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* scripts/*: Cleanups and fixes, including for compilation

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problems with Perl. (Derives from some macro expansion for THR.)
This commit is contained in:
Geoffrey Hutchison
2006-12-02 18:56:04 +00:00
parent ebe138c944
commit aa011ebe45
16 changed files with 3847 additions and 1562 deletions
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5
ChangeLog
View File

@@ -1,3 +1,8 @@
2006-12-02 Geoffrey Hutchison <babel@geoffhutchison.net>
* scripts/*: Cleanups and fixes, including for compilation
problems with Perl. (Derives from some macro expansion for THR.)
2006-12-01 Benoit Jacob <jacob@math.jussieu.fr>
* src/grid.h, src/grid.cpp: In class OBFloatGrid:

14
scripts/Makefile.am
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@@ -17,7 +17,7 @@ dist-hook:
if MAINTAINER_MODE
if BUILD_SWIG
BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
ruby/openbabel_ruby.cpp java/openbabel_java.cpp
java/openbabel_java.cpp
perl/openbabel_perl.cpp: openbabel-perl.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
$(SWIG) -perl5 -c++ -naturalvar -o $@ \
@@ -36,10 +36,6 @@ python/openbabel_python.cpp: openbabel-python.i $(top_srcdir)/src/mol.h $(top_s
cat python/openbabel.py >>python/ob.py;
mv python/ob.py python/openbabel.py;
ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
$(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
(cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
$(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
(cd java; \
@@ -47,5 +43,13 @@ java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir)
do tgt=$$(echo $${file} | sed -e "s/SWIGTYPE_p_//" | sed -e "s/std__//g" | sed -e "s/OpenBabel__//g" | sed -e "s/p_/p/g"); \
mv $$file $$tgt; done)
if BUILD_RUBY
BUILT_SOURCES += ruby/openbabel_ruby.cpp
ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
$(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
(cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
endif # BUILD_RUBY
endif # BUILD_SWIG
endif # MAINTAINER_MODE

16
scripts/Makefile.in
View File

@@ -35,6 +35,7 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@am__append_1 = ruby/openbabel_ruby.cpp
subdir = scripts
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -198,9 +199,10 @@ EXTRA_DIST = openbabel-perl.i perl \
# build the scripting language interfaces if --enable-maintainer-mode was set
# and SWIG is available -- please use the most recent version of SWIG
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ ruby/openbabel_ruby.cpp java/openbabel_java.cpp
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ python/openbabel_python.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ java/openbabel_java.cpp \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(am__append_1)
all: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) all-am
@@ -394,16 +396,16 @@ dist-hook:
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ cat python/openbabel.py >>python/ob.py;
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv python/ob.py python/openbabel.py;
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ (cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -java -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ (cd java; \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ for file in SWIGTYPE_p_*; \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ do tgt=$$(echo $${file} | sed -e "s/SWIGTYPE_p_//" | sed -e "s/std__//g" | sed -e "s/OpenBabel__//g" | sed -e "s/p_/p/g"); \
@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ mv $$file $$tgt; done)
@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ruby/openbabel_ruby.cpp: openbabel-ruby.i $(top_srcdir)/src/mol.h $(top_srcdir)/src/obconversion.h
@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ $(SWIG) -ruby -naturalvar -c++ -o $@ -I$(top_srcdir)/src $<;
@BUILD_RUBY_TRUE@@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@ (cd ruby; ruby extconf.rb --with-openbabel-include=$(includedir)/openbabel-2.0/openbabel --with-openbabel-2.0-include=$(includedir)/openbabel-2.0 --with-openbabel-lib=$(libdir) )
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:

46
scripts/java/OBRandom.java
View File

@@ -7,53 +7,19 @@
* ----------------------------------------------------------------------------- */
public class OBRandom {
public class SWIGTYPE_p_OpenBabel__OBRandom {
private long swigCPtr;
protected boolean swigCMemOwn;
protected OBRandom(long cPtr, boolean cMemoryOwn) {
swigCMemOwn = cMemoryOwn;
protected SWIGTYPE_p_OpenBabel__OBRandom(long cPtr, boolean futureUse) {
swigCPtr = cPtr;
}
protected static long getCPtr(OBRandom obj) {
return (obj == null) ? 0 : obj.swigCPtr;
}
protected void finalize() {
delete();
}
public synchronized void delete() {
if(swigCPtr != 0 && swigCMemOwn) {
swigCMemOwn = false;
openbabelJNI.delete_OBRandom(swigCPtr);
}
protected SWIGTYPE_p_OpenBabel__OBRandom() {
swigCPtr = 0;
}
public OBRandom(boolean useSys) {
this(openbabelJNI.new_OBRandom__SWIG_0(useSys), true);
protected static long getCPtr(SWIGTYPE_p_OpenBabel__OBRandom obj) {
return (obj == null) ? 0 : obj.swigCPtr;
}
public OBRandom() {
this(openbabelJNI.new_OBRandom__SWIG_1(), true);
}
public void Seed(int seed) {
openbabelJNI.OBRandom_Seed(swigCPtr, this, seed);
}
public void TimeSeed() {
openbabelJNI.OBRandom_TimeSeed(swigCPtr, this);
}
public int NextInt() {
return openbabelJNI.OBRandom_NextInt(swigCPtr, this);
}
public double NextFloat() {
return openbabelJNI.OBRandom_NextFloat(swigCPtr, this);
}
}

