</td>\n",
|
848 |
-
" <td>None</td>\n",
|
849 |
-
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
850 |
-
" <td>0.00024</td>\n",
|
851 |
-
" </tr>\n",
|
852 |
-
" <tr>\n",
|
853 |
-
" <th>1</th>\n",
|
854 |
-
" <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
|
855 |
-
" <td>None</td>\n",
|
856 |
-
" <td>None</td>\n",
|
857 |
-
" <td>0.25</td>\n",
|
858 |
-
" <td>None</td>\n",
|
859 |
-
" <td>None</td>\n",
|
860 |
-
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
861 |
-
" <td>0.00025</td>\n",
|
862 |
-
" </tr>\n",
|
863 |
-
" <tr>\n",
|
864 |
-
" <th>2</th>\n",
|
865 |
-
" <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
|
866 |
-
" <td>None</td>\n",
|
867 |
-
" <td>None</td>\n",
|
868 |
-
" <td>0.41</td>\n",
|
869 |
-
" <td>None</td>\n",
|
870 |
-
" <td>None</td>\n",
|
871 |
-
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
872 |
-
" <td>0.00041</td>\n",
|
873 |
-
" </tr>\n",
|
874 |
-
" <tr>\n",
|
875 |
-
" <th>3</th>\n",
|
876 |
-
" <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
|
877 |
-
" <td>None</td>\n",
|
878 |
-
" <td>None</td>\n",
|
879 |
-
" <td>0.8</td>\n",
|
880 |
-
" <td>None</td>\n",
|
881 |
-
" <td>None</td>\n",
|
882 |
-
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
883 |
-
" <td>0.00080</td>\n",
|
884 |
-
" </tr>\n",
|
885 |
-
" <tr>\n",
|
886 |
-
" <th>4</th>\n",
|
887 |
-
" <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
|
888 |
-
" <td>None</td>\n",
|
889 |
-
" <td>None</td>\n",
|
890 |
-
" <td>0.99</td>\n",
|
891 |
-
" <td>None</td>\n",
|
892 |
-
" <td>None</td>\n",
|
893 |
-
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
894 |
-
" <td>0.00099</td>\n",
|
895 |
-
" </tr>\n",
|
896 |
-
" <tr>\n",
|
897 |
-
" <th>...</th>\n",
|
898 |
-
" <td>...</td>\n",
|
899 |
-
" <td>...</td>\n",
|
900 |
-
" <td>...</td>\n",
|
901 |
-
" <td>...</td>\n",
|
902 |
-
" <td>...</td>\n",
|
903 |
-
" <td>...</td>\n",
|
904 |
-
" <td>...</td>\n",
|
905 |
-
" <td>...</td>\n",
|
906 |
-
" </tr>\n",
|
907 |
-
" <tr>\n",
|
908 |
-
" <th>4453</th>\n",
|
909 |
-
" <td>CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c...</td>\n",
|
910 |
-
" <td>9.4</td>\n",
|
911 |
-
" <td>None</td>\n",
|
912 |
-
" <td>None</td>\n",
|
913 |
-
" <td>None</td>\n",
|
914 |
-
" <td>None</td>\n",
|
915 |
-
" <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
|
916 |
-
" <td>0.00940</td>\n",
|
917 |
-
" </tr>\n",
|
918 |
-
" <tr>\n",
|
919 |
-
" <th>4454</th>\n",
|
920 |
-
" <td>CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc...</td>\n",
|
921 |
-
" <td>11</td>\n",
|
922 |
-
" <td>None</td>\n",
|
923 |
-
" <td>None</td>\n",
|
924 |
-
" <td>None</td>\n",
|
925 |
-
" <td>None</td>\n",
|
926 |
-
" <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
|
927 |
-
" <td>0.01100</td>\n",
|
928 |
-
" </tr>\n",
|
929 |
-
" <tr>\n",
|
930 |
-
" <th>4455</th>\n",
|
931 |
-
" <td>CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=...</td>\n",
|
932 |
-
" <td>355</td>\n",
|
933 |
-
" <td>None</td>\n",
|
934 |
-
" <td>None</td>\n",
|
935 |
-
" <td>None</td>\n",
|
936 |
-
" <td>None</td>\n",
|
937 |
-
" <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
|
938 |
-
" <td>0.35500</td>\n",
|
939 |
-
" </tr>\n",
|
940 |
-
" <tr>\n",
|
941 |
-
" <th>4456</th>\n",
|
942 |
-
" <td>COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(...</td>\n",
|
943 |
-
" <td>17</td>\n",
|
944 |
-
" <td>None</td>\n",
|
945 |
-
" <td>None</td>\n",
|
946 |
-
" <td>None</td>\n",
|
947 |
-
" <td>None</td>\n",
|
948 |
-
" <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
|
949 |
-
" <td>0.01700</td>\n",
|
950 |
-
" </tr>\n",
|
951 |
-
" <tr>\n",
|
952 |
-
" <th>4457</th>\n",
|
953 |
-
" <td>CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=...</td>\n",
|
954 |
-
" <td>76</td>\n",
|
955 |
-
" <td>None</td>\n",
|
956 |
-
" <td>None</td>\n",
|
957 |
-
" <td>None</td>\n",
|
958 |
-
" <td>None</td>\n",
|
959 |
-
" <td>MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE...</td>\n",
|
960 |
-
" <td>0.07600</td>\n",
|
961 |
-
" </tr>\n",
|
962 |
-
" </tbody>\n",
|
963 |
-
"</table>\n",
|
964 |
-
"<p>2389700 rows × 8 columns</p>\n",
|
965 |
-
"</div>"
|
966 |
-
],
|
967 |
-
"text/plain": [
|
968 |
-
" Ligand SMILES IC50 (nM) \\\n",
|
969 |
-
"0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 None \n",
|
970 |
-
"1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... None \n",
|
971 |
-
"2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... None \n",
|
972 |
-
"3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... None \n",
|
973 |
-
"4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... None \n",
|
974 |
-
"... ... ... \n",
|
975 |
-
"4453 CC(C)C[C@H](NC(=O)N1CCC(CC1)C(=O)Nc1ccc(cc1)-c... 9.4 \n",
|
976 |
-
"4454 CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)c1cncc... 11 \n",
|
977 |
-
"4455 CC(C)C[C@H](NC(=O)N1CCCC(C1)C(=O)Nc1cnccn1)C(=... 355 \n",
|
978 |
-
"4456 COc1ccc(NC(=O)N2CCC(CC2)C(=O)N[C@@H](CC(C)C)C(... 17 \n",
|
979 |
-
"4457 CC(C)C[C@H](NC(=O)C1CCN(CC1)C(=O)Nc1cnccn1)C(=... 76 \n",
|
980 |
-
"\n",
|
981 |
-
" KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
|
982 |
-
"0 None 0.24 None None \n",
|
983 |
-
"1 None 0.25 None None \n",
|
984 |
-
"2 None 0.41 None None \n",
|
985 |
-
"3 None 0.8 None None \n",
|
986 |
-
"4 None 0.99 None None \n",
|
987 |
-
"... ... ... ... ... \n",
|
988 |
-
"4453 None None None None \n",
|
989 |
-
"4454 None None None None \n",
|
990 |
-
"4455 None None None None \n",
|
991 |
-
"4456 None None None None \n",
|
992 |
-
"4457 None None None None \n",
|
993 |
-
"\n",
|
994 |
-
" seq affinity_uM \n",
|
995 |
-
"0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00024 \n",
|
996 |
-
"1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00025 \n",
|
997 |
-
"2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00041 \n",
|
998 |
-
"3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00080 \n",
|
999 |
-
"4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 \n",
|
1000 |
-
"... ... ... \n",
|
1001 |
-
"4453 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.00940 \n",
|
1002 |
-
"4454 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01100 \n",
|
1003 |
-
"4455 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.35500 \n",
|
1004 |
-
"4456 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.01700 \n",
|
1005 |
-
"4457 MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVE... 0.07600 \n",
|
1006 |
-
"\n",
|
1007 |
-
"[2389700 rows x 8 columns]"
|
1008 |
-
]
|
1009 |
-
},
|
1010 |
-
"execution_count": 5,
|
1011 |
-
"metadata": {},
|
1012 |
-
"output_type": "execute_result"
|
1013 |
-
}
|
1014 |
-
],
|
1015 |
-
"source": [
|
1016 |
-
"df_affinity"
|
1017 |
-
]
|
1018 |
-
},
|
1019 |
{
|
1020 |
"cell_type": "code",
|
1021 |
"execution_count": null,
|
|
|
2 |
"cells": [
|
3 |
{
|
4 |
"cell_type": "code",
|
5 |
+
"execution_count": 2,
|
6 |
"id": "ecce356e-321b-441e-8a5d-a20bf72f8691",
|
7 |
"metadata": {},
|
8 |
"outputs": [],
|
|
|
12 |
},
|
13 |
{
|
14 |
"cell_type": "code",
|
15 |
+
"execution_count": 2,
|
16 |
"id": "89cbcd82-4ca2-4aba-95b7-e58c0ceed770",
|
17 |
"metadata": {},
|
18 |
"outputs": [],
|
|
|
22 |
},
|
23 |
{
|
24 |
"cell_type": "code",
|
25 |
+
"execution_count": 3,
|
26 |
"id": "a870d8d7-374b-4474-b9ee-305bbf9f17a9",
|
27 |
"metadata": {},
|
28 |
"outputs": [],
|
|
|
32 |
},
|
33 |
{
|
34 |
"cell_type": "code",
|
35 |
+
"execution_count": 5,
|
36 |
"id": "e9f76b32-e8f0-47ee-b592-a91a88f4f93e",
|
37 |
"metadata": {},
|
38 |
+
"outputs": [
|
39 |
+
{
|
40 |
+
"data": {
|
41 |
+
"application/vnd.jupyter.widget-view+json": {
|
42 |
+
"model_id": "c988bc89781242ec8c8b7f8fd0b1c233",
|
43 |
+
"version_major": 2,
|
44 |
+
"version_minor": 0
|
45 |
+
},
|
46 |
+
"text/plain": [
|
47 |
+
" 0%| | 0/13 [00:00<?, ?it/s]"
|
48 |
+
]
|
49 |
+
},
|
50 |
+
"metadata": {},
|
51 |
+
"output_type": "display_data"
|
52 |
+
}
|
53 |
+
],
|
54 |
"source": [
|
55 |
"for i in tqdm.notebook.tqdm(range(0,13)):\n",
|
56 |
" mycol = 'BindingDB Target Chain Sequence.{}'.format(i)\n",
|
|
|
75 |
},
|
76 |
{
|
77 |
"cell_type": "code",
|
78 |
+
"execution_count": 15,
|
79 |
"id": "be79bbcf-0622-4d1e-8f08-a723a4167d8b",
|
80 |
"metadata": {},
|
81 |
"outputs": [],
|
|
|
89 |
},
|
90 |
{
|
91 |
"cell_type": "code",
|
92 |
+
"execution_count": 16,
|
93 |
"id": "35ca09cb-6264-4526-b504-0d29236a03c1",
|
94 |
"metadata": {},
|
95 |
"outputs": [],
|
|
|
99 |
},
|
100 |
{
|
101 |
"cell_type": "code",
|
102 |
+
"execution_count": 17,
|
103 |
"id": "ba518a9a-0d15-47be-977b-e2dfe2511529",
|
104 |
"metadata": {},
|
105 |
"outputs": [
|
|
|
211 |
"4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
|
212 |
]
|
213 |
},
|
214 |
+
"execution_count": 17,
|
215 |
"metadata": {},
|
216 |
"output_type": "execute_result"
|
217 |
}
|
|
|
222 |
},
|
223 |
{
|
224 |
"cell_type": "code",
|
225 |
+
"execution_count": 9,
|
226 |
"id": "f504d7aa-dfc1-4346-a136-8814c4b5d979",
|
227 |
"metadata": {},
|
228 |
"outputs": [],
|
|
|
232 |
},
|
233 |
{
|
234 |
"cell_type": "code",
|
235 |
+
"execution_count": 4,
|
236 |
"id": "d7eafa69-4606-4b34-ae8f-8c6462dcb004",
|
237 |
"metadata": {},
|
238 |
"outputs": [],
|
239 |
"source": [
|
240 |
+
"ddf = dd.read_parquet('../binding_affinity/bindingdb/parquet_data/all_targets')"
|
241 |
]
|
242 |
},
|
243 |
{
|
244 |
"cell_type": "code",
|
245 |
+
"execution_count": 5,
|
246 |
"id": "b151868a-0cd6-405e-8401-f79918fb0b07",
|
247 |
"metadata": {},
|
248 |
"outputs": [
|
|
|
277 |
" <th>seq</th>\n",
|
278 |
" </tr>\n",
|
279 |
" <tr>\n",
|
280 |
+
" <th>npartitions=483</th>\n",
|
281 |
" <th></th>\n",
|
282 |
" <th></th>\n",
|
283 |
" <th></th>\n",
|
|
|
341 |
" </tbody>\n",
|
342 |
"</table>\n",
|
343 |
"</div>\n",
|
344 |
+
"<div>Dask Name: read-parquet, 483 tasks</div>"
|
345 |
],
|
346 |
"text/plain": [
|
347 |
"Dask DataFrame Structure:\n",
|
348 |
" Ligand SMILES IC50 (nM) KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) seq\n",
|
349 |
+
"npartitions=483 \n",
|
350 |
" object object object object object object object\n",
|
351 |
" ... ... ... ... ... ... ...\n",
|
352 |
"... ... ... ... ... ... ... ...\n",
|
353 |
" ... ... ... ... ... ... ...\n",
|
354 |
" ... ... ... ... ... ... ...\n",
|
355 |
+
"Dask Name: read-parquet, 483 tasks"
|
356 |
]
|
357 |
},
|
358 |
+
"execution_count": 5,
|
359 |
"metadata": {},
|
360 |
"output_type": "execute_result"
|
361 |
}
|
|
|
366 |
},
|
367 |
{
|
368 |
"cell_type": "code",
|
369 |
+
"execution_count": 6,
|
370 |
"id": "c00102b8-f4be-4ebd-8d30-7a2c7fc2d05e",
|
371 |
"metadata": {},
|
372 |
"outputs": [],
|
|
|
376 |
},
|
377 |
{
|
378 |
"cell_type": "code",
|
379 |
+
"execution_count": 8,
|
380 |
"id": "c5337e06-1e45-4180-90ed-49ac9ecdd24a",
|
381 |
"metadata": {},
|
382 |
"outputs": [
|
|
|
412 |
" </thead>\n",
|
413 |
" <tbody>\n",
|
414 |
" <tr>\n",
|
415 |
+
" <th>0</th>\n",
|
416 |
+
" <td>COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1</td>\n",
|
|
|
417 |
" <td>None</td>\n",
|
418 |
" <td>None</td>\n",
|
419 |
+
" <td>0.24</td>\n",
|
420 |
" <td>None</td>\n",
|
421 |
" <td>None</td>\n",
|
422 |
+
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
423 |
" </tr>\n",
|
424 |
" <tr>\n",
|
425 |
+
" <th>1</th>\n",
|
426 |
+
" <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn...</td>\n",
|
|
|
427 |
" <td>None</td>\n",
|
428 |
" <td>None</td>\n",
|
429 |
+
" <td>0.25</td>\n",
|
430 |
" <td>None</td>\n",
|
431 |
" <td>None</td>\n",
|
432 |
+
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
433 |
" </tr>\n",
|
434 |
" <tr>\n",
|
435 |
+
" <th>2</th>\n",
|
436 |
+
" <td>O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=...</td>\n",
|
|
|
437 |
" <td>None</td>\n",
|
438 |
" <td>None</td>\n",
|
439 |
+
" <td>0.41</td>\n",
|
440 |
" <td>None</td>\n",
|
441 |
" <td>None</td>\n",
|
442 |
+
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
443 |
" </tr>\n",
|
444 |
" <tr>\n",
|
445 |
+
" <th>3</th>\n",
|
446 |
+
" <td>OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@...</td>\n",
|
|
|
447 |
" <td>None</td>\n",
