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rdkit/Code/GraphMol/MolDraw2D/MolDraw2D.cpp

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//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
// Original author: David Cosgrove (AstraZeneca)
// 27th May 2014
//
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DDetails.h>
#include <cstdlib>
#include <limits>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <boost/assign/list_of.hpp>
using namespace boost;
using namespace std;
namespace RDKit {
// ****************************************************************************
MolDraw2D::MolDraw2D( int width, int height ) :
width_( width ) , height_( height ) , scale_( 1.0 ) , x_trans_( 0.0 ) ,
y_trans_( 0.0 ) , font_size_( 0.5 ), curr_width_(2), fill_polys_(true) {
}
// ****************************************************************************
void MolDraw2D::drawMolecule( const ROMol &mol ,
const vector<int> *highlight_atoms ,
const map<int,DrawColour> *highlight_atom_map ) {
vector<int> highlight_bonds;
if(highlight_atoms){
for(vector<int>::const_iterator ai=highlight_atoms->begin();
ai!=highlight_atoms->end();++ai){
for(vector<int>::const_iterator aj=ai+1;
aj!=highlight_atoms->end();++aj){
const Bond *bnd=mol.getBondBetweenAtoms(*ai,*aj);
if(bnd) highlight_bonds.push_back(bnd->getIdx());
}
}
}
drawMolecule(mol,highlight_atoms,&highlight_bonds,highlight_atom_map);
}
void MolDraw2D::doContinuousHighlighting( const ROMol &mol ,
const vector<int> *highlight_atoms ,
const vector<int> *highlight_bonds ,
const map<int,DrawColour> *highlight_atom_map,
const map<int,DrawColour> *highlight_bond_map ) {
int orig_lw=lineWidth();
bool orig_fp=fillPolys();
ROMol::VERTEX_ITER this_at , end_at;
if(highlight_bonds){
boost::tie( this_at , end_at ) = mol.getVertices();
while( this_at != end_at ) {
int this_idx = mol[*this_at]->getIdx();
ROMol::OEDGE_ITER nbr , end_nbr;
boost::tie( nbr , end_nbr ) = mol.getAtomBonds( mol[*this_at].get() );
while( nbr != end_nbr ) {
const BOND_SPTR bond = mol[*nbr];
++nbr;
int nbr_idx = bond->getOtherAtomIdx( this_idx );
if( nbr_idx < static_cast<int>( at_cds_.size() ) && nbr_idx > this_idx ) {
if(std::find(highlight_bonds->begin(),highlight_bonds->end(),bond->getIdx()) != highlight_bonds->end()){
DrawColour col=drawOptions().highlightColour;
if(highlight_bond_map &&
highlight_bond_map->find(bond->getIdx())!=highlight_bond_map->end()){
col = highlight_bond_map->find(bond->getIdx())->second;
}
setLineWidth(orig_lw*8);
pair<float,float> at1_cds = at_cds_[this_idx];
pair<float,float> at2_cds = at_cds_[nbr_idx];
drawLine( at1_cds , at2_cds , col , col);
}
}
}
++this_at;
}
}
if(highlight_atoms){
boost::tie( this_at , end_at ) = mol.getVertices();
while( this_at != end_at ) {
int this_idx = mol[*this_at]->getIdx();
if(std::find(highlight_atoms->begin(),highlight_atoms->end(),this_idx) != highlight_atoms->end()){
DrawColour col=drawOptions().highlightColour;
if(highlight_atom_map &&
highlight_atom_map->find(this_idx)!=highlight_atom_map->end()){
col = highlight_atom_map->find(this_idx)->second;
}
std::pair<double,double> p1=at_cds_[this_idx];
std::pair<double,double> p2=at_cds_[this_idx];
p1.first -= 0.4;
p1.second -= 0.4;
p2.first += 0.4;
p2.second += 0.4;
setColour(col);
setFillPolys(true);
setLineWidth(1);
drawEllipse(p1,p2);
}
++this_at;
}
}
setLineWidth(orig_lw);
setFillPolys(orig_fp);
}
void MolDraw2D::drawMolecule( const ROMol &mol ,
const vector<int> *highlight_atoms ,
const vector<int> *highlight_bonds ,
const map<int,DrawColour> *highlight_atom_map,
const map<int,DrawColour> *highlight_bond_map ) {
clearDrawing();
extractAtomCoords( mol );
extractAtomSymbols( mol );
calculateScale();
setFontSize( font_size_ );
if(drawOptions().continuousHighlight){
// if we're doing continuous highlighting, start by drawing the highlights
