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Chemical Data Processing Library Python API - Version 1.2.0
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Chemical Data Processing Library Python API - Version 1.2.0
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Implements the 2D visualization of chemical structures. More...
Inheritance diagram for CDPL.Vis.StructureView2D:Public Member Functions | |
| None | __init__ () |
| Initializes the StructureView2D instance. | |
| None | __init__ (Chem.MolecularGraph molgraph) |
Constructs and initializes a StructureView2D instance for the visualization of the chemical structure specified by molgraph. More... | |
| None | setStructure (Chem.MolecularGraph molgraph) |
| Specifies the chemical structure to visualize. More... | |
| Chem.MolecularGraph | getStructure () |
| Returns a reference to the visualized chemical structure. More... | |
| FontMetrics | getFontMetrics () |
| Returns a reference to the used font metrics object. More... | |
| Public Member Functions inherited from CDPL.Vis.View2D | |
| None | render (Renderer2D renderer) |
| Renders the visual representation of the model using the specified Vis.Renderer2D instance. More... | |
| None | setFontMetrics (FontMetrics font_metrics) |
| Specifies a font metrics object that will be used to measure the dimension of text labels. More... | |
| None | getModelBounds (Rectangle2D bounds) |
| Calculates the bounding rectangle of the visualized model. More... | |
| Public Member Functions inherited from CDPL.Base.ControlParameterContainer | |
| None | setParameter (LookupKey key, Any value) |
| bool | removeParameter (LookupKey key) |
| Removes the entry for the control-parameter specified by key. More... | |
| Any | getParameter (LookupKey key, bool throw_=False, bool local=False) |
| Returns the value of the control-parameter specified by key. More... | |
| Any | getParameterOrDefault (LookupKey key, Any def_value, bool local=False) |
| bool | isParameterSet (LookupKey key, bool local=False) |
| Tells whether or not a value has been assigned to the control-parameter specified by key. More... | |
| None | clearParameters () |
| Erases all container entries. More... | |
| None | addParameters (ControlParameterContainer cntnr) |
Adds the control-parameter value entries in the ControlParameterContainer instance cntnr. More... | |
| None | copyParameters (ControlParameterContainer cntnr) |
| Replaces the current set of properties by a copy of the entries in cntnr. More... | |
| int | getNumParameters () |
| Returns the number of container entries. More... | |
| int | registerParameterChangedCallback (VoidLookupKeyAnyFunctor func) |
| Registers a callback target function that gets invoked when the value of a control-parameter has changed. More... | |
| None | unregisterParameterChangedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| int | registerParameterRemovedCallback (VoidLookupKeyFunctor func) |
| Registers a callback target function that gets invoked when a control-parameter entry has been removed. More... | |
| None | unregisterParameterRemovedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| int | registerParentChangedCallback (VoidFunctor func) |
| Registers a callback target function that gets invoked when the parent container has been changed or was detached. More... | |
| None | unregisterParentChangedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| ControlParameterContainer | getParent () |
| Returns a reference to the parent control-parameter container. More... | |
| None | setParent (ControlParameterContainer cntnr) |
| Sets or removes the parent control-parameter container used to resolve requests for missing entries. More... | |
| list | getParameterKeys () |
| list | getParameterValues () |
| list | getParameters () |
| Returns a reference to itself. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| Any | __getitem__ (LookupKey key) |
| None | __setitem__ (LookupKey key, Any value) |
| bool | __delitem__ (LookupKey self) |
| bool | __contains__ (LookupKey self, bool key) |
Returns the result of the membership test operation self in arg1. More... | |
| int | __len__ () |
Properties | |
| structure = property(getStructure, setStructure) | |
| fontMetrics = property(getFontMetrics, setFontMetrics) | |
| Properties inherited from CDPL.Base.ControlParameterContainer | |
| objectID = property(getObjectID) | |
| parent = property(getParent, setParent) | |
| parameterKeys = property(getParameterKeys) | |
| parameterValues = property(getParameterValues) | |
| parameters = property(getParameters) | |
| numParameters = property(getNumParameters) | |
Implements the 2D visualization of chemical structures.
