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updates for 1.9.11
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added SPEC file to qt5 branch and checking in fixes for 1.9.11
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@bryanherger
bryanherger committed Dec 24, 2016
1 parent e8bab78 commit d4c27d9
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9 changes: 6 additions & 3 deletions README.md
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Expand Up @@ -4,11 +4,14 @@ Welcome to XDrawChem!

Please visit the project page at http://www.woodsidelabs.com/chemistry/xdrawchem.php

Current release (1.9.10-1) source tarball and RPM are at SourceForge: https://sourceforge.net/projects/xdrawchem/files/xdrawchem/1.9.10/
Current release (1.9.11-1) source tarball and RPM are at SourceForge: https://sourceforge.net/projects/xdrawchem/files/xdrawchem/1.9.10/

This package conatins two versions of XDrawChem:
This repository conatins three (!) versions of XDrawChem:

xdrawchem - this is the main development version. It is based on Qt 3.x.
xdrawchem-qt5 - this is the main development and release version (1.9.11 onwards). It is based on Qt 5.x.
(Starting with 1.10.x, this will be "xdrawchem" and the legacy version will be "xdrawchem-qt3")

xdrawchem - this is the legacy Qt3 version (1.9.10 and prior). It is based on Qt 3.x.

xdrawchem-qt4 - this is a contributed version. It is based on Qt 4.
Eventually, this will become the main version, but most distributions
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47 changes: 47 additions & 0 deletions xdrawchem-qt5/SPECS/xdrawchem.spec
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@@ -0,0 +1,47 @@
Summary: XDrawChem is an application for drawing and analyzing chemical structures and reactions.
Name: xdrawchem
Version: 1.9.11
Release: 1
License: GPL
Group: Applications/Productivity
URL: http://www.woodsidelabs.com/chemistry/xdrawchem.php
Source0: https://sourceforge.net/projects/%{name}/files/%{name}/%{version}/%{name}-%{version}-%{release}.rpmsrc.tar.gz
Requires: openbabel qt5-qtbase
BuildRequires: openbabel openbabel-devel qt5-qtbase-devel
BuildRoot: /var/tmp/%{name}-buildroot

%description
XDrawChem is an application for drawing and analyzing chemical structures and reactions.

%prep
%setup -q

%build
[ "$RPM_BUILD_ROOT" != "/" ] && rm -rf $RPM_BUILD_ROOT
mkdir -p $RPM_BUILD_ROOT
qmake-qt5 PREFIX="/usr/local"
make

%install
install -D -m 0755 bin/xdrawchem $RPM_BUILD_ROOT/usr/local/bin/xdrawchem
mkdir -p $RPM_BUILD_ROOT/usr/local/share/xdrawchem
chmod 0755 $RPM_BUILD_ROOT/usr/local/share/xdrawchem
cp ring/* $RPM_BUILD_ROOT/usr/local/share/xdrawchem
mkdir -p $RPM_BUILD_ROOT/usr/local/share/xdrawchem/doc
chmod 0755 $RPM_BUILD_ROOT/usr/local/share/xdrawchem/doc
cp doc/* $RPM_BUILD_ROOT/usr/local/share/xdrawchem/doc

%clean
make clean
[ "$RPM_BUILD_ROOT" != "/" ] && rm -rf $RPM_BUILD_ROOT

%files
%defattr(-,root,root)
%doc README.txt INSTALL.txt TODO.txt COPYRIGHT.txt
/usr/local/bin/xdrawchem
/usr/local/share/xdrawchem/*

%changelog
* Sun Dec 11 2016 Bryan Herger <bherger@users.sf.net>
- initial version of spec file

4 changes: 3 additions & 1 deletion xdrawchem-qt5/xdrawchem.pro
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
TEMPLATE = app
TARGET = xdrawchem-qt5
TARGET = xdrawchem

# edit to match your OB install
INCLUDEPATH += /usr/include/openbabel-2.0
Expand Down Expand Up @@ -29,6 +29,8 @@ doc.path = $${PREFIX}/share/xdrawchem/doc
doc.files = doc/*
INSTALLS += ringdir doc
QMAKE_CXXFLAGS_DEBUG += -O0 -g3
QMAKE_CXXFLAGS_GNUCXX11 =
QMAKE_CXXFLAGS_CXX11 =

