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// $Id: MolDrawing.h 1777 2011-07-01 03:52:01Z glandrum $
//
// Copyright (C) 2009-2010 Greg Landrum
//
// @@ 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.
//
#ifndef _RD_MOLDRAWING_H_
#define _RD_MOLDRAWING_H_
#include <vector>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <GraphMol/RDKitBase.h>
#include <Geometry/point.h>
/***********
Return Format: vector of ints
RESOLUTION dots_per_angstrom
BOUNDS x1 y1 x2 y2
LINE width dashed atom1_atnum atom2_atnum x1 y1 x2 y2
WEDGE dashed atom1_atnum atom2_atnum x1 y1 x2 y2 x3 y3
ATOM idx atnum x y num_chars char1-charx orient
*************/
namespace RDKit {
namespace Drawing {
typedef int ElementType;
typedef enum {
LINE=1,
WEDGE,
ATOM,
BOUNDS,
RESOLUTION
} PrimType;
typedef enum {
C=0,
N,
E,
S,
W
} OrientType;
std::vector<ElementType> DrawMol(const ROMol &mol,int confId=-1,
const std::vector<int> *highlightAtoms=0,
unsigned int dotsPerAngstrom=100,
double dblBondOffset=0.3,
double dblBondLengthFrac=0.8){
std::vector<ElementType> res;
res.push_back(RESOLUTION);
res.push_back(static_cast<ElementType>(dotsPerAngstrom));
const Conformer &conf=mol.getConformer(confId);
const RDGeom::POINT3D_VECT &locs=conf.getPositions();
//------------
// do the bounding box
//------------
double minx=1e6,miny=1e6,maxx=-1e6,maxy=-1e6;
BOOST_FOREACH( const RDGeom::Point3D &pt,locs){
minx=std::min(pt.x,minx);
miny=std::min(pt.y,miny);
maxx=std::max(pt.x,maxx);
maxy=std::max(pt.y,maxy);
}
double dimx=(maxx-minx),dimy=(maxy-miny);
res.push_back(BOUNDS);
res.push_back(static_cast<ElementType>(dotsPerAngstrom*0));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*0));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*dimx));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*dimy));
// loop over atoms:
ROMol::VERTEX_ITER bAts,eAts;
boost::tie(bAts,eAts)=mol.getVertices();
while(bAts!=eAts){
int a1Idx=mol[*bAts]->getIdx();
RDGeom::Point2D a1(locs[a1Idx].x-minx,locs[a1Idx].y-miny);
ROMol::OEDGE_ITER nbr,endNbrs;
RDGeom::Point2D nbrSum(0,0);
boost::tie(nbr,endNbrs) = mol.getAtomBonds(mol[*bAts].get());
while(nbr!=endNbrs){
const BOND_SPTR bond=mol[*nbr];
++nbr;
int a2Idx=bond->getOtherAtomIdx(a1Idx);
int lineWidth=1;
if(highlightAtoms
&&
std::find(highlightAtoms->begin(),highlightAtoms->end(),a1Idx)
!= highlightAtoms->end()
&&
std::find(highlightAtoms->begin(),highlightAtoms->end(),a2Idx)
!= highlightAtoms->end() ){
lineWidth=3;
}
RDGeom::Point2D a2(locs[a2Idx].x-minx,locs[a2Idx].y-miny);
nbrSum+=a2-a1;
if(a2Idx<a1Idx) continue;
res.push_back(LINE);
res.push_back(lineWidth);
res.push_back(0);
res.push_back(mol[*bAts]->getAtomicNum());
res.push_back(mol.getAtomWithIdx(a2Idx)->getAtomicNum());
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a1.x));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a1.y));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a2.x));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a2.y));
if(bond->getBondType()==Bond::DOUBLE ||
bond->getBondType()==Bond::AROMATIC ||
bond->getBondType()==Bond::TRIPLE ){
RDGeom::Point2D obv=a2-a1;
RDGeom::Point2D perp=obv;
perp.rotate90();
perp.normalize();
if( (bond->getBondType()==Bond::DOUBLE ||
bond->getBondType()==Bond::AROMATIC) &&
mol.getRingInfo()->numBondRings(bond->getIdx())){
// we're in a ring... we might need to flip sides:
ROMol::OEDGE_ITER nbr2,endNbrs2;
boost::tie(nbr2,endNbrs2) = mol.getAtomBonds(mol[*bAts].get());
while(nbr2!=endNbrs2){
const BOND_SPTR bond2=mol[*nbr2];
++nbr2;
if(bond2->getIdx()==bond->getIdx() ||
!mol.getRingInfo()->numBondRings(bond2->getIdx())) continue;
bool sharedRing=false;
BOOST_FOREACH(const INT_VECT &ring,mol.getRingInfo()->bondRings()){
if(std::find(ring.begin(),ring.end(),bond->getIdx())!=ring.end() &&
std::find(ring.begin(),ring.end(),bond2->getIdx())!=ring.end()){
sharedRing=true;
break;
}
}
if(sharedRing){
// these two bonds share a ring.
