mirror of
https://github.com/rdkit/rdkit.git
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8bed437c5f
* Address minor compilation warning messages
Addresses trivial compilation warning messages:
[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o
rdkit/Code/GraphMol/AddHs.cpp:497:9: warning: unused variable 'dblBond' [-Wunused-variable]
Bond *dblBond = nullptr;
^
1 warning generated.
[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o
rdkit/Code/GraphMol/Chirality.cpp:1738:62: warning: unused parameter 'mol' [-Wunused-parameter]
bool isBondCandidateForStereo(const Bond *bond, const ROMol &mol) {
^
1 warning generated.
[ 44%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o
rdkit/Code/GraphMol/molopstest.cpp:4694:12: warning: unused variable 'nm' [-Wunused-variable]
ROMol *nm = MolOps::renumberAtoms(*m, nVect);
^
rdkit/Code/GraphMol/molopstest.cpp:6941:16: warning: unused variable 'm' [-Wunused-variable]
RWMol *m = SmilesToMol(smiles);
^
2 warnings generated.
[ 42%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o
rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:14: warning: unused parameter 'argc' [-Wunused-parameter]
int main(int argc, char *argv[]) {
^
rdkit/Code/GraphMol/testPicklerGlobalSettings.cpp:257:26: warning: unused parameter 'argv' [-Wunused-parameter]
int main(int argc, char *argv[]) {
^
2 warnings generated.
[ 55%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o
rdkit/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:176:20: warning: unused variable 'NUM_FUNCS' [-Wunused-const-variable]
const unsigned int NUM_FUNCS =
^
1 warning generated.
[ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/ReCharge.cpp.o
rdkit/Code/GraphMol/StructChecker/ReCharge.cpp:405:17: warning: unused variable 'atom' [-Wunused-variable]
const Atom &atom = *Mol.getAtomWithIdx(i);
^
1 warning generated.
[ 84%] Building CXX object Code/GraphMol/StructChecker/CMakeFiles/StructChecker.dir/Tautomer.cpp.o
rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:12: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (-1 == ti || -1 == tj) continue;
~~ ^ ~~
rdkit/Code/GraphMol/StructChecker/Tautomer.cpp:61:24: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (-1 == ti || -1 == tj) continue;
~~ ^ ~~
2 warnings generated.
[ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o
rdkit/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:428:9: warning: unused variable 'res' [-Wunused-variable]
int res = decomp.add(*mol);
^
1 warning generated.
[ 96%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o
rdkit/Code/SimDivPickers/testPickers.cpp:19:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
return abs((double)i - (double)j);
^
rdkit/Code/SimDivPickers/testPickers.cpp:19:10: note: use function 'std::abs' instead
return abs((double)i - (double)j);
^~~
std::abs
1 warning generated.
* Close open file handles during build set-up
Under Python3, the update_pains.py file generated warning
messages like:
== Done updating pains files
/Code/GraphMol/FilterCatalog/update_pains.py:140: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/../../../Data/Pains/wehi_pains.csv'
mode='r' encoding='UTF-8'>
for smiles, name in csv.reader(open(PAINS_CSV)):
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_a.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_b.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
/Code/GraphMol/FilterCatalog/update_pains.py:169: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/Code/GraphMol/FilterCatalog/pains_c.in' mode='r'
encoding='UTF-8'>
t = open(filename).read()
RDKit
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
- BSD license - a business friendly license for open source
- Core data structures and algorithms in C++
- Python (2.x and 3.x) wrapper generated using Boost.Python
- Java and C# wrappers generated with SWIG
- 2D and 3D molecular operations
- Descriptor and Fingerprint generation for machine learning
- Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
- Cheminformatics nodes for KNIME
- Contrib folder with useful community-contributed software harnessing the power of the RDKit
Web presence
- RDKit web page
- Blog
- Documentation also available at ReadTheDocs
Code
Community
Materials from user group meetings
Documentation
Available on the RDKit page and in the Docs folder on GitHub
Installation
Installation instructions are available in Docs/Book/Install.md.
Binary distributions, anaconda, homebrew
- Windows binaries are available with each release.
- RPMs for RedHat Enterprise Linux, Centos, and Fedora. Contributed by Gianluca Sforna.
- homebrew formula for building on the Mac. Contributed by Eddie Cao.
- recipes for building using the excellent conda package manager. Contributed by Riccardo Vianello.
Projects using RDKit
- ChEMBL Beaker - standalone web server wrapper for RDKit and OSRA
- myChEMBL (blog post, paper) - A virtual machine implementation of open data and cheminformatics tools
- sdf_viewer.py - an interactive SDF viewer
- sdf2ppt - Reads an SDFile and displays molecules as image grid in powerpoint/openoffice presentation.
- MolGears - A cheminformatics tool for bioactive molecules
- PYPL - Simple cartridge that lets you call Python scripts from Oracle PL/SQL.
- shape-it-rdkit - Gaussian molecular overlap code shape-it (from silicos it) ported to RDKit backend
- WONKA - Tool for analysis and interrogation of protein-ligand crystal structures
- OOMMPPAA - Tool for directed synthesis and data analysis based on protein-ligand crystal structures
- DeepChem - Machine learning library for small molecules
License
Code released under the BSD license.