RDKit
Open-source cheminformatics and machine learning.
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#include <DrawMol.h>
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virtualdefault |
RDKit::MolDraw2D_detail::DrawMol::DrawMol | ( | const ROMol & | mol, |
const std::string & | legend, | ||
int | width, | ||
int | height, | ||
const MolDrawOptions & | drawOptions, | ||
DrawText & | textDrawer, | ||
const std::vector< int > * | highlightAtoms = nullptr , |
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const std::vector< int > * | highlightBonds = nullptr , |
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const std::map< int, DrawColour > * | highlightAtomMap = nullptr , |
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const std::map< int, DrawColour > * | highlightBondMap = nullptr , |
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const std::vector< std::pair< DrawColour, DrawColour > > * | bondColours = nullptr , |
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const std::map< int, double > * | highlight_radii = nullptr , |
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bool | includeAnnotations = true , |
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int | confId = -1 , |
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bool | isReactionMol = false |
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) |
mol | : the molecule to draw |
legend | : the legend (to be drawn under the molecule) |
width | : width (in pixels) of the rendering set this to -1 to have the canvas size set automatically |
height | : height (in pixels) of the rendering set this to -1 to have the canvas size set automatically |
drawOptions | : a MolDrawOptions object from the owning MolDraw2D |
textDrawer | : a DrawText object from the owning MolDraw2D |
highlightAtoms | : (optional) vector of atom ids to highlight |
highlightBonds | : (optional) vector of bond ids to highlight |
highlightAtomMap | : (optional) map from atomId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlightBondMap | : (optional) map from bondId -> DrawColour providing the highlight colors. If not provided the default highlight colour from drawOptions() will be used. |
highlightRadii | : (optional) map from atomId -> radius (in molecule coordinates) for the radii of atomic highlights. If not provided the default value from drawOptions() will be used. |
confId | : (optional) conformer ID to be used for atomic coordinates |
RDKit::MolDraw2D_detail::DrawMol::DrawMol | ( | int | width, |
int | height, | ||
const MolDrawOptions & | drawOptions, | ||
DrawText & | textDrawer, | ||
double | xmin, | ||
double | xmax, | ||
double | ymin, | ||
double | ymax, | ||
double | scale, | ||
double | fontscale | ||
) |
Make a DrawMol when there's no molecule to draw, but we still want a DrawMol in the MolDraw2D for scale, conversion of atom coords to draw coords etc. And so DrawMol starts sounding like a poor name for the class.
width | : width (in pixels) of the rendering |
height | : height (in pixels) of the rendering |
drawOptions | : a MolDrawOptions object from the owning MolDraw2D |
textDrawer | : a DrawText object from the owning MolDraw2D |
xmin | : minimum value expected in X |
xmax | : miaximum value expected in X |
ymin | : minimum value expected in Y |
ymax | : maximum value expected in Y |
scale | : scale to use |
fontscale | : font scale to use |
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delete |
void RDKit::MolDraw2D_detail::DrawMol::adjustBondEndsForLabels | ( | int | begAtIdx, |
int | endAtIdx, | ||
Point2D & | begCds, | ||
Point2D & | endCds | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::adjustBondsOnSolidWedgeEnds | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::bondInsideRing | ( | const Bond & | bond, |
double | offset, | ||
Point2D & | l2s, | ||
Point2D & | l2f | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::bondNonRing | ( | const Bond & | bond, |
double | offset, | ||
Point2D & | l2s, | ||
Point2D & | l2f | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::calcAnnotationPosition | ( | const Atom * | atom, |