//DEFINES += QT_NO_CAST_TO_ASCII
CONFIG += debug
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2 changes: 1 addition & 1 deletion xdrawchem-qt5/xdrawchem/atom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ class Atom
n->bondOrderSum = bondOrderSum;
//System->arraycopy(nodeTable, 0, n->nodeTable, 0, 10);
for (int f = 0; f < 10; f++)
n->nodeTable.insert(f, nodeTable[f]); // shallow copy!
n->nodeTable.replace(f, nodeTable[f]); // shallow copy!
// the rest are deep copies.
n->intnodeTable = intnodeTable;
n->bondTable = bondTable;
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8 changes: 4 additions & 4 deletions xdrawchem-qt5/xdrawchem/molecule_smiles.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ void Molecule::SDG( bool coord )
a1 = atoms.at( c1 );
for ( c2 = 0; c2 < tmp_pt->neighbors.count(); c2++ ) {
refnum = tmp_pt->neighbors.at( c2 )->serial;
a1->nodeTable.insert( c2, atoms.at( refnum ) );
a1->nodeTable.replace( c2, atoms.at( refnum ) );
a1->bondTable[c2] = tmp_pt->bondorder[c2];
a1->intnodeTable[c2] = refnum;
}
Expand All @@ -106,12 +106,12 @@ void Molecule::SDG( bool coord )
c2 = 0;
for (tmp_pt = tmp_ring->first(); tmp_pt != 0; tmp_pt = tmp_ring->next()) {
a1 = atoms.at(tmp_pt->serial);
ring1->insert(c2, a1);
ring1->replace(c2, a1);
qInfo() << "RA" << c2 << ":" << tmp_pt->serial ;
c2++;
}
ring1->sort2();
s1.insert(c1, ring1);
s1.replace(c1, ring1);
c1++;
}
*/
Expand Down Expand Up @@ -463,7 +463,7 @@ void Molecule::FromSMILES(QString sm) {
int ringnum = tmp_token.right(1).toInt();
flag = true;
if (ring_array_status[ringnum] == false) { // save this atom
ring_closure_array.insert(ringnum, new_pt);
ring_closure_array.replace(ringnum, new_pt);
ring_array_status[ringnum] = true;
} else { // do ring closure
tmp_pt = ring_closure_array.at(ringnum);
Expand Down
56 changes: 40 additions & 16 deletions xdrawchem-qt5/xdrawchem/sdg.h
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Original file line number Diff line number Diff line change
Expand Up @@ -68,11 +68,16 @@ class SPoint {
y = (double)y1;
}

/** Constructs a point as a dublicate of another point */
/** Constructs a point as a duplicate of another point */
SPoint(const SPoint &p){
x = p.x;
y = p.y;
}

/** return this SPoint as a QString */
QString toString() {
return QString("(%1,%2)").arg(x).arg(y);
}
};

/** Construct that stores the parameters needed for the placement of
Expand Down Expand Up @@ -135,6 +140,7 @@ class SDG {
ringTracker = 0;
ddebug = 0;
draw();
drawStatus("at end");
}

/** Performs the actual calculation of the coordinated based on a
Expand All @@ -154,7 +160,7 @@ class SDG {
atomSet[i]->status = 0;
atomSet[i]->ringCounter = 0;
}

drawStatus("start");
sortBondList();
for (int f = 0; f < atomSet.count(); f++)
{
Expand All @@ -170,6 +176,7 @@ class SDG {
sssr = sorf.findSSSR(atomSet); //should be passed from Molecule()
sssr.sort();
sssr.makeNodeRingLists(atomSet);
drawStatus("after sssr");

if (sssr.size() > 0){
/* We have rings
Expand Down Expand Up @@ -203,6 +210,7 @@ class SDG {
}
}
positionRingAtoms(complRing, SPoint(0,0), (double)0, 0, complRingSize - 1);
drawStatus("208");
ring = sssr.at(complRing);
ring->status = 1;

Expand All @@ -215,6 +223,7 @@ class SDG {
for (int f = 0; f < sssr.size(); f++){
if ((sssr.at(f))->status == 1) {
positionRingSubstituents(f);
drawStatus("222");
//if (true) return;
stillThere = true;
}
Expand Down Expand Up @@ -278,14 +287,21 @@ class SDG {
int whatToDraw(){
for (int f = 0; f < atomSet.count(); f++){
if (atomSet[f]->status == 1){
qDebug() << "whatToDraw(): " << f ;
qInfo() << "whatToDraw(): " << f ;
return f;
}
}
qDebug() << "whatToDraw(): -1" ;
qInfo() << "whatToDraw(): -1" ;
return -1;
}

/** Scans the array of nodes for those that have not been finally drawn */

void drawStatus(QString note){
// debug: what actually happened here?
for (int ii = 0; ii < atomSet.count(); ii++) { qInfo() << note << ":SDG pos:" << ii << ":status:" << atomSet[ii]->status << ":(" << atomSet[ii]->x << "," << atomSet[ii]->y << ")"; }
}

