Compile, Link and Run RDKit C++ API Examples

Cheminformatics Tutorials - Herong's Tutorial Examples

∟RDKit: Open-Source Cheminformatics Software

∟Compile, Link and Run RDKit C++ API Examples

This section provides a tutorial example on how to compile, link and run RDKit C++ API examples provided in the RDKit source package.

With RDKit installed and tested, now I can some example C++ programs provided in the RDKit source package to try its C++ API.

1. Locate the source code of example programs.

herong$ cd ~/rdkit/Docs/Book/C++Examples

herong$ ls -l
total 80
-rwxr-xr-x. 1 herong herong 1666 Apr  7 18:43 CMakeLists.txt
-rwxr-xr-x. 1 herong herong 1241 Apr  7 18:43 example10.cpp
-rwxr-xr-x. 1 herong herong 1671 Apr  7 18:43 example11.cpp
-rwxr-xr-x. 1 herong herong 2240 Apr  7 18:43 example12.cpp
-rwxr-xr-x. 1 herong herong 2298 Apr  7 18:43 example13.cpp
-rwxr-xr-x. 1 herong herong 3084 Apr  7 18:43 example14.cpp
-rwxr-xr-x. 1 herong herong 2312 Apr  7 18:43 example15.cpp
-rwxr-xr-x. 1 herong herong 1278 Apr  7 18:43 example16.cpp
-rwxr-xr-x. 1 herong herong 4547 Apr  7 18:43 example17.cpp
-rwxr-xr-x. 1 herong herong 1029 Apr  7 18:43 example1.cpp
-rwxr-xr-x. 1 herong herong 1876 Apr  7 18:43 example2.cpp
-rwxr-xr-x. 1 herong herong 1419 Apr  7 18:43 example3.cpp
-rwxr-xr-x. 1 herong herong 1970 Apr  7 18:43 example4.cpp
-rwxr-xr-x. 1 herong herong 1476 Apr  7 18:43 example5.cpp
-rwxr-xr-x. 1 herong herong 1669 Apr  7 18:43 example6.cpp
-rwxr-xr-x. 1 herong herong 1993 Apr  7 18:43 example7.cpp
-rwxr-xr-x. 1 herong herong  674 Apr  7 18:43 example8.cpp
-rwxr-xr-x. 1 herong herong 1478 Apr  7 18:43 example9.cpp
-rwxr-xr-x. 1 herong herong 1458 Apr  7 18:43 FindMyRDKit.cmake

2. Compile the first example, example1.cpp, with CPATH environment variable for RDKit header files.

herong$ export CPATH=/home/herong/rdkit/Code

herong$ g++ -c example1.cpp

herong$ ls -l example1.*
-rwxr-xr-x. 1 herong herong  1029 Apr  7 18:43 example1.cpp
-rw-rw-r--. 1 herong herong 94960 Apr 11 22:13 example1.o

3. Link the object code, example1.o, with RDKit dynamic libraries.

herong$ export LIBRARY_PATH=/home/herong/rdkit/lib

herong$ export RDKIT_LIBS="-lRDKitFileParsers -lRDKitDepictor \
   -lRDKitMolAlign \
   -lRDKitMolTransforms -lRDKitEigenSolvers -lRDKitAlignment \
   -lRDKitForceFieldHelpers -lRDKitSmilesParse -lRDKitSubstructMatch \
   -lRDKitForceField -lRDKitOptimizer -lRDKitTrajectory -lRDKitGraphMol \
   -lRDKitRingDecomposerLib -lRDKitRDGeometryLib -lRDKitDataStructs \
   -lRDKitRDGeneral -lRDKitcoordgen -lRDKitmaeparser"

herong$ g++ $RDKIT_LIBS -o example1 example1.o

herong$ ls -l example1
-rwxrwxr-x. 1 herong herong 55608 Apr 11 22:22 example1

4. Run the executable code, example1, with LD_LIBRARY_PATH for RDKit dynamic libraries.

herong$ export LD_LIBRARY_PATH=/home/herong/rdkit/lib

herong$ ./example1
Number of atoms 7
Number of atoms : 11
Explicit valence for atom # 1 O, 3, is greater than permitted
Can't kekulize mol.  Unkekulized atoms: 0 1 2

