svn commit: r561406 - in head/science: gchemutils kalzium luscus molsketch xdrawchem xdrawchem/files
Yuri Victorovich
yuri at FreeBSD.org
Wed Jan 13 00:31:41 UTC 2021
Author: yuri
Date: Wed Jan 13 00:31:38 2021
New Revision: 561406
URL: https://svnweb.freebsd.org/changeset/ports/561406
Log:
science/openbabel: Upgrade 2.4.1 -> 3.1.1
PR: 252309
Submitted by: thierry
Added:
head/science/xdrawchem/files/
head/science/xdrawchem/files/patch-xdrawchem.pro (contents, props changed)
head/science/xdrawchem/files/patch-xdrawchem_ioiface.cpp (contents, props changed)
head/science/xdrawchem/files/patch-xdrawchem_ioiface.h (contents, props changed)
head/science/xdrawchem/files/patch-xdrawchem_molecule.h (contents, props changed)
head/science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp (contents, props changed)
head/science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp (contents, props changed)
Modified:
head/science/gchemutils/Makefile
head/science/kalzium/Makefile
head/science/luscus/Makefile
head/science/molsketch/Makefile
head/science/molsketch/distinfo
head/science/molsketch/pkg-plist
head/science/xdrawchem/Makefile
Modified: head/science/gchemutils/Makefile
==============================================================================
--- head/science/gchemutils/Makefile Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/gchemutils/Makefile Wed Jan 13 00:31:38 2021 (r561406)
@@ -3,7 +3,7 @@
PORTNAME= gchemutils
PORTVERSION= 0.14.16
-PORTREVISION= 4
+PORTREVISION= 5
CATEGORIES= science
MASTER_SITES= SAVANNAH/${PORTNAME}/${PORTVERSION:R}
DISTNAME= gnome-chemistry-utils-${PORTVERSION}
@@ -62,8 +62,9 @@ PLIST_SUB+= GNUMERIC=""
PLIST_SUB+= GNUMERIC="@comment "
.endif
-post-patch:
- @${REINPLACE_CMD} -e 's|-ldl||g' ${WRKSRC}/libs/gcp/Makefile.in
+pre-configure:
+ ${REINPLACE_CMD} -e 's|-ldl||g' ${WRKSRC}/libs/gcp/Makefile.in
+ ${REINPLACE_CMD} -e 's|openbabel-2.0|openbabel-3|' ${WRKSRC}/${CONFIGURE_SCRIPT}
post-install:
@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so.*
Modified: head/science/kalzium/Makefile
==============================================================================
--- head/science/kalzium/Makefile Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/kalzium/Makefile Wed Jan 13 00:31:38 2021 (r561406)
@@ -2,14 +2,18 @@
PORTNAME= kalzium
DISTVERSION= ${KDE_APPLICATIONS_VERSION}
+PORTREVISION= 1
CATEGORIES= science education kde kde-applications
PATCH_SITES= https://invent.kde.org/education/kalzium/commit/
PATCHFILES= 2b9ebd85.diff:-p1
MAINTAINER= kde at FreeBSD.org
-COMMENT= Periodic table of elements for KDE 4
+COMMENT= Periodic table of elements for KDE
+LICENSE= GPLv2 LGPL20 GFDL
+LICENSE_COMB= multi
+
LIB_DEPENDS= libopenbabel.so:science/openbabel \
libAvogadroCore.so:science/avogadrolibs
BUILD_DEPENDS= ${LOCALBASE}/lib/ocaml/facile/facile.a:math/facile \
@@ -33,6 +37,19 @@ USE_QT= concurrent core dbus declarative gui network
USE_LDCONFIG= yes
+CMF= . compoundviewer compoundviewer/widgets src
+
OPTIONS_DEFINE= DOCS
+
+post-patch:
+ ${CP} ${WRKSRC}/cmake/modules/FindOpenBabel2.cmake \
+ ${WRKSRC}/cmake/modules/FindOpenBabel3.cmake
+ ${REINPLACE_CMD} -e 's|OPENBABEL2|OPENBABEL3|g;s|OpenBabel2|OpenBabel3|' \
+ -e 's|openbabel-2.0|openbabel-3|;s|openbabel-2|openbabel-3|' \
+ ${WRKSRC}/cmake/modules/FindOpenBabel3.cmake
+.for c in ${CMF}
+ ${REINPLACE_CMD} -e 's|OpenBabel2|OpenBabel3|;s|OPENBABEL2|OPENBABEL3|;s|OpenBabel3_|OPENBABEL3_|;s|OPENBABEL3_INCLUDE_DIRS|OPENBABEL3_INCLUDE_DIR|;s|OPENBABEL2_|OPENBABEL3_|' \
+ ${WRKSRC}/${c}/CMakeLists.txt
+.endfor
.include <bsd.port.mk>
Modified: head/science/luscus/Makefile
==============================================================================
--- head/science/luscus/Makefile Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/luscus/Makefile Wed Jan 13 00:31:38 2021 (r561406)
@@ -2,7 +2,7 @@
PORTNAME= luscus
DISTVERSION= 0.8.6
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= science
MASTER_SITES= SF/${PORTNAME}/
DISTNAME= ${PORTNAME}_${DISTVERSION}
@@ -19,7 +19,7 @@ LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \
libfreetype.so:print/freetype2 \
libgdkglext-x11-1.0.so:x11-toolkits/gtkglext
RUN_DEPENDS= bash:shells/bash \
- babel:science/openbabel
+ obabel:science/openbabel # see https://sourceforge.net/p/luscus/tickets/5/
USES= cmake compiler:c++11-lang gettext-runtime gl gnome pkgconfig \
shebangfix xorg
Modified: head/science/molsketch/Makefile
==============================================================================
--- head/science/molsketch/Makefile Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/molsketch/Makefile Wed Jan 13 00:31:38 2021 (r561406)
@@ -1,11 +1,10 @@
