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From 2fb8dea9d1ace5b1fc1ddcf0f7034cf119763b53 Mon Sep 17 00:00:00 2001
From: Andrius Merkys <andrius.merkys@gmail.com>
Date: Wed, 8 Jan 2020 11:47:58 +0200
Subject: [PATCH] Migrating xdrawchem to Open Babel 3.
---
xdrawchem-qt5/xdrawchem.pro | 4 ++--
xdrawchem-qt5/xdrawchem/ioiface.cpp | 8 ++++----
xdrawchem-qt5/xdrawchem/ioiface.h | 3 +++
xdrawchem-qt5/xdrawchem/molecule.h | 4 ++++
xdrawchem-qt5/xdrawchem/molecule_obmol.cpp | 10 +++++-----
xdrawchem-qt5/xdrawchem/molecule_smiles.cpp | 8 +++-----
6 files changed, 21 insertions(+), 16 deletions(-)
diff --git a/xdrawchem-qt5/xdrawchem.pro b/xdrawchem-qt5/xdrawchem.pro
index e8e1886..2b4e2a2 100644
--- a/xdrawchem-qt5/xdrawchem.pro
+++ b/xdrawchem-qt5/xdrawchem.pro
@@ -2,8 +2,8 @@ TEMPLATE = app
TARGET = xdrawchem
# edit to match your OB install
-exists(/usr/include/openbabel-2.0/openbabel/mol.h) {
-INCLUDEPATH += /usr/include/openbabel-2.0
+exists(/usr/include/openbabel3/openbabel/mol.h) {
+INCLUDEPATH += /usr/include/openbabel3
LIBS += -lopenbabel
}
exists(/usr/local/include/openbabel-2.0/openbabel/mol.h) {
diff --git a/xdrawchem-qt5/xdrawchem/ioiface.cpp b/xdrawchem-qt5/xdrawchem/ioiface.cpp
index acba119..5123970 100644
--- a/xdrawchem-qt5/xdrawchem/ioiface.cpp
+++ b/xdrawchem-qt5/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];
diff --git a/xdrawchem-qt5/xdrawchem/ioiface.h b/xdrawchem-qt5/xdrawchem/ioiface.h
index 9db30f8..dd671da 100644
--- a/xdrawchem-qt5/xdrawchem/ioiface.h
+++ b/xdrawchem-qt5/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;
diff --git a/xdrawchem-qt5/xdrawchem/molecule.h b/xdrawchem-qt5/xdrawchem/molecule.h
index f11cb73..cf57096 100644
--- a/xdrawchem-qt5/xdrawchem/molecule.h
+++ b/xdrawchem-qt5/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>
diff --git a/xdrawchem-qt5/xdrawchem/molecule_obmol.cpp b/xdrawchem-qt5/xdrawchem/molecule_obmol.cpp
index b48d860..50dd949 100644
--- a/xdrawchem-qt5/xdrawchem/molecule_obmol.cpp
+++ b/xdrawchem-qt5/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];
diff --git a/xdrawchem-qt5/xdrawchem/molecule_smiles.cpp b/xdrawchem-qt5/xdrawchem/molecule_smiles.cpp
index 5d7c8b3..4bf9fbb 100644
--- a/xdrawchem-qt5/xdrawchem/molecule_smiles.cpp
+++ b/xdrawchem-qt5/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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