5. Repeat for other examples.

herong$ g++ $RDKIT_LIBS -o example2 example2.cpp
/usr/bin/ld: /home/herong/rdkit/lib/libRDKitmaeparser.so: undefined
   reference to symbol '_ZN5boost9iostreams4zlib4okayE'
//usr/lib64/libboost_iostreams.so.1.66.0: error adding symbols:
   DSO missing from command line
collect2: error: ld returned 1 exit status

herong$ g++ $RDKIT_LIBS -o example3 example3.cpp
herong$ ./example3
C[C@H](O)c1ccccc1
CC(O)c1ccccc1
c1ccncc1
c1ccncc1
c1ccncc1
C[C@H](O)C1=CC=CC=C1
...

herong$ g++ $RDKIT_LIBS -o example4 example4.cpp
/tmp/ccxa2yre.o: In function `RDKit::DGeomHelpers::EmbedMolecule(...)':
example4.cpp: undefined reference to `RDKit::DGeomHelpers::EmbedMultipleConfs(...)'
collect2: error: ld returned 1 exit status

herong$ g++ $RDKIT_LIBS -o example5 example5.cpp
herong$ ./example5
mol-295
     RDKit          3D

 20 22  0  0  1  0  0  0  0  0999 V2000
    2.3200    0.0800   -0.1000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8400   -1.2200    0.1200 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800    0.0800    0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
...

herong$ g++ $RDKIT_LIBS -o example6 example6.cpp
herong$ ./example6
6 8 6
6 8 6
1 1 1
0 0 0
0 to 0 is 1
No bond between 0 and 3
1 : 8
0 : 6

herong$ g++ $RDKIT_LIBS -o example7 example7.cpp
herong$ ./example7
0 1 2 2 1 1
0 1 2 1 1 1 1
Bond 1 is in a ring
Atom 2 is in ring of size 3 : 1
Atom 2 is in ring of size 4 : 1
Atom 2 is in ring of size 5 : 0
Bond 1 is in ring of size 3 : 1
Atom 1 is in ring of size 5 : 0
Number of symmetric SSSR rings : 2
1 2 3
4 5 2 3
Number of SSSR rings : 2

herong$ g++ $RDKIT_LIBS -o example8 example8.cpp
herong$ ./example8
Number of atoms : 3
Number of atoms : 9
Number of atoms : 3

herong$ g++ $RDKIT_LIBS -o example9 example9.cpp
herong$ ./example9
Order : 12
Aromatic : 1
After default Kekulize : Order : 2
After default Kekulize : Aromatic : 0
After Kekulize, markAtomsBonds false : Aromatic : 1
After Kekulize, markAtomsBonds true : Aromatic : 0
Order : 12
Aromatic : 1

herong$ g++ $RDKIT_LIBS -o example10 example10.cpp
herong$ ./example10
CoordGen support not available

herong$ g++ $RDKIT_LIBS -o example11 example11.cpp
/tmp/ccv0U38c.o: In function `main':
example11.cpp:(.text+0x9fc): undefined reference to `RDKit::DGeomHelpers::ETKDG'
...

herong$ g++ $RDKIT_LIBS -o example12 example12.cpp
herong$ ./example12
c1ccncc1
Wrote 5289 molecules
Read mol of name : 1
Read 5289 molecules.

herong$ g++ $RDKIT_LIBS -o example13 example13.cpp
/tmp/ccLRCjCS.o: In function `main':
example13.cpp:(.text+0x1af): undefined reference
   to `RDKit::MolDraw2D::drawMolecule(...)'
...

herong$ g++ $RDKIT_LIBS -o example14 example14.cpp
herong$ ./example14
Pattern matched molecule :
(0,0)(1,5)(2,6)
Match 1 : (0,0)(1,5)(2,6)
Match 2 : (0,4)(1,5)(2,6)
There were 22 hits in the file.
SMILES match
SMARTS match
SMILES match
Not SMARTS match
SMARTS match

herong$ g++ $RDKIT_LIBS -o example15 example15.cpp
herong$ ./example15
SMARTS 1 match
SMARTS 2 match
SMARTS 3 match
SMARTS 1 chiral match
Not SMARTS 2 chiral match
SMARTS 3 chiral match
Chiral mol, non-chiral query : match
Non-chiral mol, chiral query : NO match

herong$ g++ $RDKIT_LIBS -o example16 example16.cpp
herong$ ./example16
0 1 3 4
Match 1 : 1 7 8 10

herong$ g++ $RDKIT_LIBS -o example17 example17.cpp
/tmp/ccHQoWV7.o: In function `main':
example17.cpp:(.text+0x6d2): undefined reference
   to `RDKit::MolDraw2D::drawMolecule(...)'