|
448 |
" <td>None</td>\n",
|
449 |
+
" <td>0.8</td>\n",
|
450 |
" <td>None</td>\n",
|
451 |
" <td>None</td>\n",
|
452 |
+
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
453 |
" </tr>\n",
|
454 |
" <tr>\n",
|
455 |
+
" <th>4</th>\n",
|
456 |
+
" <td>OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H...</td>\n",
|
|
|
457 |
" <td>None</td>\n",
|
458 |
" <td>None</td>\n",
|
459 |
+
" <td>0.99</td>\n",
|
460 |
" <td>None</td>\n",
|
461 |
" <td>None</td>\n",
|
462 |
+
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM...</td>\n",
|
463 |
" </tr>\n",
|
464 |
" </tbody>\n",
|
465 |
"</table>\n",
|
466 |
"</div>"
|
467 |
],
|
468 |
"text/plain": [
|
469 |
+
" Ligand SMILES IC50 (nM) \\\n",
|
470 |
+
"0 COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC1CCN(C)CC1 None \n",
|
471 |
+
"1 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(C\\C=C\\c2cn... None \n",
|
472 |
+
"2 O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(CC2CC2)C(=... None \n",
|
473 |
+
"3 OCCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@... None \n",
|
474 |
+
"4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... None \n",
|
475 |
"\n",
|
476 |
+
" KEGG ID of Ligand Ki (nM) Kd (nM) EC50 (nM) \\\n",
|
477 |
+
"0 None 0.24 None None \n",
|
478 |
+
"1 None 0.25 None None \n",
|
479 |
+
"2 None 0.41 None None \n",
|
480 |
+
"3 None 0.8 None None \n",
|
481 |
+
"4 None 0.99 None None \n",
|
482 |
"\n",
|
483 |
+
" seq \n",
|
484 |
+
"0 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
|
485 |
+
"1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
|
486 |
+
"2 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
|
487 |
+
"3 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... \n",
|
488 |
+
"4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... "
|
489 |
+
]
|
490 |
+
},
|
491 |
+
"execution_count": 8,
|
492 |
+
"metadata": {},
|
493 |
+
"output_type": "execute_result"
|
494 |
+
}
|
495 |
+
],
|
496 |
+
"source": [
|
497 |
+
"ddf_nonnull.head()"
|
498 |
+
]
|
499 |
+
},
|
500 |
+
{
|
501 |
+
"cell_type": "code",
|
502 |
+
"execution_count": 17,
|
503 |
+
"id": "7b423365-4989-4325-a5a5-845d852d52e9",
|
504 |
+
"metadata": {},
|
505 |
+
"outputs": [
|
506 |
+
{
|
507 |
+
"data": {
|
508 |
+
"text/plain": [
|
509 |
+
"2512985"
|
510 |
]
|
511 |
},
|
512 |
+
"execution_count": 17,
|
513 |
"metadata": {},
|
514 |
"output_type": "execute_result"
|
515 |
}
|
516 |
],
|
517 |
"source": [
|
518 |
+
"len(ddf_nonnull)"
|
519 |
]
|
520 |
},
|
521 |
{
|
522 |
"cell_type": "code",
|
523 |
+
"execution_count": 11,
|
524 |
"id": "872edb84-3459-43d9-8e0e-e2a6b5d281eb",
|
525 |
"metadata": {},
|
526 |
"outputs": [],
|
|
|
535 |
"\n",
|
536 |
" vals = []\n",
|
537 |
" \n",
|
538 |
+
" try:\n",
|
539 |
+
" ic50 = ureg(str(ic50)+'nM').m_as(ureg.uM)\n",
|
540 |
+
" vals.append(ic50)\n",
|
541 |
+
" except:\n",
|
542 |
+
" pass\n",
|
543 |
"\n",
|
544 |
" try:\n",
|
545 |
" Ki = ureg(str(Ki)+'nM').m_as(ureg.uM)\n",
|
|
|
553 |
" except:\n",
|
554 |
" pass\n",
|
555 |
"\n",
|
556 |
+
" try:\n",
|
557 |
+
" ec50 = ureg(str(ec50)+'nM').m_as(ureg.uM)\n",
|
558 |
+
" vals.append(ec50)\n",
|
559 |
+
" except:\n",
|
560 |
+
" pass\n",
|
561 |
"\n",
|
562 |
" if len(vals) > 0:\n",
|
563 |
" vals = np.array(vals)\n",
|
|
|
568 |
},
|
569 |
{
|
570 |
"cell_type": "code",
|
571 |
+
"execution_count": 12,
|
572 |
"id": "b3cff13c-19b2-4413-a84b-d99062f516a7",
|
573 |
"metadata": {},
|
574 |
"outputs": [],
|
|
|
578 |
},
|
579 |
{
|
580 |
"cell_type": "code",
|
581 |
+
"execution_count": 13,
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
582 |
"id": "ca9795de-e821-4dc3-a7bf-70ade9e4c7f0",
|
583 |
"metadata": {},
|
584 |
"outputs": [
|
|
|
598 |
},
|
599 |
{
|
600 |
"cell_type": "code",
|
601 |
+
"execution_count": 14,
|
602 |
"id": "4356a3e2-fede-48e7-a486-343661fe0a0a",
|
603 |
"metadata": {},
|
604 |
"outputs": [],
|
|
|
609 |
},
|
610 |
{
|
611 |
"cell_type": "code",
|
612 |
+
"execution_count": 15,
|
613 |
"id": "e91c3af8-84a5-42a2-9e25-49cb2f320b0b",
|
614 |
"metadata": {},
|
615 |
"outputs": [],
|
|
|
619 |
},
|
620 |
{
|
621 |
"cell_type": "code",
|
622 |
+
"execution_count": 16,
|
623 |
+
"id": "f602fdbe-7083-436c-9eac-9d97fbc8be67",
|
624 |
+
"metadata": {},
|
625 |
+
"outputs": [
|
626 |
+
{
|
627 |
+
"data": {
|
628 |
+
"text/plain": [
|
629 |
+
"2512985"
|
630 |
+
]
|
631 |
+
},
|
632 |
+
"execution_count": 16,
|
633 |
+
"metadata": {},
|
634 |
+
"output_type": "execute_result"
|
635 |
+
}
|
636 |
+
],
|
637 |
+
"source": [
|
638 |
+
"len(df_affinity)"
|
639 |
+
]
|
640 |
+
},
|
641 |
+
{
|
642 |
+
"cell_type": "code",
|
643 |
+
"execution_count": 18,
|
644 |
"id": "27194288-cf3e-4c30-ad55-3b0998fdf939",
|
645 |
"metadata": {},
|
646 |
"outputs": [
|
|
|
758 |
"4 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKM... 0.00099 "
|
759 |
]
|
760 |
},
|
761 |
+
"execution_count": 18,
|
762 |
"metadata": {},
|
763 |
"output_type": "execute_result"
|
764 |
}
|
|
|
769 |
},
|
770 |
{
|
771 |
"cell_type": "code",
|
772 |
+
"execution_count": 19,
|
773 |
"id": "603fd298-0aa6-4097-b298-c55db013548c",
|
774 |
"metadata": {},
|
775 |
"outputs": [
|
776 |
{
|
777 |
"data": {
|
778 |
"text/plain": [
|
779 |
+
"2512985"
|
780 |
]
|
781 |
},
|
782 |
+
"execution_count": 19,
|
783 |
"metadata": {},
|
784 |
"output_type": "execute_result"
|
785 |
}
|
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|
790 |
},
|
791 |
{
|
792 |
"cell_type": "code",
|
793 |
+
"execution_count": 20,
|
794 |
"id": "d95ad9a9-d4ca-4679-8a33-235fe6e7047f",
|
795 |
"metadata": {},
|
796 |
"outputs": [
|
797 |
{
|
798 |
"data": {
|
799 |
"text/plain": [
|
800 |
+
"2510716"
|
801 |
]
|
802 |
},
|
803 |
+
"execution_count": 20,
|
804 |
"metadata": {},
|
805 |
"output_type": "execute_result"
|
806 |
}
|
|
|
809 |
"len(df_affinity[~df_affinity['affinity_uM'].isnull()])"
|
810 |
]
|
811 |
},
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812 |
{
|
813 |
"cell_type": "code",
|
814 |
"execution_count": null,
|
biolip.ipynb
CHANGED
@@ -2,28 +2,25 @@
|
|
2 |
"cells": [
|
3 |
{
|
4 |
"cell_type": "code",
|
5 |
-
"execution_count":
|
6 |
-
"id": "
|
7 |
"metadata": {},
|
8 |
"outputs": [],
|
9 |
"source": [
|
10 |
-
"
|
11 |
-
"from Bio.PDB import * \n"
|
12 |
]
|
13 |
},
|
14 |
{
|
15 |
-
"cell_type": "
|
16 |
-
"
|
17 |
-
"id": "26bc18a2-a6eb-49d3-be80-876ddc7dd8e1",
|
18 |
"metadata": {},
|
19 |
-
"outputs": [],
|
20 |
"source": [
|
21 |
-
"
|
22 |
]
|
23 |
},
|
24 |
{
|
25 |
"cell_type": "code",
|
26 |
-
"execution_count":
|
27 |
"id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
|
28 |
"metadata": {},
|
29 |
"outputs": [],
|
@@ -36,18 +33,18 @@
|
|
36 |
},
|
37 |
{
|
38 |
"cell_type": "code",
|
39 |
-
"execution_count":
|
40 |
"id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
|
41 |
"metadata": {},
|
42 |
"outputs": [],
|
43 |
"source": [
|
44 |
-
"base = 'biolip/data/
|
45 |
"df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'"
|
46 |
]
|
47 |
},
|
48 |
{
|
49 |
"cell_type": "code",
|
50 |
-
"execution_count":
|
51 |
"id": "bd8671da-66ad-40ad-b221-e33228be65f4",
|
52 |
"metadata": {},
|
53 |
"outputs": [],
|
@@ -57,7 +54,7 @@
|
|
57 |
},
|
58 |
{
|
59 |
"cell_type": "code",
|
60 |
-
"execution_count":
|
61 |
"id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
|
62 |
"metadata": {},
|
63 |
"outputs": [],
|
@@ -68,7 +65,7 @@
|
|
68 |
},
|
69 |
{
|
70 |
"cell_type": "code",
|
71 |
-
"execution_count":
|
72 |
"id": "97af5533-10fe-4419-a998-ed80b7d26690",
|
73 |
"metadata": {},
|
74 |
"outputs": [],
|
@@ -78,7 +75,7 @@
|
|
78 |
"import re\n",
|
79 |
"ureg = UnitRegistry()\n",
|
80 |
"\n",
|
81 |
-
"quantities = ['ki','kd','ka','k1/2','kb']\n",
|
82 |
"\n",
|
83 |
"others = set()\n",
|
84 |
"def to_uM(affinities):\n",
|
@@ -182,7 +179,31 @@
|
|
182 |
},
|
183 |
{
|
184 |
"cell_type": "code",
|
185 |
-
"execution_count":
|
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|
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|
186 |
"id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
|
187 |
"metadata": {},
|
188 |
"outputs": [],
|
@@ -192,17 +213,17 @@
|
|
192 |
},
|
193 |
{
|
194 |
"cell_type": "code",
|
195 |
-
"execution_count":
|
196 |
"id": "6b9526ec-b134-4ecb-8fea-b493c3fdac22",
|
197 |
"metadata": {},
|
198 |
"outputs": [
|
199 |
{
|
200 |
"data": {
|
201 |
"text/plain": [
|
202 |
-
"{'deltag', 'deltah', '
|
203 |
]
|
204 |
},
|
205 |
-
"execution_count":
|
206 |
"metadata": {},
|
207 |
"output_type": "execute_result"
|
208 |
}
|
@@ -213,7 +234,7 @@
|
|
213 |
},
|
214 |
{
|
215 |
"cell_type": "code",
|
216 |
-
"execution_count":
|
217 |
"id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
|
218 |
"metadata": {},
|
219 |
"outputs": [
|
@@ -264,7 +285,7 @@
|
|
264 |
" <td>Ki=1.5uM (GTT-EAA)</td>\n",
|
265 |
" <td>None</td>\n",
|
266 |
" <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
|
267 |
-
" <td>biolip/data/
|
268 |
" <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
|
269 |
" <td>1.5000</td>\n",
|
270 |
" </tr>\n",
|
@@ -279,7 +300,7 @@
|
|
279 |
" <td>Ki=24uM (SAS)</td>\n",
|
280 |
" <td>None</td>\n",
|
281 |
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
|
282 |
-
" <td>biolip/data/
|
283 |
" <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
|
284 |
" <td>24.0000</td>\n",
|
285 |
" </tr>\n",
|
@@ -294,7 +315,7 @@
|
|
294 |
" <td>Ki=6uM (BIS)</td>\n",
|
295 |
" <td>None</td>\n",
|
296 |
" <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
|
297 |
-
" <td>biolip/data/
|
298 |
" <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
|
299 |
" <td>6.0000</td>\n",
|
300 |
" </tr>\n",
|
@@ -309,7 +330,7 @@
|
|
309 |
" <td>None</td>\n",
|
310 |
" <td>Kd=10000nM</td>\n",
|
311 |
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
|
312 |
-
" <td>biolip/data/
|
313 |
" <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
|
314 |
" <td>10.0000</td>\n",
|
315 |
" </tr>\n",
|
@@ -324,7 +345,7 @@
|
|
324 |
" <td>None</td>\n",
|
325 |
" <td>Kd=175000nM</td>\n",
|
326 |
" <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
|
327 |
-
" <td>biolip/data/
|
328 |
" <td>c1ccccc1</td>\n",
|
329 |
" <td>175.0000</td>\n",
|
330 |
" </tr>\n",
|
@@ -354,7 +375,7 @@
|
|
354 |
" <td>Ki=4.5nM (5-mer)</td>\n",
|
355 |
" <td>None</td>\n",
|
356 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
357 |
-
" <td>biolip/data/
|
358 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
359 |
" <td>0.0045</td>\n",
|
360 |
" </tr>\n",
|
@@ -369,7 +390,7 @@
|
|
369 |
" <td>Ki=4.5nM (5-mer)</td>\n",
|
370 |
" <td>None</td>\n",
|
371 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
372 |
-
" <td>biolip/data/
|
373 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
374 |
" <td>0.0045</td>\n",
|
375 |
" </tr>\n",
|
@@ -384,7 +405,7 @@
|
|
384 |
" <td>Kd=125uM (NAP)</td>\n",
|
385 |
" <td>None</td>\n",
|
386 |
" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
|
387 |
-
" <td>biolip/data/
|
388 |
" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
|
389 |
" <td>125.0000</td>\n",
|
390 |
" </tr>\n",
|
@@ -399,7 +420,7 @@
|
|
399 |
" <td>Ki=2000nM (4-mer)</td>\n",
|
400 |
" <td>None</td>\n",
|
401 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
402 |
-
" <td>biolip/data/
|
403 |
" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
404 |
" <td>2.0000</td>\n",
|
405 |
" </tr>\n",
|
@@ -414,13 +435,13 @@
|
|
414 |
" <td>None</td>\n",
|
415 |
" <td>None</td>\n",
|
416 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
417 |
-
" <td>biolip/data/
|
418 |
" <td>CC[Se]C(=N)N</td>\n",
|
419 |
" <td>0.0390</td>\n",
|
420 |
" </tr>\n",
|
421 |
" </tbody>\n",
|
422 |
"</table>\n",
|
423 |
-
"<p>
|
424 |
"</div>"
|
425 |
],
|
426 |
"text/plain": [
|
@@ -463,18 +484,18 @@
|
|
463 |
"105133 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
|
464 |
"105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
|
465 |
"\n",
|
466 |
-
"
|
467 |
-
"38 biolip/data/
|
468 |
-
"43 biolip/data/
|
469 |
-
"53 biolip/data/
|
470 |
-
"54 biolip/data/
|
471 |
-
"55 biolip/data/
|
472 |
-
"...
