Discover UnixJunkie/opdb Open Source project

dolog

A dumb OCaml logger

Molecular Generation by Fast Assembly of SMILES Fragments

FASMIFRA

Minimalist OCaml library for command line parsing

minicli

DAFT Allows File Transfers

daft

Bisector tree implementation in OCaml

bisec-tree

3D diverse conformers generation using rdkit

smi2sdf3d

Chemoinformatics tool for ligand-based virtual screening

ACPC

MolEnc: a molecular encoder using rdkit and OCaml.

molenc

interval-tree

tree for float intervals

Classification and Regression Performance Metrics library

cpmlib

The dumb OCaml key-value store

dokeysto

Mirror of https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl/

dimorphite_dl

Gradient boosting for OCaml using the R xgboost package under the carpet

orxgboost

Minimalist persistent hashtbl OCaml library

phashtbl

Efficient OCaml marshaling to and from bigarrays

bytearray

open/close binary channels with LZ4 compression in the background

lz4-chans

convert molecules to their ECFP4 fingerprint using rdkit

mol2ecfp4

backup of silicos-it's align-it-1.0.4

align-it

orf

OCaml Random Forests

Function to generate almost uniformly points on a sphere

genspir

trial at reviving the ancient library

ocaml-ancient

hoogle_for_ocaml

Same as https://www.haskell.org/hoogle/ but for OCaml programmers

Shell

hts_shrink

Reference implementation of the Distance-Based Boolean Applicability Domain for HTS datasets

Wrapper on top of liblinear-tools

cpu

Core pinning for OCaml

linwrap

ligand-based virtual screening with consensus queries

consent

get line at index i from file f (a missing unix command); will crash early and loud if any problem on the contrary to awk

get_line

A protein fragments picker

fragger

module for 3D vectors (implemented as a record of x, y and z floats)

vector3

Thin OCaml wrapper for the ranger (C++) random forests implementation

oranger

Skip list implementation in OCaml

slist

Deprecated; replaced by: https://github.com/UnixJunkie/cpu

setcore

UNIX-fun

Some configuration files to make life under UNIX fun

OCaml wrapper on top of R to perform Multiple Linear Regression

omlr

OPAM repository tree fingerprinter and differ using a Merkle tree

opmer

Command line recipes for the working chemoinformatician

chemoinfo_recipes

ocamlmath

import of http://www.irem.sciences.univ-nantes.fr/Calcul/Ocaml/ocamlmath-0.4.tbz

HTML

rankers

Reference implementation of the Vanishing Ranking Kernels (VRK) method

Parallel and Distributed execution of command lines, pardi !

pardi

mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/

EDTSurf

OCaml implementation of a kd-tree

okdt

OCaml library for basic operations on files made of lines of text

line-oriented

EleKit2 computes the electrostatic complementarity between a docked ligand and its protein receptor

elekit2

carbon

Incomplete SMILES parser

mirror of Open Molecule Generator from https://git.code.sf.net/p/openmg/code

OMG

parpair

compute in parallel the application of one (or two) function(s) on a pair of elements

Entropy-accelerated exact clustering of protein decoys (PDB files).

Durandal

Access the Linear or RBF kernel SVM from OCaml using the R e1071 or svmpath packages

orsvm-e1071

Synthetic Accessibility (SA) score

SA_score

Wrapper on top of libsvm-tools

svmwrap

some scripts using deepchem

deepchem-playground

almost mirror of https://github.com/flatkinson/standardiser

standardizer

Jupyter Notebook

pharmer

mirror of https://svn.code.sf.net/p/pharmer/code/trunk

A dumb, source to source, preprocessor for OCaml code

batpp

OCaml implementation of a never empty list

onelist

wrapper shell script to run opam faster when your $HOME is served via NFS

nfsopam

Shell

elekit

EleKit measures the similarity of electrostatic potentials between a small molecule and a protein.

Performance benchmark for Parmap and Parany

gram-matrix-bench

set operations on unsorted text file lines, a missing UNIX command

ofts

OCaml fuzzy type search

setop

LigGrep is a program for identifying docked poses that participate in user-specified receptor/ligand interactions. It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.

ligprep

OCaml wrapper to the R randomForest package

orrandomForest

paf

Pipes and forks

MOL2 file format specification

mol2-file-format-spec

interlig

mirror of https://bitbucket.org/clami66/interlig

Two datasets for Ligand-Based Virtual Screening benchmarking without decoys

findrotatable

findrotatable.pl

Perl

lbvs_no_decoys

PAR

Execute shell commands in a parallel and/or distributed way

Regressor in OCaml using a Deep Neural Network

odnnr

ocamlpvm

PVM bindings for OCaml

mirror of vina.scripps.edu/download v1.1.2

autodock-vina

My copy of the Tox21 dataset

tox21

pychem

backup copy of https://code.google.com/archive/p/pychem/downloads

OCaml wrapper to the pls R package (Partial Least Squares / PLS regression)

oplsr

Durandal exact clustering for protein decoys using QCP RMSD

durandal_qcp

how to quickly get an rpm or deb package for a recent version of the compiler

create-ocaml-pkg

Shell

meta-caret

OCaml wrapper for the R caret package

arpeggio

mirror of https://bitbucket.org/harryjubb/arpeggio

Comes from https://pubs.acs.org/doi/10.1021/acs.jcim.9b00375

novartis-realistic-train-test-split

a toy compiler training project

mini-ml-exercise

Simple Molecular Interaction Potential Generator in Python (mirror of https://sourceforge.net/projects/mipgen/)

mipgen

mirror of https://spotlite.nih.gov/opensource/tox21baseline.git

tox21baseline

Java

Open3DALIGN

mirror of https://svn.code.sf.net/p/open3dalign/open3dalign_svn/trunk

rdock

mirror of https://sourceforge.net/projects/rdock/

A DSL for operations over files

shlang

ocaml_SFS

OCaml implementation of Marc Alexa's Super-Fibonacci Spirals (CVPR 2022)

mirror of http://jcompoundmapper.sourceforge.net/

jcompoundmapper

Java

ACP4

Coming soon...

batlist_bench_01

benchmarks for BatList's favg and fsum

aricomp

an arithmetic compressor

RetroPath3

mirror of https://bitbucket.org/dalke/propbox

propbox

backup of silicos-it's filter-it-1.0.2

filter-it

mirror of http://www.mayachemtools.org/download/mayachemtools.tar.bz2 as of 25/09/2022

mayachemtools

Perl

shape-it

backup of silicos-it's shape-it-1.0.1.tar.gz

mirror of https://gitlab.com/CaflischLab/SEED.git

SEED

mirror of https://bitbucket.org/AstexUK/pli

PLI

molecular-datasets

A collection of molecular datasets for meta-learning.

HTML

100

liblinear-ranksvm

mirror of https://www.csie.ntu.edu.tw/~cjlin/libsvmtools/ranksvm/liblinear-ranksvm-2.11.zip