Attachment 221140 Details for Bug 252309 – science/xdrawchem: chase the upgrade to OpenBabel 3

[patch] science/xdrawchem: chase the upgrade to OpenBabel 3

science_xdrawchem.diff (text/plain), 9.85 KB, created by Thierry Thomas on 2020-12-31 16:34:52 UTC

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Creator: Thierry Thomas

Created: 2020-12-31 16:34:52 UTC

Size: 9.85 KB

patch

obsolete

>Index: science/xdrawchem/Makefile
>===================================================================
>--- science/xdrawchem/Makefile	(revision 558294)
>+++ science/xdrawchem/Makefile	(working copy)
>@@ -2,7 +2,7 @@
> 
> PORTNAME=	xdrawchem
> DISTVERSION=	1.10.2-1
>-PORTREVISION=	3
>+PORTREVISION=	4
> CATEGORIES=	science
> 
> MAINTAINER=	yuri@FreeBSD.org
>@@ -21,6 +21,10 @@
> 
> WRKSRC_SUBDIR=	${PORTNAME}-qt5
> 
>+pre-configure:
>+	${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|'	\
>+		${WRKSRC}/xdrawchem.pro
>+
> post-install:
> 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
> 
>Index: science/xdrawchem/files/patch-xdrawchem.pro
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem.pro	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem.pro	(working copy)
>@@ -0,0 +1,13 @@
>+--- xdrawchem.pro.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem.pro
>+@@ -6,8 +6,8 @@ exists(/usr/include/openbabel-2.0/openbabel/mol.h) {
>+ INCLUDEPATH += /usr/include/openbabel-2.0
>+ LIBS += -lopenbabel
>+ }
>+-exists(/usr/local/include/openbabel-2.0/openbabel/mol.h) {
>+-INCLUDEPATH += /usr/local/include/openbabel-2.0
>++exists(%%LOCALBASE%%/include/openbabel3/openbabel/mol.h) {
>++INCLUDEPATH += %%LOCALBASE%%/include/openbabel3
>+ LIBS += -lopenbabel
>+ }
>+ exists(/Developer/openbabel-2.4.1/include/openbabel/mol.h) {
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem.pro
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: science/xdrawchem/files/patch-xdrawchem_ioiface.cpp
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem_ioiface.cpp	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem_ioiface.cpp	(working copy)
>@@ -0,0 +1,38 @@
>+--- xdrawchem/ioiface.cpp.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem/ioiface.cpp
>+@@ -193,7 +193,7 @@ void IOIface::convertToChemData()
>+         int bondorder = bond->GetBondOrder();
>+ 
>+         //set elements
>+-        if ( !atom1->IsCarbon() ) {
>++        if ( atom1->GetAtomicNum() != 6 ) {
>+             QString str( "<element>" );
>+             str += IOIface::symbol[atom1->GetAtomicNum() - 1];
>+             str += "</element>";
>+@@ -201,7 +201,7 @@ void IOIface::convertToChemData()
>+ 
>+         }
>+ 
>+-        if ( !atom2->IsCarbon() ) {
>++        if ( atom2->GetAtomicNum() != 6 ) {
>+             QString str( "<element>" );
>+ 
>+             str += IOIface::symbol[atom2->GetAtomicNum() - 1];
>+@@ -216,7 +216,7 @@ void IOIface::convertToChemData()
>+ 
>+         //label atoms if not Carbon
>+ 
>+-        if ( !atom1->IsCarbon() ) {
>++        if ( atom1->GetAtomicNum() != 6 ) {
>+ 
>+             text = new Text( chemdata->getRender2D() );
>+             QString str = IOIface::symbol[atom1->GetAtomicNum() - 1];
>+@@ -229,7 +229,7 @@ void IOIface::convertToChemData()
>+             //qDebug() << "ioiface(1) text:" << str;
>+         }
>+ 
>+-        if ( !atom2->IsCarbon() ) {
>++        if ( atom2->GetAtomicNum() != 6 ) {
>+ 
>+             text = new Text( chemdata->getRender2D() );
>+             QString str = IOIface::symbol[atom2->GetAtomicNum() - 1];
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem_ioiface.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: science/xdrawchem/files/patch-xdrawchem_ioiface.h
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem_ioiface.h	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem_ioiface.h	(working copy)
>@@ -0,0 +1,12 @@
>+--- xdrawchem/ioiface.h.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem/ioiface.h
>+@@ -20,6 +20,9 @@
>+ 
>+ #include "chemdata.h"
>+ 
>++#include <openbabel/atom.h>
>++#include <openbabel/bond.h>
>++#include <openbabel/math/vector3.h>
>+ #include <openbabel/mol.h>
>+ 
>+ using namespace OpenBabel;
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem_ioiface.h
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: science/xdrawchem/files/patch-xdrawchem_molecule.h
