OpenBabel is needed. Install it via conda:
conda install -c conda-forge openbabel
Then adapt the Makefile (example from add_mols)
XX = g++
OBDIR = <path/to/directory>/anaconda3/envs/openbabel
INCLUDE = -I <path/to/directory>/anaconda3/envs/openbabel/include/openbabel3
LIBS = -L <path/to/directory>/anaconda3/envs/openbabel/lib
CXX_FLAGS = -std=c++17 -O3 -march=native -Wall
LINKER_FLAGS = -lopenbabel
all: add_mols
add_mols: src/add_mols.cpp src/utils.hpp
$(CXX) $(INCLUDE) $(LIBS) $(CXX_FLAGS) src/add_mols.cpp -o add_mols $(LINKER_FLAGS)
clean:
rm -f add_mols
rm -f mols_combined.xyz
If it compiles but after running the executable following error appears:
error while loading shared libraries: libopenbabel.so.7: cannot open shared object file: No such file or directory
Add following line to your .bashrc:
LD_LIBRARY_PATH=<path/to/directory>/anaconda3/envs/openbabel/lib/:$LD_LIBRARY_PATH'
convert: reads in a molecule using a specified file format and converts it to a desired format.
conv --f_in <full path to molecule> --format_in <input format> --format_out <output format>
add_mols: reading in 2 smiles codes, add hydrogens, generates 3D geometries, puts molecule in the same 'file' moves them apart and minimizes the energy using a forcefield and finally saves them as an xyz file.
add_mols --target 'O=Cl(=O)([O-])=O' --ligand 'C12=C(C=CC=C2)C=C3C=CC=CC3=[NH+]1'
TODO: a lot!
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent