ChEMBL distributes precomputed RDKit-Morgan fingerprints in FPS format. I've reformatted the ChEMBL 34 fingerprints into FPB format along with an embedded chemfp license key to enable the full range of chemfp functionality when working with that data set.
I've also removed the ChEMBL 31 dataset. If you need it, please …
read moreAfter over a year of development, I'm pleased to announce the release of chemfp 4.1. For full details read What’s new in chemfp 4.1 from the documentation.
Here are some of the highlights.
CXSMILES is now the default for SMILES input, across all of the supported toolkits …
I'm pleased to announce the release of chemfp 4.0.
The two themes of this release are diversity selection and improving the user-interface for interactive use.
Chemfp 4.0 adds implementations of the MaxMin, heapsweep, and sphere exclusion algorithms for diversity selection.
MaxMin is an approximate iterative method …
read moreI've just released a preview release of chemfp, version 4.0b2. It includes a new "chemfp" command, diversity selection, a "high-level" API, pandas integration, progress bars, new output formats, and more.
It is ready for production use. What remains is to improve test coverage and update the documentation.
To install …
read moreThe newly released chemfp 3.5.1 adds support for licensed FPB files. These are cheminformatics fingerprint datasets which can be used under the terms of chemfp's base license agreement even without a chemfp license key or source code distribution.
As the first (and so far only) data set, I've …
read moreI've just released chemfp 3.5, which is the latest version of the commercial chemfp development track. To install it on Linux-based OSes do the following:
python -m pip install chemfp -i https://chemfp.com/packages/
These are available at no cost under the Chemfp Base License Agreement. This license …
read moreI've just released chemfp 3.5b1, which is the latest version of the commercial chemfp development track. This is a beta version meant primarily as a way to get feedback about the new CDK support. See the previous posting for examples of the new features.
Because it is a beta …
read moreI've just released chemfp 3.5a1, which is an EXPERIMENTAL version with support for CDK. I'm looking for friendly users to try it out. It depends on JPype for the Python/Java interface. To install them, for Python 3.7 or later, on Linux-based OSes, do:
python -m pip install …I've just released chemfp 3.4.1, which is the latest version of the commercial chemfp development track. Use the following to download pre-compiled packages for most Linux-based operating systems:
python -m pip install chemfp -i https://chemp.com/packages/
These are available at no cost under the Chemfp Base …
read moreI've just released chemfp 1.6.1, which is the latest version of the no-cost/open source chemfp development track. You can download it from PyPI using:
python -m pip install chemfp
This minor release added specialized POPCNT implementations for all 8-byte-multiple fingerprint lengths up to 1024 bytes, plus a …
read moreI've just released chemfp 3.4, which is the latest version of the commercial chemfp development track. Use the following to download pre-compiled packages for most Linux-based operating systems:
python -m pip install chemfp -i https://chemp.com/packages/
These are available at no cost under the Chemfp Base License …
read moreI've just released chemfp 1.6, which is the latest version of the no-cost/open source chemfp development track. You can download it from PyPI using:
python -m pip install chemfp
The main goal of this release was to improve the no-cost/free software version of chemfp for use as …
read moreMy paper "The chemfp project" has been accepted and published by the Journal of Cheminformatics.
It's an open access paper, which means you can read it right now.
read moreI've written a paper describing all aspects of the chemfp project, including the FPS and FPB file formats, methods for fast popcount calculation and similarity search, and the experience of running chemfp as a commercial free software project.
It's been submitted to a journal. A preprint is available from ChemRxiv …
read moreChemfp 3.3 is now available to licensed users. If you are interested in purchasing a chemfp license, email me.
This release focused on squeezing out even more performance for machines with the POPCNT and AVX2 instruction sets. I believe chemfp is the fastest available single-threaded similarity search program for …
read moreChemfp 1.5 is now available
for download
or through PyPI as pip install chemfp.
The knearest and count searches are about 10% faster. They now use a fast integer test to reject obvious mismatches before doing the computationally expensive divison operation. This optimization was already available in threshold search …
read moreAndrew Dalke, the primary author of chemfp, will be at the 11th ICCS conference from 27-31 May 2018.
He will be presenting a poster on "mmpdb: A Matched Molecular Pair Platform for Large Multi-Property Datasets", which is a summary of the work published in JCIM doi:10.1021/acs …
read moreUntil now chemfp has only been available under the MIT license, which is a permissive free/open source software license.
This was true for both the 1.x development track, which is available for no cost, and the 3.x track, which was only available after paying for it.
Chemfp …
read moreI've just released chemfp 1.4, the newest version of the chemfp 1.x development track.
This version mostly contains bug fixes and internal improvements. The biggest additions are the fpcat command-line program, support for Dave Cosgrove's 'flush' fingerprintfile format, and support for 'fromAtoms' in some of the RDKit fingerprints …
read moreI've just released chemfp 3.2, available immediately for paying chemfp customers. If you are interested in purchasing a chemfp license, email me.
This version mostly contains bug fixes and internal improvements. The biggest additions are support for Dave Cosgrove's 'flush' fingerprint file format, and support for 'fromAtoms' in some …
read moreI made a minor release of the chemfp_converters package for better chemfp integration. If chemfp_converters is installed then chemfp will use it to read and write flush files.
You can download chemfp_converters-0.9.1.tar.gz or use pip to install or upgrade chemfp from PyPI.
The changes are:
flush …
I've released chemfp_converters, a package to convert between the
chemfp formats and other fingerprint file formats.
The command-line tools fs2fps and fps2fs convert from/to Open Babel's "FastSearch" format.
The command-line tools flush2fps and fps2flush convert from/to Dave Cosgrove's "flush".
The command-line tools fpbin2fps and fps2fpbin convert from/to …