doContinuousHighlighting(mol,highlight_atoms,highlight_bonds,
highlight_atom_map,highlight_bond_map);
// at this point we shouldn't be doing any more higlighting, so blow out those variables:
highlight_bonds=NULL;
highlight_atoms=NULL;
} else if(drawOptions().circleAtoms && highlight_atoms){
ROMol::VERTEX_ITER this_at , end_at;
boost::tie( this_at , end_at ) = mol.getVertices();
setFillPolys(false);
while( this_at != end_at ) {
int this_idx = mol[*this_at]->getIdx();
if(std::find(highlight_atoms->begin(),highlight_atoms->end(),this_idx) != highlight_atoms->end()){
if(highlight_atom_map && highlight_atom_map->find(this_idx)!=highlight_atom_map->end()){
setColour(highlight_atom_map->find(this_idx)->second);
} else {
setColour(drawOptions().highlightColour);
}
std::pair<double,double> p1=at_cds_[this_idx];
std::pair<double,double> p2=at_cds_[this_idx];
p1.first -= 0.3;
p1.second -= 0.3;
p2.first += 0.3;
p2.second += 0.3;
drawEllipse(p1,p2);
}
++this_at;
}
setFillPolys(true);
}
ROMol::VERTEX_ITER this_at , end_at;
boost::tie( this_at , end_at ) = mol.getVertices();
while( this_at != end_at ) {
int this_idx = mol[*this_at]->getIdx();
ROMol::OEDGE_ITER nbr , end_nbr;
boost::tie( nbr , end_nbr ) = mol.getAtomBonds( mol[*this_at].get() );
while( nbr != end_nbr ) {
const BOND_SPTR bond = mol[*nbr];
++nbr;
int nbr_idx = bond->getOtherAtomIdx( this_idx );
if( nbr_idx < static_cast<int>( at_cds_.size() ) && nbr_idx > this_idx ) {
drawBond( mol , bond , this_idx , nbr_idx , highlight_atoms ,
highlight_atom_map, highlight_bonds, highlight_bond_map );
}
}
++this_at;
}
for( int i = 0 , is = atom_syms_.size() ; i < is ; ++i ) {
if( !atom_syms_[i].first.empty() ) {
drawAtomLabel( i , highlight_atoms , highlight_atom_map );
}
}
}
// ****************************************************************************
// transform a set of coords in the molecule's coordinate system
// to drawing system coordinates
pair<float,float> MolDraw2D::getDrawCoords( const std::pair<float, float> &mol_cds ) const {
float x = scale_ * ( mol_cds.first - x_min_ + x_trans_ );
float y = scale_ * ( mol_cds.second - y_min_ + y_trans_ );
return make_pair( x , y );
}
// ****************************************************************************
pair<float,float> MolDraw2D::getDrawCoords( int at_num ) const {
return getDrawCoords( at_cds_[at_num] );
}
// ****************************************************************************
pair<float,float> MolDraw2D::getAtomCoords( const pair<int, int> &screen_cds) const {
int x = int( float( screen_cds.first ) / scale_ + x_min_ - x_trans_ );
int y = int( float( screen_cds.second ) / scale_ + y_min_ - y_trans_ );
return make_pair( x , y );
}
// ****************************************************************************
pair<float,float> MolDraw2D::getAtomCoords( int at_num ) const {
return at_cds_[at_num];
}
// ****************************************************************************
void MolDraw2D::setFontSize( float new_size ) {
font_size_ = new_size;
}
// ****************************************************************************
void MolDraw2D::calculateScale() {
x_min_ = y_min_ = numeric_limits<float>::max();
float x_max( -numeric_limits<float>::max() ) , y_max( -numeric_limits<float>::max() );
for( int i = 0 , is = at_cds_.size() ; i < is ; ++i ) {
const pair<float,float> &pt = at_cds_[i];
x_min_ = std::min( pt.first , x_min_ );
y_min_ = std::min( pt.second , y_min_ );
x_max = std::max( pt.first , x_max );
y_max = std::max( pt.second , y_max );
}
x_range_ = x_max - x_min_;
y_range_ = y_max - y_min_;
scale_ = std::min( float( width_ ) / x_range_ , float( height_ ) / y_range_ );
// we may need to adjust the scale if there are atom symbols that go off
// the edges, and we probably need to do it iteratively because get_string_size
// uses the current value of scale_.