40
scripts/java/openbabel.java
View File

@@ -12,18 +12,6 @@ public class openbabel implements openbabelConstants {
return openbabelJNI.OpenDatafile(SWIGTYPE_p_std__ifstream.getCPtr(fs), filename);
}
public static void DoubleMultiply(long arg0, long arg1, DoubleType arg2) {
openbabelJNI.DoubleMultiply(arg0, arg1, DoubleType.getCPtr(arg2), arg2);
}
public static void DoubleAdd(DoubleType arg0, long arg1) {
openbabelJNI.DoubleAdd(DoubleType.getCPtr(arg0), arg0, arg1);
}
public static long DoubleModulus(DoubleType arg0, long arg1) {
return openbabelJNI.DoubleModulus(DoubleType.getCPtr(arg0), arg0, arg1);
}
public static double dot(vector3 v1, vector3 v2) {
return openbabelJNI.dot(vector3.getCPtr(v1), v1, vector3.getCPtr(v2), v2);
}
@@ -464,14 +452,34 @@ public class openbabel implements openbabelConstants {
return openbabelJNI.I_get();
}
public static long get_1MA() {
return openbabelJNI._1MA_get();
}
public static long get_5MC() {
return openbabelJNI._5MC_get();
}
public static long getOMC() {
return openbabelJNI.OMC_get();
}
public static long get_1MG() {
return openbabelJNI._1MG_get();
}
public static long get_2MG() {
return openbabelJNI._2MG_get();
}
public static long getM2G() {
return openbabelJNI.M2G_get();
}
public static long get_7MG() {
return openbabelJNI._7MG_get();
}
public static long getOMG() {
return openbabelJNI.OMG_get();
}
@@ -484,6 +492,10 @@ public class openbabel implements openbabelConstants {
return openbabelJNI.H2U_get();
}
public static long get_5MU() {
return openbabelJNI._5MU_get();
}
public static long getPSU() {
return openbabelJNI.PSU_get();
}
@@ -626,6 +638,10 @@ public class openbabel implements openbabelConstants {
return openbabelJNI.tokenize__SWIG_4(SWIGTYPE_p_std__vectorTstd__string_t.getCPtr(arg0), SWIGTYPE_p_std__string.getCPtr(arg1));
}
public static void ThrowError(String str) {
openbabelJNI.ThrowError__SWIG_0(str);
}
public static void ThrowError(SWIGTYPE_p_std__string str) {
openbabelJNI.ThrowError__SWIG_1(SWIGTYPE_p_std__string.getCPtr(str));
}

25
scripts/java/openbabelJNI.java
View File

@@ -189,22 +189,6 @@ class openbabelJNI {
public final static native void delete_OBSqrtTbl(long jarg1);
public final static native double OBSqrtTbl_Sqrt(long jarg1, OBSqrtTbl jarg1_, double jarg2);
public final static native void OBSqrtTbl_Init(long jarg1, OBSqrtTbl jarg1_, double jarg2, double jarg3);
public final static native void DoubleType_hi_set(long jarg1, DoubleType jarg1_, long jarg2);
public final static native long DoubleType_hi_get(long jarg1, DoubleType jarg1_);
public final static native void DoubleType_lo_set(long jarg1, DoubleType jarg1_, long jarg2);
public final static native long DoubleType_lo_get(long jarg1, DoubleType jarg1_);
public final static native long new_DoubleType();
public final static native void delete_DoubleType(long jarg1);
public final static native void DoubleMultiply(long jarg1, long jarg2, long jarg3, DoubleType jarg3_);
public final static native void DoubleAdd(long jarg1, DoubleType jarg1_, long jarg2);
public final static native long DoubleModulus(long jarg1, DoubleType jarg1_, long jarg2);
public final static native long new_OBRandom__SWIG_0(boolean jarg1);
public final static native long new_OBRandom__SWIG_1();
public final static native void OBRandom_Seed(long jarg1, OBRandom jarg1_, int jarg2);
public final static native void OBRandom_TimeSeed(long jarg1, OBRandom jarg1_);
public final static native int OBRandom_NextInt(long jarg1, OBRandom jarg1_);
public final static native double OBRandom_NextFloat(long jarg1, OBRandom jarg1_);
public final static native void delete_OBRandom(long jarg1);
public final static native long new_vector3__SWIG_0(double jarg1, double jarg2, double jarg3);
public final static native long new_vector3__SWIG_1(double jarg1, double jarg2);
public final static native long new_vector3__SWIG_2(double jarg1);
@@ -217,7 +201,7 @@ class openbabelJNI {
public final static native void vector3_SetZ(long jarg1, vector3 jarg1_, double jarg2);
public final static native void vector3_Get(long jarg1, vector3 jarg1_, long jarg2);
public final static native long vector3_AsArray(long jarg1, vector3 jarg1_);
public final static native void vector3_randomUnitVector__SWIG_0(long jarg1, vector3 jarg1_, long jarg2, OBRandom jarg2_);
public final static native void vector3_randomUnitVector__SWIG_0(long jarg1, vector3 jarg1_, long jarg2);
public final static native void vector3_randomUnitVector__SWIG_1(long jarg1, vector3 jarg1_);
public final static native long vector3_normalize(long jarg1, vector3 jarg1_);
public final static native boolean vector3_CanBeNormalized(long jarg1, vector3 jarg1_);
@@ -712,11 +696,17 @@ class openbabelJNI {
public final static native long U_get();
public final static native long UPLUS_get();
public final static native long I_get();
public final static native long _1MA_get();
public final static native long _5MC_get();
public final static native long OMC_get();
public final static native long _1MG_get();
public final static native long _2MG_get();
public final static native long M2G_get();
public final static native long _7MG_get();
public final static native long OMG_get();
public final static native long YG_get();
public final static native long H2U_get();
public final static native long _5MU_get();
public final static native long PSU_get();
public final static native long UNK_get();
public final static native long ACE_get();
@@ -1165,6 +1155,7 @@ class openbabelJNI {
public final static native boolean tokenize__SWIG_2(long jarg1, long jarg2, String jarg3, int jarg4);
public final static native boolean tokenize__SWIG_3(long jarg1, long jarg2, String jarg3);
public final static native boolean tokenize__SWIG_4(long jarg1, long jarg2);
public final static native void ThrowError__SWIG_0(String jarg1);
public final static native void ThrowError__SWIG_1(long jarg1);
public final static native void CartesianToInternal(long jarg1, long jarg2, OBMol jarg2_);
public final static native void InternalToCartesian(long jarg1, long jarg2, OBMol jarg2_);