|
473 |
-
"105118 biolip/data/
|
474 |
-
"105119 biolip/data/
|
475 |
-
"105124 biolip/data/
|
476 |
-
"105133 biolip/data/
|
477 |
-
"105138 biolip/data/
|
478 |
"\n",
|
479 |
" smiles affinity_uM \n",
|
480 |
"38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
|
@@ -489,10 +510,10 @@
|
|
489 |
"105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
|
490 |
"105138 CC[Se]C(=N)N 0.0390 \n",
|
491 |
"\n",
|
492 |
-
"[
|
493 |
]
|
494 |
},
|
495 |
-
"execution_count":
|
496 |
"metadata": {},
|
497 |
"output_type": "execute_result"
|
498 |
}
|
@@ -503,7 +524,7 @@
|
|
503 |
},
|
504 |
{
|
505 |
"cell_type": "code",
|
506 |
-
"execution_count":
|
507 |
"id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
|
508 |
"metadata": {},
|
509 |
"outputs": [],
|
@@ -513,9 +534,30 @@
|
|
513 |
},
|
514 |
{
|
515 |
"cell_type": "code",
|
516 |
-
"execution_count":
|
517 |
"id": "68dd5e45-b31d-492d-a47e-39072b67fa72",
|
518 |
"metadata": {},
|
|
|
|
|
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|
|
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|
|
|
|
|
|
519 |
"outputs": [],
|
520 |
"source": []
|
521 |
}
|
|
|
2 |
"cells": [
|
3 |
{
|
4 |
"cell_type": "code",
|
5 |
+
"execution_count": 3,
|
6 |
+
"id": "26bc18a2-a6eb-49d3-be80-876ddc7dd8e1",
|
7 |
"metadata": {},
|
8 |
"outputs": [],
|
9 |
"source": [
|
10 |
+
"import pandas as pd"
|
|
|
11 |
]
|
12 |
},
|
13 |
{
|
14 |
+
"cell_type": "markdown",
|
15 |
+
"id": "dbef8a5d-8603-4f40-aa98-fe50aa1160f6",
|
|
|
16 |
"metadata": {},
|
|
|
17 |
"source": [
|
18 |
+
"the binding affinities are **only** present in the 2013 snapshot, not in the updated ones"
|
19 |
]
|
20 |
},
|
21 |
{
|
22 |
"cell_type": "code",
|
23 |
+
"execution_count": 48,
|
24 |
"id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
|
25 |
"metadata": {},
|
26 |
"outputs": [],
|
|
|
33 |
},
|
34 |
{
|
35 |
"cell_type": "code",
|
36 |
+
"execution_count": 49,
|
37 |
"id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
|
38 |
"metadata": {},
|
39 |
"outputs": [],
|
40 |
"source": [
|
41 |
+
"base = 'biolip/data/ligand/'\n",
|
42 |
"df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'"
|
43 |
]
|
44 |
},
|
45 |
{
|
46 |
"cell_type": "code",
|
47 |
+
"execution_count": 50,
|
48 |
"id": "bd8671da-66ad-40ad-b221-e33228be65f4",
|
49 |
"metadata": {},
|
50 |
"outputs": [],
|
|
|
54 |
},
|
55 |
{
|
56 |
"cell_type": "code",
|
57 |
+
"execution_count": 51,
|
58 |
"id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
|
59 |
"metadata": {},
|
60 |
"outputs": [],
|
|
|
65 |
},
|
66 |
{
|
67 |
"cell_type": "code",
|
68 |
+
"execution_count": 57,
|
69 |
"id": "97af5533-10fe-4419-a998-ed80b7d26690",
|
70 |
"metadata": {},
|
71 |
"outputs": [],
|
|
|
75 |
"import re\n",
|
76 |
"ureg = UnitRegistry()\n",
|
77 |
"\n",
|
78 |
+
"quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50','km']\n",
|
79 |
"\n",
|
80 |
"others = set()\n",
|
81 |
"def to_uM(affinities):\n",
|
|
|
179 |
},
|
180 |
{
|
181 |
"cell_type": "code",
|
182 |
+
"execution_count": 58,
|
183 |
+
"id": "d2fab1e6-ec5b-46f9-a4a2-f3744128c777",
|
184 |
+
"metadata": {},
|
185 |
+
"outputs": [
|
186 |
+
{
|
187 |
+
"data": {
|
188 |
+
"text/plain": [
|
189 |
+
"Index(['pdb', 'chain', 'l_id', 'l_chain', 'affinity_lit', 'affinity_moad',\n",
|
190 |
+
" 'affinity_pdbbind-cn', 'affinity_bindingdb', 'seq', 'ligand_fn',\n",
|
191 |
+
" 'smiles', 'affinity_uM'],\n",
|
192 |
+
" dtype='object')"
|
193 |
+
]
|
194 |
+
},
|
195 |
+
"execution_count": 58,
|
196 |
+
"metadata": {},
|
197 |
+
"output_type": "execute_result"
|
198 |
+
}
|
199 |
+
],
|
200 |
+
"source": [
|
201 |
+
"df_affinity.columns"
|
202 |
+
]
|
203 |
+
},
|
204 |
+
{
|
205 |
+
"cell_type": "code",
|
206 |
+
"execution_count": 59,
|
207 |
"id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
|
208 |
"metadata": {},
|
209 |
"outputs": [],
|
|
|
213 |
},
|
214 |
{
|
215 |
"cell_type": "code",
|
216 |
+
"execution_count": 60,
|
217 |
"id": "6b9526ec-b134-4ecb-8fea-b493c3fdac22",
|
218 |
"metadata": {},
|
219 |
"outputs": [
|
220 |
{
|
221 |
"data": {
|
222 |
"text/plain": [
|
223 |
+
"{'deltag', 'deltah', 'none'}"
|
224 |
]
|
225 |
},
|
226 |
+
"execution_count": 60,
|
227 |
"metadata": {},
|
228 |
"output_type": "execute_result"
|
229 |
}
|
|
|
234 |
},
|
235 |
{
|
236 |
"cell_type": "code",
|
237 |
+
"execution_count": 61,
|
238 |
"id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
|
239 |
"metadata": {},
|
240 |
"outputs": [
|
|
|
285 |
" <td>Ki=1.5uM (GTT-EAA)</td>\n",
|
286 |
" <td>None</td>\n",
|
287 |
" <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
|
288 |
+
" <td>biolip/data/ligand/11gs_EAA_A_1.pdb</td>\n",
|
289 |
" <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
|
290 |
" <td>1.5000</td>\n",
|
291 |
" </tr>\n",
|
|
|
300 |
" <td>Ki=24uM (SAS)</td>\n",
|
301 |
" <td>None</td>\n",
|
302 |
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
|
303 |
+
" <td>biolip/data/ligand/13gs_SAS_A_1.pdb</td>\n",
|
304 |
" <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
|
305 |
" <td>24.0000</td>\n",
|
306 |
" </tr>\n",
|
|
|
315 |
" <td>Ki=6uM (BIS)</td>\n",
|
316 |
" <td>None</td>\n",
|
317 |
" <td>EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKV...</td>\n",
|
318 |
+
" <td>biolip/data/ligand/16pk_BIS_A_1.pdb</td>\n",
|
319 |
" <td>O[C@@H]1[C@@H](CO[P@](=O)(O[P@@](=O)(C(CCCC(P(...</td>\n",
|
320 |
" <td>6.0000</td>\n",
|
321 |
" </tr>\n",
|
|
|
330 |
" <td>None</td>\n",
|
331 |
" <td>Kd=10000nM</td>\n",
|
332 |
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
|
333 |
+
" <td>biolip/data/ligand/17gs_GTX_A_1.pdb</td>\n",
|
334 |
" <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
|
335 |
" <td>10.0000</td>\n",
|
336 |
" </tr>\n",
|
|
|
345 |
" <td>None</td>\n",
|
346 |
" <td>Kd=175000nM</td>\n",
|
347 |
" <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
|
348 |
+
" <td>biolip/data/ligand/181l_BNZ_A_1.pdb</td>\n",
|
349 |
" <td>c1ccccc1</td>\n",
|
350 |
" <td>175.0000</td>\n",
|
351 |
" </tr>\n",
|
|
|
375 |
" <td>Ki=4.5nM (5-mer)</td>\n",
|
376 |
" <td>None</td>\n",
|
377 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
378 |
+
" <td>biolip/data/ligand/9hvp_0E9_A_1.pdb</td>\n",
|
379 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
380 |
" <td>0.0045</td>\n",
|
381 |
" </tr>\n",
|
|
|
390 |
" <td>Ki=4.5nM (5-mer)</td>\n",
|
391 |
" <td>None</td>\n",
|
392 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
393 |
+
" <td>biolip/data/ligand/9hvp_0E9_A_1.pdb</td>\n",
|
394 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
395 |
" <td>0.0045</td>\n",
|
396 |
" </tr>\n",
|
|
|
405 |
" <td>Kd=125uM (NAP)</td>\n",
|
406 |
" <td>None</td>\n",
|
407 |
" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
|
408 |
+
" <td>biolip/data/ligand/9icd_NAP_A_1.pdb</td>\n",
|
409 |
" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
|
410 |
" <td>125.0000</td>\n",
|
411 |
" </tr>\n",
|
|
|
420 |
" <td>Ki=2000nM (4-mer)</td>\n",
|
421 |
" <td>None</td>\n",
|
422 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
423 |
+
" <td>biolip/data/ligand/9lpr_III_P_1.pdb</td>\n",
|
424 |
" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
425 |
" <td>2.0000</td>\n",
|
426 |
" </tr>\n",
|
|
|
435 |
" <td>None</td>\n",
|
436 |
" <td>None</td>\n",
|
437 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
438 |
+
" <td>biolip/data/ligand/9nse_ISU_B_2.pdb</td>\n",
|
439 |
" <td>CC[Se]C(=N)N</td>\n",
|
440 |
" <td>0.0390</td>\n",
|
441 |
" </tr>\n",
|
442 |
" </tbody>\n",
|
443 |
"</table>\n",
|
444 |
+
"<p>12851 rows × 12 columns</p>\n",
|
445 |
"</div>"
|
446 |
],
|
447 |
"text/plain": [
|
|
|
484 |
"105133 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
|
485 |
"105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
|
486 |
"\n",
|
487 |
+
" ligand_fn \\\n",
|
488 |
+
"38 biolip/data/ligand/11gs_EAA_A_1.pdb \n",
|
489 |
+
"43 biolip/data/ligand/13gs_SAS_A_1.pdb \n",
|
490 |
+
"53 biolip/data/ligand/16pk_BIS_A_1.pdb \n",
|
491 |
+
"54 biolip/data/ligand/17gs_GTX_A_1.pdb \n",
|
492 |
+
"55 biolip/data/ligand/181l_BNZ_A_1.pdb \n",
|
493 |
+
"... ... \n",
|
494 |
+
"105118 biolip/data/ligand/9hvp_0E9_A_1.pdb \n",
|
495 |
+
"105119 biolip/data/ligand/9hvp_0E9_A_1.pdb \n",
|
496 |
+
"105124 biolip/data/ligand/9icd_NAP_A_1.pdb \n",
|
497 |
+
"105133 biolip/data/ligand/9lpr_III_P_1.pdb \n",
|
498 |
+
"105138 biolip/data/ligand/9nse_ISU_B_2.pdb \n",
|
499 |
"\n",
|
500 |
" smiles affinity_uM \n",
|
501 |
"38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.5000 \n",
|
|
|
510 |
"105133 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
|
511 |
"105138 CC[Se]C(=N)N 0.0390 \n",
|
512 |
"\n",
|
513 |
+
"[12851 rows x 12 columns]"
|
514 |
]
|
515 |
},
|
516 |
+
"execution_count": 61,
|
517 |
"metadata": {},
|
518 |
"output_type": "execute_result"
|
519 |
}
|
|
|
524 |
},
|
525 |
{
|
526 |
"cell_type": "code",
|
527 |
+
"execution_count": 63,
|
528 |
"id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
|
529 |
"metadata": {},
|
530 |
"outputs": [],
|
|
|
534 |
},
|
535 |
{
|
536 |
"cell_type": "code",
|
537 |
+
"execution_count": 64,
|
538 |
"id": "68dd5e45-b31d-492d-a47e-39072b67fa72",
|
539 |
"metadata": {},
|
540 |
+
"outputs": [
|
541 |
+
{
|
542 |
+
"data": {
|
543 |
+
"text/plain": [
|
544 |
+
"13645"
|
545 |
+
]
|
546 |
+
},
|
547 |
+
"execution_count": 64,
|
548 |
+
"metadata": {},
|
549 |
+
"output_type": "execute_result"
|
550 |
+
}
|
551 |
+
],
|
552 |
+
"source": [
|
553 |
+
"len(df_affinity)"
|
554 |
+
]
|
555 |
+
},
|
556 |
+
{
|
557 |
+
"cell_type": "code",
|
558 |
+
"execution_count": null,
|
559 |
+
"id": "cf11317d-bbab-40f1-a8a2-b6fd6126e998",
|
560 |
+
"metadata": {},
|
561 |
"outputs": [],
|
562 |
"source": []
|
563 |
}
|
biolip.py
CHANGED
@@ -34,7 +34,7 @@ if __name__ == '__main__':
|
|
34 |
df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain',
|
35 |
13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb',
|
36 |
19: 'seq'})
|
37 |
-
base = 'biolip/data/
|
38 |
df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'
|
39 |
smiles = list(executor.map(parse_ligand, df['ligand_fn']))
|
40 |
df['smiles'] = smiles
|
|
|
34 |
df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain',
|
35 |
13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb',
|
36 |
19: 'seq'})
|
37 |
+
base = 'biolip/data/ligand/'
|
38 |
df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'
|
39 |
smiles = list(executor.map(parse_ligand, df['ligand_fn']))
|
40 |
df['smiles'] = smiles
|
biolip.slurm
CHANGED
@@ -1,9 +1,9 @@
|
|
1 |
#!/bin/bash
|
2 |
-
#SBATCH -J
|
3 |
#SBATCH -p batch
|
4 |
#SBATCH -A BIP214
|
5 |
#SBATCH -t 3:00:00
|
6 |
-
#SBATCH -N
|
7 |
#SBATCH --ntasks-per-node=32
|
8 |
|
9 |
export PYTHONUNBUFFERED=1
|
|
|
1 |
#!/bin/bash
|
2 |
+
#SBATCH -J preprocess_biolip
|
3 |
#SBATCH -p batch
|
4 |
#SBATCH -A BIP214
|
5 |
#SBATCH -t 3:00:00
|
6 |
+
#SBATCH -N 11
|
7 |
#SBATCH --ntasks-per-node=32
|
8 |
|
9 |
export PYTHONUNBUFFERED=1
|
combine_dbs.ipynb
CHANGED
@@ -2,7 +2,7 @@
|
|
2 |
"cells": [
|
3 |
{
|
4 |
"cell_type": "code",
|
5 |
-
"execution_count":
|
6 |
"id": "95bd761a-fe51-4a8e-bc70-1365260ba5f8",
|
7 |
"metadata": {},
|
8 |
"outputs": [],
|
@@ -12,7 +12,7 @@
|
|
12 |
},
|
13 |
{
|
14 |
"cell_type": "code",
|
15 |
-
"execution_count":
|
16 |
"id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
|
17 |
"metadata": {},
|
18 |
"outputs": [],
|
@@ -23,7 +23,7 @@
|
|
23 |
},
|
24 |
{
|
25 |
"cell_type": "code",
|
26 |
-
"execution_count":
|
27 |
"id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
|
28 |
"metadata": {},
|
29 |
"outputs": [
|
@@ -57,32 +57,32 @@
|
|
57 |
" <tr>\n",
|
58 |
" <th>0</th>\n",
|
59 |
" <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
|
60 |
-
" <td>
|
61 |
" <td>0.026</td>\n",
|
62 |
" </tr>\n",
|
63 |
" <tr>\n",
|
64 |
" <th>1</th>\n",
|
65 |
-
" <td>
|
66 |
-
" <td>OC[C
|
67 |
-
" <td>
|
68 |
" </tr>\n",
|
69 |
" <tr>\n",
|
70 |
" <th>2</th>\n",
|
71 |
-
" <td>
|
72 |
-
" <td>
|
73 |
-
" <td>
|
74 |
" </tr>\n",
|
75 |
" <tr>\n",
|
76 |
" <th>3</th>\n",
|
77 |
-
" <td>
|
78 |
-
" <td>
|
79 |
-
" <td>
|
80 |
" </tr>\n",
|
81 |
" <tr>\n",
|
82 |
" <th>4</th>\n",
|
83 |
-
" <td>
|
84 |
-
" <td>
|
85 |
-
" <td>0.
