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signaturizer
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8cf0fed4
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8cf0fed4
authored
Jul 01, 2020
by
Martino Bertoni
🌋
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README.md
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# Signaturizer
Generate Chemical Checker signatures from molecules SMILES.
# Install from PyPI

```
Bioactivity signatures are multi-dimensional vectors that capture biological
traits of the molecule (for example, its target profile) in a numerical vector
format that is akin to the structural descriptors or fingerprints used in the
field of chemoinformatics.
Our
**signaturizers**
relate to bioactivities of 25 different types (including
target profiles, cellular response and clinical outcomes) and can be used as
drop-in replacements for chemical descriptors in day-to-day chemoinformatics
tasks.
For and overview of the different bioctivity descriptors available please check
the original Chemical Checker
[
paper
](
https://www.nature.com/articles/s41587-020-0502-7
)
or
[
website
](
https://chemicalchecker.com/
)
# Installation
## from PyPI
```
bash
pip
install
signaturizer
```
#
Install
from Git repository
#
#
from Git repository
```
```
bash
pip
install
git+http://gitlabsbnb.irbbarcelona.org/packages/signaturizer.git
```
# Example
# Usage
## Generating Bioactivity Signatures
```
python
from
signaturizer
import
Signaturizer
# load the
bioactivity space predictor
# load the
predictor for B1 space (representing the Mode of Action)
sign
=
Signaturizer
(
'/aloy/web_checker/exported_smilespreds/B1'
)
# prepare a list of SMILES strings
smiles
=
[
'C'
,
'CCC'
]
...
...
@@ -34,7 +60,7 @@ results = sign.predict(smiles, 'destination.h5')
```
#
Example Multiple
Signatures
#
#
Generating Multiple Bioactivity
Signatures
```
python
from
signaturizer
import
Signaturizer
# load the bioactivity space predictor for all space
...
...
@@ -46,4 +72,4 @@ smiles = ['C', 'CCC']
results
=
sign
.
predict
(
smiles
)
print
(
results
.
signature
.
shape
)
# (2, 3200)
```
\ No newline at end of file
```
images/cc_signatures.jpg
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