while( 1 ) {
for( int i = 0 , is = atom_syms_.size() ; i < is ; ++i ) {
if( !atom_syms_[i].first.empty() ) {
float atsym_width , atsym_height;
getStringSize( atom_syms_[i].first , atsym_width , atsym_height );
float this_x = at_cds_[i].first;
float this_y = at_cds_[i].second + atsym_height;
if( W == atom_syms_[i].second ) {
this_x -= atsym_width;
} else if( E == atom_syms_[i].second ) {
this_x += atsym_width;
}
x_max = std::max( x_max , this_x );
x_min_ = std::min( x_min_ , this_x );
y_max = std::max( y_max , this_y );
}
}
float old_scale = scale_;
x_range_ = x_max - x_min_;
y_range_ = y_max - y_min_;
scale_ = std::min( float( width_ ) / x_range_ , float( height_ ) / y_range_ );
if( fabs( scale_ - old_scale ) < 0.1 ) {
break;
}
}
// put a 5% buffer round the drawing and calculate a final scale
x_min_ -= 0.05 * x_range_;
x_range_ *= 1.1;
y_min_ -= 0.05 * y_range_;
y_range_ *= 1.1;
scale_ = std::min( float( width_ ) / x_range_ , float( height_ ) / y_range_ );
float x_mid = x_min_ + 0.5 * x_range_;
float y_mid = y_min_ + 0.5 * y_range_;
pair<float,float> mid = getDrawCoords( make_pair( x_mid , y_mid ) );
x_trans_ = ( width_ / 2 - mid.first ) / scale_;
y_trans_ = ( height_ / 2 - mid.second ) / scale_;
}
// ****************************************************************************
// establishes whether to put string draw mode into super- or sub-script
// mode based on contents of instring from i onwards. Increments i appropriately
// and returns true or false depending on whether it did something or not.
bool MolDraw2D::setStringDrawMode( const string &instring , int &draw_mode ,
int &i ) const {
string bit1 = instring.substr( i , 5 );
string bit2 = instring.substr( i , 6 );
// could be markup for super- or sub-script
if( string( "<sub>" ) == bit1 ) {
draw_mode = 2;
i += 4;
return true;
} else if( string( "<sup>" ) == bit1 ) {
draw_mode = 1;
i += 4;
return true;
} else if( string( "</sub>") == bit2 ) {
draw_mode = 0;
i += 5;
return true;
} else if( string( "</sup>") == bit2 ) {
draw_mode = 0;
i += 5;
return true;
}
return false;
}
// ****************************************************************************
void MolDraw2D::drawLine( const pair<float, float> &cds1 ,
const pair<float, float> &cds2 ,
const DrawColour &col1 , const DrawColour &col2) {
if( col1 == col2 ) {
setColour( col1 );
drawLine( cds1 , cds2 );
} else {
pair<float,float> mid( 0.5 * ( cds1.first + cds2.first ) ,
0.5 * ( cds1.second + cds2.second ) );
setColour( col1 );
drawLine( cds1 , mid );
setColour( col2 );
drawLine( mid , cds2 );
}
}
// ****************************************************************************
// draws the string centred on cds
void MolDraw2D::drawString( const string &str ,
const pair<float,float> &cds ) {
float string_width , string_height;
getStringSize( str , string_width , string_height );
float draw_x = cds.first - string_width / 2.0;
float draw_y = cds.second - string_height / 2.0;
float full_font_size = fontSize();
int draw_mode = 0; // 0 for normal, 1 for superscript, 2 for subscript
string next_char( " " );
for( int i = 0 , is = str.length() ; i < is ; ++i ) {
// setStringDrawMode moves i along to the end of any <sub> or <sup>
// markup
if( '<' == str[i] && setStringDrawMode( str , draw_mode , i ) ) {
continue;
}
char next_c = str[i];
next_char[0] = next_c;
float char_width , char_height;
getStringSize( next_char , char_width , char_height );
// these font sizes and positions work best for Qt, IMO. They may want
// tweaking for a more general solution.
if( 2 == draw_mode ) {
// y goes from top to bottom, so add for a subscript!