307
scripts/java/openbabel_java.cpp
View File

@@ -3364,223 +3364,6 @@ SWIGEXPORT void JNICALL Java_openbabelJNI_OBSqrtTbl_1Init(JNIEnv *jenv, jclass j
}
SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleType_1hi_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int arg2 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
arg2 = (unsigned int)jarg2;
if (arg1) (arg1)->hi = arg2;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleType_1hi_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
jlong jresult = 0 ;
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
result = (unsigned int) ((arg1)->hi);
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleType_1lo_1set(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int arg2 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
arg2 = (unsigned int)jarg2;
if (arg1) (arg1)->lo = arg2;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleType_1lo_1get(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
jlong jresult = 0 ;
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
result = (unsigned int) ((arg1)->lo);
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1DoubleType(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
OpenBabel::DoubleType *result = 0 ;
(void)jenv;
(void)jcls;
result = (OpenBabel::DoubleType *)new OpenBabel::DoubleType();
*(OpenBabel::DoubleType **)&jresult = result;
return jresult;
}
SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1DoubleType(JNIEnv *jenv, jclass jcls, jlong jarg1) {
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
(void)jenv;
(void)jcls;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
delete arg1;
}
SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleMultiply(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jobject jarg3_) {
unsigned int arg1 ;
unsigned int arg2 ;
OpenBabel::DoubleType *arg3 = (OpenBabel::DoubleType *) 0 ;
(void)jenv;
(void)jcls;
(void)jarg3_;
arg1 = (unsigned int)jarg1;
arg2 = (unsigned int)jarg2;
arg3 = *(OpenBabel::DoubleType **)&jarg3;
OpenBabel::DoubleMultiply(arg1,arg2,arg3);
}
SWIGEXPORT void JNICALL Java_openbabelJNI_DoubleAdd(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int arg2 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
arg2 = (unsigned int)jarg2;
OpenBabel::DoubleAdd(arg1,arg2);
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_DoubleModulus(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
jlong jresult = 0 ;
OpenBabel::DoubleType *arg1 = (OpenBabel::DoubleType *) 0 ;
unsigned int arg2 ;
unsigned int result;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::DoubleType **)&jarg1;
arg2 = (unsigned int)jarg2;
result = (unsigned int)OpenBabel::DoubleModulus(arg1,arg2);
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBRandom_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jboolean jarg1) {
jlong jresult = 0 ;
bool arg1 ;
OpenBabel::OBRandom *result = 0 ;
(void)jenv;
(void)jcls;
arg1 = jarg1 ? true : false;
result = (OpenBabel::OBRandom *)new OpenBabel::OBRandom(arg1);
*(OpenBabel::OBRandom **)&jresult = result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1OBRandom_1_1SWIG_11(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
OpenBabel::OBRandom *result = 0 ;
(void)jenv;
(void)jcls;
result = (OpenBabel::OBRandom *)new OpenBabel::OBRandom();
*(OpenBabel::OBRandom **)&jresult = result;
return jresult;
}
SWIGEXPORT void JNICALL Java_openbabelJNI_OBRandom_1Seed(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jint jarg2) {
OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
int arg2 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::OBRandom **)&jarg1;
arg2 = (int)jarg2;
(arg1)->Seed(arg2);
}
SWIGEXPORT void JNICALL Java_openbabelJNI_OBRandom_1TimeSeed(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::OBRandom **)&jarg1;
(arg1)->TimeSeed();
}
SWIGEXPORT jint JNICALL Java_openbabelJNI_OBRandom_1NextInt(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
jint jresult = 0 ;
OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
int result;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::OBRandom **)&jarg1;
result = (int)(arg1)->NextInt();
jresult = (jint)result;
return jresult;
}
SWIGEXPORT jdouble JNICALL Java_openbabelJNI_OBRandom_1NextFloat(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_) {
jdouble jresult = 0 ;
OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
double result;
(void)jenv;
(void)jcls;
(void)jarg1_;
arg1 = *(OpenBabel::OBRandom **)&jarg1;
result = (double)(arg1)->NextFloat();
jresult = (jdouble)result;
return jresult;
}
SWIGEXPORT void JNICALL Java_openbabelJNI_delete_1OBRandom(JNIEnv *jenv, jclass jcls, jlong jarg1) {
OpenBabel::OBRandom *arg1 = (OpenBabel::OBRandom *) 0 ;
(void)jenv;
(void)jcls;
arg1 = *(OpenBabel::OBRandom **)&jarg1;
delete arg1;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_new_1vector3_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jdouble jarg1, jdouble jarg2, jdouble jarg3) {
jlong jresult = 0 ;
double arg1 ;
@@ -3757,14 +3540,13 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_vector3_1AsArray(JNIEnv *jenv, jclass
}
SWIGEXPORT void JNICALL Java_openbabelJNI_vector3_1randomUnitVector_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2, jobject jarg2_) {
SWIGEXPORT void JNICALL Java_openbabelJNI_vector3_1randomUnitVector_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jlong jarg1, jobject jarg1_, jlong jarg2) {
OpenBabel::vector3 *arg1 = (OpenBabel::vector3 *) 0 ;
OpenBabel::OBRandom *arg2 = (OpenBabel::OBRandom *) 0 ;
(void)jenv;
(void)jcls;
(void)jarg1_;
(void)jarg2_;
arg1 = *(OpenBabel::vector3 **)&jarg1;
arg2 = *(OpenBabel::OBRandom **)&jarg2;
(arg1)->randomUnitVector(arg2);
@@ -11653,6 +11435,30 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_I_1get(JNIEnv *jenv, jclass jcls) {
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__11MA_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_1MA;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__15MC_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_5MC;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMC_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
@@ -11665,6 +11471,30 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMC_1get(JNIEnv *jenv, jclass jcls) {
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__11MG_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_1MG;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__12MG_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_2MG;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_M2G_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
@@ -11677,6 +11507,18 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_M2G_1get(JNIEnv *jenv, jclass jcls) {
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__17MG_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_7MG;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_OMG_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
@@ -11713,6 +11555,18 @@ SWIGEXPORT jlong JNICALL Java_openbabelJNI_H2U_1get(JNIEnv *jenv, jclass jcls) {
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI__15MU_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
(void)jenv;
(void)jcls;
result = (unsigned int)(unsigned int)OpenBabel::OBResidueIndex::_5MU;
jresult = (jlong)result;
return jresult;
}
SWIGEXPORT jlong JNICALL Java_openbabelJNI_PSU_1get(JNIEnv *jenv, jclass jcls) {
jlong jresult = 0 ;
unsigned int result;
@@ -18414,6 +18268,21 @@ SWIGEXPORT jboolean JNICALL Java_openbabelJNI_tokenize_1_1SWIG_14(JNIEnv *jenv,
}
SWIGEXPORT void JNICALL Java_openbabelJNI_ThrowError_1_1SWIG_10(JNIEnv *jenv, jclass jcls, jstring jarg1) {
char *arg1 = (char *) 0 ;
(void)jenv;
(void)jcls;
arg1 = 0;
if (jarg1) {
arg1 = (char *)jenv->GetStringUTFChars(jarg1, 0);
if (!arg1) return ;
}
OpenBabel::ThrowError(arg1);
if (arg1) jenv->ReleaseStringUTFChars(jarg1, (const char *)arg1);
}
SWIGEXPORT void JNICALL Java_openbabelJNI_ThrowError_1_1SWIG_11(JNIEnv *jenv, jclass jcls, jlong jarg1) {
std::string *arg1 = 0 ;

