Welcome to the Eli Lilly LillyMol implementation.

This version is updated by ianiwatson@gmail to use some Google
tooling, bazel, protocol buffers, the Google test infrastructure
and RE2.

Building is now more complex. You will need to install

bazel https://docs.bazel.build/versions/master/install.html
protocol buffers https://github.com/protocolbuffers/protobuf/releases/tag/v3.12.3
RE2 https://github.com/google/re2
Gunit https://github.com/google/googletest

This is complex. 

Basically install these packages somewhere, then update the file WORKSPACE to
reflect where they are installed. Currently they are pointing to
/home/ian/pub/... You will need to install these packages somewhere on your
system and update the WORKSPACE file to point to the right locations. Expect
some pain doing this.
And no, I do not fully understand Bazel, it is very complex. Within Google it
just works, but outside it is hard.

Here are some typical build commands I used:

bazel test --cxxopt=-std=c++17 --cxxopt=-msse4 Molecule_Lib:all
bazel build --cxxopt=-std=c++17 --cxxopt=-msse4 Molecule_Tools:all

The ZLIB requirement mentioned below is probably not needed any more
since most systems will have an up to date zlib installed by default.

I do most development on an Ubuntu 19.10 system.

REQUIREMENT:

This software requires following packages to build
1. GCC >= 7.2.1 (see https://gcc.gnu.org/install/index.html)
Example command(using module load): module load gcc/7.2.1

2. zlib >= 1.2.11 (see http://www.zlib.net/)
Example command(using module load): module load zlib/1.2.11
You need to define the location for zlib.a in makefile.public.*
You may also need to add the location of zlib.h to CPATH


BUILD:
1. Start console

2. Load required packages

3. Pull down the code from repo

4. Enter the root directory of the code

5. Edit the makefile.public.Linux-gcc-7.2.1 (or corresponding version) to add the local path for the zlib library
Example: ZLIB = /zlib/zlib-1.2.11/lib

6. Run makeall.sh (Skip step 7 if you run this command) 

7. Alternatively, you can run following commands: 
    make veryclean
    make copy_include
    make library
    make copy_library
    make exe
    make copy_exe


EXECUTION:
See Wiki page for sample commands
See the example folder for data used in the sample commands 
Example to verify a generated command:
    cd bin/Linux-gcc-7.2.1/
    ./common_names
Note: This command shall print out the help menu on screen if it is built successfully
      This approach can be used to verify if each command is built successfully
Example to run sample commands:
    cd example/common_names/
    ../../bin/Linux-gcc-7.2.1/common_names input1.smi input2.smi -S ./output -s 10000 -r 10000 -D + -v
	


DIRECTORY:
src:                             source code
example:                         data for sample commands (see Wiki page)
test:                            test scripts for each command
bin(generated after build):      all generated executables
lib(generated after build):      all generated library files
include(generated after build):  shared include files
contrib:                         legacy tools, data and queries


TEST:
See the test folder for the test case for each command
Example to run a test:
    cd test/common_names/case_1/
    ./test_case_1.sh
Note: Test shall print out TEST PASS if it is successful, otherwise it shall
      print out TEST FAIL

LICENSE:
Consult the LICENSE file for details of the license