mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-09 12:38:03 -05:00
Merge branch 'khoran-R-script'
This commit is contained in:
Geoff Hutchison
@@ -505,6 +505,9 @@ option(PERL_BINDINGS "Build Perl bindings" OFF)
|
||||
# Should Java bindings be built?
|
||||
option(JAVA_BINDINGS "Build Java bindings" OFF)
|
||||
|
||||
# Should R bindings be built?
|
||||
option(R_BINDINGS "Build R bindings" OFF)
|
||||
|
||||
# Should CSharp bindings be built?
|
||||
option(CSHARP_BINDINGS "Build Csharp bindings" OFF)
|
||||
|
||||
@@ -515,6 +518,7 @@ if(ALL_BINDINGS)
|
||||
set(PERL_BINDINGS ON)
|
||||
set(JAVA_BINDINGS ON)
|
||||
set(CSHARP_BINDINGS ON)
|
||||
set(R_BINDINGS ON)
|
||||
endif()
|
||||
|
||||
add_subdirectory(scripts)
|
||||
|
||||
+58
-3
@@ -170,15 +170,15 @@ endif (JAVA_BINDINGS)
|
||||
|
||||
if (DO_JAVA_BINDINGS)
|
||||
|
||||
include_directories(
|
||||
${JNI_INCLUDE_DIRS}
|
||||
include_directories(
|
||||
${JNI_INCLUDE_DIRS}
|
||||
)
|
||||
|
||||
if (RUN_SWIG)
|
||||
add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/java/openbabel-java.cpp
|
||||
COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/java/org/openbabel
|
||||
COMMAND ${SWIG_EXECUTABLE} -java -package org.openbabel -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/java/openbabel-java.cpp ${eigen_define} -outdir ${openbabel_BINARY_DIR}/scripts/java/org/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-java.i
|
||||
COMMAND ${JAVA_COMPILE} ARGS "java/org/openbabel/*.java"
|
||||
COMMAND ${JAVA_COMPILE} ARGS "java/org/openbabel/*.java"
|
||||
COMMAND ${CMAKE_COMMAND} -E chdir ${openbabel_BINARY_DIR}/scripts/java ${JAVA_ARCHIVE} cf openbabel.jar org
|
||||
COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_BINARY_DIR}/scripts/java/openbabel.jar ${openbabel_SOURCE_DIR}/scripts/java
|
||||
COMMAND ${CMAKE_COMMAND} -E remove_directory ${openbabel_BINARY_DIR}/scripts/java/org
|
||||
@@ -211,6 +211,61 @@ if (DO_JAVA_BINDINGS)
|
||||
|
||||
endif (DO_JAVA_BINDINGS)
|
||||
|
||||
|
||||
###################
|
||||
# R
|
||||
###################
|
||||
|
||||
if (R_BINDINGS)
|
||||
if (EXISTS ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp OR RUN_SWIG)
|
||||
|
||||
if (RUN_SWIG)
|
||||
set(DO_R_BINDINGS ON BOOL)
|
||||
endif (RUN_SWIG)
|
||||
|
||||
|
||||
else (EXISTS ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp OR RUN_SWIG)
|
||||
message(STATUS "Warning: R bindings NOT found. Generate using -DRUN_SWIG.")