4
scripts/java/vector3.java
View File

@@ -81,8 +81,8 @@ public class vector3 {
return (cPtr == 0) ? null : new SWIGTYPE_p_double(cPtr, false);
}
public void randomUnitVector(OBRandom oeRand) {
openbabelJNI.vector3_randomUnitVector__SWIG_0(swigCPtr, this, OBRandom.getCPtr(oeRand), oeRand);
public void randomUnitVector(SWIGTYPE_p_OpenBabel__OBRandom oeRand) {
openbabelJNI.vector3_randomUnitVector__SWIG_0(swigCPtr, this, SWIGTYPE_p_OpenBabel__OBRandom.getCPtr(oeRand));
}
public void randomUnitVector() {

8
scripts/openbabel-perl.i
View File

@@ -9,12 +9,18 @@
#include "obutil.h"
#include "rand.h"
#include "math/vector3.h"
#include "math/matrix3x3.h"
#include "generic.h"
#include "base.h"
#include "mol.h"
#include "atom.h"
#include "bond.h"
#include "residue.h"
#include "internalcoord.h"
#include "ring.h"
#include "obconversion.h"
#include "oberror.h"
@@ -45,6 +51,7 @@ namespace std {
%apply std::string &OUTPUT { std::string &to };
%include "data.h"
%include "rand.h"
%include "obutil.h"
%include "math/vector3.h"
%import "math/matrix3x3.h"
@@ -59,6 +66,7 @@ namespace std {
%include "oberror.h"
%include "obconversion.h"
%include "residue.h"
%include "internalcoord.h"
%include "atom.h"
%include "bond.h"
%include "mol.h"

8
scripts/openbabel-python.i
View File

@@ -8,12 +8,18 @@
#include "obutil.h"
#include "rand.h"
#include "math/vector3.h"
#include "math/matrix3x3.h"
#include "generic.h"
#include "base.h"
#include "mol.h"
#include "atom.h"
#include "bond.h"
#include "residue.h"
#include "internalcoord.h"
#include "ring.h"
#include "obconversion.h"
#include "oberror.h"
@@ -44,6 +50,7 @@ namespace std {
%apply std::string &OUTPUT { std::string &to };
%include "data.h"
%include "rand.h"
%include "obutil.h"
%include "math/vector3.h"
%import "math/matrix3x3.h"
@@ -58,6 +65,7 @@ namespace std {
%include "oberror.h"
%include "obconversion.h"
%include "residue.h"
%include "internalcoord.h"
%include "atom.h"
%include "bond.h"
%include "mol.h"

