mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-10 04:58:04 -05:00
Merged revisions 3063-3068,3070 via svnmerge from
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x ........ r3063 | baoilleach | 2009-06-16 19:40:47 +0200 (Tue, 16 Jun 2009) | 3 lines The first of a series of commits where I try to get the CSharp bindings into shape. Moving Windows-specific files away from scripts/csharp into windows-vc2005/OBCSharp ........ r3064 | baoilleach | 2009-06-16 20:05:21 +0200 (Tue, 16 Jun 2009) | 1 line Create openbabel-mono.i, a mono-specific version of openbabel-csharp.i, primarily for use on Linux/MacOSX. It is currently an exact checkout of svn r2805 of openbabel-csharp.i. ........ r3065 | baoilleach | 2009-06-16 20:17:22 +0200 (Tue, 16 Jun 2009) | 1 line Update windows release build to use libstdinchi.lib ........ r3066 | baoilleach | 2009-06-16 21:24:16 +0200 (Tue, 16 Jun 2009) | 1 line Updates to Windows CSharp build files ........ r3067 | baoilleach | 2009-06-16 22:17:06 +0200 (Tue, 16 Jun 2009) | 7 lines Changelog for previous commits 2009-06-16 Noel O'Boyle <baoilleach@gmail.com> * windows-vc2005/OBCSharp and CSharp files in scripts: Separate .NET and Mono SWIG files. Move .NET files to windows-vc2005. Update relevant files. ........ r3068 | mr_grieves | 2009-06-17 22:18:51 +0200 (Wed, 17 Jun 2009) | 2 lines Skip selective dynamics line if present -- Thanks for janneb in #avogadro for pointing this out. Also include 'K' and 'k' in coordinate type selection. ........ r3070 | baoilleach | 2009-06-18 11:06:34 +0200 (Thu, 18 Jun 2009) | 1 line Minor updates to scripting READMEs ........
This commit is contained in:
Tim Vandermeersch
@@ -0,0 +1,343 @@
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//Rename GetType methods. GetType() is a member of the base C# object
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//and should retain its default meaning in all derived classes
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%rename(GetAtomType) OpenBabel::OBAtom::GetType();
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%rename(GetBondType) OpenBabel::OBBond::GetType();
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%rename(GetFormatType) OpenBabel::OBFormat::GetType();
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%rename(GetRingType) OpenBabel::OBRing::GetType();
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%rename(SetAtomType) OpenBabel::OBAtom::SetType(const char *);
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%rename(SetBondType) OpenBabel::OBBond::SetType(const char *);
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%rename(SetFormatType) OpenBabel::OBFormat::SetType(const char *);
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%rename(SetRingType) OpenBabel::OBRing::SetType(const char *);
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//renamed to avoid confusion with similarly named types in
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//the System.Windows.Media.Media3d namespace and because all C# class names should start with a capital
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//letter
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%rename(OBVector3) *::vector3;
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%rename(OBMatrix3x3) OpenBabel::matrix3x3;
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%rename(OBTransform3d) OpenBabel::transform3d;
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//renamed these because all public methods of a C# class should start with
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//a capital letter. As swig for c# matures this may become uneccesary.
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%rename(DistSq) OpenBabel::vector3::distSq(const vector3 &) const;
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%rename(RandomUnitVector) OpenBabel::vector3::randomUnitVector(OBRandom *);
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%rename(RandomUnitVector) OpenBabel::vector3::randomUnitVector();
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%rename(Normalize) OpenBabel::vector3::normalize();
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//changed this name slightly to match DistSq(vector3)
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%rename(LengthSq) OpenBabel::vector3::length_2() const;
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%rename(Length) OpenBabel::vector3::length() const;
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%rename(CreateOrthoVector) OpenBabel::vector3::createOrthoVector(vector3 &) const;
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//marks certain classes as partial for people who want to add methods and properties
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//when using OBDotNet to build their own apis (ChemSharp will provide an example of this)
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//this change can be made to other classes if needed in the future.