|
||||
|
||||
endif (EXISTS ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp OR RUN_SWIG)
|
||||
endif (R_BINDINGS)
|
||||
|
||||
if (DO_R_BINDINGS)
|
||||
|
||||
|
||||
include_directories(/usr/share/R/include )
|
||||
if (RUN_SWIG)
|
||||
add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp
|
||||
COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/R
|
||||
COMMAND ${SWIG_EXECUTABLE} -r -package openbabelR -c++ -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp ${eigen_define} -outdir ${openbabel_BINARY_DIR}/scripts/R ${openbabel_SOURCE_DIR}/scripts/openbabel-R.i
|
||||
COMMAND sed -i -e "'s/reg\.finalizer(\(.*\)) /reg.finalizer(\1); /g'" ${openbabel_BINARY_DIR}/scripts/R/openbabelR.R
|
||||
MAIN_DEPENDENCY openbabel-R.i
|
||||
)
|
||||
endif (RUN_SWIG)
|
||||
|
||||
add_library(bindings_R MODULE ${openbabel_SOURCE_DIR}/scripts/R/openbabel-R.cpp)
|
||||
if(BINDINGS_ONLY)
|
||||
target_link_libraries(bindings_R R ${BABEL_SYSTEM_LIBRARY})
|
||||
else()
|
||||
target_link_libraries(bindings_R R ${BABEL_LIBRARY})
|
||||
endif()
|
||||
|
||||
set_target_properties(bindings_R PROPERTIES
|
||||
OUTPUT_NAME openbabel_R)
|
||||
if(NOT BINDINGS_ONLY)
|
||||
add_dependencies(bindings_R openbabel)
|
||||
endif()
|
||||
add_dependencies(bindings_R R)
|
||||
|
||||
install(TARGETS bindings_R
|
||||
LIBRARY DESTINATION ${LIB_INSTALL_DIR}
|
||||
COMPONENT bindings_R)
|
||||
install(FILES ${openbabel_SOURCE_DIR}/scripts/R/openbabel_java.R
|
||||
DESTINATION ${LIB_INSTALL_DIR}
|
||||
COMPONENT bindings_R)
|
||||
|
||||
endif (DO_R_BINDINGS)
|
||||
|
||||
###################
|
||||
# Perl
|
||||
###################
|
||||
|
||||
@@ -0,0 +1,51 @@
|
||||
OpenBabel R bindings
|
||||
=====================
|
||||
|
||||
This module provides an R interface to the Open Babel chemistry library.
|
||||
|
||||
Open Babel is a chemical toolbox designed to speak the many languages
|
||||
of chemical data. It's an open, collaborative project allowing anyone
|
||||
to search, convert, analyze, or store data from molecular modeling,
|
||||
chemistry, solid-state materials, biochemistry, or related areas.
|
||||
|
||||
The code is generated using the SWIG package and provides access to
|
||||
almost all of the Open Babel interfaces via R, including the base
|
||||
classes OBMol, OBAtom, OBBond, and OBResidue, as well as the
|
||||
conversion framework OBConversion, fingerprints, and descriptors.
|
||||
|
||||
|
||||
There are two ways to use this binding. You can either build an
|
||||
R package which wraps the C++ library (see examples directory for such
|
||||
a package) and then import it into your R code, or you can use the
|
||||
generated openbabelR.R and openbabel-R.cpp files directly in your
|
||||
own package.
|
||||
|
||||
To use the first Method, copy the openbabelR directory from the examples
|
||||
directory somewhere. In the R subdirectory place a copy of or a link to
|
||||
the openbabelR.R file (found in <build dir>/scripts/R/openbabelR.R).
|
||||
In the src subdirectory, do the same for the openbabel-R.cpp file (found
|
||||
in <source dir>/scripts/R/openbabel-R.cpp). You then need to edit
|
||||
the file src/Makevars to point to the open babel include and lib
|
||||
directories. Finally, install the package with "R CMD INSTALL openbabelR".
|
||||
You can then use this library in your code by calling "library(openbabelR)".
|
||||
|
||||
To use the second method, copy the .R and .cpp files into an existing R
|
||||
package, in the same way as the first method. You will also need to
|
||||
edit the .R file to replace all occurances of "PACKAGE=openbabelR"
|
||||
with "PACKAGE=<your package name>". I recommend using search and
|
||||
replaceAll for this as there are a few thousand occurances.
|
||||
You also need to copy the file examples/openbabelR/R/init.R into
|
||||
your packages R directory. The key thing is that the library be
|
||||
loaded with LOCAL=FALSE, otherwise openbabel will not be able to
|
||||
access any of its plugins.
|
||||
|
||||
Finally, if OpenBabel has not been installed globally, ensure
|
||||
the following environment variables are set:
|
||||
|
||||
export LD_LIBRARY_PATH=<openbabel build dir>/lib
|
||||
export BABEL_DATADIR=<openbabel source dir>/data
|
||||
export BABEL_LIBDIR=$LD_LIBRARY_PATH
|
||||
|
||||
You can test the first method with the test.R script in the
|
||||
examples directory. Run is as: R --vanilla --slave < test.R .
|
||||
|
||||
@@ -0,0 +1,10 @@
|
||||
Package: openbabelR
|
||||
Type: Package
|
||||
Title: R interface to OpenBabel
|
||||
Version: 0.99.0
|
||||
Date: 2013-10-21
|
||||
Author: your name
|
||||
Maintainer: name@example.com
|
||||
Description: example package
|
||||
License: file LICENSE
|
||||
Depends: R (>= 2.15.1)
|
||||
@@ -0,0 +1 @@
|
||||
exportPattern("^[^\\.]")