|
86 |
" </tr>\n",
|
87 |
" </tbody>\n",
|
88 |
"</table>\n",
|
@@ -91,20 +91,20 @@
|
|
91 |
"text/plain": [
|
92 |
" seq \\\n",
|
93 |
"0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
|
94 |
-
"1
|
95 |
-
"2
|
96 |
-
"3
|
97 |
-
"4
|
98 |
"\n",
|
99 |
" smiles affinity_uM \n",
|
100 |
-
"0
|
101 |
-
"1 OC[C
|
102 |
-
"2
|
103 |
-
"3
|
104 |
-
"4
|
105 |
]
|
106 |
},
|
107 |
-
"execution_count":
|
108 |
"metadata": {},
|
109 |
"output_type": "execute_result"
|
110 |
}
|
@@ -115,7 +115,7 @@
|
|
115 |
},
|
116 |
{
|
117 |
"cell_type": "code",
|
118 |
-
"execution_count":
|
119 |
"id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
|
120 |
"metadata": {},
|
121 |
"outputs": [],
|
@@ -135,7 +135,7 @@
|
|
135 |
},
|
136 |
{
|
137 |
"cell_type": "code",
|
138 |
-
"execution_count":
|
139 |
"id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
|
140 |
"metadata": {},
|
141 |
"outputs": [],
|
@@ -146,7 +146,7 @@
|
|
146 |
},
|
147 |
{
|
148 |
"cell_type": "code",
|
149 |
-
"execution_count":
|
150 |
"id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
|
151 |
"metadata": {},
|
152 |
"outputs": [
|
@@ -227,7 +227,7 @@
|
|
227 |
"4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
|
228 |
]
|
229 |
},
|
230 |
-
"execution_count":
|
231 |
"metadata": {},
|
232 |
"output_type": "execute_result"
|
233 |
}
|
@@ -238,7 +238,7 @@
|
|
238 |
},
|
239 |
{
|
240 |
"cell_type": "code",
|
241 |
-
"execution_count":
|
242 |
"id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
|
243 |
"metadata": {},
|
244 |
"outputs": [],
|
@@ -249,7 +249,7 @@
|
|
249 |
},
|
250 |
{
|
251 |
"cell_type": "code",
|
252 |
-
"execution_count":
|
253 |
"id": "25553199-1715-40fb-9260-427bdd6c3706",
|
254 |
"metadata": {},
|
255 |
"outputs": [
|
@@ -294,15 +294,15 @@
|
|
294 |
" </tr>\n",
|
295 |
" <tr>\n",
|
296 |
" <th>2</th>\n",
|
297 |
-
" <td>
|
298 |
-
" <td>
|
299 |
-
" <td>
|
300 |
" </tr>\n",
|
301 |
" <tr>\n",
|
302 |
" <th>3</th>\n",
|
303 |
-
" <td>
|
304 |
-
" <td>
|
305 |
-
" <td>
|
306 |
" </tr>\n",
|
307 |
" <tr>\n",
|
308 |
" <th>4</th>\n",
|
@@ -317,71 +317,71 @@
|
|
317 |
" <td>...</td>\n",
|
318 |
" </tr>\n",
|
319 |
" <tr>\n",
|
320 |
-
" <th>
|
321 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
322 |
" <td>None</td>\n",
|
323 |
" <td>127.226463</td>\n",
|
324 |
" </tr>\n",
|
325 |
" <tr>\n",
|
326 |
-
" <th>
|
327 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
328 |
" <td>None</td>\n",
|
329 |
" <td>127.226463</td>\n",
|
330 |
" </tr>\n",
|
331 |
" <tr>\n",
|
332 |
-
" <th>
|
333 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
334 |
" <td>None</td>\n",
|
335 |
" <td>169.204738</td>\n",
|
336 |
" </tr>\n",
|
337 |
" <tr>\n",
|
338 |
-
" <th>
|
339 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
340 |
" <td>None</td>\n",
|
341 |
" <td>169.204738</td>\n",
|
342 |
" </tr>\n",
|
343 |
" <tr>\n",
|
344 |
-
" <th>
|
345 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
346 |
" <td>None</td>\n",
|
347 |
" <td>169.204738</td>\n",
|
348 |
" </tr>\n",
|
349 |
" </tbody>\n",
|
350 |
"</table>\n",
|
351 |
-
"<p>
|
352 |
"</div>"
|
353 |
],
|
354 |
"text/plain": [
|
355 |
" seq \\\n",
|
356 |
"0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
357 |
"1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
358 |
-
"2
|
359 |
-
"3
|
360 |
"4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
|
361 |
"... ... \n",
|
362 |
-
"
|
363 |
-
"
|
364 |
-
"
|
365 |
-
"
|
366 |
-
"
|
367 |
"\n",
|
368 |
" smiles affinity_uM \n",
|
369 |
"0 NP(=O)(N)O 0.000620 \n",
|
370 |
"1 CC(=O)NO 2.600000 \n",
|
371 |
-
"2
|
372 |
-
"3
|
373 |
"4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
|
374 |
"... ... ... \n",
|
375 |
-
"
|
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-
"
|
377 |
-
"
|
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-
"
|
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"
|
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"\n",
|
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-
"[
|
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]
|
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},
|
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-
"execution_count":
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
@@ -392,7 +392,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -403,7 +403,7 @@
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|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "cee93018-601d-458b-af44-bd978da7a2bc",
|
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"metadata": {},
|
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"outputs": [
|
@@ -535,7 +535,7 @@
|
|
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"[13645 rows x 3 columns]"
|
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]
|
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},
|
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-
"execution_count":
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
@@ -546,7 +546,7 @@
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|
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},
|
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{
|
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"cell_type": "code",
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"execution_count":
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"id": "195f92db-fe06-4d03-8500-8d6c310a3347",
|
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"metadata": {},
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"outputs": [],
|
@@ -556,17 +556,17 @@
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|
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},
|
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{
|
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"cell_type": "code",
|
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"execution_count":
|
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"id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
|
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"metadata": {},
|
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"outputs": [
|
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{
|
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"data": {
|
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"text/plain": [
|
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-
"
|
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]
|
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},
|
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"execution_count":
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|
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}
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},
|
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{
|
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"cell_type": "code",
|
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"execution_count":
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"id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
|
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"metadata": {},
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"outputs": [
|
@@ -607,7 +607,7 @@
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -617,7 +617,7 @@
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|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -627,7 +627,7 @@
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|
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},
|
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{
|
629 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -638,17 +638,17 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
|
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"metadata": {},
|
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"outputs": [
|
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{
|
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"data": {
|
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"text/plain": [
|
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-
"
|
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]
|
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},
|
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-
"execution_count":
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
@@ -659,7 +659,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -670,7 +670,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "80c15210-1af3-436e-970b-f81fc596fb41",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -680,7 +680,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
|
685 |
"metadata": {},
|
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"outputs": [
|
@@ -696,7 +696,7 @@
|
|
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"dtype: object"
|
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]
|
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},
|
699 |
-
"execution_count":
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
@@ -707,7 +707,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -717,7 +717,7 @@
|
|
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},
|
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{
|
719 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
|
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"metadata": {},
|
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"outputs": [
|
@@ -756,62 +756,62 @@
|
|
756 |
" <tbody>\n",
|
757 |
" <tr>\n",
|
758 |
" <th>0</th>\n",
|
759 |
-
" <td>
|
760 |
-
" <td>
|
761 |
-
" <td>0.
|
762 |
-
" <td>
|
763 |
-
" <td>
|
764 |
-
" <td>
|
765 |
-
" <td>
|
766 |
-
" <td>
|
767 |
-
" <td>
|
768 |
" </tr>\n",
|
769 |
" <tr>\n",
|
770 |
" <th>1</th>\n",
|
771 |
-
" <td>
|
772 |
-
" <td>
|
773 |
-
" <td>
|
774 |
-
" <td>
|
775 |
-
" <td>
|
776 |
-
" <td>
|
777 |
-
" <td>
|
778 |
-
" <td>
|
779 |
" <td>124</td>\n",
|
780 |
" </tr>\n",
|
781 |
" <tr>\n",
|
782 |
" <th>2</th>\n",
|
783 |
-
" <td>
|
784 |
-
" <td>
|
785 |
-
" <td>
|
786 |
-
" <td>
|
787 |
-
" <td>
|
788 |
-
" <td>
|
789 |
-
" <td>
|
790 |
-
" <td>
|
791 |
" <td>252</td>\n",
|
792 |
" </tr>\n",
|
793 |
" <tr>\n",
|
794 |
" <th>3</th>\n",
|
795 |
-
" <td>
|
796 |
-
" <td>OC[C
|
797 |
-
" <td>
|
798 |
" <td>0</td>\n",
|
799 |
-
" <td>
|
800 |
-
" <td>
|
801 |
-
" <td>
|
802 |
-
" <td>
|
803 |
-
" <td>
|
804 |
" </tr>\n",
|
805 |
" <tr>\n",
|
806 |
" <th>4</th>\n",
|
807 |
-
" <td>
|
808 |
-
" <td>C
|
809 |
-
" <td>0.