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%typemap(csclassmodifiers) OpenBabel::OBAtom "public partial class"
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%typemap(csclassmodifiers) OpenBabel::OBMol "public partial class"
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%typemap(csclassmodifiers) OpenBabel::OBBond "public partial class"
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%typemap(csclassmodifiers) OpenBabel::matrix3x3 "public partial class"
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%typemap(csclassmodifiers) OpenBabel::OBRing "public partial class"
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%typemap(csclassmodifiers) OpenBabel::vector3 "public partial class"
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%typemap(csclassmodifiers) OpenBabel::OBElementTable "public partial class"
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//adds the ignored operators back into the OBVector3 class
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//with companion methods for use by .Net languages that don't support operator
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//overloading
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%typemap(cscode) OpenBabel::vector3
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%{
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public static OBVector3 Add(OBVector3 vecA, OBVector3 vecB)
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{
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return new OBVector3(vecA.x()+vecB.x(), vecA.y()+vecB.y(),vecA.z()+vecB.z());
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}
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public static OBVector3 operator +(OBVector3 vecA, OBVector3 vecB)
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{
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return new OBVector3(vecA.x()+vecB.x(), vecA.y()+vecB.y(),vecA.z()+vecB.z());
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}
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public static OBVector3 Mul(double d, OBVector3 vec)
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{
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return new OBVector3(d*vec.x(),d*vec.y(),d*vec.z());
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}
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public static OBVector3 operator *(double d, OBVector3 vec)
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{
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return new OBVector3(d*vec.x(),d*vec.y(),d*vec.z());
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}
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public static OBVector3 operator *(OBVector3 vec, double d)
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{
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return new OBVector3(d*vec.x(),d*vec.y(),d*vec.z());
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}
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public static OBVector3 Sub(OBVector3 vecA, OBVector3 vecB)
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{
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return new OBVector3(vecA.x()-vecB.x(), vecA.y()-vecB.y(),vecA.z()-vecB.z());
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}
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public static OBVector3 operator -(OBVector3 vecA, OBVector3 vecB)
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{
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return new OBVector3(vecA.x()-vecB.x(), vecA.y()-vecB.y(),vecA.z()-vecB.z());
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}
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public void Negate()
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{
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SetX(-x());
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SetY(-y());
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SetZ(-z());
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}
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public static OBVector3 operator -(OBVector3 vec)
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{
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return new OBVector3(-vec.x(),-vec.y(),-vec.z());
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}
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public double this[int index]
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{
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get
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{
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if(index == 0)
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return x();
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else if(index == 1)
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return y();
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else if(index == 2)
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return z();
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else
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throw new IndexOutOfRangeException("Largest allowable index is 2");
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}
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}
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%}
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%include "carrays.i"
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%define WRAP_ARRAY(TYPE, NAME)
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%array_class(TYPE,NAME)
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%typemap(cstype) TYPE * "NAME"
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%typemap(csout, excode=SWIGEXCODE) TYPE *
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{
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IntPtr cPtr = $imcall;$excode
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$csclassname ret = null;
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if (cPtr != IntPtr.Zero)
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{
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ret = new $csclassname(cPtr,true);
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}
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return NAME.frompointer(ret);
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}
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%typemap(csin, pre=" $csclassname temp$csinput = $csinput.cast();")
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TYPE * "$csclassname.getCPtr(temp$csinput)"
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%typemap(csvarin, excode=SWIGEXCODE2) TYPE * %{
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set
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{
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$csclassname tempvalue = value.cast();
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$imcall;$excode
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} %}
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%typemap(csvarout, excode=SWIGEXCODE2) TYPE * %{
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get
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{
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IntPtr cPtr = $imcall;
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$csclassname tmp = new $csclassname(cPtr,true);$excode
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return NAME.frompointer(tmp);
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} %}
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%enddef
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WRAP_ARRAY(double,double_array)
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%module openbabelcsharp
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%{
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// used to set import/export for Cygwin DLLs
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#ifdef WIN32
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#define USING_OBDLL
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#endif
