nanomelt 1.0.0__tar.gz

nanomelt-1.0.0/LICENSE

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nanomelt-1.0.0/MANIFEST.in

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+include environment.yml

nanomelt-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: nanomelt
+Version: 1.0.0
+Summary: A nanobody thermostability prediction tool
+Author: Aubin Ramon
+Author-email: ar2033@cam.ac.uk
+License: CC BY-NC-SA 4.0
+License-File: LICENSE
+Requires-Dist: scikit-learn
+Requires-Dist: joblib
+Requires-Dist: fair-esm
+Requires-Dist: ablang
+Requires-Dist: peptides
+Requires-Dist: Immunebuilder
+Requires-Dist: transformers
+Requires-Dist: antiberty
+Requires-Dist: xgboost
+Requires-Dist: lightgbm
+Requires-Dist: kmedoids
+Requires-Dist: kneed
+Requires-Dist: matplotlib
+
+See READ.me in GitLab repository https://gitlab.developers.cam.ac.uk/ch/sormanni/nanomelt.git

nanomelt-1.0.0/README.md

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+# NanoMelt: semi-supervised ensemble model for nanobody thermostability prediction
+
+</div>
+
+## License
+
+Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) (see License file).
+This software is not to be used for commerical purposes.
+
+## Reference
+
+> Original publication (mAbs 2025): https://doi.org/10.1080/19420862.2024.2442750
+
+
+## Presentation
+
+NanoMelt is a semi-supervised ensemble model trained to predict the apparent
+melting temperatures of nanobodies. 
+
+The model involves a Ridge stacking of multiple Gaussian Process Regressors (GPRs)
+and Suppot Vector Regressors (SVRs) combined with diverse pre-trained nanobody embeddings 
+(i.e., one-hot, VHSE, ESM-1b, and ESM-2).
+
+* NanoMelt can be used via:
+    - `nanomelt predict`: to directly predict the apparent melting temperatures of given nanobodies, or
+    - `nanomelt train`: to retrain a custom model with your own dataset. 
+
+<strong>A webserver for nanobody thermostability prediction is available at https://www-cohsoftware.ch.cam.ac.uk/</strong>
+
+You can find the parsed datasets of nanobody thermostabily in the `/datasets` directory. 
+All Jupyter notebooks used to create the figures in the original publication are available in the `/notebooks` directory. 
+
+## Setup NanoMelt 
+
+> **Compatible with 3.12**
+
+We recommend running NanoMelt on a `GPU` for optimal performance, as it relies on ESM models to generate input embeddings.
+
+**Step 1. Ensure all conda dependencies are installed**
+
+```bash
+conda install -c conda-forge openmm pdbfixer biopython
+```
+
+**Step 2. Install ANARCI**
+
+```bash
+# For Linux (x86_64)
+conda install -c bioconda anarci
+
+# For Apple Silicon (arm64), due to limited support, the following steps are recommended
+conda install -c biocore hmmer
+git clone https://github.com/oxpig/ANARCI.git
+cd ANARCI
+python setup.py install
+conda install nomkl #Optional, for compatibility with numpy
+```
+
+**Step 3. Install NanoMelt from PyPI**
+```
+# Install from PyPI
+pip install nanomelt
+```
+
+## NanoMelt command-line interface
+
+### 1 - Prediction of nanobody apparent melting temperatures
+
+To predict the apparent melting temperature of nanobody sequences, use the `nanobody predict` command line. Parallelisation can be applied by specifying the number of cpus `-ncpu`. NanoMelt will automatically search for CUDA or Apple MX GPU to accelerate the embedding step. 
+
+<details>
+    <summary>See <strong>nanomelt predict</strong> command line description</summary>
+
+```
+nanomelt predict [-h] [-i INPUT_FILEPATH_OR_SEQ] [-o OUTPUT_SAVEFP] [-align] [-ncpu NCPU]
+
+Predict nanobody apparent melting temperatures with NanoMelt
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT_FILEPATH_OR_SEQ, --input_filepath_or_seq INPUT_FILEPATH_OR_SEQ
+                        Filepath to the fasta file .fa to score or directly a single string sequence (default: to_score.fa)
+  -o OUTPUT_SAVEFP, --output_savefp OUTPUT_SAVEFP