setFontSize( 0.75 * full_font_size );
char_width *= 0.5;
drawChar( next_c , getDrawCoords( make_pair( draw_x , draw_y + 0.5 * char_height ) ) );
setFontSize( full_font_size );
} else if( 1 == draw_mode ) {
setFontSize( 0.75 * full_font_size );
char_width *= 0.5;
drawChar( next_c , getDrawCoords( make_pair( draw_x , draw_y - 0.25 * char_height ) ) );
setFontSize( full_font_size );
} else {
drawChar( next_c , getDrawCoords( make_pair( draw_x , draw_y ) ) );
}
draw_x += char_width;
}
}
// ****************************************************************************
DrawColour MolDraw2D::getColour( int atom_idx ,
const std::vector<int> *highlight_atoms ,
const std::map<int,DrawColour> *highlight_map ) {
PRECONDITION(atom_idx>=0,"bad atom_idx");
PRECONDITION(atomic_nums_.size()>atom_idx,"bad atom_idx");
DrawColour retval = getColourByAtomicNum( atomic_nums_[atom_idx] );
// set contents of highlight_atoms to red
if( highlight_atoms && highlight_atoms->end() != find( highlight_atoms->begin() ,
highlight_atoms->end() , atom_idx ) ) {
retval = drawOptions().highlightColour;
}
// over-ride with explicit colour from highlight_map if there is one
if(highlight_map){
map<int,DrawColour>::const_iterator p = highlight_map->find( atom_idx );
if( p != highlight_map->end() ) {
retval = p->second;
}
}
return retval;
}
// ****************************************************************************
DrawColour MolDraw2D::getColourByAtomicNum( int atomic_num ) {
// RGB values taken from Qt's QColor. The seem to work pretty well on my
// machine. Using them as fractions of 255, as that's the way Cairo does it.
DrawColour res(0.,1.,1.); // default to cyan
switch( atomic_num ) {
case 0 : res=DrawColour(0.5,0.5,0.5); break;
case 1 : res=DrawColour(0.55,0.55,0.55); break;
case 6 : res=DrawColour(0.0,0.0,0.0); break;
case 7 : res=DrawColour(0.0,0.0,1.0); break;
case 8 : res=DrawColour(1.0,0.0,0.0); break;
case 9 : res=DrawColour(0.2,0.8,0.8); break;
case 15 : res=DrawColour(1.0,0.5,0.0); break;
case 16 : res=DrawColour(0.8,0.8,0.0); break;
case 17 : res=DrawColour(0.0,0.802,0.0); break;
case 35 : res=DrawColour(0.5,0.3,0.1); break;
case 53 : res=DrawColour(0.63,0.12,0.94); break;
default : break;
}
return res;
}
// ****************************************************************************
void MolDraw2D::extractAtomCoords( const ROMol &mol ) {
at_cds_.clear();
atomic_nums_.clear();
const RDGeom::POINT3D_VECT &locs = mol.getConformer( -1 ).getPositions();
ROMol::VERTEX_ITER this_at , end_at;
tie( this_at , end_at ) = mol.getVertices();
while( this_at != end_at ) {
int this_idx = mol[*this_at]->getIdx();
at_cds_.push_back( make_pair( locs[this_idx].x , locs[this_idx].y ) );
++this_at;
}
}
// ****************************************************************************
void MolDraw2D::extractAtomSymbols( const ROMol &mol ) {
ROMol::VERTEX_ITER atom , end_atom;
tie( atom , end_atom ) = mol.getVertices();
while( atom != end_atom ) {
ROMol::OEDGE_ITER nbr , end_nbrs;
const Atom *at1 = mol[*atom].get();
tie( nbr , end_nbrs ) = mol.getAtomBonds( at1 );
pair<float,float> &at1_cds = at_cds_[at1->getIdx()];
pair<float,float> nbr_sum( 0.0 , 0.0 );
while( nbr != end_nbrs ) {
const BOND_SPTR bond = mol[*nbr];
++nbr;
pair<float,float> &at2_cds = at_cds_[bond->getOtherAtomIdx( at1->getIdx() )];
nbr_sum.first += at2_cds.first - at1_cds.first;
nbr_sum.second += at2_cds.second - at1_cds.second;
}
atom_syms_.push_back( getAtomSymbolAndOrientation( *at1 , nbr_sum ) );
atomic_nums_.push_back( at1->getAtomicNum() );
++atom;
}
}
// ****************************************************************************
