Rust crate for linking against the RDKit C++ API

#3

Introduces a feature flag for dynamic-linking-from-conda which changes build.rs to prefer dynamic linking and it invokes the conda info --base to find where packages exist.

@iwatobipen does this work for you?

In the project which depends on rdkit-sys you'll want to do something like:

[dependencies]
rdkit-sys = { git = "[email protected]:rdkit-rs/rdkit-sys.git", branch = "conda-build", features = ["dynamic-linking-from-conda"] }

also, you need to make sure that the conda packages are in your library path, on linux it'll be something like:

export LD_LIBRARY_PATH=$(conda info --base)/lib

before you can use the code. The Dockerfile.conda in this PR shows an example of how you can update your /etc/ld.so.conf.d/conda to include that conda path all the time (although the conda project does not recommend it).

Hi,

I’m a relatively new user of Rust (more familiar with Python & R) and hoping to integrate Rust and RDKit (trying to start a cheminformatics project in Rust), so I was quite excited to come across this crate, rdkit-sys, online. I was running it on VS code on Mac OS, by using the latest version 0.2.16 of rdkit-sys in the cargo.toml. However, when I ran it via cargo check or cargo test, it showed a set of errors like this after compilation (in total it appeared twice):

warning: /usr/local/include/rdkit/RDGeneral/Dict.h:261:26: error: no template named 'is_same_v' in namespace 'std'; did you mean 'is_same'? warning: static_assert(! std::is_same_v<T, std::string_view>, warning: ~~~~~^~~~~~~~~ warning: is_same

warning: /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/type_traits:547:61: note: 'is_same' declared here warning: template <class _Tp, class _Up> struct _LIBCPP_TEMPLATE_VIS is_same : public false_type {}; warning:

Prior to this, I’ve already installed rdkit and relevant dependencies via Homebrew. It appeared there might be conflicts between one of the RDKit files and one of the llvm files (this was as far as I could tell if I went back to these files). So either I’m missing something obvious here (being quite new in the coding world) or I wasn’t doing something correctly?

Hoping someone might be able to enlighten me on this one... (might be due to a silly thing I've missed).

Many thanks, J

The Boost library returns explicit bitvects as vectors of u64 (so whole CPU words). but libraries like tantivy expect vectors of u8. we should add a helper function for converting Vec<u64> to Vec<u8>

Dear, Thanks for sharing uself chemoinformaitcs package of Rust! I would like to ask you if I could build the code with rdkit which is installed from conda. By using conda env, I couldn't solve the issue which related static link. Any suggestion, advicces are greatly appreciated. Thanks,

Taka