|
||||
@@ -0,0 +1,6 @@
|
||||
|
||||
.onLoad <- function(libname,pkgname) {
|
||||
|
||||
library.dynam(pkgname,package=pkgname,lib.loc=libname,local=FALSE)
|
||||
|
||||
}
|
||||
@@ -0,0 +1 @@
|
||||
../../../../../build/scripts/R/openbabelR.R
|
||||
@@ -0,0 +1,2 @@
|
||||
PKG_CXXFLAGS += -I<open babel src dir>/include/ -I/usr/include/eigen3
|
||||
PKG_LIBS += -I<open babel build dir>/lib -lopenbabel
|
||||
@@ -0,0 +1 @@
|
||||
../../../openbabel-R.cpp
|
||||
@@ -0,0 +1,49 @@
|
||||
library(openbabelR)
|
||||
|
||||
convertTest <- function(){
|
||||
smi = "cc1cccc1c"
|
||||
|
||||
inStr = openbabelR:::istreamFromString(smi)
|
||||
outStr = openbabelR:::ostreamToString()
|
||||
|
||||
conv = openbabelR:::OBConversion(inStr,outStr)
|
||||
|
||||
message("setting formats")
|
||||
openbabelR:::OBConversion_SetInAndOutFormats(conv,"SMI","SDF")
|
||||
|
||||
message("converting")
|
||||
openbabelR:::OBConversion_Convert(conv)
|
||||
|
||||
str = openbabelR:::stringFromOstream(outStr)
|
||||
print(str)
|
||||
|
||||
}
|
||||
descriptorTest <- function(){
|
||||
mol = openbabelR:::OBMol()
|
||||
|
||||
smi = "cc1cccc1c"
|
||||
inStr = openbabelR:::istreamFromString(smi)
|
||||
|
||||
conv = openbabelR:::OBConversion(inStr)
|
||||
|
||||
message("setting formats")
|
||||
openbabelR:::OBConversion_SetInAndOutFormats(conv,"SMI","SDF")
|
||||
|
||||
message("reading mol")
|
||||
openbabelR:::OBConversion_Read(conv,mol)
|
||||
message("finding type")
|
||||
desc = openbabelR:::OBDescriptor_FindType("logP")
|
||||
|
||||
message("predicting")
|
||||
p= openbabelR:::OBDescriptor_Predict(desc,mol)
|
||||
message("value: ",p)
|
||||
|
||||
strDesc = openbabelR:::OBDescriptor_FindType("cansmi")
|
||||
cansmi = openbabelR:::stringp()
|
||||
openbabelR:::OBDescriptor_GetStringValue(strDesc,mol,cansmi$cast())
|
||||
message("cansmi: ",cansmi$value())
|
||||
|
||||
}
|
||||
|
||||
convertTest()
|
||||
descriptorTest()
|
||||
@@ -0,0 +1,444 @@
|
||||
%module openbabel_R
|
||||
%{
|
||||
#include <R.h>
|
||||
// used to set import/export for Cygwin DLLs
|
||||
#ifdef WIN32
|
||||
#define USING_OBDLL
|
||||
#endif
|
||||
|
||||
|
||||
#include <openbabel/obutil.h>
|
||||
#include <openbabel/rand.h>
|
||||
#include <openbabel/math/vector3.h>
|
||||
#include <openbabel/math/matrix3x3.h>
|
||||
#include <openbabel/math/transform3d.h>
|
||||
#include <openbabel/math/spacegroup.h>
|
||||
|
||||
#include <openbabel/generic.h>
|
||||
#include <openbabel/griddata.h>
|
||||
|
||||
#include <openbabel/base.h>
|
||||
#include <openbabel/mol.h>
|
||||
#include <openbabel/atom.h>
|
||||
#include <openbabel/bond.h>
|
||||
#include <openbabel/reaction.h>
|
||||
#include <openbabel/residue.h>
|
||||
#include <openbabel/internalcoord.h>
|
||||
|
||||
#include <openbabel/ring.h>
|
||||
#include <openbabel/obconversion.h>
|
||||
#include <openbabel/oberror.h>
|
||||
#include <openbabel/plugin.h>
|
||||
#include <openbabel/fingerprint.h>
|
||||
#include <openbabel/descriptor.h>
|
||||
#include <openbabel/format.h>
|
||||
|
||||
#include <openbabel/builder.h>
|
||||
#include <openbabel/op.h>
|
||||
|
||||
#include <openbabel/bitvec.h>
|
||||
#include <openbabel/data.h>
|
||||
#include <openbabel/parsmart.h>
|
||||
#include <openbabel/alias.h>
|
||||
#include <openbabel/atomclass.h>
|
||||
|
||||