8
scripts/openbabel-ruby.i
View File

@@ -9,12 +9,18 @@
#include <math.h>
#include "obutil.h"
#include "rand.h"
#include "math/vector3.h"
#include "math/matrix3x3.h"
#include "generic.h"
#include "base.h"
#include "mol.h"
#include "atom.h"
#include "bond.h"
#include "residue.h"
#include "internalcoord.h"
#include "ring.h"
#include "obconversion.h"
#include "oberror.h"
@@ -44,6 +50,7 @@ namespace std {
%apply std::string &OUTPUT { std::string &to };
%include "data.h"
%include "rand.h"
%include "obutil.h"
%include "math/vector3.h"
%import "math/matrix3x3.h"
@@ -58,6 +65,7 @@ namespace std {
%include "oberror.h"
%include "obconversion.h"
%include "residue.h"
%include "internalcoord.h"
%include "atom.h"
%include "bond.h"
%include "mol.h"

214
scripts/perl/OpenBabel.pm
View File

@@ -741,85 +741,6 @@ sub ACQUIRE {
}
############# Class : Chemistry::OpenBabel::OBStopwatch ##############
package Chemistry::OpenBabel::OBStopwatch;
use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
@ISA = qw( Chemistry::OpenBabel );
%OWNER = ();
%ITERATORS = ();
*Start = *Chemistry::OpenBabelc::OBStopwatch_Start;
*Lap = *Chemistry::OpenBabelc::OBStopwatch_Lap;
*Elapsed = *Chemistry::OpenBabelc::OBStopwatch_Elapsed;
sub new {
my $pkg = shift;
my $self = Chemistry::OpenBabelc::new_OBStopwatch(@_);
bless $self, $pkg if defined($self);
}
sub DESTROY {
return unless $_[0]->isa('HASH');
my $self = tied(%{$_[0]});
return unless defined $self;
delete $ITERATORS{$self};
if (exists $OWNER{$self}) {
Chemistry::OpenBabelc::delete_OBStopwatch($self);
delete $OWNER{$self};
}
}
sub DISOWN {
my $self = shift;
my $ptr = tied(%$self);
delete $OWNER{$ptr};
}
sub ACQUIRE {
my $self = shift;
my $ptr = tied(%$self);
$OWNER{$ptr} = 1;
}
############# Class : Chemistry::OpenBabel::OBSqrtTbl ##############
package Chemistry::OpenBabel::OBSqrtTbl;
use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
@ISA = qw( Chemistry::OpenBabel );
%OWNER = ();
%ITERATORS = ();
sub new {
my $pkg = shift;
my $self = Chemistry::OpenBabelc::new_OBSqrtTbl(@_);
bless $self, $pkg if defined($self);
}
sub DESTROY {
return unless $_[0]->isa('HASH');
my $self = tied(%{$_[0]});
return unless defined $self;
delete $ITERATORS{$self};
if (exists $OWNER{$self}) {
Chemistry::OpenBabelc::delete_OBSqrtTbl($self);
delete $OWNER{$self};
}
}
*Sqrt = *Chemistry::OpenBabelc::OBSqrtTbl_Sqrt;
*Init = *Chemistry::OpenBabelc::OBSqrtTbl_Init;
sub DISOWN {
my $self = shift;
my $ptr = tied(%$self);
delete $OWNER{$ptr};
}
sub ACQUIRE {
my $self = shift;
my $ptr = tied(%$self);
$OWNER{$ptr} = 1;
}
############# Class : Chemistry::OpenBabel::DoubleType ##############
package Chemistry::OpenBabel::DoubleType;
@@ -902,6 +823,85 @@ sub ACQUIRE {
}
############# Class : Chemistry::OpenBabel::OBStopwatch ##############
package Chemistry::OpenBabel::OBStopwatch;
use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
@ISA = qw( Chemistry::OpenBabel );
%OWNER = ();
%ITERATORS = ();
*Start = *Chemistry::OpenBabelc::OBStopwatch_Start;
*Lap = *Chemistry::OpenBabelc::OBStopwatch_Lap;
*Elapsed = *Chemistry::OpenBabelc::OBStopwatch_Elapsed;
sub new {
my $pkg = shift;
my $self = Chemistry::OpenBabelc::new_OBStopwatch(@_);
bless $self, $pkg if defined($self);
}
sub DESTROY {
return unless $_[0]->isa('HASH');
my $self = tied(%{$_[0]});
return unless defined $self;
delete $ITERATORS{$self};
if (exists $OWNER{$self}) {
Chemistry::OpenBabelc::delete_OBStopwatch($self);
delete $OWNER{$self};
}
}
sub DISOWN {
my $self = shift;
my $ptr = tied(%$self);
delete $OWNER{$ptr};
}
sub ACQUIRE {
my $self = shift;
my $ptr = tied(%$self);
$OWNER{$ptr} = 1;
}
############# Class : Chemistry::OpenBabel::OBSqrtTbl ##############
package Chemistry::OpenBabel::OBSqrtTbl;