# $FreeBSD$
PORTNAME= molsketch
-DISTVERSION= 0.6.0
-PORTREVISION= 1
+DISTVERSION= 0.7.0
DISTVERSIONSUFFIX= -src
CATEGORIES= science
-MASTER_SITES= SF/${PORTNAME}/Molsketch/Nitrogen%20${DISTVERSION}/
+MASTER_SITES= SF/${PORTNAME}/Molsketch/Oxygen%20${DISTVERSION}/
DISTNAME= Molsketch-${DISTVERSIONFULL}
MAINTAINER= yuri at FreeBSD.org
Modified: head/science/molsketch/distinfo
==============================================================================
--- head/science/molsketch/distinfo Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/molsketch/distinfo Wed Jan 13 00:31:38 2021 (r561406)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1552970968
-SHA256 (Molsketch-0.6.0-src.tar.gz) = 999751d0dca25fe5c0b117dddd8a43f2583bb9e2df7fd14cddfa859896389537
-SIZE (Molsketch-0.6.0-src.tar.gz) = 1680065
+TIMESTAMP = 1609181842
+SHA256 (Molsketch-0.7.0-src.tar.gz) = 2a8b181793f6df8892c55399c13674ecf688403ad402c9fead20f4916715bb9d
+SIZE (Molsketch-0.7.0-src.tar.gz) = 1874764
Modified: head/science/molsketch/pkg-plist
==============================================================================
--- head/science/molsketch/pkg-plist Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/molsketch/pkg-plist Wed Jan 13 00:31:38 2021 (r561406)
@@ -22,6 +22,7 @@ include/libmolsketch/actions/itemgrouptypeaction.h
include/libmolsketch/actions/itemtypeaction.h
include/libmolsketch/actions/itemtypeselectionaction.h
include/libmolsketch/actions/itemtypewidget.h
+include/libmolsketch/actions/lineupaction.h
include/libmolsketch/actions/linewidthaction.h
include/libmolsketch/actions/mechanismarrowaction.h
include/libmolsketch/actions/multiaction.h
@@ -46,6 +47,7 @@ include/libmolsketch/coordinatemodel.h
include/libmolsketch/coordinatetableview.h
include/libmolsketch/electronsystem.h
include/libmolsketch/element.h
+include/libmolsketch/elementalignment.h
include/libmolsketch/fileio.h
include/libmolsketch/fontchooser.h
include/libmolsketch/frame.h
@@ -56,15 +58,14 @@ include/libmolsketch/helptextemptydock.h
include/libmolsketch/helptextonemptylabel.h
include/libmolsketch/librarymodel.h
include/libmolsketch/libraryview.h
-include/libmolsketch/lineupaction.h
include/libmolsketch/lonepair.h
include/libmolsketch/math2d.h
-include/libmolsketch/mimemolecule.h
include/libmolsketch/molecule.h
include/libmolsketch/moleculemodelitem.h
include/libmolsketch/moleculepopup.h
include/libmolsketch/molscene.h
include/libmolsketch/molview.h
+include/libmolsketch/neighboralignment.h
include/libmolsketch/propertiesdock.h
include/libmolsketch/propertieswidget.h
include/libmolsketch/qtversionmacros.h
Modified: head/science/xdrawchem/Makefile
==============================================================================
--- head/science/xdrawchem/Makefile Wed Jan 13 00:29:40 2021 (r561405)
+++ head/science/xdrawchem/Makefile Wed Jan 13 00:31:38 2021 (r561406)
@@ -2,7 +2,7 @@
PORTNAME= xdrawchem
DISTVERSION= 1.10.2-1
-PORTREVISION= 3
+PORTREVISION= 4
CATEGORIES= science
MAINTAINER= yuri at FreeBSD.org
@@ -20,6 +20,10 @@ USE_QT= core gui network printsupport widgets xml bui
USE_GL= gl
WRKSRC_SUBDIR= ${PORTNAME}-qt5
+
+pre-configure:
+ ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' \
+ ${WRKSRC}/xdrawchem.pro
post-install:
@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
Added: head/science/xdrawchem/files/patch-xdrawchem.pro
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem.pro Wed Jan 13 00:31:38 2021 (r561406)
@@ -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) {
Added: head/science/xdrawchem/files/patch-xdrawchem_ioiface.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem_ioiface.cpp Wed Jan 13 00:31:38 2021 (r561406)
@@ -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];
Added: head/science/xdrawchem/files/patch-xdrawchem_ioiface.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem_ioiface.h Wed Jan 13 00:31:38 2021 (r561406)
@@ -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;
Added: head/science/xdrawchem/files/patch-xdrawchem_molecule.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem_molecule.h Wed Jan 13 00:31:38 2021 (r561406)
@@ -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>
+
Added: head/science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem_molecule__obmol.cpp Wed Jan 13 00:31:38 2021 (r561406)
@@ -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];
Added: head/science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/science/xdrawchem/files/patch-xdrawchem_molecule__smiles.cpp Wed Jan 13 00:31:38 2021 (r561406)
@@ -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 );
+ }
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