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem_molecule.h	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem_molecule.h	(working copy)
>@@ -0,0 +1,13 @@
>+--- xdrawchem/molecule.h.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem/molecule.h
>+@@ -3,6 +3,10 @@
>+ #ifndef MOLECULE_H
>+ #define MOLECULE_H
>+ 
>++#include <openbabel/atom.h>
>++#include <openbabel/bond.h>
>++#include <openbabel/elements.h>
>++#include <openbabel/math/vector3.h>
>+ #include <openbabel/mol.h>
>+ #include <openbabel/obconversion.h>
>+ 
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem_molecule.h
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp	(working copy)
>@@ -0,0 +1,47 @@
>+--- xdrawchem/molecule_obmol.cpp.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem/molecule_obmol.cpp
>+@@ -58,7 +58,7 @@ bool Molecule::convertFromOBMol( OBMol * obmol )
>+     Point point;
>+     Text *text;
>+ 
>+-    std::vector < OBEdgeBase * >::iterator bonditr;
>++    std::vector < OBBond * >::iterator bonditr;
>+     std::map < Point, DPoint *, pt_cmp > points;
>+     std::map < Point, DPoint *, pt_cmp >::iterator itr;
>+ 
>+@@ -133,7 +133,7 @@ bool Molecule::convertFromOBMol( OBMol * obmol )
>+         int bondorder = bond->GetBondOrder();
>+ 
>+         //set elements
>+-        if ( !atom1->IsCarbon() ) {
>++        if ( atom1->GetAtomicNum() != 6 ) {
>+             QString str( "<element>" );
>+ 
>+             str += symbol[atom1->GetAtomicNum() - 1];
>+@@ -142,7 +142,7 @@ bool Molecule::convertFromOBMol( OBMol * obmol )
>+ 
>+         }
>+ 
>+-        if ( !atom2->IsCarbon() ) {
>++        if ( atom2->GetAtomicNum() != 6 ) {
>+             QString str( "<element>" );
>+ 
>+             str += symbol[atom2->GetAtomicNum() - 1];
>+@@ -155,7 +155,7 @@ bool Molecule::convertFromOBMol( OBMol * obmol )
>+ 
>+         //label atoms if not Carbon
>+ 
>+-        if ( !atom1->IsCarbon() ) {
>++        if ( atom1->GetAtomicNum() != 6 ) {
>+ 
>+             text = new Text( r );
>+             QString str = symbol[atom1->GetAtomicNum() - 1];
>+@@ -167,7 +167,7 @@ bool Molecule::convertFromOBMol( OBMol * obmol )
>+             addText( text );
>+         }
>+ 
>+-        if ( !atom2->IsCarbon() ) {
>++        if ( atom2->GetAtomicNum() != 6 ) {
>+ 
>+             text = new Text( r );
>+             QString str = symbol[atom2->GetAtomicNum() - 1];
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp
>===================================================================
>--- science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp	(nonexistent)
>+++ science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp	(working copy)
>@@ -0,0 +1,32 @@
>+--- xdrawchem/molecule_smiles.cpp.orig	2017-01-09 12:25:32 UTC
>++++ xdrawchem/molecule_smiles.cpp
>+@@ -254,8 +254,6 @@ void Molecule::FromSMILES( QString sm )
>+ 
>+     DPoint *thisDPoint;
>+ 
>+-    OpenBabel::OBElementTable etable;
>+-
>+     std::vector < OpenBabel::OBNodeBase * >::iterator ait;
>+ 
>+     std::map < OpenBabel::OBAtom *, DPoint * >hashit;
>+@@ -265,9 +263,9 @@ void Molecule::FromSMILES( QString sm )
>+ 
>+         qInfo() << "Adding OBAtom: " << i++ << " of element#: " <<
>+           thisAtom->GetAtomicNum() << " type: " <<
>+-          etable.GetSymbol(thisAtom->GetAtomicNum()) ;
>++          OBElements::GetSymbol(thisAtom->GetAtomicNum()) ;
>+         thisDPoint = new DPoint;
>+-        tmp_element = etable.GetSymbol( thisAtom->GetAtomicNum() );
>++        tmp_element = OBElements::GetSymbol( thisAtom->GetAtomicNum() );
>+ 
>+         tmp_element_mask = tmp_element;
>+         tmp_element_mask.fill( ' ' );   // fix the mask characters
>+@@ -292,7 +290,7 @@ void Molecule::FromSMILES( QString sm )
>+ 
>+     OpenBabel::OBBond * thisBond;
>+ 
>+-    std::vector < OpenBabel::OBEdgeBase * >::iterator bit;
>++    std::vector < OpenBabel::OBBond * >::iterator bit;
>+     for ( thisBond = myMol.BeginBond( bit ); thisBond; thisBond = myMol.NextBond( bit ) ) {
>+         addBond( hashit[thisBond->GetBeginAtom()], hashit[thisBond->GetEndAtom()], 1, thisBond->GetBondOrder(), QColor( 0, 0, 0 ), true );
>+     }
>
>Property changes on: science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 252309: 221136 | 221137 | 221138 | 221139 | 221140