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#include <openbabel/obutil.h>
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#include <openbabel/rand.h>
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#include <openbabel/math/vector3.h>
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#include <openbabel/math/matrix3x3.h>
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#include <openbabel/math/transform3d.h>
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#include <openbabel/generic.h>
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#include <openbabel/base.h>
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#include <openbabel/mol.h>
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#include <openbabel/atom.h>
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#include <openbabel/bond.h>
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#include <openbabel/residue.h>
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#include <openbabel/internalcoord.h>
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#include <openbabel/ring.h>
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#include <openbabel/obconversion.h>
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#include <openbabel/oberror.h>
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#include <openbabel/plugin.h>
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#include <openbabel/fingerprint.h>
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#include <openbabel/descriptor.h>
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#include <openbabel/format.h>
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#include <openbabel/forcefield.h>
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#include <openbabel/op.h>
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#include <openbabel/bitvec.h>
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#include <openbabel/data.h>
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#include <openbabel/parsmart.h>
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#include <openbabel/alias.h>
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#include <openbabel/atomclass.h>
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#include <openbabel/kinetics.h>
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#include <openbabel/rotamer.h>
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%}
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%module VecMath
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%{
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#include <openbabel/math/vector3.h>
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#include <openbabel/math/matrix3x3.h>
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#include <openbabel/math/transform3d.h>
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%}
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%ignore *::operator=;
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%ignore *::operator++;
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%ignore *::operator-=;
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%ignore *::operator+=;
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%ignore *::operator bool;
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%ignore *::operator*=;
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%ignore *::operator/=;
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%ignore *::operator <<;
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%ignore *::operator==;
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%ignore *::operator-;
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//%ignore *::operator*;
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%ignore *::operator !=;
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%include "std_string.i"
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%include "std_map.i"
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%include "std_vector.i"
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%template (vectorInt) std::vector<int>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(vectorInt, std::vector<int>);
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// Note that the following line will fail if the space between
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// the two greater-than signs is removed!
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%template (vvInt) std::vector<std::vector<int> >;
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%template (vectorUnsignedInt) std::vector<unsigned int>;
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%template (vectorDouble) std::vector<double>;
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%template (vectorString) std::vector<std::string>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBVector3, OpenBabel::vector3);
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%template (vectorOBVector3) std::vector<OpenBabel::vector3>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBMol, OpenBabel::OBMol);
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%template (vectorMol) std::vector<OpenBabel::OBMol>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBBond, OpenBabel::OBBond);
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%template (vectorBond) std::vector<OpenBabel::OBBond>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBResidue, OpenBabel::OBResidue);
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%template (vectorResidue) std::vector<OpenBabel::OBResidue>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBRing, OpenBabel::OBRing);
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%template (vectorRing) std::vector<OpenBabel::OBRing>;
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// Note that vectors of pointers need slightly different syntax
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBRing, OpenBabel::OBRing*);
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%template (vectorpRing) std::vector<OpenBabel::OBRing*>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBGenericData, OpenBabel::OBGenericData*);
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%template (vectorpData) std::vector<OpenBabel::OBGenericData*>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBInternalCoord, OpenBabel::OBInternalCoord*);
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%template (vectorpInternalCoord) std::vector<OpenBabel::OBInternalCoord*>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBAtom, OpenBabel::OBAtom*);
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%template (vectorpAtom) std::vector<OpenBabel::OBAtom*>;
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SWIG_STD_VECTOR_SPECIALIZE_MINIMUM(OBBond, OpenBabel::OBBond*);
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%template (vectorpBond) std::vector<OpenBabel::OBBond*>;
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%import <openbabel/babelconfig.h>
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%include <openbabel/data.h>
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%include <openbabel/rand.h>
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%include <openbabel/obutil.h>
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%include <openbabel/math/vector3.h>
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%include <openbabel/math/matrix3x3.h>
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%include <openbabel/math/transform3d.h>
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%include <openbabel/math/spacegroup.h>
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%include <openbabel/base.h>
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%include <openbabel/generic.h>
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%define CAST_GENERICDATA_TO(subclass)
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%extend OpenBabel::OBGenericData {
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OpenBabel::OB ## subclass *To ## subclass() {
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return (OpenBabel::OB ## subclass *) $self;
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}