DrawAnnotation & | annot | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::calcAnnotationPosition | ( | const Bond * | bond, |
DrawAnnotation & | annot | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::calcDoubleBondLines | ( | double | offset, |
const Bond & | bond, | ||
Point2D & | l1s, | ||
Point2D & | l1f, | ||
Point2D & | l2s, | ||
Point2D & | l2f | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::calcMeanBondLength | ( | ) |
OrientType RDKit::MolDraw2D_detail::DrawMol::calcRadicalRect | ( | const Atom * | atom, |
StringRect & | rad_rect | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::calcTripleBondLines | ( | double | offset, |
const Bond & | bond, | ||
Point2D & | l1s, | ||
Point2D & | l1f, | ||
Point2D & | l2s, | ||
Point2D & | l2f | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::calculateScale | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::changeToDrawCoords | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::createDrawObjects | ( | ) |
int RDKit::MolDraw2D_detail::DrawMol::doesNoteClash | ( | const DrawAnnotation & | annot | ) | const |
int RDKit::MolDraw2D_detail::DrawMol::doesRectClash | ( | const StringRect & | rect, |
double | padding | ||
) | const |
Point2D RDKit::MolDraw2D_detail::DrawMol::doubleBondEnd | ( | unsigned int | at1, |
unsigned int | at2, | ||
unsigned int | at3, | ||
double | offset, | ||
bool | trunc | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::doubleBondTerminal | ( | Atom * | at1, |
Atom * | at2, | ||
double | offset, | ||
Point2D & | l1s, | ||
Point2D & | l1f, | ||
Point2D & | l2s, | ||
Point2D & | l2f | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::extractAtomCoords | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractAtomNotes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractAtomSymbols | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractAttachments | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractBondNotes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractBonds | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractBrackets | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractCloseContacts | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractLegend | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractLinkNodes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractMolNotes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractRadicals | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractRegions | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractSGroupData | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractStereoGroups | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::extractVariableBonds | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::findExtremes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::findOtherBondVecs | ( | const Atom * | atom, |
const Atom * | otherAtom, | ||
std::vector< Point2D > & | otherBondVecs | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::finishCreateDrawObjects | ( | ) |
OrientType RDKit::MolDraw2D_detail::DrawMol::getAtomOrientation | ( | const Atom & | atom | ) | const |
std::string RDKit::MolDraw2D_detail::DrawMol::getAtomSymbol | ( | const Atom & | atom, |
OrientType | orientation | ||
) | const |
std::pair< std::string, OrientType > RDKit::MolDraw2D_detail::DrawMol::getAtomSymbolAndOrientation | ( | const Atom & | atom | ) | const |
std::pair< DrawColour, DrawColour > RDKit::MolDraw2D_detail::DrawMol::getBondColours | ( | Bond * | bond | ) |
DrawColour RDKit::MolDraw2D_detail::DrawMol::getColour | ( | int | atom_idx | ) | const |
Point2D RDKit::MolDraw2D_detail::DrawMol::getDrawCoords | ( | const Point2D & | atCds, |
const Point2D & | trans, | ||
const Point2D & | scaleFactor, | ||
const Point2D & | toCentre | ||
) | const |
void RDKit::MolDraw2D_detail::DrawMol::getDrawTransformers | ( | Point2D & | trans, |
Point2D & | scale, | ||
Point2D & | toCentre | ||
) | const |
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inline |
Definition at line 201 of file DrawMol.h.
References fontScale_.