void MolDraw2D::drawBond( const ROMol &mol , const BOND_SPTR &bond ,
int at1_idx , int at2_idx ,
const vector<int> *highlight_atoms ,
const map<int,DrawColour> *highlight_atom_map ,
const vector<int> *highlight_bonds ,
const map<int,DrawColour> *highlight_bond_map
) {
static const DashPattern noDash;
static const DashPattern dots=assign::list_of(2)(6);
static const DashPattern dashes=assign::list_of(6)(6);
const Atom *at1 = mol.getAtomWithIdx( at1_idx );
const Atom *at2 = mol.getAtomWithIdx( at2_idx );
const float double_bond_offset = 0.1;
pair<float,float> at1_cds = at_cds_[at1_idx];
pair<float,float> at2_cds = at_cds_[at2_idx];
adjustBondEndForLabel( at1_idx , at2_cds , at1_cds );
adjustBondEndForLabel( at2_idx , at1_cds , at2_cds );
bool highlight_bond=false;
if(highlight_bonds &&
std::find(highlight_bonds->begin(),highlight_bonds->end(),bond->getIdx()) != highlight_bonds->end()){
highlight_bond=true;
}
DrawColour col1,col2;
int orig_lw=lineWidth();
if( !highlight_bond ){
col1 = getColour( at1_idx );
col2 = getColour( at2_idx );
} else {
if(highlight_bond_map &&
highlight_bond_map->find(bond->getIdx())!=highlight_bond_map->end()){
col1 = col2 = highlight_bond_map->find(bond->getIdx())->second;
} else {
col1 = col2 = drawOptions().highlightColour;
}
if( drawOptions().continuousHighlight ){
setLineWidth(orig_lw*8);
} else {
setLineWidth(orig_lw*2);
}
}
// it's a double bond and one end is 1-connected, do two lines parallel
// to the atom-atom line.
if( ( bond->getBondType() == Bond::DOUBLE ) &&
( 1 == at1->getDegree() || 1 == at2->getDegree() ) ) {
pair<float,float> perp = calcPerpendicular( at1_cds , at2_cds );
drawLine( make_pair( at1_cds.first + double_bond_offset * perp.first ,
at1_cds.second + double_bond_offset * perp.second ) ,
make_pair( at2_cds.first + double_bond_offset * perp.first ,
at2_cds.second + double_bond_offset * perp.second ) , col1 , col2 );
drawLine( make_pair( at1_cds.first - double_bond_offset * perp.first ,
at1_cds.second - double_bond_offset * perp.second ) ,
make_pair( at2_cds.first - double_bond_offset * perp.first ,
at2_cds.second - double_bond_offset * perp.second ) , col1 , col2 );
if( bond->getBondType() == Bond::TRIPLE ) {
drawLine( at1_cds , at2_cds , col1 , col2 );
}
} else if( Bond::SINGLE == bond->getBondType() &&
( Bond::BEGINWEDGE == bond->getBondDir() || Bond::BEGINDASH == bond->getBondDir() ) ) {
if( at1->getChiralTag() != Atom::CHI_TETRAHEDRAL_CW &&
at1->getChiralTag() != Atom::CHI_TETRAHEDRAL_CCW ) {
swap( at1_cds , at2_cds );
swap( col1 , col2 );
}
if( Bond::BEGINWEDGE == bond->getBondDir() ) {
drawWedgedBond( at1_cds , at2_cds , false , col1 , col2 );
} else {
drawWedgedBond( at1_cds , at2_cds , true , col1 , col2 );
}
} else {
// in all other cases, we will definitely want to draw a line between the
// two atoms
drawLine( at1_cds , at2_cds , col1 , col2 );
if( Bond::TRIPLE == bond->getBondType() ) {
// 2 further lines, a bit shorter and offset on the perpendicular
pair<float,float> perp = calcPerpendicular( at1_cds , at2_cds );
float dbo = 2.0 * double_bond_offset;
float end1_trunc = 1 == at1->getDegree() ? 0.0 : 0.1;
float end2_trunc = 1 == at2->getDegree() ? 0.0 : 0.1;
float bv[2] = { at1_cds.first - at2_cds.first , at1_cds.second - at2_cds.second };
float px1 = at1_cds.first - end1_trunc * bv[0] + dbo * perp.first;
float py1 = at1_cds.second - end1_trunc * bv[1] + dbo * perp.second;
float px2 = at2_cds.first + end2_trunc * bv[0] + dbo * perp.first;
float py2 = at2_cds.second + end2_trunc * bv[1] + dbo * perp.second;
drawLine( make_pair( px1 , py1 ) , make_pair( px2 , py2 ) , col1 , col2 );