StructureView2D visualizes chemical structures in the form of 2D structure diagrams (also known as skeletal formulas [WSKF] or structural formulas [WSTF]) that allow for an easy perception of important chemical characteristics like constitution, connectivity and stereochemistry.
Graphical details of the generated structure diagrams (colors, fonts, line-widths etc.) are configurable on a StructureView2D instance level by control-parameters and on a visualized data object level by setting appropriate Chem.Atom, Chem.Bond or Chem.MolecularGraph properties. Properties of the visualized data objects have a higher priority than equivalent control-parameters of the StructureView2D instance and properties of Chem.Atom or Chem.Bond objects override corresponding properties of the parent Chem.MolecularGraph instance.
StructureView2D supports the following control-parameters:
| Control-Parameter | Description |
|---|---|
| Vis.ControlParameter.VIEWPORT | Specifies a rectangular viewport area which constrains the location and size of the generated structure diagram |
| Vis.ControlParameter.SIZE_ADJUSTMENT | Specifies how to adjust the size of the structure diagram relative to the available viewport area |
| Vis.ControlParameter.ALIGNMENT | Specifies the alignment of the structure diagram within the viewport area |
| Vis.ControlParameter.BACKGROUND_COLOR | Specifies the backround color of the structure diagram |
| Vis.ControlParameter.ATOM_COLOR | Specifies the color of atom labels |
| Vis.ControlParameter.ATOM_COLOR_TABLE | Specifies a lookup table for the atom type dependent coloring of atom labels |
| Vis.ControlParameter.USE_CALCULATED_ATOM_COORDINATES | Specifies whether or not to use calculated atom coordinates |
| Vis.ControlParameter.ATOM_LABEL_FONT | Specifies the font for atom element and query match expression labels |
| Vis.ControlParameter.ATOM_LABEL_SIZE | Specifies the size of atom element and query match expression labels |
| Vis.ControlParameter.SECONDARY_ATOM_LABEL_FONT | Specifies the font for text labels that show the value of various atomic properties |
| Vis.ControlParameter.SECONDARY_ATOM_LABEL_SIZE | Specifies the size of text labels that show the value of various atomic properties |
| Vis.ControlParameter.ATOM_CONFIGURATION_LABEL_FONT | Specifies the font for atom configuration labels |
| Vis.ControlParameter.ATOM_CONFIGURATION_LABEL_SIZE | Specifies the size of atom configuration labels |
| Vis.ControlParameter.ATOM_CONFIGURATION_LABEL_COLOR | Specifies the color of atom configuration labels |
| Vis.ControlParameter.ATOM_CUSTOM_LABEL_FONT | Specifies the font for atom custom labels |
| Vis.ControlParameter.ATOM_CUSTOM_LABEL_SIZE | Specifies the size of atom custom labels |
| Vis.ControlParameter.ATOM_CUSTOM_LABEL_COLOR | Specifies the color of atom custom labels |
| Vis.ControlParameter.ATOM_LABEL_MARGIN | Specifies the margin of free space around atom labels |
| Vis.ControlParameter.RADICAL_ELECTRON_DOT_SIZE | Specifies the size of radical electron dots |
| Vis.ControlParameter.ATOM_HIGHLIGHT_AREA_SIZE | Specifies the minimum size of atom highlighting areas |
| Vis.ControlParameter.ATOM_HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling atom highlighting areas |
| Vis.ControlParameter.ATOM_HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing atom highlighting area outlines |
| Vis.ControlParameter.SHOW_EXPLICIT_HYDROGENS | Specifies whether or not to show explicit hydrogen atoms |
| Vis.ControlParameter.SHOW_CARBONS | Specifies whether or not to show the element label of carbon atoms |
| Vis.ControlParameter.SHOW_CHARGES | Specifies whether or not to show the formal charge of atoms |
| Vis.ControlParameter.SHOW_ISOTOPES | Specifies whether or not to show the isotopic mass of atoms |
| Vis.ControlParameter.SHOW_HYDROGEN_COUNTS | Specifies whether or not to show the implicit hydrogen count of connected atoms |