|
810 |
-
" <td>
|
811 |
-
" <td>
|
812 |
-
" <td>
|
813 |
-
" <td>
|
814 |
-
" <td>
|
815 |
" <td>252</td>\n",
|
816 |
" </tr>\n",
|
817 |
" <tr>\n",
|
@@ -827,7 +827,7 @@
|
|
827 |
" <td>...</td>\n",
|
828 |
" </tr>\n",
|
829 |
" <tr>\n",
|
830 |
-
" <th>
|
831 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
832 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
833 |
" <td>0.0045</td>\n",
|
@@ -839,7 +839,7 @@
|
|
839 |
" <td>252</td>\n",
|
840 |
" </tr>\n",
|
841 |
" <tr>\n",
|
842 |
-
" <th>
|
843 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
844 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
845 |
" <td>0.0045</td>\n",
|
@@ -851,7 +851,7 @@
|
|
851 |
" <td>252</td>\n",
|
852 |
" </tr>\n",
|
853 |
" <tr>\n",
|
854 |
-
" <th>
|
855 |
" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
|
856 |
" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
|
857 |
" <td>125.0000</td>\n",
|
@@ -863,7 +863,7 @@
|
|
863 |
" <td>124</td>\n",
|
864 |
" </tr>\n",
|
865 |
" <tr>\n",
|
866 |
-
" <th>
|
867 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
868 |
" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
869 |
" <td>2.0000</td>\n",
|
@@ -875,7 +875,7 @@
|
|
875 |
" <td>204</td>\n",
|
876 |
" </tr>\n",
|
877 |
" <tr>\n",
|
878 |
-
" <th>
|
879 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
880 |
" <td>CC[Se]C(=N)N</td>\n",
|
881 |
" <td>0.0390</td>\n",
|
@@ -888,53 +888,53 @@
|
|
888 |
" </tr>\n",
|
889 |
" </tbody>\n",
|
890 |
"</table>\n",
|
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-
"<p>
|
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"</div>"
|
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],
|
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"text/plain": [
|
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|
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|
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|
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|
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|
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|
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|
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|
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"[
|
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]
|
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},
|
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-
"execution_count":
|
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|
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}
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@@ -945,7 +945,7 @@
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},
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{
|
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"execution_count":
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"id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
|
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"metadata": {},
|
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"outputs": [
|
@@ -955,7 +955,7 @@
|
|
955 |
"Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
|
956 |
]
|
957 |
},
|
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-
"execution_count":
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|
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"output_type": "execute_result"
|
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}
|
@@ -966,7 +966,7 @@
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{
|
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"execution_count":
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"id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
|
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|
@@ -976,7 +976,7 @@
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|
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},
|
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{
|
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|
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-
"execution_count":
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"id": "27fa2150-8152-444b-ba5b-24bea39fc098",
|
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"metadata": {},
|
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"outputs": [
|
@@ -986,7 +986,7 @@
|
|
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"Index(['smiles', 'affinity_uM'], dtype='object')"
|
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]
|
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},
|
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-
"execution_count":
|
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"metadata": {},
|
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|
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}
|
@@ -997,7 +997,7 @@
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|
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|
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{
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|
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|
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|
@@ -1008,7 +1008,7 @@
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|
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@@ -1018,7 +1018,7 @@
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{
|
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|
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|
@@ -1026,7 +1026,7 @@
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|
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"name": "stderr",
|
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|
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"text": [
|
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-
"/ccs/proj/stf006/glaser/conda-envs/
|
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" result = getattr(ufunc, method)(*inputs, **kwargs)\n"
|
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|
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|
@@ -1037,7 +1037,7 @@
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|
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{
|
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|
@@ -1071,38 +1071,38 @@
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|
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" <tbody>\n",
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|
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|
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|
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|
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" </tr>\n",
|
1079 |
" <tr>\n",
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|
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" <td>...</td>\n",
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" </tr>\n",
|
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|
|
|
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" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
|
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" <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
|
1118 |
" <td>8.0000</td>\n",
|
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" <td>5.096910</td>\n",
|
1120 |
" </tr>\n",
|
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" <tr>\n",
|
1122 |
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" <th>
|
1123 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
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" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
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" <td>0.0045</td>\n",
|
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" <td>8.346787</td>\n",
|
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" </tr>\n",
|
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" <th>
|
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|
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" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
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" <th>488475</th>\n",
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" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
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" <th>
|
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" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
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" <td>CC[Se]C(=N)N</td>\n",
|
1146 |
" <td>0.0390</td>\n",
|
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-
"image/png": "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\n",
|
1387 |
"text/plain": [
|
1388 |
"<Figure size 432x288 with 1 Axes>"
|
1389 |
]
|
@@ -1395,7 +1362,7 @@
|
|
1395 |
}
|
1396 |
],
|
1397 |
"source": [
|
1398 |
-
"ax = df['neg_log10_affinity_M'].hist(bins=
|
1399 |
"ax.set_xlabel('-$\\log_{10}$ affinity[M]',fontsize=16)\n",
|
1400 |
"ax.set_ylabel('probability',fontsize=16)\n",
|
1401 |
"ax.figure.savefig('affinity_neglog10_M.pdf')"
|
@@ -1403,17 +1370,17 @@
|
|
1403 |
},
|
1404 |
{
|
1405 |
"cell_type": "code",
|
1406 |
-
"execution_count":
|
1407 |
"id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
|
1408 |
"metadata": {},
|
1409 |
"outputs": [
|
1410 |
{
|
1411 |
"data": {
|
1412 |
"text/plain": [
|
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-
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"execution_count":
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"output_type": "execute_result"
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}
|
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"len(df)"
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{
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"cell_type": "code",
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"execution_count": null,
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-
"id": "
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"metadata": {},
|
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"outputs": [],
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"source": []
|
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2 |
"cells": [
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 3,
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"id": "95bd761a-fe51-4a8e-bc70-1365260ba5f8",
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"metadata": {},
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"outputs": [],
|
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},
|
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{
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"cell_type": "code",
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+
"execution_count": 5,
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"id": "b0859483-5e19-4280-9f53-0d00a6f22d34",
|
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"metadata": {},
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"outputs": [],
|
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},
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{
|
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"cell_type": "code",
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+
"execution_count": 6,
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"id": "f30732b7-7444-47ad-84e7-566e7a6f2f8e",
|
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"metadata": {},
|
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"outputs": [
|
|
|
57 |
" <tr>\n",
|
58 |
" <th>0</th>\n",
|
59 |
" <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
|
60 |
+
" <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
|
61 |
" <td>0.026</td>\n",
|
62 |
" </tr>\n",
|
63 |
" <tr>\n",
|
64 |
" <th>1</th>\n",
|
65 |
+
" <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
|
66 |
+
" <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
|
67 |
+
" <td>500.000</td>\n",
|
68 |
" </tr>\n",
|
69 |
" <tr>\n",
|
70 |
" <th>2</th>\n",
|
71 |
+
" <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
|
72 |
+
" <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
|
73 |
+
" <td>0.023</td>\n",
|
74 |
" </tr>\n",
|
75 |
" <tr>\n",
|
76 |
" <th>3</th>\n",
|
77 |
+
" <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
|
78 |
+
" <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
|
79 |
+
" <td>6.430</td>\n",
|
80 |
" </tr>\n",
|
81 |
" <tr>\n",
|
82 |
" <th>4</th>\n",
|
83 |
+
" <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
|
84 |
+
" <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
|
85 |
+
" <td>0.185</td>\n",
|
86 |
" </tr>\n",
|
87 |
" </tbody>\n",
|
88 |
"</table>\n",
|
|
|
91 |
"text/plain": [
|
92 |
" seq \\\n",
|
93 |
"0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
|
94 |
+
"1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
|
95 |
+
"2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
|
96 |
+
"3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
|
97 |
+
"4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
|
98 |
"\n",
|
99 |
" smiles affinity_uM \n",
|
100 |
+
"0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.026 \n",
|
101 |
+
"1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.000 \n",
|
102 |
+
"2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.023 \n",
|
103 |
+
"3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.430 \n",
|
104 |
+
"4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.185 "
|
105 |
]
|
106 |
},
|
107 |
+
"execution_count": 6,
|
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"metadata": {},
|
109 |
"output_type": "execute_result"
|
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}
|
|
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 7,
|
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"id": "2787b9fd-3d6f-4ae3-a3ad-d3539b72782b",
|
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"metadata": {},
|
121 |
"outputs": [],
|
|
|
135 |
},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 8,
|
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"id": "d1abe1c8-ac66-4289-8964-367a5b18528d",
|
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"metadata": {},
|
141 |
"outputs": [],
|
|
|
146 |
},
|
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{
|
148 |
"cell_type": "code",
|
149 |
+
"execution_count": 9,
|
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"id": "988bab9c-5147-44e2-92ef-902eaf3c5a90",
|
151 |
"metadata": {},
|
152 |
"outputs": [
|
|
|
227 |
"4 OCCCCCN1[C@H](Cc2ccccc2)[C@H](O)[C@@H](O)[C@@H... 0.00099 "
|
228 |
]
|
229 |
},
|
230 |
+
"execution_count": 9,
|
231 |
"metadata": {},
|
232 |
"output_type": "execute_result"
|
233 |
}
|
|
|
238 |
},
|
239 |
{
|
240 |
"cell_type": "code",
|
241 |
+
"execution_count": 10,
|
242 |
"id": "d7bfee2a-c4e6-48c9-b0c6-52f6a69c7453",
|
243 |
"metadata": {},
|
244 |
"outputs": [],
|
|
|
249 |
},
|
250 |
{
|
251 |
"cell_type": "code",
|
252 |
+
"execution_count": 11,
|
253 |
"id": "25553199-1715-40fb-9260-427bdd6c3706",
|
254 |
"metadata": {},
|
255 |
"outputs": [
|
|
|
294 |
" </tr>\n",
|
295 |
" <tr>\n",
|
296 |
" <th>2</th>\n",
|
297 |
+
" <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
|
298 |
+
" <td>C#CCCOP(=O)(O)OP(=O)(O)O</td>\n",
|
299 |
+
" <td>0.580000</td>\n",
|
300 |
" </tr>\n",
|
301 |
" <tr>\n",
|
302 |
" <th>3</th>\n",
|
303 |
+
" <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
|
304 |
+
" <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
|
305 |
+
" <td>0.770000</td>\n",
|
306 |
" </tr>\n",
|
307 |
" <tr>\n",
|
308 |
" <th>4</th>\n",
|
|
|
317 |
" <td>...</td>\n",
|
318 |
" </tr>\n",
|
319 |
" <tr>\n",
|
320 |
+
" <th>25420</th>\n",
|
321 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
322 |
" <td>None</td>\n",
|
323 |
" <td>127.226463</td>\n",
|
324 |
" </tr>\n",
|
325 |
" <tr>\n",
|
326 |
+
" <th>25421</th>\n",
|
327 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
328 |
" <td>None</td>\n",
|
329 |
" <td>127.226463</td>\n",
|
330 |
" </tr>\n",
|
331 |
" <tr>\n",
|
332 |
+
" <th>25422</th>\n",
|
333 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
334 |
" <td>None</td>\n",
|
335 |
" <td>169.204738</td>\n",
|
336 |
" </tr>\n",
|
337 |
" <tr>\n",
|
338 |
+
" <th>25423</th>\n",
|
339 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
340 |
" <td>None</td>\n",
|
341 |
" <td>169.204738</td>\n",
|
342 |
" </tr>\n",
|
343 |
" <tr>\n",
|
344 |
+
" <th>25424</th>\n",
|