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inline |
void RDKit::MolDraw2D_detail::DrawMol::makeAtomCircleHighlights | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::makeDativeBond | ( | Bond * | bond, |
double | offset, | ||
const std::pair< DrawColour, DrawColour > & | cols | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeDoubleBondLines | ( | Bond * | bond, |
double | doubleBondOffset, | ||
const std::pair< DrawColour, DrawColour > & | cols | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeHighlightEnd | ( | const Atom * | end1, |
const Atom * | end2, | ||
double | lineWidth, | ||
const std::vector< Atom * > & | end1HighNbrs, | ||
std::vector< Point2D > & | points | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeTripleBondLines | ( | Bond * | bond, |
double | doubleBondOffset, | ||
const std::pair< DrawColour, DrawColour > & | cols | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeWavyBond | ( | Bond * | bond, |
double | offset, | ||
const std::pair< DrawColour, DrawColour > & | cols | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeWedgedBond | ( | Bond * | bond, |
const std::pair< DrawColour, DrawColour > & | cols | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::makeZeroBond | ( | Bond * | bond, |
const std::pair< DrawColour, DrawColour > & | cols, | ||
const DashPattern & | dashPattern | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::newBondLine | ( | const Point2D & | pt1, |
const Point2D & | pt2, | ||
const DrawColour & | col1, | ||
const DrawColour & | col2, | ||
int | atom1Idx, | ||
int | atom2Idx, | ||
int | bondIdx, | ||
const DashPattern & | dashPattern | ||
) |
void RDKit::MolDraw2D_detail::DrawMol::partitionForLegend | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::resetEverything | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::resolveAtomSymbolClashes | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::setScale | ( | double | newScale, |
double | newFontScale, | ||
bool | ignoreFontLimits = true |
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) |
void RDKit::MolDraw2D_detail::DrawMol::smoothBondJoins | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::tagAtomsWithCoords | ( | ) |
void RDKit::MolDraw2D_detail::DrawMol::transformAll | ( | const Point2D * | trans = nullptr , |
Point2D * | scale = nullptr , |
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const Point2D * | toCentre = nullptr |
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) |
Point2D RDKit::MolDraw2D_detail::DrawMol::transformPoint | ( | const Point2D & | pt, |
const Point2D * | trans = nullptr , |
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Point2D * | scale = nullptr , |
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const Point2D * | toCentre = nullptr |
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) | const |
int RDKit::MolDraw2D_detail::DrawMol::activeAtmIdxOffset_ = 0 |
int RDKit::MolDraw2D_detail::DrawMol::activeBndIdxOffset_ = 0 |
std::vector<std::unique_ptr<DrawAnnotation> > RDKit::MolDraw2D_detail::DrawMol::annotations_ |
std::vector<Point2D> RDKit::MolDraw2D_detail::DrawMol::atCds_ |
std::vector<int> RDKit::MolDraw2D_detail::DrawMol::atomicNums_ |
std::vector<std::unique_ptr<AtomSymbol> > RDKit::MolDraw2D_detail::DrawMol::atomLabels_ |
std::vector<std::pair<std::string, OrientType> > RDKit::MolDraw2D_detail::DrawMol::atomSyms_ |
std::vector<std::pair<DrawColour, DrawColour> > RDKit::MolDraw2D_detail::DrawMol::bondColours_ |
std::vector<std::unique_ptr<DrawShape> > RDKit::MolDraw2D_detail::DrawMol::bonds_ |
std::unique_ptr<RWMol> RDKit::MolDraw2D_detail::DrawMol::drawMol_ |
const MolDrawOptions& RDKit::MolDraw2D_detail::DrawMol::drawOptions_ |
double RDKit::MolDraw2D_detail::DrawMol::fontScale_ |
Definition at line 301 of file DrawMol.h.
Referenced by getFontScale().
std::map<int, DrawColour> RDKit::MolDraw2D_detail::DrawMol::highlightAtomMap_ |
std::vector<int> RDKit::MolDraw2D_detail::DrawMol::highlightAtoms_ |
std::map<int, DrawColour> RDKit::MolDraw2D_detail::DrawMol::highlightBondMap_ |
std::vector<int> RDKit::MolDraw2D_detail::DrawMol::highlightBonds_ |
std::vector<std::unique_ptr<DrawShape> > RDKit::MolDraw2D_detail::DrawMol::highlights_ |
bool RDKit::MolDraw2D_detail::DrawMol::includeAnnotations_ |
std::vector<std::unique_ptr<DrawAnnotation> > RDKit::MolDraw2D_detail::DrawMol::legends_ |
double RDKit::MolDraw2D_detail::DrawMol::meanBondLength_ = 0.0 |
std::vector<std::unique_ptr<DrawShape> > RDKit::MolDraw2D_detail::DrawMol::postShapes_ |
std::vector<std::unique_ptr<DrawShape> > RDKit::MolDraw2D_detail::DrawMol::preShapes_ |
std::vector<std::tuple<StringRect, OrientType, int> > RDKit::MolDraw2D_detail::DrawMol::radicals_ |
double RDKit::MolDraw2D_detail::DrawMol::scale_ |
Definition at line 301 of file DrawMol.h.
Referenced by getScale().
std::vector<int> RDKit::MolDraw2D_detail::DrawMol::singleBondLines_ |