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};
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%enddef
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CAST_GENERICDATA_TO(AngleData)
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CAST_GENERICDATA_TO(AtomClassData)
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CAST_GENERICDATA_TO(ChiralData)
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CAST_GENERICDATA_TO(CommentData)
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CAST_GENERICDATA_TO(ConformerData)
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CAST_GENERICDATA_TO(ExternalBondData)
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CAST_GENERICDATA_TO(GridData)
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CAST_GENERICDATA_TO(MatrixData)
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CAST_GENERICDATA_TO(NasaThermoData)
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CAST_GENERICDATA_TO(PairData)
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// CAST_GENERICDATA_TO(PairTemplate)
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CAST_GENERICDATA_TO(RateData)
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CAST_GENERICDATA_TO(RotamerList)
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CAST_GENERICDATA_TO(RotationData)
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CAST_GENERICDATA_TO(SerialNums)
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CAST_GENERICDATA_TO(SetData)
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CAST_GENERICDATA_TO(SymmetryData)
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CAST_GENERICDATA_TO(TorsionData)
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CAST_GENERICDATA_TO(UnitCell)
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CAST_GENERICDATA_TO(VectorData)
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CAST_GENERICDATA_TO(VibrationData)
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CAST_GENERICDATA_TO(VirtualBond)
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%include <openbabel/griddata.h> // Needs to come after generic.h
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%include <openbabel/chains.h>
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//# %import <openbabel/bitvec.h>
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%include <openbabel/typer.h>
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%include <openbabel/plugin.h>
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%include <openbabel/oberror.h>
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%include <openbabel/format.h>
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%include <openbabel/obconversion.h>
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%include <openbabel/residue.h>
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%include <openbabel/internalcoord.h>
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%include <openbabel/atom.h>
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%include <openbabel/bond.h>
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%ignore OpenBabel::OBMol::SetData;
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%include <openbabel/mol.h>
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%include <openbabel/ring.h>
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%include <openbabel/parsmart.h>
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%include <openbabel/alias.h>
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%include <openbabel/atomclass.h>
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%include <openbabel/fingerprint.h>
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%include <openbabel/descriptor.h>
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%include <openbabel/forcefield.h>
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%include <openbabel/op.h>
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%include <openbabel/bitvec.h>
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# The following %ignores avoid warning messages due to shadowed classes.
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# This does not imply a loss of functionality as (in this case)
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# the shadowed class is identical (from the point of view of SWIG) to
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# the shadowing class.
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# This is because C++ references (&) are transformed by SWIG back into
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# pointers, so that OBAtomIter(OBMol &) would be treated the same as
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# OBAtomIter(OBMol *).
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%ignore OBAtomAtomIter(OBAtom &);
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%ignore OBAtomBondIter(OBAtom &);
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%ignore OBMolAngleIter(OBMol &);
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%ignore OBMolAtomIter(OBMol &);
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%ignore OBMolAtomBFSIter(OBMol &);
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%ignore OBMolAtomDFSIter(OBMol &);
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%ignore OBMolAtomBFSIter(OBMol &, int);
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%ignore OBMolAtomDFSIter(OBMol &, int);
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%ignore OBMolBondIter(OBMol &);
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%ignore OBMolPairIter(OBMol &);
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%ignore OBMolRingIter(OBMol &);
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%ignore OBMolTorsionIter(OBMol &);
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%ignore OBResidueIter(OBMol &);
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%ignore OBResidueAtomIter(OBResidue &);
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%include <openbabel/obiter.h>
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@@ -1,5 +1,5 @@
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openbabel version 1.2
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================================
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||||
OpenBabel Python bindings version 1.5
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||||
=====================================
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||||
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||||
This is a Python interface to the Open Babel chemistry library.
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||||
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||||
@@ -29,8 +29,8 @@ installed Open Babel):
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DEPENDENCIES
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||||
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||||
python-2.3 or a more recent version.
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||||
openbabel-2.1 or a more recent version.
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||||
python-2.4 or a more recent version.
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||||
openbabel-2.2.2 or a more recent version.
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||||
|
||||
Note that if you are trying to build/run this Python code in the Open
|
||||
Babel source/build directory BEFORE you install Open Babel, you may
|
||||
@@ -42,7 +42,7 @@ Open Babel package and THEN rebuild this Python module.
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||||
COPYRIGHT AND LICENSE
|
||||
|
||||
Copyright (C) 2005-2007 Geoffrey R. Hutchison <babel@geoffhutchison.net>
|
||||
Some portions Copyright (C) 2006-2007 Noel O'Boyle
|
||||
Some portions Copyright (C) 2006-2009 Noel O'Boyle
|
||||
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||||
This Python module is part of the Open Babel project.
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||||
<http://openbabel.sourceforge.net/>
|
||||
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||||
Reference in New Issue
Block a user