345 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
346 |
" <td>None</td>\n",
|
347 |
" <td>169.204738</td>\n",
|
348 |
" </tr>\n",
|
349 |
" </tbody>\n",
|
350 |
"</table>\n",
|
351 |
+
"<p>25425 rows × 3 columns</p>\n",
|
352 |
"</div>"
|
353 |
],
|
354 |
"text/plain": [
|
355 |
" seq \\\n",
|
356 |
"0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
357 |
"1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
358 |
+
"2 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
|
359 |
+
"3 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
|
360 |
"4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
|
361 |
"... ... \n",
|
362 |
+
"25420 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
363 |
+
"25421 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
364 |
+
"25422 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
365 |
+
"25423 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
366 |
+
"25424 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
367 |
"\n",
|
368 |
" smiles affinity_uM \n",
|
369 |
"0 NP(=O)(N)O 0.000620 \n",
|
370 |
"1 CC(=O)NO 2.600000 \n",
|
371 |
+
"2 C#CCCOP(=O)(O)OP(=O)(O)O 0.580000 \n",
|
372 |
+
"3 C#CCOP(=O)(O)OP(=O)(O)O 0.770000 \n",
|
373 |
"4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... 15.000000 \n",
|
374 |
"... ... ... \n",
|
375 |
+
"25420 None 127.226463 \n",
|
376 |
+
"25421 None 127.226463 \n",
|
377 |
+
"25422 None 169.204738 \n",
|
378 |
+
"25423 None 169.204738 \n",
|
379 |
+
"25424 None 169.204738 \n",
|
380 |
"\n",
|
381 |
+
"[25425 rows x 3 columns]"
|
382 |
]
|
383 |
},
|
384 |
+
"execution_count": 11,
|
385 |
"metadata": {},
|
386 |
"output_type": "execute_result"
|
387 |
}
|
|
|
392 |
},
|
393 |
{
|
394 |
"cell_type": "code",
|
395 |
+
"execution_count": 12,
|
396 |
"id": "b2c936bc-cdc8-4bc1-b92d-f8755fd65f0a",
|
397 |
"metadata": {},
|
398 |
"outputs": [],
|
|
|
403 |
},
|
404 |
{
|
405 |
"cell_type": "code",
|
406 |
+
"execution_count": 13,
|
407 |
"id": "cee93018-601d-458b-af44-bd978da7a2bc",
|
408 |
"metadata": {},
|
409 |
"outputs": [
|
|
|
535 |
"[13645 rows x 3 columns]"
|
536 |
]
|
537 |
},
|
538 |
+
"execution_count": 13,
|
539 |
"metadata": {},
|
540 |
"output_type": "execute_result"
|
541 |
}
|
|
|
546 |
},
|
547 |
{
|
548 |
"cell_type": "code",
|
549 |
+
"execution_count": 14,
|
550 |
"id": "195f92db-fe06-4d03-8500-8d6c310a3347",
|
551 |
"metadata": {},
|
552 |
"outputs": [],
|
|
|
556 |
},
|
557 |
{
|
558 |
"cell_type": "code",
|
559 |
+
"execution_count": 15,
|
560 |
"id": "d25c1e24-6566-4944-a0b4-944b3c8dbc6f",
|
561 |
"metadata": {},
|
562 |
"outputs": [
|
563 |
{
|
564 |
"data": {
|
565 |
"text/plain": [
|
566 |
+
"2574545"
|
567 |
]
|
568 |
},
|
569 |
+
"execution_count": 15,
|
570 |
"metadata": {},
|
571 |
"output_type": "execute_result"
|
572 |
}
|
|
|
577 |
},
|
578 |
{
|
579 |
"cell_type": "code",
|
580 |
+
"execution_count": 16,
|
581 |
"id": "c8287da2-cfdf-4d89-b175-f4c6b38ff8ac",
|
582 |
"metadata": {},
|
583 |
"outputs": [
|
|
|
607 |
},
|
608 |
{
|
609 |
"cell_type": "code",
|
610 |
+
"execution_count": 18,
|
611 |
"id": "59a6706d-dab9-4ee0-8ef6-33537a3622a4",
|
612 |
"metadata": {},
|
613 |
"outputs": [],
|
|
|
617 |
},
|
618 |
{
|
619 |
"cell_type": "code",
|
620 |
+
"execution_count": 19,
|
621 |
"id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
|
622 |
"metadata": {},
|
623 |
"outputs": [],
|
|
|
627 |
},
|
628 |
{
|
629 |
"cell_type": "code",
|
630 |
+
"execution_count": 20,
|
631 |
"id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
|
632 |
"metadata": {},
|
633 |
"outputs": [],
|
|
|
638 |
},
|
639 |
{
|
640 |
"cell_type": "code",
|
641 |
+
"execution_count": 21,
|
642 |
"id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
|
643 |
"metadata": {},
|
644 |
"outputs": [
|
645 |
{
|
646 |
"data": {
|
647 |
"text/plain": [
|
648 |
+
"2568079"
|
649 |
]
|
650 |
},
|
651 |
+
"execution_count": 21,
|
652 |
"metadata": {},
|
653 |
"output_type": "execute_result"
|
654 |
}
|
|
|
659 |
},
|
660 |
{
|
661 |
"cell_type": "code",
|
662 |
+
"execution_count": 22,
|
663 |
"id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
|
664 |
"metadata": {},
|
665 |
"outputs": [],
|
|
|
670 |
},
|
671 |
{
|
672 |
"cell_type": "code",
|
673 |
+
"execution_count": 23,
|
674 |
"id": "80c15210-1af3-436e-970b-f81fc596fb41",
|
675 |
"metadata": {},
|
676 |
"outputs": [],
|
|
|
680 |
},
|
681 |
{
|
682 |
"cell_type": "code",
|
683 |
+
"execution_count": 24,
|
684 |
"id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
|
685 |
"metadata": {},
|
686 |
"outputs": [
|
|
|
696 |
"dtype: object"
|
697 |
]
|
698 |
},
|
699 |
+
"execution_count": 24,
|
700 |
"metadata": {},
|
701 |
"output_type": "execute_result"
|
702 |
}
|
|
|
707 |
},
|
708 |
{
|
709 |
"cell_type": "code",
|
710 |
+
"execution_count": 25,
|
711 |
"id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
|
712 |
"metadata": {},
|
713 |
"outputs": [],
|
|
|
717 |
},
|
718 |
{
|
719 |
"cell_type": "code",
|
720 |
+
"execution_count": 26,
|
721 |
"id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
|
722 |
"metadata": {},
|
723 |
"outputs": [
|
|
|
756 |
" <tbody>\n",
|
757 |
" <tr>\n",
|
758 |
" <th>0</th>\n",
|
759 |
+
" <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
|
760 |
+
" <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
|
761 |
+
" <td>0.0260</td>\n",
|
762 |
+
" <td>0</td>\n",
|
763 |
+
" <td>0</td>\n",
|
764 |
+
" <td>805306368</td>\n",
|
765 |
+
" <td>272271360</td>\n",
|
766 |
+
" <td>890245320</td>\n",
|
767 |
+
" <td>136</td>\n",
|
768 |
" </tr>\n",
|
769 |
" <tr>\n",
|
770 |
" <th>1</th>\n",
|
771 |
+
" <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
|
772 |
+
" <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
|
773 |
+
" <td>500.0000</td>\n",
|
774 |
+
" <td>2147483648</td>\n",
|
775 |
+
" <td>3242590208</td>\n",
|
776 |
+
" <td>1914732547</td>\n",
|
777 |
+
" <td>994116706</td>\n",
|
778 |
+
" <td>3748288829</td>\n",
|
779 |
" <td>124</td>\n",
|
780 |
" </tr>\n",
|
781 |
" <tr>\n",
|
782 |
" <th>2</th>\n",
|
783 |
+
" <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
|
784 |
+
" <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
|
785 |
+
" <td>0.0230</td>\n",
|
786 |
+
" <td>131072</td>\n",
|
787 |
+
" <td>1109655552</td>\n",
|
788 |
+
" <td>2123376961</td>\n",
|
789 |
+
" <td>3477340882</td>\n",
|
790 |
+
" <td>2951175957</td>\n",
|
791 |
" <td>252</td>\n",
|
792 |
" </tr>\n",
|
793 |
" <tr>\n",
|
794 |
" <th>3</th>\n",
|
795 |
+
" <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
|
796 |
+
" <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
|
797 |
+
" <td>6.4300</td>\n",
|
798 |
" <td>0</td>\n",
|
799 |
+
" <td>6685696</td>\n",
|
800 |
+
" <td>2033191680</td>\n",
|
801 |
+
" <td>1345701844</td>\n",
|
802 |
+
" <td>2133187096</td>\n",
|
803 |
+
" <td>220</td>\n",
|
804 |
" </tr>\n",
|
805 |
" <tr>\n",
|
806 |
" <th>4</th>\n",
|
807 |
+
" <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
|
808 |
+
" <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
|
809 |
+
" <td>0.1850</td>\n",
|
810 |
+
" <td>1048576</td>\n",
|
811 |
+
" <td>1107427332</td>\n",
|
812 |
+
" <td>2109513024</td>\n",
|
813 |
+
" <td>4081492984</td>\n",
|
814 |
+
" <td>4026260436</td>\n",
|
815 |
" <td>252</td>\n",
|
816 |
" </tr>\n",
|
817 |
" <tr>\n",
|
|
|
827 |
" <td>...</td>\n",
|
828 |
" </tr>\n",
|
829 |
" <tr>\n",
|
830 |
+
" <th>2568074</th>\n",
|
831 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
832 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
833 |
" <td>0.0045</td>\n",
|
|
|
839 |
" <td>252</td>\n",
|
840 |
" </tr>\n",
|
841 |
" <tr>\n",
|
842 |
+
" <th>2568075</th>\n",
|
843 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
844 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
845 |
" <td>0.0045</td>\n",
|
|
|
851 |
" <td>252</td>\n",
|
852 |
" </tr>\n",
|
853 |
" <tr>\n",
|
854 |
+
" <th>2568076</th>\n",
|
855 |
" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
|
856 |
" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
|
857 |
" <td>125.0000</td>\n",
|
|
|
863 |
" <td>124</td>\n",
|
864 |
" </tr>\n",
|
865 |
" <tr>\n",
|
866 |
+
" <th>2568077</th>\n",
|
867 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
868 |
" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
869 |
" <td>2.0000</td>\n",
|
|
|
875 |
" <td>204</td>\n",
|
876 |
" </tr>\n",
|
877 |
" <tr>\n",
|
878 |
+
" <th>2568078</th>\n",
|
879 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
880 |
" <td>CC[Se]C(=N)N</td>\n",
|
881 |
" <td>0.0390</td>\n",
|
|
|
888 |
" </tr>\n",
|
889 |
" </tbody>\n",
|
890 |
"</table>\n",
|
891 |
+
"<p>2568079 rows × 9 columns</p>\n",
|
892 |
"</div>"
|
893 |
],
|
894 |
"text/plain": [
|
895 |
+
" seq \\\n",
|
896 |
+
"0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
|
897 |
+
"1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
|
898 |
+
"2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
|
899 |
+
"3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
|
900 |
+
"4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
|
901 |
+
"... ... \n",
|
902 |
+
"2568074 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
|
903 |
+
"2568075 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
|
904 |
+
"2568076 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
|
905 |
+
"2568077 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
|
906 |
+
"2568078 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
|
907 |
"\n",
|
908 |
+
" smiles affinity_uM \\\n",
|
909 |
+
"0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
|
910 |
+
"1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.0000 \n",
|
911 |
+
"2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.0230 \n",
|
912 |
+
"3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
|
913 |
+
"4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
|
914 |
+
"... ... ... \n",
|
915 |
+
"2568074 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
|
916 |
+
"2568075 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
|
917 |
+
"2568076 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.0000 \n",
|
918 |
+
"2568077 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
|
919 |
+
"2568078 CC[Se]C(=N)N 0.0390 \n",
|
920 |
"\n",
|
921 |
+
" 0 1 2 3 4 5 \n",
|
922 |
+
"0 0 0 805306368 272271360 890245320 136 \n",
|
923 |
+
"1 2147483648 3242590208 1914732547 994116706 3748288829 124 \n",
|
924 |
+
"2 131072 1109655552 2123376961 3477340882 2951175957 252 \n",
|
925 |
+
"3 0 6685696 2033191680 1345701844 2133187096 220 \n",
|
926 |
+
"4 1048576 1107427332 2109513024 4081492984 4026260436 252 \n",
|
927 |
+
"... ... ... ... ... ... ... \n",
|
928 |
+
"2568074 65536 393216 964698368 369403648 4284858000 252 \n",
|
929 |
+
"2568075 65536 393216 964698368 369403648 4284858000 252 \n",
|
930 |
+
"2568076 67108864 1115688962 1771869508 4018431718 3744193341 124 \n",
|
931 |
+
"2568077 2097152 137216 958148868 1746307978 2067783280 204 \n",
|
932 |
+
"2568078 16 6144 537396736 2170880 1510015504 192 \n",
|
933 |
"\n",
|
934 |
+
"[2568079 rows x 9 columns]"
|
935 |
]
|
936 |
},
|
937 |
+
"execution_count": 26,
|
938 |
"metadata": {},
|
939 |
"output_type": "execute_result"
|
940 |
}
|
|
|
945 |
},
|
946 |
{
|
947 |
"cell_type": "code",
|
948 |
+
"execution_count": 27,
|
949 |
"id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
|
950 |
"metadata": {},
|
951 |
"outputs": [
|
|
|
955 |
"Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
|
956 |
]
|
957 |
},
|
958 |
+
"execution_count": 27,
|
959 |
"metadata": {},
|
960 |
"output_type": "execute_result"
|
961 |
}
|
|
|
966 |
},
|
967 |
{
|
968 |
"cell_type": "code",
|
969 |
+
"execution_count": 28,
|
970 |
"id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
|
971 |
"metadata": {},
|
972 |
"outputs": [],
|
|
|
976 |
},
|
977 |
{
|
978 |
"cell_type": "code",
|
979 |
+
"execution_count": 29,
|
980 |
"id": "27fa2150-8152-444b-ba5b-24bea39fc098",
|
981 |
"metadata": {},
|
982 |
"outputs": [
|
|
|
986 |
"Index(['smiles', 'affinity_uM'], dtype='object')"
|
987 |
]
|
988 |
},
|
989 |
+
"execution_count": 29,
|
990 |
"metadata": {},
|
991 |
"output_type": "execute_result"
|
992 |
}
|
|
|
997 |
},
|
998 |
{
|
999 |
"cell_type": "code",
|
1000 |
+
"execution_count": 30,
|
1001 |
"id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
|
1002 |
"metadata": {},
|
1003 |
"outputs": [],
|
|
|
1008 |
},
|
1009 |
{
|
1010 |
"cell_type": "code",
|
1011 |
+
"execution_count": 31,
|
1012 |
"id": "6a704c5e-68a6-418f-bcad-8688a13ca1d6",
|
1013 |
"metadata": {},
|
1014 |
"outputs": [],
|
|
|
1018 |
},
|
1019 |
{
|
1020 |
"cell_type": "code",
|
1021 |
+
"execution_count": 32,
|
1022 |
"id": "0cad3882-975d-4693-aad1-63ec26646bd0",
|
1023 |
"metadata": {},
|
1024 |
"outputs": [
|
|
|
1026 |
"name": "stderr",
|
1027 |
"output_type": "stream",
|
1028 |
"text": [
|
1029 |
+
"/ccs/proj/stf006/glaser/conda-envs/dask/lib/python3.9/site-packages/pandas/core/arraylike.py:358: RuntimeWarning: divide by zero encountered in log\n",
|
1030 |
" result = getattr(ufunc, method)(*inputs, **kwargs)\n"
|
1031 |
]
|
1032 |
}
|
|
|
1037 |
},
|
1038 |
{
|
1039 |
"cell_type": "code",
|
1040 |
+
"execution_count": 33,
|
1041 |
"id": "c200e29a-3f14-41f4-b620-ccce0eb0d5ce",
|
1042 |
"metadata": {},
|
1043 |
"outputs": [
|
|
|
1071 |
" <tbody>\n",
|
1072 |
" <tr>\n",
|
1073 |
" <th>0</th>\n",
|
1074 |
+
" <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
|
1075 |
+
" <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
|
1076 |
+
" <td>0.0260</td>\n",
|
1077 |
+
" <td>7.585027</td>\n",
|
1078 |
" </tr>\n",
|
1079 |
" <tr>\n",
|
1080 |
" <th>1</th>\n",
|
1081 |
+
" <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
|
1082 |
+
" <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",
|
1083 |
+
" <td>500.0000</td>\n",
|
1084 |
+
" <td>3.301030</td>\n",
|
1085 |
" </tr>\n",
|
1086 |
" <tr>\n",
|
1087 |
" <th>2</th>\n",
|
1088 |
+
" <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
|
1089 |
+
" <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",
|
1090 |
+
" <td>0.0230</td>\n",
|
1091 |
+
" <td>7.638272</td>\n",
|
1092 |
" </tr>\n",
|
1093 |
" <tr>\n",
|
1094 |
" <th>3</th>\n",
|
1095 |
+
" <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",
|
1096 |
+
" <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",
|
1097 |
+
" <td>6.4300</td>\n",
|
1098 |
+
" <td>5.191789</td>\n",
|
1099 |
" </tr>\n",
|
1100 |
" <tr>\n",
|
1101 |
" <th>4</th>\n",
|
1102 |
+
" <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",
|
1103 |
+
" <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",
|
1104 |
+
" <td>0.1850</td>\n",
|
1105 |
+
" <td>6.732828</td>\n",
|
1106 |
" </tr>\n",
|
1107 |
" <tr>\n",
|
1108 |
" <th>...</th>\n",
|
|
|
1112 |
" <td>...</td>\n",
|
1113 |
" </tr>\n",
|
1114 |
" <tr>\n",
|
1115 |
+
" <th>1929143</th>\n",
|
1116 |
+
" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
|
1117 |
+
" <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
|
1118 |
+
" <td>8.0000</td>\n",
|
1119 |
+
" <td>5.096910</td>\n",
|
1120 |
+
" </tr>\n",
|
1121 |
+
" <tr>\n",
|
1122 |
+
" <th>1929144</th>\n",
|
1123 |
" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
|
1124 |
" <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
|
1125 |
" <td>8.0000</td>\n",
|
1126 |
" <td>5.096910</td>\n",
|
1127 |
" </tr>\n",
|
1128 |
" <tr>\n",
|
1129 |
+
" <th>1929145</th>\n",
|
1130 |
" <td>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM...</td>\n",
|
1131 |
" <td>O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=...</td>\n",
|
1132 |
" <td>0.0045</td>\n",
|
1133 |
" <td>8.346787</td>\n",
|
1134 |
" </tr>\n",
|
1135 |
" <tr>\n",
|
1136 |
+
" <th>1929146</th>\n",
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1137 |
" <td>ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...</td>\n",
|
1138 |
" <td>CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]...</td>\n",
|
1139 |
" <td>2.0000</td>\n",
|
1140 |
" <td>5.698970</td>\n",
|
1141 |
" </tr>\n",
|
1142 |
" <tr>\n",
|
1143 |
+
" <th>1929147</th>\n",
|
1144 |
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
|
1145 |
" <td>CC[Se]C(=N)N</td>\n",
|
1146 |
" <td>0.0390</td>\n",
|
|
|
1148 |
" </tr>\n",
|
1149 |
" </tbody>\n",
|
1150 |
"</table>\n",
|
1151 |
+
"<p>1929148 rows × 4 columns</p>\n",
|
1152 |
"</div>"
|
1153 |
],
|
1154 |
"text/plain": [
|
1155 |
+
" seq \\\n",
|
1156 |
+
"0 MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",
|
1157 |
+