#include <openbabel/kinetics.h>
|
||||
#include <openbabel/rotor.h>
|
||||
#include <openbabel/rotamer.h>
|
||||
#include <openbabel/spectrophore.h>
|
||||
|
||||
#include <openbabel/chargemodel.h>
|
||||
#include <openbabel/graphsym.h>
|
||||
#include <openbabel/isomorphism.h>
|
||||
#include <openbabel/query.h>
|
||||
#include <openbabel/canon.h>
|
||||
|
||||
#include <openbabel/stereo/tetrahedral.h>
|
||||
#include <openbabel/stereo/cistrans.h>
|
||||
#include <openbabel/stereo/squareplanar.h>
|
||||
#include <openbabel/stereo/bindings.h>
|
||||
%}
|
||||
|
||||
|
||||
#ifdef HAVE_EIGEN
|
||||
%{
|
||||
#include <openbabel/forcefield.h>
|
||||
#include <openbabel/conformersearch.h>
|
||||
#include <openbabel/math/align.h>
|
||||
%}
|
||||
#endif
|
||||
|
||||
%include "std_map.i"
|
||||
%include "std_vector.i"
|
||||
%include "std_string.i"
|
||||
%include "std_pair.i"
|
||||
%include "cpointer.i"
|
||||
|
||||
%pointer_class(std::string,stringp)
|
||||
%typemap("rtype") const std::string & "character"; //add typemap for const references
|
||||
%typemap("rtype") std::string *, std::string &; // remove erroneous typemap in swig libraries
|
||||
|
||||
%typemap(scoercein) const std::string &
|
||||
%{ $input = as($input, "character"); %}
|
||||
%typemap(scoercein) std::string *, std::string &;
|
||||
|
||||
|
||||
|
||||
%inline %{
|
||||
|
||||
#include <iostream>
|
||||
std::istream* istreamFromString(std::string str){
|
||||
return new std::istringstream(str);
|
||||
}
|
||||
std::istream* istreamFromFile(const char *filename) {
|
||||
return new std::ifstream(filename);
|
||||
}
|
||||
std::ostream* ostreamToString(){
|
||||
return new std::ostringstream();
|
||||
}
|
||||
std::ostream* ostreamToFile(const char *filename) {
|
||||
return new std::ofstream(filename);
|
||||
}
|
||||
const std::string stringFromOstream(const std::ostringstream* os){
|
||||
// return (os->str()).c_str();
|
||||
return os->str();
|
||||
}
|
||||
|
||||
%}
|
||||
|
||||
|
||||
namespace std {
|
||||
|
||||
%define VVTEMPLATE_WRAP(name, T)
|
||||
%feature("ignore") vector< vector<T> >::append;
|
||||
%feature("ignore") vector< vector<T> >::assign;
|
||||
%feature("ignore") vector< vector<T> >::back;
|
||||
%feature("ignore") vector< vector<T> >::begin;
|
||||
%feature("ignore") vector< vector<T> >::capacity;
|
||||
%feature("ignore") vector< vector<T> >::clear;
|
||||
%feature("ignore") vector< vector<T> >::empty;
|
||||
%feature("ignore") vector< vector<T> >::end;
|
||||
%feature("ignore") vector< vector<T> >::erase;
|
||||
%feature("ignore") vector< vector<T> >::front;
|
||||
%feature("ignore") vector< vector<T> >::get_allocator;
|
||||
%feature("ignore") vector< vector<T> >::insert;
|
||||
%feature("ignore") vector< vector<T> >::pop;
|
||||
%feature("ignore") vector< vector<T> >::pop_back;
|
||||
%feature("ignore") vector< vector<T> >::push_back;
|
||||
%feature("ignore") vector< vector<T> >::rbegin;
|
||||
%feature("ignore") vector< vector<T> >::rend;
|
||||
%feature("ignore") vector< vector<T> >::reserve;
|
||||
%feature("ignore") vector< vector<T> >::resize;
|
||||
%feature("ignore") vector< vector<T> >::swap;
|
||||
%template(vectorv ## name) vector< vector<T> >;
|
||||
%enddef
|
||||
|
||||
%define VECTORTEMPLATE_WRAP(vectorname, T)
|
||||
%feature("ignore") vector<T>::append;