| Vis.ControlParameter.SHOW_NON_CARBON_HYDROGEN_COUNTS | Specifies whether or not to show the implicit hydrogen count of connected non-carbon atoms |
| Vis.ControlParameter.SHOW_ATOM_QUERY_INFOS | Specifies whether or not to show query atom match expressions |
| Vis.ControlParameter.SHOW_ATOM_REACTION_INFOS | Specifies whether or not to show reaction atom-atom mapping numbers |
| Vis.ControlParameter.SHOW_RADICAL_ELECTRONS | Specifies whether or not to draw radical electron dots |
| Vis.ControlParameter.SHOW_ATOM_CONFIGURATION_LABELS | Specifies whether or not to show atom confiuration labels |
| Vis.ControlParameter.SHOW_ATOM_CUSTOM_LABELS | Specifies whether or not to show atom confiuration labels |
| Vis.ControlParameter.ENABLE_ATOM_HIGHLIGHTING | Specifies whether or not to enable the highlighting of atoms |
| Vis.ControlParameter.HIGHLIGHT_AREA_OUTLINE_WIDTH | Specifies the line width for drawing atom or bond highlighting area outlines |
| Vis.ControlParameter.BOND_LENGTH | Specifies the desired average bond length |
| Vis.ControlParameter.BOND_COLOR | Specifies the color of bonds |
| Vis.ControlParameter.BOND_LINE_WIDTH | Specifies the width of bond lines |
| Vis.ControlParameter.BOND_LINE_SPACING | Specifies the distance between the lines of double and triple bonds |
| Vis.ControlParameter.STEREO_BOND_WEDGE_WIDTH | Specifies the width of wedge-shaped stereo bonds |
| Vis.ControlParameter.STEREO_BOND_HASH_SPACING | Specifies the distance between the hashes of down stereo bonds |
| Vis.ControlParameter.REACTION_CENTER_LINE_LENGTH | Specifies the length of the lines in reaction center marks |
| Vis.ControlParameter.REACTION_CENTER_LINE_SPACING | Specifies the distance between lines in reaction center marks |
| Vis.ControlParameter.DOUBLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of asymmetric double bonds have to be trimmed at each line end |
| Vis.ControlParameter.TRIPLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of triple bonds have to be trimmed at each line end |
| Vis.ControlParameter.BOND_LABEL_FONT | Specifies the font for bond labels |
| Vis.ControlParameter.BOND_LABEL_SIZE | Specifies the size of bond labels |
| Vis.ControlParameter.BOND_CONFIGURATION_LABEL_FONT | Specifies the font for bond configuration labels |
| Vis.ControlParameter.BOND_CONFIGURATION_LABEL_SIZE | Specifies the size of bond configuration labels |
| Vis.ControlParameter.BOND_CONFIGURATION_LABEL_COLOR | Specifies the color of bond configuration labels |
| Vis.ControlParameter.BOND_CUSTOM_LABEL_FONT | Specifies the font for bond custom labels |
| Vis.ControlParameter.BOND_CUSTOM_LABEL_SIZE | Specifies the size of bond custom labels |
| Vis.ControlParameter.BOND_CUSTOM_LABEL_COLOR | Specifies the color of bond custom labels |
| Vis.ControlParameter.BOND_LABEL_MARGIN | Specifies the margin of free space around bond labels |
| Vis.ControlParameter.BOND_HIGHLIGHT_AREA_WIDTH | Specifies the width of bond highlighting areas |
| Vis.ControlParameter.BOND_HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling bond highlighting areas |
| Vis.ControlParameter.BOND_HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing bond highlighting area outlines |
| Vis.ControlParameter.SHOW_BOND_REACTION_INFOS | Specifies whether or not to draw reaction center marks |
| Vis.ControlParameter.SHOW_BOND_QUERY_INFOS | Specifies whether or not to show query bond match expressions |
| Vis.ControlParameter.SHOW_STEREO_BONDS | Specifies whether or not to draw stereo bonds |
| Vis.ControlParameter.SHOW_BOND_CONFIGURATION_LABELS | Specifies whether or not to show bond confiuration labels |
| Vis.ControlParameter.SHOW_BOND_CUSTOM_LABELS | Specifies whether or not to show bond confiuration labels |
| Vis.ControlParameter.ENABLE_BOND_HIGHLIGHTING | Specifies whether or not to enable the highlighting of bonds |
Default values for most of the control-parameters are defined in namespace Vis.ControlParameterDefault.
