##Requirements
unix system (tested on Ubuntu 18.04 LTS and PharmCADD server) bash shell to run the CLI scripts conda for RDKIT (https://conda.io/projects/conda/en/latest/user-guide/install/index.html) gcc, g++, make
src/: This folder contains all C/C(++)-programs to count functional groups from a molecule.
bin/: This folder is empty, but will contains executable files (*.exe) after running "make" command inside the src/ folder
scripts/: This folder contains all scripts which call all the executable files from the bin folder to count the functional groups in a molecule. The main script file is script.sh
config/: In this folder a script file, init.sh, resides. It is required to source the root of the cloned repository (e.g.; /home/<user name>/FGCount) and path to your conda installation eg, /home/<user name>/miniconda3
example/: This folder contains an example input file (asp.smi) and a script.sh file
Step 1: Copy FGCount.git folder to your account
Step 2: Install miniconda (https://docs.conda.io/en/latest/miniconda.html)
Step 3: create a conda environment as
cd FGCount/
conda env create -f fgcount.yml
Step 4: Edit the init file which is located inside the "config/" folder and source the file as
source config/init.sh
Step 5: Compile all the C/C++-codes which are there inside the src/ folder
cd src
make
(Ignore messages)
Step 6: Run the script anywhere except inside the bin/, config/, scripts/ and src/ folder
If you have a SMILES code of an organic ligand molecule and the file name is asp.smi then, run the following command without .smi extention
cd example
bash script.sh asp
Output file:
• Descriptors_Final.txt: In this file, counting of functional groups is there in a column (semicolon seperated) for a query SMILES string
• FG_Binary.txt: In this file, occurance of functional groups (binary file line a fingerprint) is there for the same query