use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
@ISA = qw( Chemistry::OpenBabel );
%OWNER = ();
%ITERATORS = ();
sub new {
my $pkg = shift;
my $self = Chemistry::OpenBabelc::new_OBSqrtTbl(@_);
bless $self, $pkg if defined($self);
}
sub DESTROY {
return unless $_[0]->isa('HASH');
my $self = tied(%{$_[0]});
return unless defined $self;
delete $ITERATORS{$self};
if (exists $OWNER{$self}) {
Chemistry::OpenBabelc::delete_OBSqrtTbl($self);
delete $OWNER{$self};
}
}
*Sqrt = *Chemistry::OpenBabelc::OBSqrtTbl_Sqrt;
*Init = *Chemistry::OpenBabelc::OBSqrtTbl_Init;
sub DISOWN {
my $self = shift;
my $ptr = tied(%$self);
delete $OWNER{$ptr};
}
sub ACQUIRE {
my $self = shift;
my $ptr = tied(%$self);
$OWNER{$ptr} = 1;
}
############# Class : Chemistry::OpenBabel::vector3 ##############
package Chemistry::OpenBabel::vector3;
@@ -2124,6 +2124,55 @@ sub ACQUIRE {
}
############# Class : Chemistry::OpenBabel::OBInternalCoord ##############
package Chemistry::OpenBabel::OBInternalCoord;
use vars qw(@ISA %OWNER %ITERATORS %BLESSEDMEMBERS);
@ISA = qw( Chemistry::OpenBabel );
%OWNER = ();
%ITERATORS = ();
*swig__a_get = *Chemistry::OpenBabelc::OBInternalCoord__a_get;
*swig__a_set = *Chemistry::OpenBabelc::OBInternalCoord__a_set;
*swig__b_get = *Chemistry::OpenBabelc::OBInternalCoord__b_get;
*swig__b_set = *Chemistry::OpenBabelc::OBInternalCoord__b_set;
*swig__c_get = *Chemistry::OpenBabelc::OBInternalCoord__c_get;
*swig__c_set = *Chemistry::OpenBabelc::OBInternalCoord__c_set;
*swig__dst_get = *Chemistry::OpenBabelc::OBInternalCoord__dst_get;
*swig__dst_set = *Chemistry::OpenBabelc::OBInternalCoord__dst_set;
*swig__ang_get = *Chemistry::OpenBabelc::OBInternalCoord__ang_get;
*swig__ang_set = *Chemistry::OpenBabelc::OBInternalCoord__ang_set;
*swig__tor_get = *Chemistry::OpenBabelc::OBInternalCoord__tor_get;
*swig__tor_set = *Chemistry::OpenBabelc::OBInternalCoord__tor_set;
sub new {
my $pkg = shift;
my $self = Chemistry::OpenBabelc::new_OBInternalCoord(@_);
bless $self, $pkg if defined($self);
}
sub DESTROY {
return unless $_[0]->isa('HASH');
my $self = tied(%{$_[0]});
return unless defined $self;
delete $ITERATORS{$self};
if (exists $OWNER{$self}) {
Chemistry::OpenBabelc::delete_OBInternalCoord($self);
delete $OWNER{$self};
}
}
sub DISOWN {
my $self = shift;
my $ptr = tied(%$self);
delete $OWNER{$ptr};
}
sub ACQUIRE {
my $self = shift;
my $ptr = tied(%$self);
$OWNER{$ptr} = 1;
}
############# Class : Chemistry::OpenBabel::OBAtom ##############
package Chemistry::OpenBabel::OBAtom;
@@ -4130,7 +4179,6 @@ bless $obErrorLog, Chemistry::OpenBabel::OBMessageHandler;
*LEU = *Chemistry::OpenBabelc::LEU;
*SER = *Chemistry::OpenBabelc::SER;
*VAL = *Chemistry::OpenBabelc::VAL;
*THR = *Chemistry::OpenBabelc::THR;
*LYS = *Chemistry::OpenBabelc::LYS;
*ASP = *Chemistry::OpenBabelc::ASP;
*ILE = *Chemistry::OpenBabelc::ILE;
@@ -4156,11 +4204,17 @@ bless $obErrorLog, Chemistry::OpenBabel::OBMessageHandler;
*U = *Chemistry::OpenBabelc::U;
*UPLUS = *Chemistry::OpenBabelc::UPLUS;
*I = *Chemistry::OpenBabelc::I;
*_1MA = *Chemistry::OpenBabelc::_1MA;
*_5MC = *Chemistry::OpenBabelc::_5MC;
*OMC = *Chemistry::OpenBabelc::OMC;
*_1MG = *Chemistry::OpenBabelc::_1MG;
*_2MG = *Chemistry::OpenBabelc::_2MG;
*M2G = *Chemistry::OpenBabelc::M2G;
*_7MG = *Chemistry::OpenBabelc::_7MG;
*OMG = *Chemistry::OpenBabelc::OMG;
*YG = *Chemistry::OpenBabelc::YG;
*H2U = *Chemistry::OpenBabelc::H2U;
*_5MU = *Chemistry::OpenBabelc::_5MU;
*PSU = *Chemistry::OpenBabelc::PSU;
*UNK = *Chemistry::OpenBabelc::UNK;
*ACE = *Chemistry::OpenBabelc::ACE;

1549
scripts/perl/openbabel_perl.cpp
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File diff suppressed because it is too large Load Diff