px1 = at1_cds.first - end1_trunc * bv[0] - dbo * perp.first;
py1 = at1_cds.second - end1_trunc * bv[1] - dbo * perp.second;
px2 = at2_cds.first + end2_trunc * bv[0] - dbo * perp.first;
py2 = at2_cds.second + end2_trunc * bv[1] - dbo * perp.second;
drawLine( make_pair( px1 , py1 ) , make_pair( px2 , py2 ) , col1 , col2 );
}
// all we have left now are double bonds in a ring or not in a ring
// and multiply connected
else if( Bond::DOUBLE == bond->getBondType() || Bond::AROMATIC == bond->getBondType() ) {
pair<float,float> perp;
if( mol.getRingInfo()->numBondRings( bond->getIdx() ) ) {
// in a ring, we need to draw the bond inside the ring
perp = bondInsideRing( mol , bond , at1_cds , at2_cds );
} else {
perp = bondInsideDoubleBond( mol , bond );
}
float dbo = 2.0 * double_bond_offset;
float bv[2] = { at1_cds.first - at2_cds.first , at1_cds.second - at2_cds.second };
float px1 = at1_cds.first - 0.1 * bv[0] + dbo * perp.first;
float py1 = at1_cds.second - 0.1 * bv[1] + dbo * perp.second;
float px2 = at2_cds.first + 0.1 * bv[0] + dbo * perp.first;
float py2 = at2_cds.second + 0.1 * bv[1] + dbo * perp.second;
if(bond->getBondType()==Bond::AROMATIC) setDash(dashes);
drawLine( make_pair( px1 , py1 ) , make_pair( px2 , py2 ) , col1 , col2 );
if(bond->getBondType()==Bond::AROMATIC) setDash(noDash);
}
}
if(highlight_bond){
setLineWidth(orig_lw);
}
}
// ****************************************************************************
void MolDraw2D::drawWedgedBond( const pair<float, float> &cds1 ,
const pair<float, float> &cds2 ,
bool draw_dashed , const DrawColour &col1 ,
const DrawColour &col2) {
pair<float,float> perp = calcPerpendicular( cds1 , cds2 );
pair<float,float> disp( 0.1 * perp.first , 0.1 * perp.second );
pair<float,float> end1 , end2;
end1.first = cds2.first + disp.first;
end1.second = cds2.second + disp.second;
end2.first = cds2.first - disp.first;
end2.second = cds2.second - disp.second;
setColour( col1 );
if( draw_dashed ) {
pair<float,float> e1( end1.first - cds1.first , end1.second - cds1.second );
pair<float,float> e2( end2.first - cds1.first , end2.second - cds1.second );
for( int i = 1 ; i < 11 ; ++i ) {
if( 6 == i ) {
setColour( col2 );
}
pair<float,float> e11( cds1.first + float( i ) * 0.1 * e1.first ,
cds1.second + float( i ) * 0.1 * e1.second );
pair<float,float> e22( cds1.first + float( i ) * 0.1 * e2.first ,
cds1.second + float( i ) * 0.1 * e2.second );
drawLine( e11 , e22 );
}
} else {
if( col1 == col2 ) {
drawTriangle( cds1 , end1 , end2 );
} else {
pair<float,float> e1( end1.first - cds1.first , end1.second - cds1.second );
pair<float,float> e2( end2.first - cds1.first , end2.second - cds1.second );
pair<float,float> mid1( cds1.first + 0.5 * e1.first ,
cds1.second + 0.5 * e1.second );
pair<float,float> mid2( cds1.first + 0.5 * e2.first ,
cds1.second + 0.5 * e2.second );
drawTriangle( cds1 , mid1 , mid2 );
setColour( col2 );
drawTriangle( mid1 , end2 , end1 );
drawTriangle( mid1 , mid2 , end2 );
}
}
}
// ****************************************************************************
void MolDraw2D::drawAtomLabel( int atom_num ,
const std::vector<int> *highlight_atoms ,
const std::map<int,DrawColour> *highlight_map ) {
setColour( getColour( atom_num , highlight_atoms , highlight_map ) );
drawString( atom_syms_[atom_num].first , at_cds_[atom_num] );
}
// ****************************************************************************
// calculate normalised perpendicular to vector between two coords
pair<float,float> MolDraw2D::calcPerpendicular( const pair<float,float> &cds1 ,
const pair<float,float> &cds2 ) {