"1 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",
|
1158 |
+
"2 VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",
|
1159 |
+
"3 AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",
|
1160 |
+
"4 YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",
|
1161 |
+
"... ... \n",
|
1162 |
+
"1929143 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
|
1163 |
+
"1929144 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
|
1164 |
+
"1929145 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKM... \n",
|
1165 |
+
"1929146 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI... \n",
|
1166 |
+
"1929147 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
|
1167 |
"\n",
|
1168 |
+
" smiles affinity_uM \\\n",
|
1169 |
+
"0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.0260 \n",
|
1170 |
+
"1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.0000 \n",
|
1171 |
+
"2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.0230 \n",
|
1172 |
+
"3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.4300 \n",
|
1173 |
+
"4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.1850 \n",
|
1174 |
+
"... ... ... \n",
|
1175 |
+
"1929143 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.0000 \n",
|
1176 |
+
"1929144 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.0000 \n",
|
1177 |
+
"1929145 O[C@@H]([C@H](Cc1ccccc1)NC(=O)[C@H](C(C)C)NC(=... 0.0045 \n",
|
1178 |
+
"1929146 CC(C[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H]... 2.0000 \n",
|
1179 |
+
"1929147 CC[Se]C(=N)N 0.0390 \n",
|
1180 |
"\n",
|
1181 |
+
" neg_log10_affinity_M \n",
|
1182 |
+
"0 7.585027 \n",
|
1183 |
+
"1 3.301030 \n",
|
1184 |
+
"2 7.638272 \n",
|
1185 |
+
"3 5.191789 \n",
|
1186 |
+
"4 6.732828 \n",
|
1187 |
+
"... ... \n",
|
1188 |
+
"1929143 5.096910 \n",
|
1189 |
+
"1929144 5.096910 \n",
|
1190 |
+
"1929145 8.346787 \n",
|
1191 |
+
"1929146 5.698970 \n",
|
1192 |
+
"1929147 7.408935 \n",
|
1193 |
"\n",
|
1194 |
+
"[1929148 rows x 4 columns]"
|
1195 |
]
|
1196 |
},
|
1197 |
+
"execution_count": 33,
|
1198 |
"metadata": {},
|
1199 |
"output_type": "execute_result"
|
1200 |
}
|
|
|
1205 |
},
|
1206 |
{
|
1207 |
"cell_type": "code",
|
1208 |
+
"execution_count": 34,
|
1209 |
"id": "7f4027a2-0a5f-47bf-8a34-0c6a73b9b112",
|
1210 |
"metadata": {},
|
1211 |
"outputs": [],
|
1212 |
"source": [
|
1213 |
+
"df = df_nr[np.isfinite(df_nr['neg_log10_affinity_M'])].copy()"
|
|
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|
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|
1214 |
]
|
1215 |
},
|
1216 |
{
|
1217 |
"cell_type": "code",
|
1218 |
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"execution_count": 35,
|
1219 |
"id": "eb99774f-9bcc-454d-b5e5-a8470223d6ca",
|
1220 |
"metadata": {},
|
1221 |
"outputs": [],
|
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|
1230 |
},
|
1231 |
{
|
1232 |
"cell_type": "code",
|
1233 |
+
"execution_count": 36,
|
1234 |
"id": "4d44bd8e-f2e1-44b4-aea7-40b4437baf44",
|
1235 |
"metadata": {},
|
1236 |
+
"outputs": [],
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|
|
|
|
|
|
1237 |
"source": [
|
1238 |
"df['smiles_can'] = df['smiles'].parallel_apply(make_canonical)"
|
1239 |
]
|
1240 |
},
|
1241 |
{
|
1242 |
"cell_type": "code",
|
1243 |
+
"execution_count": 37,
|
1244 |
"id": "07ffdeb1-f4fa-4776-9fea-a18439e03d2e",
|
1245 |
"metadata": {},
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1246 |
"outputs": [],
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|
1250 |
},
|
1251 |
{
|
1252 |
"cell_type": "code",
|
1253 |
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"execution_count": 38,
|
1254 |
"id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
|
1255 |
"metadata": {},
|
1256 |
"outputs": [],
|
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|
1260 |
},
|
1261 |
{
|
1262 |
"cell_type": "code",
|
1263 |
+
"execution_count": 39,
|
1264 |
"id": "0c027988-0b44-4010-ad61-7d70eead1654",
|
1265 |
"metadata": {},
|
1266 |
"outputs": [],
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|
1270 |
},
|
1271 |
{
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1272 |
"cell_type": "code",
|
1273 |
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"execution_count": 40,
|
1274 |
"id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
|
1275 |
"metadata": {},
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1276 |
"outputs": [],
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|
1280 |
},
|
1281 |
{
|
1282 |
"cell_type": "code",
|
1283 |
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"execution_count": 41,
|
1284 |
"id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
|
1285 |
"metadata": {},
|
1286 |
"outputs": [
|
1287 |
{
|
1288 |
"data": {
|
1289 |
"text/plain": [
|
1290 |
+
"(array([6.51286529]), array([2.4379995]))"
|
1291 |
]
|
1292 |
},
|
1293 |
+
"execution_count": 41,
|
1294 |
"metadata": {},
|
1295 |
"output_type": "execute_result"
|
1296 |
}
|
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|
1301 |
},
|
1302 |
{
|
1303 |
"cell_type": "code",
|
1304 |
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"execution_count": 42,
|
1305 |
"id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
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1306 |
"metadata": {},
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1307 |
"outputs": [],
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|
1311 |
},
|
1312 |
{
|
1313 |
"cell_type": "code",
|
1314 |
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"execution_count": 43,
|
1315 |
"id": "c6c64066-4032-4247-a8b9-00388176cc7b",
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1316 |
"metadata": {},
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1317 |
"outputs": [],
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|
1321 |
},
|
1322 |
{
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1323 |
"cell_type": "code",
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1324 |
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"execution_count": 44,
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1325 |
"id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
|
1326 |
"metadata": {},
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1327 |
"outputs": [
|
|
|
1333 |
" dtype='object')"
|
1334 |
]
|
1335 |
},
|
1336 |
+
"execution_count": 44,
|
1337 |
"metadata": {},
|
1338 |
"output_type": "execute_result"
|
1339 |
}
|
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|
1344 |
},
|
1345 |
{
|
1346 |
"cell_type": "code",
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1347 |
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"execution_count": 48,
|
1348 |
"id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
|
1349 |
"metadata": {},
|
1350 |
"outputs": [
|
1351 |
{
|
1352 |
"data": {
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1353 |
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\n",
|
1354 |
"text/plain": [
|
1355 |
"<Figure size 432x288 with 1 Axes>"
|
1356 |
]
|
|
|
1362 |
}
|
1363 |
],
|
1364 |
"source": [
|
1365 |
+
"ax = df['neg_log10_affinity_M'].hist(bins=100,density=True)\n",
|
1366 |
"ax.set_xlabel('-$\\log_{10}$ affinity[M]',fontsize=16)\n",
|
1367 |
"ax.set_ylabel('probability',fontsize=16)\n",
|
1368 |
"ax.figure.savefig('affinity_neglog10_M.pdf')"
|
|
|
1370 |
},
|
1371 |
{
|
1372 |
"cell_type": "code",
|
1373 |
+
"execution_count": 49,
|
1374 |
"id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
|
1375 |
"metadata": {},
|
1376 |
"outputs": [
|
1377 |
{
|
1378 |
"data": {
|
1379 |
"text/plain": [
|
1380 |
+
"1927202"
|
1381 |
]
|
1382 |
},
|
1383 |
+
"execution_count": 49,
|
1384 |
"metadata": {},
|
1385 |
"output_type": "execute_result"
|
1386 |
}
|
|
|
1389 |
"len(df)"
|
1390 |
]
|
1391 |
},
|
1392 |
+
{
|
1393 |
+
"cell_type": "code",
|
1394 |
+
"execution_count": 54,
|
1395 |
+
"id": "b85f8b72-8dfc-4a24-b5b8-51fcbe6dcf63",
|
1396 |
+
"metadata": {},
|
1397 |
+
"outputs": [
|
1398 |
+
{
|
1399 |
+
"data": {
|
1400 |
+
"text/plain": [
|
1401 |
+
"{'with_mean': True,\n",
|
1402 |
+
" 'with_std': True,\n",
|
1403 |
+
" 'copy': True,\n",
|
1404 |
+
" 'n_features_in_': 1,\n",
|
1405 |
+
" 'n_samples_seen_': 1927202,\n",
|
1406 |
+
" 'mean_': array([6.51286529]),\n",
|
1407 |
+
" 'var_': array([2.4379995]),\n",
|
1408 |
+
" 'scale_': array([1.56140946])}"
|
1409 |
+
]
|
1410 |
+
},
|
1411 |
+
"execution_count": 54,
|
1412 |
+
"metadata": {},
|
1413 |
+
"output_type": "execute_result"
|
1414 |
+
}
|
1415 |
+
],
|
1416 |
+
"source": [
|
1417 |
+
"scaler.__dict__"
|
1418 |
+
]
|
1419 |
+
},
|
1420 |
+
{
|
1421 |
+
"cell_type": "code",
|
1422 |
+
"execution_count": 63,
|
1423 |
+
"id": "ec0ef8e2-c0e9-4c9b-bf3a-c98cc3889475",
|
1424 |
+
"metadata": {},
|
1425 |
+
"outputs": [
|
1426 |
+
{
|
1427 |
+
"data": {
|
1428 |
+
"text/plain": [
|
1429 |
+
"{'with_mean': True,\n",
|
1430 |
+
" 'with_std': True,\n",
|
1431 |
+
" 'copy': True,\n",
|
1432 |
+
" 'n_features_in_': 1,\n",
|
1433 |
+
" 'n_samples_seen_': 1927202,\n",
|
1434 |
+
" 'mean_': array([6.51286529]),\n",
|
1435 |
+
" 'var_': array([2.4379995]),\n",
|
1436 |
+
" 'scale_': array([1.56140946])}"
|
1437 |
+
]
|
1438 |
+
},
|
1439 |
+
"execution_count": 63,
|
1440 |
+
"metadata": {},
|
1441 |
+
"output_type": "execute_result"
|
1442 |
+
}
|
1443 |
+
],
|
1444 |
+
"source": [
|
1445 |
+
"scaler.__dict__"
|
1446 |
+
]
|
1447 |
+
},
|
1448 |
+
{
|
1449 |
+
"cell_type": "code",
|
1450 |
+
"execution_count": 67,
|
1451 |
+
"id": "15f8d5b9-37d5-453e-a6df-df6510cc5c81",
|
1452 |
+
"metadata": {},
|
1453 |
+
"outputs": [],
|
1454 |
+
"source": [
|
1455 |
+
"# output the normalization\n",
|
1456 |
+
"\n",
|
1457 |
+
"import json\n",
|
1458 |
+
"\n",
|
1459 |
+
"class NumpyEncoder(json.JSONEncoder):\n",
|
1460 |
+
" def default(self, obj):\n",
|
1461 |
+
" if isinstance(obj, np.ndarray):\n",
|
1462 |
+
" return obj.tolist()\n",
|
1463 |
+
" if isinstance(obj, np.int64):\n",
|
1464 |
+
" return int(obj)\n",
|
1465 |
+
" return json.JSONEncoder.default(self, obj)\n",
|
1466 |
+
" \n",
|
1467 |
+
"json.dump(scaler.__dict__,open('data/scaling.json','w'),cls=NumpyEncoder)"
|
1468 |
+
]
|
1469 |
+
},
|
1470 |
+
{
|
1471 |
+
"cell_type": "markdown",
|
1472 |
+
"id": "210b39d3-505b-4a6e-b186-35e660f4d510",
|
1473 |
+
"metadata": {},
|
1474 |
+
"source": [
|
1475 |
+
"**without KRAS**"
|
1476 |
+
]
|
1477 |
+
},
|
1478 |
+
{
|
1479 |
+
"cell_type": "code",
|
1480 |
+
"execution_count": 78,
|
1481 |
+
"id": "8dec95dc-a014-4d39-ae51-8de981173573",
|
1482 |
+
"metadata": {},
|
1483 |
+
"outputs": [],
|
1484 |
+
"source": [
|
1485 |
+
"smiles_sotorasib = 'C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1'\n",
|
1486 |
+
"seq_kras_wt = 'MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM'"
|
1487 |
+
]
|
1488 |
+
},
|
1489 |
+
{
|
1490 |
+
"cell_type": "code",
|
1491 |
+
"execution_count": 81,
|
1492 |
+
"id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
|
1493 |
+
"metadata": {},
|
1494 |
+
"outputs": [],
|
1495 |
+
"source": [
|
1496 |
+
"df_nokras = df[df.seq!=seq_kras_wt]"
|
1497 |
+
]
|
1498 |
+
},
|
1499 |
+
{
|
1500 |
+
"cell_type": "code",
|
1501 |
+
"execution_count": 83,
|
1502 |
+
"id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
|
1503 |
+
"metadata": {},
|
1504 |
+
"outputs": [
|
1505 |
+
{
|
1506 |
+
"data": {
|
1507 |
+
"text/plain": [
|
1508 |
+
"1926945"
|
1509 |
+
]
|
1510 |
+
},
|
1511 |
+
"execution_count": 83,
|
1512 |
+
"metadata": {},
|
1513 |
+
"output_type": "execute_result"
|
1514 |
+
}
|
1515 |
+
],
|
1516 |
+
"source": [
|
1517 |
+
"len(df_nokras)"
|
1518 |
+
]
|
1519 |
+
},
|
1520 |
+
{
|
1521 |
+
"cell_type": "code",
|
1522 |
+
"execution_count": 84,
|
1523 |
+
"id": "47966268-c97c-4bd9-9c90-eb568249f2ef",
|
1524 |
+
"metadata": {},
|
1525 |
+
"outputs": [],
|
1526 |
+
"source": [
|
1527 |
+
"df_nokras.to_parquet('data/all_nokras.parquet')"
|
1528 |
+
]
|
1529 |
+
},
|
1530 |
{
|
1531 |
"cell_type": "code",
|
1532 |
"execution_count": null,
|
1533 |
+
"id": "bfbf0bcd-8cd5-4efa-a9ca-f8d7ee5870e0",
|
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|
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"source": [
|
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+
"quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50']"
|
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]
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 8,
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"id": "52c0c66c-1eb0-415b-b019-bc77419ccbd7",
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"metadata": {},
|
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "e5b4dd41-1389-408d-bee6-6dbeefc1d5c7",
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"metadata": {},
|
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"outputs": [],
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 10,
|
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"id": "61b8276c-54fe-4989-af5f-723994e1df7e",
|
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"metadata": {},
|
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"outputs": [],
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 11,
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"id": "342c8ef3-6808-471b-baa4-f9bdc7f6e8d6",
|
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"metadata": {},
|
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"outputs": [
|
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"88806"
|
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]
|
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},
|
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+
"execution_count": 11,
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"metadata": {},
|
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"output_type": "execute_result"
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 12,
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"id": "8bb2dfac-5f11-455c-9dee-3607b47b4232",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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+
"execution_count": 13,
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"id": "b5c0fa42-b595-4b96-b2d5-57f0031427dc",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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+
"execution_count": 14,
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"id": "27c4865b-5337-48e0-9be7-a913b31cfae1",
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"metadata": {},
|
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"outputs": [
|
|
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"88806"
|
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]
|
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},
|
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+
"execution_count": 14,
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
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},
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{
|
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"cell_type": "code",
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"execution_count": 15,
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"id": "f3daf4ad-0205-48c0-8c38-36aa4eb561e0",
|
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"metadata": {},
|
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"outputs": [
|
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{
|
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"data": {
|
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"text/plain": [
|
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+
"25490"
|
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]
|
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},
|
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+
"execution_count": 15,
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 23,
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"id": "0dc39f62-5b18-4a86-9a44-17d1925da2ad",
|
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"metadata": {},
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"outputs": [],
|
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},
|
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{
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"cell_type": "code",
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+
"execution_count": 15,
|
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+