+                        Filename of the .csv file to save the predictions in (default: nanomelt_run.csv)
+  -align, --do_align    Do the alignment and the cleaning of the given sequences before training. This step can takes a lot of time if the number of
+                        sequences is huge. (default: False)
+  -ncpu NCPU, --ncpu NCPU
+                        If ncpu>1 will parallelise the alignment process (default: 1)
+```
+</details>
+
+
+\
+Testing files are presented in `/test`, with examples of output files.
+
+Examples of `nanomelt predict` usage:
+
+```bash
+# For one single sequence
+nanomelt predict -i QVQLVESGGGLVQAGGSLRLSCAASGYIFGRNAMGWYRQAPGKERELVAGITRRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADPASPAYGDYWGQGTQVTVSS -align
+
+# Predict the apparent melting temepatures for a set of sequences in a fasta file
+nanomelt predict -i test/application6.fa  -o test/NanoMeltrun_application6.csv -align
+```
+
+Additionally, NanoMelt can be used directly via its in-built function `NanoMeltPredPipe()`. It takes as inputs a list of SeqRecords (seq_records, see BioPython). 
+See description of function for further details. For instance:
+
+```bash
+# Import
+from nanomelt.model.nanomelt import NanoMeltPredPipe
+
+# Run the model
+data = NanoMeltPredPipe(seq_records, do_align=True, ncpus=4, verbose=True)
+```
+
+### 2 - Re-training NanoMelt
+
+To re-train NanoMelt on a custom input dataset of nanobody sequences with their respective melting temperature, use the `nanomelt train` command line.
+Be careful with the format of your input file (see command line description).
+
+<details>
+    <summary>See <strong>nanomelt train</strong> command line description</summary>
+
+```
+nanomelt train [-h] [-i INPUT_CSV] [-od OUTPUT_DIR] [-align] [-ncpu NCPU]
+
+Train NanoMelt with a new input dataset.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT_CSV, --input_csv INPUT_CSV
+                        Filepath to the .csv file of the nanobody dataset. It needs to have at least columns with Id, Sequence, Experimental method
+                        and Measured apparent melting temperature (C). (default: new_nano_thermostability_dataset.csv)
+  -od OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        Filepath to the output dir where to save the saved models (default: nanomelt_retrain)
+  -align, --do_align    Do the alignment and the cleaning of the given sequences before training. This step can takes a lot of time if the number of
+                        sequences is huge. (default: False)
+  -ncpu NCPU, --ncpu NCPU
+                        If ncpu>1 will parallelise the algnment process (default: 1)
+```
+
+</details>
+
+Example of usage of `nanomelt train`:
+
+```bash
+# Train.
+nanomelt train -i datasets/NanoMelt_640_nanobody_apparent_melting_temperatures.csv -od test/nanomelt_retrain -align -ncpu 4
+```
+
+## Issues
+
+- The installation of OpenMM might create troubles with your device. If you have an `import error` with `lib glibxx_3.4.30`, you could solve it with `export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH` (issue due to AbNatiV installation).
+
+If you experience any issues please add an issue to the [Gitlab] or contact directly ar2033@cam.ac.uk.
+
+## Contact
+
+Please contact ar2033@cam.ac.uk to report issues of for any questions.
+
+

nanomelt-1.0.0/environment.yml

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+name: nanomelt
+channels:
+  - nodefaults
+  - bioconda
+  - biocore
+  - conda-forge
+dependencies:
+  - python>=3.8
+  - poetry
+  - hmmer
+  - anarci
+  - biopython
+  - nomkl
+  - openmm
+  - pdbfixer
+  - pip
+  - pip:
+    - scikit-learn
+    - joblib 
+    - fair-esm
+    - ablang
+    - peptides
+    - Immunebuilder
+    - transformers
+    - antiberty
+    - xgboost
+    - lightgbm
+    - kmedoids
+    - kneed
+    - matplotlib
+

nanomelt-1.0.0/nanomelt/__init__.py

@@ -0,0 +1,3 @@
+"""
+ Copyright 2024. Aubin Ramon and Pietro Sormanni. CC BY-NC-SA 4.0
+"""