float bv[2] = { cds1.first - cds2.first , cds1.second - cds2.second };
float perp[2] = { -bv[1] , bv[0] };
float perp_len = sqrt( perp[0] * perp[0] + perp[1] * perp[1] );
perp[0] /= perp_len; perp[1] /= perp_len;
return make_pair( perp[0] , perp[1] );
}
// ****************************************************************************
// cds1 and cds2 are 2 atoms in a ring. Returns the perpendicular pointing into
// the ring
pair<float,float> MolDraw2D::bondInsideRing( const ROMol &mol , const BOND_SPTR &bond ,
const pair<float,float> &cds1 ,
const pair<float,float> &cds2 ) {
Atom *bgn_atom = bond->getBeginAtom();
ROMol::OEDGE_ITER nbr2 , end_nbrs2;
tie( nbr2 , end_nbrs2 ) = mol.getAtomBonds( bgn_atom );
while( nbr2 != end_nbrs2 ) {
const BOND_SPTR bond2 = mol[*nbr2];
++nbr2;
if( bond2->getIdx() == bond->getIdx() ||
!mol.getRingInfo()->numBondRings( bond2->getIdx() ) ) {
continue;
}
bool same_ring = false;
BOOST_FOREACH( const INT_VECT &ring , mol.getRingInfo()->bondRings() ) {
if( find( ring.begin() , ring.end() , bond->getIdx() ) != ring.end() &&
find( ring.begin() , ring.end() , bond2->getIdx() ) != ring.end() ) {
same_ring = true;
break;
}
}
if( same_ring ) {
// bond and bond2 are in the same ring, so use their vectors to define
// the sign of the perpendicular.
int atom3 = bond2->getOtherAtomIdx( bond->getBeginAtomIdx() );
return calcInnerPerpendicular( cds1 , cds2 , at_cds_[atom3] );
}
}
return calcPerpendicular( cds1 , cds2 );
}
// ****************************************************************************
// cds1 and cds2 are 2 atoms in a chain double bond. Returns the perpendicular
// pointing into the inside of the bond
pair<float,float> MolDraw2D::bondInsideDoubleBond( const ROMol &mol , const BOND_SPTR &bond ) {
// a chain double bond, were it looks nicer IMO if the 2nd line is inside
// the angle of outgoing bond. Unless it's an allene, where nothing
// looks great.
const Atom *at1 = bond->getBeginAtom();
const Atom *at2 = bond->getEndAtom();
const Atom *bond_atom , *end_atom;
if( at1->getDegree() > 1 ) {
bond_atom = at1;
end_atom = at2;
} else {
bond_atom = at2;
end_atom = at1;
}
int at3 = -1; // to stop the compiler whinging.
ROMol::OEDGE_ITER nbr2 , end_nbrs2;
tie( nbr2 , end_nbrs2 ) = mol.getAtomBonds( bond_atom );
while( nbr2 != end_nbrs2 ) {
const BOND_SPTR bond2 = mol[*nbr2];
++nbr2;
if( bond != bond2 ) {
at3 = bond2->getOtherAtomIdx( bond_atom->getIdx() );
break;
}
}
return calcInnerPerpendicular( at_cds_[end_atom->getIdx()] ,
at_cds_[bond_atom->getIdx()] , at_cds_[at3] );
}
// ****************************************************************************
// calculate normalised perpendicular to vector between two coords, such that
// it's inside the angle made between (1 and 2) and (2 and 3).
pair<float,float> MolDraw2D::calcInnerPerpendicular( const pair<float,float> &cds1 ,
const pair<float,float> &cds2 ,
const pair<float,float> &cds3 ) {
pair<float,float> perp = calcPerpendicular( cds1 , cds2 );
float v1[2] = { cds1.first - cds2.first , cds1.second - cds2.second };
float v2[2] = { cds2.first - cds3.first , cds2.second - cds3.second };
float obv[2] = { v1[0] - v2[0] , v1[1] - v2[1] };
// if dot product of centre_dir and perp < 0.0, they're pointing in opposite
// directions, so reverse perp
if( obv[0] * perp.first + obv[1] * perp.second < 0.0 ) {
perp.first *= -1.0;
perp.second *= - 1.0;
}
return perp;
}
// ****************************************************************************
// take the coords for atnum, with neighbour nbr_cds, and move cds out to accommodate
// the label associated with it.