/** Takes care of drawing an ring-less graph once one start
atom has been placed. */

Expand Down Expand Up @@ -399,7 +415,7 @@ class SDG {
// ringType = 1 : spiro annulation requested;
// ringType = 2 : regular 1-bond annulation requested;
// ringType = 3 : annulation with more than two shared atoms
//System.out.println("Ring to substitute: " + ringIndex);
qInfo() << "Ring to substitute: " << ringIndex;
double ph = 0.0174532925;
Ring *ring = sssr.at(ringIndex);
int k = ring->size();
Expand Down Expand Up @@ -435,6 +451,7 @@ class SDG {
which already has been positioned by the calling
method */
handleRestOfRingSubstituents(ringIndex);
drawStatus("451");
return;

}
Expand All @@ -458,7 +475,7 @@ class SDG {
/* we found another ring to which atom belongs
which is not yet positioned. Let's remember it. */
secondRing = sssr.at(tempRing);
qDebug() << "secondRing:" << secondRing->getSortedString() ;
qInfo() << "secondRing:" << secondRing->getSortedString() ;
secondRingNumber = tempRing;
size = (getIntersection(ring->getNodeNumberList(), secondRing->getNodeNumberList())).count();
if (secondRing->notAllPositioned(atomSet)){
Expand Down Expand Up @@ -530,7 +547,7 @@ class SDG {
SPoint(atomSet[tempAtom]->x, atomSet[tempAtom]->y), rad);

if (alph != (double) 0.0)
//qDebug() << "Invoking rot-Atom() from line 538" ;
//qInfo() << "Invoking rot-Atom() from line 538" ;
tempPoint = rotAtom(SPoint(atomSet[tempAtom]->x, atomSet[tempAtom]->y), tempPoint, alph);

secondRing->x = tempPoint.x;
Expand Down Expand Up @@ -713,7 +730,7 @@ class SDG {
//System.out.println("Bicyclo");
for (il = 0; il < km; il++) {
if (atomSet[secondRing->getNodeNumber(il)]->status <= 0) {
//qDebug() << "Invoking rot-Atom() from line 719" ;
//qInfo() << "Invoking rot-Atom() from line 719" ;
temp2Point = rotAtom(SPoint(secondRing->x,secondRing->y), tempPoint, alph);
atomSet[secondRing->getNodeNumber(il)]->status = 1;
atomSet[secondRing->getNodeNumber(il)]->x = temp2Point.x;
Expand Down Expand Up @@ -777,7 +794,7 @@ class SDG {
x2 = round(center2.x * roundFactor) / roundFactor;
y2 = round(center2.y * roundFactor) / roundFactor;
angle = 360 / (sssr.at(numberOfSecondRing))->size();
qDebug() << "FRP:" << x1 << "," << y1 << ";" << x2 << "," << y2 ;
qInfo() << "FRP:" << x1 << "," << y1 << ";" << x2 << "," << y2 ;
FusedRingParams fRP;
// First block
if (x2 > x1 && y2 >= y1){
Expand Down Expand Up @@ -963,6 +980,7 @@ class SDG {
'vector' in distance 'distance' from origin. Originally called
'neuat()' */
SPoint placeAtom(SPoint origin, SPoint vector, double distance){
qInfo() << "placeAtom " << origin.toString() << " " << vector.toString() << " d=" << distance;
double a, b, cc;
a = vector.x - origin.x;
b = vector.y - origin.y;
Expand All @@ -974,11 +992,12 @@ class SDG {

/** Rotates the atom at Point 'point' around the Point 'center' with the angle 'angle' */
SPoint rotAtom(SPoint center, SPoint point, double angle){
qInfo() << "rotAtom " << center.toString() << " " << point.toString() << " a=" << angle;
double ph = 0.0174532925;
double p, co, si, x1, y1, x, y;

// make aliphatics look good
//qDebug() << "ANGLE:" << angle;
//qInfo() << "ANGLE:" << angle;

if (arerings == true) {
if (ncalls == 0) {
Expand Down Expand Up @@ -1010,7 +1029,7 @@ class SDG {
}
}