|
||||
%feature("ignore") vector<T>::assign;
|
||||
%feature("ignore") vector<T>::back;
|
||||
%feature("ignore") vector<T>::begin;
|
||||
%feature("ignore") vector<T>::capacity;
|
||||
%feature("ignore") vector<T>::clear;
|
||||
%feature("ignore") vector<T>::empty;
|
||||
%feature("ignore") vector<T>::end;
|
||||
%feature("ignore") vector<T>::erase;
|
||||
%feature("ignore") vector<T>::front;
|
||||
%feature("ignore") vector<T>::get_allocator;
|
||||
%feature("ignore") vector<T>::insert;
|
||||
%feature("ignore") vector<T>::pop;
|
||||
%feature("ignore") vector<T>::pop_back;
|
||||
%feature("ignore") vector<T>::push_back;
|
||||
%feature("ignore") vector<T>::rbegin;
|
||||
%feature("ignore") vector<T>::rend;
|
||||
%feature("ignore") vector<T>::reserve;
|
||||
%feature("ignore") vector<T>::resize;
|
||||
%feature("ignore") vector<T>::swap;
|
||||
%template(vector ## vectorname) vector<T>;
|
||||
%enddef
|
||||
|
||||
%define VECTORPAIRTEMPLATE_WRAP(vectorname, T1, T2)
|
||||
%feature("ignore") vector< pair<T1, T2> >::append;
|
||||
%feature("ignore") vector< pair<T1, T2> >::assign;
|
||||
%feature("ignore") vector< pair<T1, T2> >::back;
|
||||
%feature("ignore") vector< pair<T1, T2> >::begin;
|
||||
%feature("ignore") vector< pair<T1, T2> >::capacity;
|
||||
%feature("ignore") vector< pair<T1, T2> >::clear;
|
||||
%feature("ignore") vector< pair<T1, T2> >::empty;
|
||||
%feature("ignore") vector< pair<T1, T2> >::end;
|
||||
%feature("ignore") vector< pair<T1, T2> >::erase;
|
||||
%feature("ignore") vector< pair<T1, T2> >::front;
|
||||
%feature("ignore") vector< pair<T1, T2> >::get_allocator;
|
||||
%feature("ignore") vector< pair<T1, T2> >::insert;
|
||||
%feature("ignore") vector< pair<T1, T2> >::pop;
|
||||
%feature("ignore") vector< pair<T1, T2> >::pop_back;
|
||||
%feature("ignore") vector< pair<T1, T2> >::push_back;
|
||||
%feature("ignore") vector< pair<T1, T2> >::rbegin;
|
||||
%feature("ignore") vector< pair<T1, T2> >::rend;
|
||||
%feature("ignore") vector< pair<T1, T2> >::reserve;
|
||||
%feature("ignore") vector< pair<T1, T2> >::resize;
|
||||
%feature("ignore") vector< pair<T1, T2> >::swap;
|
||||
%template(vpair ## vectorname) vector< pair<T1, T2> >;
|
||||
%enddef
|
||||
|
||||
VECTORTEMPLATE_WRAP(Int, int)
|
||||
VECTORTEMPLATE_WRAP(UnsignedInt, unsigned int)
|
||||
VVTEMPLATE_WRAP(Int, int)
|
||||
VECTORTEMPLATE_WRAP(Double, double)
|
||||
VECTORTEMPLATE_WRAP(String, std::string)
|
||||
VECTORTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
|
||||
VVTEMPLATE_WRAP(Vector3, OpenBabel::vector3)
|
||||
VECTORTEMPLATE_WRAP(OBMol, OpenBabel::OBMol)
|
||||
VECTORTEMPLATE_WRAP(OBBond, OpenBabel::OBBond)
|
||||
VECTORTEMPLATE_WRAP(OBResidue, OpenBabel::OBResidue)
|
||||
VECTORTEMPLATE_WRAP(OBRing, OpenBabel::OBRing)
|
||||
VECTORTEMPLATE_WRAP(pOBRing, OpenBabel::OBRing*)
|
||||
VECTORTEMPLATE_WRAP(pOBGenericData, OpenBabel::OBGenericData*)
|
||||
VECTORTEMPLATE_WRAP(pOBInternalCoord, OpenBabel::OBInternalCoord*)
|
||||
|
||||
%template(pairUIntUInt) pair<unsigned int, unsigned int>;
|
||||
VECTORPAIRTEMPLATE_WRAP(UIntUInt, unsigned int, unsigned int);
|
||||
%template(vvpairUIntUInt) vector< vector< pair<unsigned int, unsigned int> > >;
|
||||
}
|
||||
|
||||
%define CAST_GENERICDATA_TO(subclass)
|
||||
%inline %{
|
||||
