fpembed 0.1.4__tar.gz → 0.1.6__tar.gz

{fpembed-0.1.4 → fpembed-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fpembed
-Version: 0.1.4
+Version: 0.1.6
 Summary: Generalized fingerprint embedding library
 License-Expression: MIT
 Requires-Python: >=3.9
@@ -20,6 +20,10 @@ Dynamic: license-file
 
 # FPembed - Generalized Molecular Fingerprint Embeddings
 
+[![PyPI version](https://badge.fury.io/py/fpembed.svg)](https://badge.fury.io/py/fpembed)
+[![DOI](https://zenodo.org/badge/1223653010.svg)](https://doi.org/10.5281/zenodo.21447996)
+
+
 A lightweight Python package for generating compressed molecular fingerprint embeddings, backed by [scikit-fingerprints](https://github.com/scikit-fingerprints/scikit-fingerprints). Supports ten binary fingerprint types through a single unified class.
 
 FPembed compresses standard molecular fingerprints using weighted binary masking, producing compact float vectors suitable for machine-learning models. The package accepts SMILES, SELFIES, and RDKit Mol objects as input.
@@ -66,12 +70,12 @@ FPembed supports six compression methods, selectable via the `method` parameter
 
 | Method (`method` value) | Category | `method_params` | Dynamic Range / Distance Preservation | Complexity |
 |-------------------------|----------|-----------------|---------------------------------------|------------|
-| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L) |
-| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L) |
-| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L) |
-| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L) |
+| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L)       |
+| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L)       |
+| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L)       |
+| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L)       |
 | `hadamard` | global | `seed` (int) | orthogonal projection | O(L log L) |
-| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L·D) |
+| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L D)     |
 
 ### The `method` Parameter
 
@@ -132,7 +136,7 @@ print(emb.shape)  # (1, 128)
 
 ### Choosing a Method
 
-Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L·D) complexity.
+Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L D) complexity.
 
 ### Performance Characteristics
 
@@ -141,7 +145,7 @@ All methods produce the same output dimensionality (D = L / compression) but dif
 | Method | Speed                                    | Precomputed Memory                   | Best For |
 |--------|------------------------------------------|--------------------------------------|----------|
 | Block-wise (all four) | Fastest - single vectorized einsum, O(L) | Negligible (C-length weight vector)  | Default choice; large batches |
-| Random projection | Fast - BLAS matmul, O(L·D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
+| Random projection | Fast - BLAS matmul, O(L D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
 | Hadamard (SRHT) | Slowest - pure-Python FWHT, O(L log L)   | L-length sign vector (~16 KB)        | Small-scale experiments; future optimization |
 
 Block-wise methods are ~2–5x faster than random projection and orders of magnitude faster than Hadamard in practice. Random projection's memory cost grows quadratically with fingerprint size.
@@ -390,6 +394,14 @@ The following datasets are included in `examples/datasets/` (obtained from their
 
 This project is licensed under the terms of the MIT open source license. Please refer to the [LICENSE](LICENSE) for the full terms.
 
+## Legal & Trademark Notice
+
+The source code of this project is licensed under the permissive **MIT License**. You are free to use, modify, and distribute the code, even for commercial purposes, as long as the original copyright notice is retained.
+
+However, the name **"FPembed"**, its branding, and identifiers are the intellectual property of the project author (@Sciencealone). 
+* **Commercial Branding:** The unauthorized use of the name "FPembed" to brand, market, or promote commercial software, corporate AI engines, or proprietary services within the fields of bioinformatics, chemoinformatics, and AI drug discovery is strictly prohibited.
+* **Community Protection:** This notice is established to prevent public confusion and to protect the open-source community from misleading corporate misrepresentations. For licensing queries regarding the project name, please open an issue or contact the author directly.
+
 ## AI disclosure
 
 AI usage during project development is declared in [aidecl.yaml](aidecl.yaml) following the [AI Declaration Format](https://ai-declaration.org/).