int a3Idx=bond2->getOtherAtomIdx(a1Idx);
if(a3Idx!=a2Idx){
RDGeom::Point2D a3(locs[a3Idx].x-minx,locs[a3Idx].y-miny);
RDGeom::Point2D obv2=a3-a1;
if(obv2.dotProduct(perp)<0){
perp*=-1;
}
}
}
}
}
perp *= dblBondOffset;
RDGeom::Point2D offsetStart=a1 + obv*(.5*(1.-dblBondLengthFrac));
obv *= dblBondLengthFrac;
res.push_back(LINE);
res.push_back(lineWidth);
if( bond->getBondType()==Bond::AROMATIC ){
res.push_back(1);
} else {
res.push_back(0);
}
res.push_back(mol[*bAts]->getAtomicNum());
res.push_back(mol.getAtomWithIdx(a2Idx)->getAtomicNum());
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.x+perp.x)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.y+perp.y)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.x+obv.x+perp.x)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.y+obv.y+perp.y)));
if(bond->getBondType()==Bond::TRIPLE){
res.push_back(LINE);
res.push_back(lineWidth);
res.push_back(0);
res.push_back(mol[*bAts]->getAtomicNum());
res.push_back(mol.getAtomWithIdx(a2Idx)->getAtomicNum());
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.x-perp.x)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.y-perp.y)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.x+obv.x-perp.x)));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*(offsetStart.y+obv.y-perp.y)));
}
}
}
double massDiff=fabs(PeriodicTable::getTable()->getAtomicWeight(mol[*bAts]->getAtomicNum()) -
mol[*bAts]->getMass());
static double massTol=0.001;
if(mol[*bAts]->getAtomicNum()!=6 ||
mol[*bAts]->getFormalCharge()!=0 ||
massDiff>massTol ){
res.push_back(ATOM);
res.push_back(mol[*bAts]->getAtomicNum());
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a1.x));
res.push_back(static_cast<ElementType>(dotsPerAngstrom*a1.y));
std::string symbol=mol[*bAts]->getSymbol();
bool leftToRight=true;
if(mol[*bAts]->getDegree()==1 && nbrSum.x>0){
leftToRight=false;
}
if(massDiff>massTol){
symbol = boost::lexical_cast<std::string>(int(mol[*bAts]->getMass()+.1))+symbol;
}
if(mol[*bAts]->getAtomicNum()!=6){
int nHs=mol[*bAts]->getTotalNumHs();
if(nHs>0){
std::string h="H";
if(nHs>1) {
h += boost::lexical_cast<std::string>(nHs);
}
if(leftToRight) symbol += h;
else symbol = h+symbol;
}
}
if( mol[*bAts]->getFormalCharge()!=0 ){
int chg=mol[*bAts]->getFormalCharge();
std::string sgn="+";
if(chg<0){
sgn="-";
}
chg=abs(chg);
if(chg>1){
sgn += boost::lexical_cast<std::string>(chg);
}
if(leftToRight) symbol+=sgn;
else symbol = sgn+symbol;
}
res.push_back(static_cast<ElementType>(symbol.length()));
BOOST_FOREACH(char c, symbol){
res.push_back(static_cast<ElementType>(c));
}
OrientType orient=C;
if(mol[*bAts]->getDegree()==1){
double islope=0;
if(fabs(nbrSum.y)>1){
islope=nbrSum.x/fabs(nbrSum.y);
} else {
islope=nbrSum.x;
}
if(fabs(islope)>.85){
if(islope>0){
orient=W;
} else {
orient=E;
}
} else {
if(nbrSum.y>0){
orient=N;
} else {
orient=S;
}
}
}
res.push_back(static_cast<ElementType>(orient));
}
++bAts;
}
return res;
}
} // end of namespace Drawing
} // end of namespace RDKit
#endif
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