OpenBabel::OB ## subclass *to ## subclass(OpenBabel::OBGenericData *data) {
|
||||
return (OpenBabel::OB ## subclass *) data;
|
||||
}
|
||||
%}
|
||||
%enddef
|
||||
%inline %{ // cant use macro -- AliasData not OBAliasData
|
||||
OpenBabel::AliasData *toAliasData(OpenBabel::OBGenericData *data) {
|
||||
return (OpenBabel::AliasData*) data;
|
||||
}
|
||||
%}
|
||||
CAST_GENERICDATA_TO(AngleData)
|
||||
CAST_GENERICDATA_TO(AtomClassData)
|
||||
CAST_GENERICDATA_TO(ChiralData)
|
||||
CAST_GENERICDATA_TO(CommentData)
|
||||
CAST_GENERICDATA_TO(ConformerData)
|
||||
CAST_GENERICDATA_TO(ExternalBondData)
|
||||
CAST_GENERICDATA_TO(GridData)
|
||||
CAST_GENERICDATA_TO(MatrixData)
|
||||
CAST_GENERICDATA_TO(NasaThermoData)
|
||||
CAST_GENERICDATA_TO(PairData)
|
||||
// CAST_GENERICDATA_TO(PairTemplate)
|
||||
CAST_GENERICDATA_TO(RateData)
|
||||
CAST_GENERICDATA_TO(RotamerList)
|
||||
CAST_GENERICDATA_TO(RotationData)
|
||||
CAST_GENERICDATA_TO(SerialNums)
|
||||
CAST_GENERICDATA_TO(SetData)
|
||||
CAST_GENERICDATA_TO(SymmetryData)
|
||||
CAST_GENERICDATA_TO(TorsionData)
|
||||
CAST_GENERICDATA_TO(UnitCell)
|
||||
CAST_GENERICDATA_TO(VectorData)
|
||||
CAST_GENERICDATA_TO(VibrationData)
|
||||
CAST_GENERICDATA_TO(VirtualBond)
|
||||
|
||||
%ignore *::operator=;
|
||||
%ignore *::operator==;
|
||||
%ignore *::operator!=;
|
||||
%ignore *::operator<<;
|
||||
%ignore *::operator();
|
||||
%ignore *::operator*;
|
||||
%ignore *::operator*=;
|
||||
%ignore *::operator+;
|
||||
%ignore *::operator+=;
|
||||
%ignore *::operator-;
|
||||
%ignore *::operator-=;
|
||||
%ignore *::operator++;
|
||||
%ignore *::operator--;
|
||||
%ignore *::operator/;
|
||||
%ignore *::operator/=;
|
||||
%ignore *::operator bool;
|
||||
%ignore *::operator[];
|
||||
|
||||
%import <openbabel/babelconfig.h>
|
||||
|
||||
%warnfilter(516) OpenBabel::OBElementTable; // Ignoring std::string methods in favour of char* ones
|
||||
%include <openbabel/data.h>
|
||||
%include <openbabel/rand.h>
|
||||
%include <openbabel/obutil.h>
|
||||
%warnfilter(516) OpenBabel::vector3; // Using the const x(), y() and z() in favour of the non-const
|
||||
%include <openbabel/math/vector3.h>
|
||||
%warnfilter(503) OpenBabel::matrix3x3; // Not wrapping any of the overloaded operators
|
||||
%include <openbabel/math/matrix3x3.h>
|
||||
%include <openbabel/math/transform3d.h>
|
||||
%warnfilter(516) OpenBabel::SpaceGroup; // Ignoring std::string methods in favour of char* ones
|
||||
%include <openbabel/math/spacegroup.h>
|
||||
|
||||
# CloneData should be used instead of the following method
|
||||
%ignore OpenBabel::OBBase::SetData;
|
||||
%ignore OpenBabel::OBBase::GetData(char const *);
|
||||
%ignore OpenBabel::OBBase::HasData(char const *);
|
||||
%include <openbabel/base.h>
|
||||
|
||||
%warnfilter(516) OpenBabel::OBPairData; // Ignoring std::string methods in favour of char* ones
|
||||
%warnfilter(516) OpenBabel::OBSetData;
|
||||
%warnfilter(516) OpenBabel::OBCommentData;
|
||||
%warnfilter(516) OpenBabel::OBUnitCell; // Ignoring const methods in favour of non-const ones
|
||||
%include <openbabel/generic.h>
|
||||
%include <openbabel/griddata.h>
|
||||
|
||||
%include <openbabel/chains.h>
|
||||
%include <openbabel/typer.h>
|
||||
|
||||
// To avoid warning in plugin.h about "Nothing known about std::binary_function"