264
scripts/python/openbabel.py
View File

@@ -566,31 +566,6 @@ OBResidueData_swigregister(OBResidueData)
OpenDatafile = _openbabel.OpenDatafile
FILE_SEP_CHAR = _openbabel.FILE_SEP_CHAR
class OBStopwatch(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def Start(*args): return _openbabel.OBStopwatch_Start(*args)
def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
def __init__(self, *args):
_openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
__swig_destroy__ = _openbabel.delete_OBStopwatch
__del__ = lambda self : None;
OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
OBStopwatch_swigregister(OBStopwatch)
class OBSqrtTbl(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
__swig_destroy__ = _openbabel.delete_OBSqrtTbl
__del__ = lambda self : None;
def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
OBSqrtTbl_swigregister(OBSqrtTbl)
class DoubleType(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
@@ -620,6 +595,31 @@ class OBRandom(object):
OBRandom_swigregister = _openbabel.OBRandom_swigregister
OBRandom_swigregister(OBRandom)
class OBStopwatch(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def Start(*args): return _openbabel.OBStopwatch_Start(*args)
def Lap(*args): return _openbabel.OBStopwatch_Lap(*args)
def Elapsed(*args): return _openbabel.OBStopwatch_Elapsed(*args)
def __init__(self, *args):
_openbabel.OBStopwatch_swiginit(self,_openbabel.new_OBStopwatch(*args))
__swig_destroy__ = _openbabel.delete_OBStopwatch
__del__ = lambda self : None;
OBStopwatch_swigregister = _openbabel.OBStopwatch_swigregister
OBStopwatch_swigregister(OBStopwatch)
class OBSqrtTbl(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.OBSqrtTbl_swiginit(self,_openbabel.new_OBSqrtTbl(*args))
__swig_destroy__ = _openbabel.delete_OBSqrtTbl
__del__ = lambda self : None;
def Sqrt(*args): return _openbabel.OBSqrtTbl_Sqrt(*args)
def Init(*args): return _openbabel.OBSqrtTbl_Init(*args)
OBSqrtTbl_swigregister = _openbabel.OBSqrtTbl_swigregister
OBSqrtTbl_swigregister(OBSqrtTbl)
class vector3(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
@@ -1264,6 +1264,113 @@ AA_HIS = _openbabel.AA_HIS
AA_CYS = _openbabel.AA_CYS
AA_MET = _openbabel.AA_MET
AA_TRP = _openbabel.AA_TRP
class OBInternalCoord(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
_a = _swig_property(_openbabel.OBInternalCoord__a_get, _openbabel.OBInternalCoord__a_set)
_b = _swig_property(_openbabel.OBInternalCoord__b_get, _openbabel.OBInternalCoord__b_set)
_c = _swig_property(_openbabel.OBInternalCoord__c_get, _openbabel.OBInternalCoord__c_set)
_dst = _swig_property(_openbabel.OBInternalCoord__dst_get, _openbabel.OBInternalCoord__dst_set)
_ang = _swig_property(_openbabel.OBInternalCoord__ang_get, _openbabel.OBInternalCoord__ang_set)
_tor = _swig_property(_openbabel.OBInternalCoord__tor_get, _openbabel.OBInternalCoord__tor_set)
def __init__(self, *args):
_openbabel.OBInternalCoord_swiginit(self,_openbabel.new_OBInternalCoord(*args))
__swig_destroy__ = _openbabel.delete_OBInternalCoord
__del__ = lambda self : None;
OBInternalCoord_swigregister = _openbabel.OBInternalCoord_swigregister
OBInternalCoord_swigregister(OBInternalCoord)
ACIDIC = cvar.ACIDIC
ACYCLIC = cvar.ACYCLIC
ALIPHATIC = cvar.ALIPHATIC
AROMATIC = cvar.AROMATIC
BASIC = cvar.BASIC
BURIED = cvar.BURIED
CHARGED = cvar.CHARGED
CYCLIC = cvar.CYCLIC
HYDROPHOBIC = cvar.HYDROPHOBIC
LARGE = cvar.LARGE
MEDIUM = cvar.MEDIUM
NEGATIVE = cvar.NEGATIVE
NEUTRAL = cvar.NEUTRAL
POLAR = cvar.POLAR
POSITIVE = cvar.POSITIVE
SMALL = cvar.SMALL
SURFACE = cvar.SURFACE
ALPHA_CARBON = cvar.ALPHA_CARBON
AMINO_BACKBONE = cvar.AMINO_BACKBONE
BACKBONE = cvar.BACKBONE
CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
LIGAND = cvar.LIGAND
NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
SIDECHAIN = cvar.SIDECHAIN
SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
ALA = cvar.ALA
GLY = cvar.GLY
LEU = cvar.LEU
SER = cvar.SER
VAL = cvar.VAL
THR = cvar.THR
LYS = cvar.LYS
ASP = cvar.ASP
ILE = cvar.ILE
ASN = cvar.ASN
GLU = cvar.GLU