"id": "719d147f-75eb-4ead-a54f-4b448a62a9a0",
|
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+
"metadata": {},
|
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+
"outputs": [],
|
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+
"source": []
|
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+
},
|
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+
{
|
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+
"cell_type": "code",
|
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+
"execution_count": 24,
|
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"id": "6d158a41-64c6-4fa2-92d5-562aa11e8924",
|
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"metadata": {},
|
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"outputs": [],
|
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 25,
|
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"id": "901fe6c6-dc8c-4ce4-82c6-1fb0b718287a",
|
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"metadata": {},
|
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"outputs": [],
|
|
|
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},
|
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{
|
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"cell_type": "code",
|
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+
"execution_count": 26,
|
231 |
"id": "383f9a1c-ffc6-43da-ac5a-5bcb815be28b",
|
232 |
"metadata": {},
|
233 |
"outputs": [
|
|
|
317 |
" <td>NaN</td>\n",
|
318 |
" <td>NaN</td>\n",
|
319 |
" <td>NaN</td>\n",
|
320 |
+
" <td>43W:A:902</td>\n",
|
321 |
" <td>valid</td>\n",
|
322 |
+
" <td>ic50</td>\n",
|
323 |
" <td>=</td>\n",
|
324 |
+
" <td>580.00</td>\n",
|
325 |
+
" <td>nM</td>\n",
|
326 |
+
" <td>C#CCCOP(=O)(O)OP(=O)(O)O</td>\n",
|
327 |
" <td>NaN</td>\n",
|
328 |
" <td>False</td>\n",
|
329 |
+
" <td>2</td>\n",
|
330 |
+
" <td>4S3F</td>\n",
|
331 |
+
" <td>0.580000</td>\n",
|
332 |
+
" <td>4S3F</td>\n",
|
333 |
+
" <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
|
334 |
" </tr>\n",
|
335 |
" <tr>\n",
|
336 |
" <th>3</th>\n",
|
337 |
" <td>NaN</td>\n",
|
338 |
" <td>NaN</td>\n",
|
339 |
" <td>NaN</td>\n",
|
340 |
+
" <td>0CG:A:902</td>\n",
|
341 |
" <td>valid</td>\n",
|
342 |
+
" <td>ic50</td>\n",
|
343 |
" <td>=</td>\n",
|
344 |
+
" <td>770.00</td>\n",
|
345 |
+
" <td>nM</td>\n",
|
346 |
+
" <td>C#CCOP(=O)(O)OP(=O)(O)O</td>\n",
|
347 |
" <td>NaN</td>\n",
|
348 |
" <td>False</td>\n",
|
349 |
+
" <td>2</td>\n",
|
350 |
+
" <td>4S3F</td>\n",
|
351 |
+
" <td>0.770000</td>\n",
|
352 |
+
" <td>4S3F</td>\n",
|
353 |
+
" <td>MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE...</td>\n",
|
354 |
" </tr>\n",
|
355 |
" <tr>\n",
|
356 |
" <th>4</th>\n",
|
357 |
" <td>NaN</td>\n",
|
358 |
" <td>NaN</td>\n",
|
359 |
" <td>NaN</td>\n",
|
360 |
+
" <td>ADN:A:901</td>\n",
|
361 |
" <td>valid</td>\n",
|
362 |
" <td>Kd</td>\n",
|
363 |
" <td>=</td>\n",
|
|
|
393 |
" <td>...</td>\n",
|
394 |
" </tr>\n",
|
395 |
" <tr>\n",
|
396 |
+
" <th>25420</th>\n",
|
397 |
" <td>NaN</td>\n",
|
398 |
" <td>NaN</td>\n",
|
399 |
" <td>NaN</td>\n",
|
|
|
413 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
414 |
" </tr>\n",
|
415 |
" <tr>\n",
|
416 |
+
" <th>25421</th>\n",
|
417 |
" <td>NaN</td>\n",
|
418 |
" <td>NaN</td>\n",
|
419 |
" <td>NaN</td>\n",
|
|
|
433 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
434 |
" </tr>\n",
|
435 |
" <tr>\n",
|
436 |
+
" <th>25422</th>\n",
|
437 |
" <td>NaN</td>\n",
|
438 |
" <td>NaN</td>\n",
|
439 |
" <td>NaN</td>\n",
|
|
|
453 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
454 |
" </tr>\n",
|
455 |
" <tr>\n",
|
456 |
+
" <th>25423</th>\n",
|
457 |
" <td>NaN</td>\n",
|
458 |
" <td>NaN</td>\n",
|
459 |
" <td>NaN</td>\n",
|
|
|
473 |
" <td>MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG...</td>\n",
|
474 |
" </tr>\n",
|
475 |
" <tr>\n",
|
476 |
+
" <th>25424</th>\n",
|
477 |
" <td>NaN</td>\n",
|
478 |
" <td>NaN</td>\n",
|
479 |
" <td>NaN</td>\n",
|
|
|
494 |
" </tr>\n",
|
495 |
" </tbody>\n",
|
496 |
"</table>\n",
|
497 |
+
"<p>25425 rows × 17 columns</p>\n",
|
498 |
"</div>"
|
499 |
],
|
500 |
"text/plain": [
|
501 |
" 0 1 pdb ligand_name ligand_valid affinity_quantity 6 \\\n",
|
502 |
"0 NaN NaN NaN 2PA:C:613 valid Ki = \n",
|
503 |
"1 NaN NaN NaN HAE:C:800 valid Ki = \n",
|
504 |
+
"2 NaN NaN NaN 43W:A:902 valid ic50 = \n",
|
505 |
+
"3 NaN NaN NaN 0CG:A:902 valid ic50 = \n",
|
506 |
+
"4 NaN NaN NaN ADN:A:901 valid Kd = \n",
|
507 |
"... ... ... ... ... ... ... .. \n",
|
508 |
+
"25420 NaN NaN NaN MAN NAG:G:1 valid Ka = \n",
|
509 |
+
"25421 NaN NaN NaN MAN NAG:F:1 valid Ka = \n",
|
510 |
+
"25422 NaN NaN NaN NGA NAG:F:1 valid Ka = \n",
|
511 |
+
"25423 NaN NaN NaN NGA NAG:E:1 valid Ka = \n",
|
512 |
+
"25424 NaN NaN NaN NGA NAG:H:1 valid Ka = \n",
|
513 |
"\n",
|
514 |
" affinity_val affinity_unit \\\n",
|
515 |
"0 0.62 nM \n",
|
516 |
"1 2.60 uM \n",
|
517 |
+
"2 580.00 nM \n",
|
518 |
+
"3 770.00 nM \n",
|
519 |
"4 15.00 uM \n",
|
520 |
"... ... ... \n",
|
521 |
+
"25420 7860.00 M^-1 \n",
|
522 |
+
"25421 7860.00 M^-1 \n",
|
523 |
+
"25422 5910.00 M^-1 \n",
|
524 |
+
"25423 5910.00 M^-1 \n",
|
525 |
+
"25424 5910.00 M^-1 \n",
|
526 |
"\n",
|
527 |
" smiles 10 is_sep cum_sum \\\n",
|
528 |
"0 NP(=O)(N)O NaN False 1 \n",
|
529 |
"1 CC(=O)NO NaN False 1 \n",
|
530 |
+
"2 C#CCCOP(=O)(O)OP(=O)(O)O NaN False 2 \n",
|
531 |
+
"3 C#CCOP(=O)(O)OP(=O)(O)O NaN False 2 \n",
|
532 |
"4 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3... NaN False 5 \n",
|
533 |
"... ... .. ... ... \n",
|
534 |
+
"25420 NaN NaN False 10499 \n",
|
535 |
+
"25421 NaN NaN False 10499 \n",
|
536 |
+
"25422 NaN NaN False 10499 \n",
|
537 |
+
"25423 NaN NaN False 10499 \n",
|
538 |
+
"25424 NaN NaN False 10499 \n",
|
539 |
"\n",
|
540 |
" pdb_ref affinity_uM name \\\n",
|
541 |
"0 6H8J 0.000620 6H8J \n",
|
542 |
"1 6H8J 2.600000 6H8J \n",
|
543 |
+
"2 4S3F 0.580000 4S3F \n",
|
544 |
+
"3 4S3F 0.770000 4S3F \n",
|
545 |
"4 2GL0 15.000000 2GL0 \n",
|
546 |
"... ... ... ... \n",
|
547 |
+
"25420 2WDB 127.226463 2WDB \n",
|
548 |
+
"25421 2WDB 127.226463 2WDB \n",
|
549 |
+
"25422 2WDB 169.204738 2WDB \n",
|
550 |
+
"25423 2WDB 169.204738 2WDB \n",
|
551 |
+
"25424 2WDB 169.204738 2WDB \n",
|
552 |
"\n",
|
553 |
" seq \n",
|
554 |
"0 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
555 |
"1 NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVE... \n",
|
556 |
+
"2 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
|
557 |
+
"3 MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLE... \n",
|
558 |
"4 MTDMSIKFELIDVPIPQGTNVIIGQAHFIKTVEDLYEALVTSVPGV... \n",
|
559 |
"... ... \n",
|
560 |
+
"25420 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
561 |
+
"25421 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
562 |
+
"25422 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
563 |
+
"25423 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
564 |
+
"25424 MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDG... \n",
|
565 |
"\n",
|
566 |
+
"[25425 rows x 17 columns]"
|
567 |
]
|
568 |
},
|
569 |
+
"execution_count": 26,
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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}
|
|
|
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},
|
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{
|
579 |
"cell_type": "code",
|
580 |
+
"execution_count": 27,
|
581 |
"id": "bebc962b-10f7-478c-8e23-e2d3722e875c",
|
582 |
"metadata": {},
|
583 |
"outputs": [],
|
pdbbind.ipynb
CHANGED
@@ -10,7 +10,7 @@
|
|
10 |
},
|
11 |
{
|
12 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
|
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"metadata": {},
|
16 |
"outputs": [],
|
@@ -20,38 +20,31 @@
|
|
20 |
},
|
21 |
{
|
22 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
|
25 |
"metadata": {},
|
26 |
"outputs": [],
|
27 |
"source": [
|
28 |
-
"df = pd.read_table('
|
29 |
-
"df = df.rename(columns={'#': 'name','release': 'affinity'})"
|
|
|
|
|
|
|
30 |
]
|
31 |
},
|
32 |
{
|
33 |
"cell_type": "code",
|
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-
"execution_count":
|
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-
"id": "16e0fe44-96aa-4d3a-ae42-3609e895418b",
|
36 |
-
"metadata": {},
|
37 |
-
"outputs": [],
|
38 |
-
"source": [
|
39 |
-
"from numericalunits import mL, nm"
|
40 |
-
]
|
41 |
-
},
|
42 |
-
{
|
43 |
-
"cell_type": "code",
|
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-
"execution_count": 13,
|
45 |
"id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",
|
46 |
"metadata": {},
|
47 |
"outputs": [],
|
48 |
"source": [
|
49 |
-
"quantities = ['ki','kd','ka','k1/2','kb']"
|
50 |
]
|
51 |
},
|
52 |
{
|
53 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -74,7 +67,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -85,7 +78,7 @@
|
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|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
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"id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
|
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"metadata": {},
|
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"outputs": [
|
@@ -95,13 +88,13 @@
|
|
95 |
"<AxesSubplot:>"
|
96 |
]
|
97 |
},
|
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-
"execution_count":
|
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"metadata": {},
|
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"output_type": "execute_result"
|
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},
|
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{
|
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"data": {
|
104 |
-
"image/png": "
|
105 |
"text/plain": [
|
106 |
"<Figure size 432x288 with 1 Axes>"
|
107 |
]
|
@@ -118,7 +111,7 @@
|
|
118 |
},
|
119 |
{
|
120 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "aa358835-55f3-4551-9217-e76a15de4fe8",
|
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"metadata": {},
|
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"outputs": [],
|
@@ -128,17 +121,17 @@
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|
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{
|
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|
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-
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|
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|
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"metadata": {},
|
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"outputs": [],
|
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"source": [
|
136 |
-
"df_complex = pd.read_parquet('
|
137 |
]
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
|
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|
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"outputs": [],
|
@@ -148,7 +141,7 @@
|
|
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},
|
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{
|
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"cell_type": "code",
|
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-
"execution_count":
|
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"id": "4d105c42-0d11-49db-9012-52fafc9cd299",
|
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"metadata": {},
|
154 |
"outputs": [],
|
@@ -158,17 +151,17 @@
|
|
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},
|
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{
|
160 |
"cell_type": "code",
|
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-
"execution_count":
|
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"id": "2955b056-26dd-45fa-8d74-f17661253a9a",
|
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"metadata": {},
|
164 |
"outputs": [
|
165 |
{
|
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"data": {
|
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"text/plain": [
|
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-
"
|
169 |
]
|
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},
|
171 |
-
"execution_count":
|
172 |
"metadata": {},
|
173 |
"output_type": "execute_result"
|
174 |
}
|
|
|
10 |
},
|
11 |
{
|
12 |
"cell_type": "code",
|
13 |
+
"execution_count": 27,
|
14 |
"id": "86476f6e-802a-463b-a1b0-2ae228bb92af",
|
15 |
"metadata": {},
|
16 |
"outputs": [],
|
|
|
20 |
},
|
21 |
{
|
22 |
"cell_type": "code",
|
23 |
+
"execution_count": 45,
|
24 |
"id": "9b2be11c-f4bb-4107-af49-abd78052afcf",
|
25 |
"metadata": {},
|
26 |
"outputs": [],
|
27 |
"source": [
|
28 |
+
"df = pd.read_table('pdbbind/data/index/INDEX_general_PL_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
|
29 |
+
"df = df.rename(columns={'#': 'name','release': 'affinity'})\n",
|
30 |
+
"df_refined = pd.read_table('pdbbind/data/index/INDEX_refined_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",
|
31 |
+
"df_refined = df_refined.rename(columns={'#': 'name','release': 'affinity'})\n",
|
32 |
+
"df = pd.concat([df,df_refined])"
|
33 |
]
|
34 |
},
|
35 |
{
|
36 |
"cell_type": "code",
|
37 |
+
"execution_count": 46,
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
38 |
"id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",
|
39 |
"metadata": {},
|
40 |
"outputs": [],
|
41 |
"source": [
|
42 |
+
"quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50']"
|
43 |
]
|
44 |
},
|
45 |
{
|
46 |
"cell_type": "code",
|
47 |
+
"execution_count": 47,
|
48 |
"id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",
|
49 |
"metadata": {},
|
50 |
"outputs": [],
|
|
|
67 |
},
|
68 |
{
|
69 |
"cell_type": "code",
|
70 |
+
"execution_count": 48,
|
71 |
"id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",
|
72 |
"metadata": {},
|
73 |
"outputs": [],
|
|
|
78 |
},
|
79 |
{
|
80 |
"cell_type": "code",
|
81 |
+
"execution_count": 49,
|
82 |
"id": "d92f0004-68c1-4487-94b9-56b4fd598de4",
|
83 |
"metadata": {},
|
84 |
"outputs": [
|
|
|
88 |
"<AxesSubplot:>"
|
89 |
]
|
90 |
},
|
91 |
+
"execution_count": 49,
|
92 |
"metadata": {},
|
93 |
"output_type": "execute_result"
|
94 |
},
|
95 |
{
|
96 |
"data": {
|
97 |
+
"image/png": 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\n",
|
98 |
"text/plain": [
|
99 |
"<Figure size 432x288 with 1 Axes>"
|
100 |
]
|
|
|
111 |
},
|
112 |
{
|
113 |
"cell_type": "code",
|
114 |
+
"execution_count": 50,
|
115 |
"id": "aa358835-55f3-4551-9217-e76a15de4fe8",
|
116 |
"metadata": {},
|
117 |
"outputs": [],
|
|
|
121 |
},
|
122 |
{
|
123 |
"cell_type": "code",
|
124 |
+
"execution_count": 51,
|
125 |
"id": "d6dda488-f709-4fe7-b372-080042cf7c66",
|
126 |
"metadata": {},
|
127 |
"outputs": [],
|
128 |
"source": [
|
129 |
+
"df_complex = pd.read_parquet('data/pdbbind_complex.parquet')"
|
130 |
]
|
131 |
},
|
132 |
{
|
133 |
"cell_type": "code",
|
134 |
+
"execution_count": 52,
|
135 |
"id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",
|
136 |
"metadata": {},
|
137 |
"outputs": [],
|
|
|
141 |
},
|
142 |
{
|
143 |
"cell_type": "code",
|
144 |
+
"execution_count": 53,
|
145 |
"id": "4d105c42-0d11-49db-9012-52fafc9cd299",
|
146 |
"metadata": {},
|
147 |
"outputs": [],
|
|
|
151 |
},
|
152 |
{
|
153 |
"cell_type": "code",
|
154 |
+
"execution_count": 54,
|
155 |
"id": "2955b056-26dd-45fa-8d74-f17661253a9a",
|
156 |
"metadata": {},
|
157 |
"outputs": [
|
158 |
{
|
159 |
"data": {
|
160 |
"text/plain": [
|
161 |
+
"24759"
|
162 |
]
|
163 |
},
|
164 |
+
"execution_count": 54,
|
165 |
"metadata": {},
|
166 |
"output_type": "execute_result"
|
167 |
}
|
pdbbind.py
CHANGED
@@ -19,7 +19,7 @@ def parse_complex(fn):
|
|
19 |
if __name__ == '__main__':
|
20 |
import glob
|
21 |
|
22 |
-
filenames = glob.glob('pdbbind/data/
|
23 |
filenames.extend(glob.glob('pdbbind/data/refined-set/*'))
|
24 |
comm = MPI.COMM_WORLD
|
25 |
with MPICommExecutor(comm, root=0) as executor:
|
|
|
19 |
if __name__ == '__main__':
|
20 |
import glob
|
21 |
|
22 |
+
filenames = glob.glob('pdbbind/data/v2020-other-PL/*')
|
23 |
filenames.extend(glob.glob('pdbbind/data/refined-set/*'))
|
24 |
comm = MPI.COMM_WORLD
|
25 |
with MPICommExecutor(comm, root=0) as executor:
|
pdbbind.slurm
CHANGED
@@ -1,7 +1,7 @@
|
|
1 |
#!/bin/bash
|
2 |
#SBATCH -J preprocess_pdbbind
|
3 |
#SBATCH -p batch
|
4 |
-
#SBATCH -A
|
5 |
#SBATCH -t 3:00:00
|
6 |
#SBATCH -N 12
|
7 |
#SBATCH --ntasks-per-node=8
|
|
|
1 |
#!/bin/bash
|
2 |
#SBATCH -J preprocess_pdbbind
|
3 |
#SBATCH -p batch
|
4 |
+
#SBATCH -A STF006
|
5 |
#SBATCH -t 3:00:00
|
6 |
#SBATCH -N 12
|
7 |
#SBATCH --ntasks-per-node=8
|