|
||||
namespace std {
|
||||
template <T1, T2, T3>
|
||||
class binary_function {};
|
||||
}
|
||||
%template(dummy) std::binary_function <const char *, const char *, bool>;
|
||||
%include <openbabel/plugin.h>
|
||||
|
||||
// To avoid warning in oberror.h about "Nothing known about std::stringbuf"
|
||||
namespace std { class stringbuf {}; }
|
||||
%warnfilter(503) OpenBabel::OBError; // Not wrapping any of the overloaded operators
|
||||
%include <openbabel/oberror.h>
|
||||
%include <openbabel/format.h>
|
||||
%ignore OpenBabel::OBConversion::FindFormat(const char *);
|
||||
%ignore OpenBabel::OBConversion::FormatFromExt(const char *);
|
||||
%include <openbabel/obconversion.h>
|
||||
%include <openbabel/residue.h>
|
||||
%include <openbabel/internalcoord.h>
|
||||
|
||||
%typemap(javacode) OpenBabel::OBAtom
|
||||
%{
|
||||
private int currentDepth = 0;
|
||||
public void SetCurrentDepth(int d) {currentDepth = d;}
|
||||
public int GetCurrentDepth() {return currentDepth;}
|
||||
%}
|
||||
%ignore OpenBabel::OBAtom::GetVector() const;
|
||||
%ignore OpenBabel::OBAtom::IsHydrogen const;
|
||||
%ignore OpenBabel::OBAtom::SetType(char const *);
|
||||
%include <openbabel/atom.h>
|
||||
%ignore OpenBabel::OBBond::GetBeginAtom() const;
|
||||
%ignore OpenBabel::OBBond::GetEndAtom() const;
|
||||
%include <openbabel/bond.h>
|
||||
%include <openbabel/reaction.h>
|
||||
|
||||
// Remove C++ iterators
|
||||
%define IGNORE_ITER(parent, iteree)
|
||||
%ignore OpenBabel::parent::Begin ## iteree ## s;
|
||||
%ignore OpenBabel::parent::End ## iteree ## s;
|
||||
%ignore OpenBabel::parent::Begin ## iteree;
|
||||
%ignore OpenBabel::parent::Next ## iteree;
|
||||
%enddef
|
||||
IGNORE_ITER(OBMol, Bond)
|
||||
IGNORE_ITER(OBMol, Atom)
|
||||
IGNORE_ITER(OBMol, Residue)
|
||||
%include <openbabel/mol.h>
|
||||
%include <openbabel/ring.h>
|
||||
%warnfilter(516) OpenBabel::OBSmartsPattern; // Using non-const versions of GetSMARTS
|
||||
%include <openbabel/parsmart.h>
|
||||
%warnfilter(516) OpenBabel::AliasData; // Ignoring std::string methods in favour of char* ones
|
||||
%include <openbabel/alias.h>
|
||||
%include <openbabel/atomclass.h>
|
||||
%ignore OpenBabel::FptIndex;
|
||||
%include <openbabel/fingerprint.h>
|
||||
%ignore OpenBabel::OBDescriptor::LessThan;
|
||||
%include <openbabel/descriptor.h>
|
||||
%include <openbabel/builder.h>
|
||||
%include <openbabel/op.h>
|
||||
|
||||
%include <openbabel/chargemodel.h>
|
||||
%include <openbabel/graphsym.h>
|
||||
%include <openbabel/isomorphism.h>
|
||||
%include <openbabel/query.h>
|
||||
%include <openbabel/canon.h>
|
||||
%include <openbabel/stereo/stereo.h>
|
||||
|
||||
%warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators
|
||||
%include <openbabel/bitvec.h>
|
||||
# Ignore shadowed method
|
||||
%ignore OpenBabel::OBRotor::GetRotAtoms() const;
|
||||
%include <openbabel/rotor.h>
|
||||
%ignore OpenBabel::Swab;
|
||||
%include <openbabel/rotamer.h>
|
||||
%include <openbabel/spectrophore.h>
|
||||
#ifdef HAVE_EIGEN
|
||||
|
||||
# Ignore shadowed methods
|
||||
%ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);
|
||||
%ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *);
|
||||
%warnfilter(516) OpenBabel::OBForceField; // Ignoring std::string methods in favour of char* ones