void MolDraw2D::adjustBondEndForLabel( int atnum , const std::pair<float,float> &nbr_cds ,
std::pair<float,float> &cds ) const {
if( atom_syms_[atnum].first.empty() ) {
return;
}
float label_width , label_height;
getStringSize( atom_syms_[atnum].first , label_width , label_height );
float lw2 = label_width / 2.0;
float lh2 = label_height / 2.0;
float x_offset = 0.0 , y_offset = 0.0;
if( fabs( nbr_cds.second - cds.second ) < 1.0e-5 ) {
// if the bond is horizontal
x_offset = lw2;
} else {
x_offset = fabs( lh2 * ( nbr_cds.first - cds.first ) / ( nbr_cds.second - cds.second ) );
if( x_offset >= lw2 ) {
x_offset = lw2;
}
}
if( nbr_cds.first < cds.first ) {
x_offset *= -1.0;
}
if( fabs( nbr_cds.first - cds.first ) < 1.0e-5 ) {
// if the bond is vertical
y_offset = lh2;
} else {
y_offset = fabs( lw2 * ( cds.second - nbr_cds.second ) / ( nbr_cds.first - cds.first ) );
if( y_offset >= lh2 ) {
y_offset = lh2;
}
}
if( nbr_cds.second < cds.second ) {
y_offset *= -1.0;
}
cds.first += x_offset;
cds.second += y_offset;
}
// ****************************************************************************
// adds XML-like annotation for super- and sub-script, in the same manner
// as MolDrawing.py. My first thought was for a LaTeX-like system, obviously...
pair<string,MolDraw2D::OrientType> MolDraw2D::getAtomSymbolAndOrientation( const Atom &atom ,
const pair<float, float> &nbr_sum ) {
string symbol( "" );
// -----------------------------------
// start with the symbol
if(drawOptions().atomLabels &&
drawOptions().atomLabels->find(atom.getIdx()) != drawOptions().atomLabels->end() ){
symbol = drawOptions().atomLabels->find(atom.getIdx())->second;
} else {
if( 6 != atom.getAtomicNum() ) {
symbol = atom.getSymbol();
}
if( 0 != atom.getIsotope() ) {
symbol = lexical_cast<string>( atom.getIsotope() ) + symbol;
}
if( atom.hasProp( "molAtomMapNumber" ) ) {
string map_num;
atom.getProp( "molAtomMapNumber" , map_num );
symbol += string( ":" ) + map_num;
}
int num_h = 6 == atom.getAtomicNum() ? 0 : atom.getTotalNumHs();
if( num_h > 0 ) {
string h( "H" );
if( num_h > 1 ) {
// put the number as a subscript
h += string( "<sub>" ) + lexical_cast<string>( num_h ) + string( "</sub>" );
}
symbol += h;
}
if( 0 != atom.getFormalCharge() ) {
int chg = atom.getFormalCharge();
string sgn = chg > 0 ? string( "+" ) : string( "-" );
chg = abs( chg );
if( chg > 1 ) {
sgn += lexical_cast<string>( chg );
}
// put the charge as a superscript
symbol += string( "<sup>" ) + sgn + string( "</sup>" );
}
}
// -----------------------------------
// now consider the orientation
OrientType orient = C;
if( 1 == atom.getDegree() ) {
float islope = 0.0;
if( fabs( nbr_sum.second ) > 1.0 ) {
islope = nbr_sum.first / fabs( nbr_sum.second );
} else {
islope = nbr_sum.first;
}
if( fabs( islope ) > 0.85 ) {
if( islope > 0.0 ) {
orient = W;
} else {
orient = E;
}
} else {
if( nbr_sum.second > 0.0 ) {
orient = N;
} else {
orient = S;
}
}
}
return make_pair( symbol , orient );
}
void MolDraw2D::drawTriangle( const std::pair<float,float> &cds1 ,
const std::pair<float,float> &cds2 ,
const std::pair<float,float> &cds3 ) {
std::vector< std::pair<float,float> > pts(3);
pts[0]=cds1;
pts[1]=cds2;
pts[2]=cds3;
drawPolygon(pts);
};
void MolDraw2D::drawEllipse(const std::pair<float,float> &cds1 ,
const std::pair<float,float> &cds2){
std::vector< std::pair<float,float> > pts;
MolDraw2D_detail::arcPoints(cds1,cds2,pts,0,360);
drawPolygon(pts);
}
} // EO namespace RDKit
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