PRO = cvar.PRO
ARG = cvar.ARG
PHE = cvar.PHE
GLN = cvar.GLN
TYR = cvar.TYR
HIS = cvar.HIS
CYS = cvar.CYS
MET = cvar.MET
TRP = cvar.TRP
ASX = cvar.ASX
GLX = cvar.GLX
PCA = cvar.PCA
HYP = cvar.HYP
A = cvar.A
C = cvar.C
G = cvar.G
T = cvar.T
U = cvar.U
UPLUS = cvar.UPLUS
I = cvar.I
_1MA = cvar._1MA
_5MC = cvar._5MC
OMC = cvar.OMC
_1MG = cvar._1MG
_2MG = cvar._2MG
M2G = cvar.M2G
_7MG = cvar._7MG
OMG = cvar.OMG
YG = cvar.YG
H2U = cvar.H2U
_5MU = cvar._5MU
PSU = cvar.PSU
UNK = cvar.UNK
ACE = cvar.ACE
FOR = cvar.FOR
HOH = cvar.HOH
DOD = cvar.DOD
SO4 = cvar.SO4
PO4 = cvar.PO4
NAD = cvar.NAD
COA = cvar.COA
NAP = cvar.NAP
NDP = cvar.NDP
AMINO = cvar.AMINO
AMINO_NUCLEO = cvar.AMINO_NUCLEO
COENZYME = cvar.COENZYME
ION = cvar.ION
NUCLEO = cvar.NUCLEO
PROTEIN = cvar.PROTEIN
PURINE = cvar.PURINE
PYRIMIDINE = cvar.PYRIMIDINE
SOLVENT = cvar.SOLVENT
WATER = cvar.WATER
OB_4RING_ATOM = _openbabel.OB_4RING_ATOM
OB_3RING_ATOM = _openbabel.OB_3RING_ATOM
OB_AROMATIC_ATOM = _openbabel.OB_AROMATIC_ATOM
@@ -1411,91 +1518,6 @@ class OBAtom(OBBase):
def MatchesSMARTS(*args): return _openbabel.OBAtom_MatchesSMARTS(*args)
OBAtom_swigregister = _openbabel.OBAtom_swigregister
OBAtom_swigregister(OBAtom)
ACIDIC = cvar.ACIDIC
ACYCLIC = cvar.ACYCLIC
ALIPHATIC = cvar.ALIPHATIC
AROMATIC = cvar.AROMATIC
BASIC = cvar.BASIC
BURIED = cvar.BURIED
CHARGED = cvar.CHARGED
CYCLIC = cvar.CYCLIC
HYDROPHOBIC = cvar.HYDROPHOBIC
LARGE = cvar.LARGE
MEDIUM = cvar.MEDIUM
NEGATIVE = cvar.NEGATIVE
NEUTRAL = cvar.NEUTRAL
POLAR = cvar.POLAR
POSITIVE = cvar.POSITIVE
SMALL = cvar.SMALL
SURFACE = cvar.SURFACE
ALPHA_CARBON = cvar.ALPHA_CARBON
AMINO_BACKBONE = cvar.AMINO_BACKBONE
BACKBONE = cvar.BACKBONE
CYSTEINE_SULPHUR = cvar.CYSTEINE_SULPHUR
LIGAND = cvar.LIGAND
NUCLEIC_BACKBONE = cvar.NUCLEIC_BACKBONE
SHAPELY_BACKBONE = cvar.SHAPELY_BACKBONE
SHAPELY_SPECIAL = cvar.SHAPELY_SPECIAL
SIDECHAIN = cvar.SIDECHAIN
SUGAR_PHOSPHATE = cvar.SUGAR_PHOSPHATE
ALA = cvar.ALA
GLY = cvar.GLY
LEU = cvar.LEU
SER = cvar.SER
VAL = cvar.VAL
THR = cvar.THR
LYS = cvar.LYS
ASP = cvar.ASP
ILE = cvar.ILE
ASN = cvar.ASN
GLU = cvar.GLU
PRO = cvar.PRO
ARG = cvar.ARG
PHE = cvar.PHE
GLN = cvar.GLN
TYR = cvar.TYR
HIS = cvar.HIS
CYS = cvar.CYS
MET = cvar.MET
TRP = cvar.TRP
ASX = cvar.ASX
GLX = cvar.GLX
PCA = cvar.PCA
HYP = cvar.HYP
A = cvar.A
C = cvar.C
G = cvar.G
T = cvar.T
U = cvar.U
UPLUS = cvar.UPLUS
I = cvar.I
OMC = cvar.OMC
M2G = cvar.M2G
OMG = cvar.OMG
YG = cvar.YG
H2U = cvar.H2U
PSU = cvar.PSU
UNK = cvar.UNK
ACE = cvar.ACE
FOR = cvar.FOR
HOH = cvar.HOH
DOD = cvar.DOD
SO4 = cvar.SO4
PO4 = cvar.PO4
NAD = cvar.NAD
COA = cvar.COA
NAP = cvar.NAP
NDP = cvar.NDP
AMINO = cvar.AMINO
AMINO_NUCLEO = cvar.AMINO_NUCLEO
COENZYME = cvar.COENZYME
ION = cvar.ION
NUCLEO = cvar.NUCLEO
PROTEIN = cvar.PROTEIN
PURINE = cvar.PURINE
PYRIMIDINE = cvar.PYRIMIDINE
SOLVENT = cvar.SOLVENT
WATER = cvar.WATER
OB_AROMATIC_BOND = _openbabel.OB_AROMATIC_BOND
OB_WEDGE_BOND = _openbabel.OB_WEDGE_BOND
@@ -2814,5 +2836,27 @@ class OBResidueAtomIter(object):
OBResidueAtomIter_swigregister = _openbabel.OBResidueAtomIter_swigregister
OBResidueAtomIter_swigregister(OBResidueAtomIter)
class doubleArray(object):
thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
__repr__ = _swig_repr
def __init__(self, *args):
_openbabel.doubleArray_swiginit(self,_openbabel.new_doubleArray(*args))
__swig_destroy__ = _openbabel.delete_doubleArray
__del__ = lambda self : None;
def __getitem__(*args): return _openbabel.doubleArray___getitem__(*args)
def __setitem__(*args): return _openbabel.doubleArray___setitem__(*args)
def cast(*args): return _openbabel.doubleArray_cast(*args)
frompointer = staticmethod(_openbabel.doubleArray_frompointer)
doubleArray_swigregister = _openbabel.doubleArray_swigregister
doubleArray_swigregister(doubleArray)
doubleArray_frompointer = _openbabel.doubleArray_frompointer
def double_array(mylist):
"""Create a C array of doubles from a list."""
c = doubleArray(len(mylist))
for i,v in enumerate(mylist):
c[i] = v
return c

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