|
||||
%include <openbabel/forcefield.h>
|
||||
|
||||
|
||||
%include <openbabel/conformersearch.h>
|
||||
%include <openbabel/math/align.h>
|
||||
#endif
|
||||
|
||||
# The following %ignores avoid warning messages due to shadowed classes.
|
||||
# This does not imply a loss of functionality as (in this case)
|
||||
# the shadowed class is identical (from the point of view of SWIG) to
|
||||
# the shadowing class.
|
||||
# This is because C++ references (&) are transformed by SWIG back into
|
||||
# pointers, so that OBAtomIter(OBMol &) would be treated the same as
|
||||
# OBAtomIter(OBMol *).
|
||||
|
||||
%ignore OBAtomAtomIter(OBAtom &);
|
||||
%ignore OBAtomBondIter(OBAtom &);
|
||||
%ignore OBMolAngleIter(OBMol &);
|
||||
%ignore OBMolAtomIter(OBMol &);
|
||||
%ignore OBMolAtomBFSIter(OBMol &);
|
||||
%ignore OBMolAtomDFSIter(OBMol &);
|
||||
%ignore OBMolAtomBFSIter(OBMol &, int);
|
||||
%ignore OBMolAtomDFSIter(OBMol &, int);
|
||||
%ignore OBMolBondIter(OBMol &);
|
||||
%ignore OBMolBondBFSIter(OBMol &);
|
||||
%ignore OBMolBondBFSIter(OBMol &, int);
|
||||
%ignore OBMolPairIter(OBMol &);
|
||||
%ignore OBMolRingIter(OBMol &);
|
||||
%ignore OBMolTorsionIter(OBMol &);
|
||||
%ignore OBResidueIter(OBMol &);
|
||||
%ignore OBResidueAtomIter(OBResidue &);
|
||||
|
||||
%ignore SpaceGroup::RegisterSpaceGroup;
|
||||
|
||||
%define WRAPITERATOR(NAME, RETURNS, OPTIONAL)
|
||||
%rename(_next) OpenBabel::NAME::next;
|
||||
%rename(inc) OpenBabel::NAME::operator++;
|
||||
%rename(HasMore) OpenBabel::NAME::operator bool;
|
||||
%typemap(javainterfaces) OpenBabel::NAME "Iterable<RETURNS>, Iterator<RETURNS>";
|
||||
%typemap(javaimports) OpenBabel::NAME " import org.openbabel.RETURNS;
|
||||
import java.util.Iterator;"
|
||||
%typemap(javacode) OpenBabel::NAME
|
||||
%{
|
||||
public Iterator<RETURNS> iterator() {
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean hasNext() {
|
||||
return HasMore();
|
||||
}
|
||||
|
||||
public RETURNS next() {
|
||||
RETURNS atom = __ref__();
|
||||
OPTIONAL
|
||||
inc();
|
||||
return atom;
|
||||
}
|
||||
|
||||
public void remove() {
|
||||
}
|
||||
%}
|
||||
%enddef
|
||||
|
||||
WRAPITERATOR(OBMolAtomIter, OBAtom, );
|
||||
WRAPITERATOR(OBMolAtomDFSIter, OBAtom, );
|
||||
WRAPITERATOR(OBMolAtomBFSIter, OBAtom, atom.SetCurrentDepth(CurrentDepth()););
|
||||
WRAPITERATOR(OBMolBondIter, OBBond, );
|
||||
WRAPITERATOR(OBMolAngleIter, vectorUnsignedInt, );
|
||||
WRAPITERATOR(OBAtomAtomIter, OBAtom, )
|
||||
WRAPITERATOR(OBAtomBondIter, OBBond, );
|
||||
WRAPITERATOR(OBMolRingIter, OBRing, );
|
||||
WRAPITERATOR(OBMolTorsionIter, vectorUnsignedInt, );
|
||||
WRAPITERATOR(OBResidueIter, OBResidue, );
|
||||
WRAPITERATOR(OBResidueAtomIter, OBAtom, );
|
||||
WRAPITERATOR(OBMolPairIter, vectorUnsignedInt, );
|
||||
|
||||
%include <openbabel/obiter.h>
|
||||
|
||||
%include "stereo.i"
|
||||
Reference in New Issue
Block a user