//qDebug() << " " << angle ;
//qInfo() << " " << angle ;
// end aliphatics garbling

p = ph * angle;
Expand All @@ -1029,6 +1048,7 @@ class SDG {
Returns "-1" if no ring was drawn or the ring number of the ring draw */
int positionAtomSubstituents(int atomIndex, SPoint point, SPoint helpPoint,
QVector<int> ilist, int modus, int ir, int igr){
qInfo() << "positionAtomSubstituents:atomIndex=" << atomIndex;
double ph = 0.0174532925;
int i, ib, /*ibb, iii, iph,*/ k;
double alph, /*b, phi,*/ rad/*, xx, yy*/;
Expand Down Expand Up @@ -1073,9 +1093,12 @@ class SDG {
for (i = 0; i < k; i++) {
tempAtom = atomSet[atomIndex]->intnodeTable[i];
if (atomSet[tempAtom]->status <= 0) {
double thisRot = rot[i];
if (thisRot > (double)359.9) thisRot = (double)0.0;
qInfo() << "placeAtom " << tempAtom << " status=" << atomSet[tempAtom]->status << " rot["<<i<<"]=" << thisRot;
tempPoint = placeAtom(helpPoint, point, bondLength);
//qDebug() << "Invoking rot-Atom() from line 1079" ;
test = rotAtom(point, tempPoint, rot[i]);
//qInfo() << "Invoking rot-Atom() from line 1079" ;
test = rotAtom(point, tempPoint, thisRot);
atomSet[tempAtom]->x = test.x;
atomSet[tempAtom]->y = test.y;
atomSet[tempAtom]->status = 1;
Expand All @@ -1102,7 +1125,7 @@ class SDG {
/* -------------------------------------------------------------*/
rad = bondLength/ 2 / sin(ph * (180.0 / igr));
tempPoint = placeAtom(SPoint(xh, yh), SPoint(x, y), rad);
//qDebug() << "Invoking rot-Atom() from line 1106" ;
//qInfo() << "Invoking rot-Atom() from line 1106" ;
tempPoint = rotAtom(SPoint(x, y), tempPoint, alph);
ring->x = tempPoint.x;
ring->y = tempPoint.y;
Expand Down Expand Up @@ -1312,7 +1335,7 @@ class SDG {
/* rotate substituents by angle pp */
/* if more than one neighbor has to be drawn */
/*----------------------------------------------*/
//qDebug() << "Invoking rot-Atom() from line 1317" ;
//qInfo() << "Invoking rot-Atom() from line 1317" ;
tempPoint = rotAtom(SPoint(x, y), SPoint(xx, yy), pp);
atomSet[atomSet[bridgeAtomNumber]->intnodeTable[i]]->x = tempPoint.x;
atomSet[atomSet[bridgeAtomNumber]->intnodeTable[i]]->y = tempPoint.y;
Expand All @@ -1330,7 +1353,7 @@ class SDG {
/* rotate substituents by angle pp */
/* if more than one neighbor has to be drawn */
/*----------------------------------------------*/
//qDebug() << "Invoking rot-Atom() from line 1335" ;
//qInfo() << "Invoking rot-Atom() from line 1335" ;
tempPoint = rotAtom(SPoint(x, y), SPoint(xx, yy), pp);
atomSet[atomSet[bridgeAtomNumber]->intnodeTable[i]]->x = tempPoint.x;
atomSet[atomSet[bridgeAtomNumber]->intnodeTable[i]]->y = tempPoint.y;
Expand Down Expand Up @@ -1389,6 +1412,7 @@ class SDG {
}
result = positionAtomSubstituents(ring->getNodeNumber(i), SPoint(atomSet[ring->getNodeNumber(i)]->x, atomSet[ring->getNodeNumber(i)]->y),
SPoint(ring->x, ring->y), ilist, ring->size(), ir, igr);
drawStatus("1406");
}
}
}
Expand Down
7 changes: 3 additions & 4 deletions xdrawchem-qt5/xdrawchem/setofrings.h
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Original file line number Diff line number Diff line change
Expand Up @@ -66,11 +66,9 @@ class setOfRings : public QVector<Ring *>
s2 = ring->getSortedString();
qInfo() << s1 << "-vs-" << s2 ;
if (s1 == s2){
qInfo("true!");
return true;
}
}
qInfo("false!");
return false;
}

Expand Down Expand Up @@ -131,8 +129,8 @@ class setOfRings : public QVector<Ring *>
void swap(int i, int j){
Ring *r;
r = at(i);
insert(i, at(j));
insert(j, r);
replace(i, at(j));
replace(j, r);
}

/** Lists the rings in this set to the console */
Expand All @@ -146,6 +144,7 @@ class setOfRings : public QVector<Ring *>
that it is part of. */

void makeNodeRingLists(QVector<Atom *> thisAtomSet){
qInfo() << "makeNodeRingLists: size = " << thisAtomSet.size();
Ring *ring = 0;
int nodeNo = -1;
for (int f = 0; f < size(); f++){
Expand Down
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