Supported Chem.MolecularGraph properties:
| Chem.MolecularGraph Property | Description | ||
|---|---|---|---|
| Vis.MolecularGraphProperty.ATOM_COLOR_TABLE | Specifies a lookup table for the atom type dependent coloring of atom labels | ||
| Vis.MolecularGraphProperty.ATOM_COLOR | Specifies the color of atom labels | ||
| Vis.MolecularGraphProperty.ATOM_LABEL_FONT | Specifies the font for atom element and query match expression labels | ||
| Vis.MolecularGraphProperty.ATOM_LABEL_SIZE | Specifies the size of atom element and query match expression labels | ||
| Vis.MolecularGraphProperty.SECONDARY_ATOM_LABEL_FONT | Specifies the font for text labels that show the value of various atomic properties | ||
| Vis.MolecularGraphProperty.SECONDARY_ATOM_LABEL_SIZE | Specifies the size of text labels that show the value of various atomic properties | ||
| Vis.MolecularGraphProperty.ATOM_CONFIGURATION_LABEL_FONT | Specifies the font for atom configuration labels | ||
| Vis.MolecularGraphProperty.ATOM_CONFIGURATION_LABEL_SIZE | Specifies the size of atom configuration labels | ||
| Vis.MolecularGraphProperty.ATOM_CONFIGURATION_LABEL_COLOR | Specifies the color of atom configuration labels | ||
| Vis.MolecularGraphProperty.ATOM_CUSTOM_LABEL_FONT | Specifies the font for atom custom labels | ||
| Vis.MolecularGraphProperty.ATOM_CUSTOM_LABEL_SIZE | Specifies the size of atom custom labels | ||
| Vis.MolecularGraphProperty.ATOM_CUSTOM_LABEL_COLOR | Specifies the color of atom custom labels | ||
| Vis.MolecularGraphProperty.ATOM_LABEL_MARGIN | Specifies the margin of free space around atom labels | ||
| Vis.MolecularGraphProperty.RADICAL_ELECTRON_DOT_SIZE | Specifies the size of radical electron dots | ||
| Vis.MolecularGraphProperty.ATOM_HIGHLIGHT_AREA_SIZE | Specifies the minimum size of atom highlighting areas | ||
| Vis.MolecularGraphProperty.ATOM_HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling atom highlighting areas | ||
| Vis.MolecularGraphProperty.ATOM_HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing atom highlighting area outlines | ||
| Vis.MolecularGraphProperty.HIGHLIGHT_AREA_OUTLINE_WIDTH | Specifies the line width for drawing atom or bond highlighting area outlines | ||
| Vis.MolecularGraphProperty.BOND_COLOR | Specifies the color of bonds | ||
| Vis.MolecularGraphProperty.BOND_LINE_WIDTH | Specifies the width of bond lines | ||
| Vis.MolecularGraphProperty.BOND_LINE_SPACING | Specifies the distance between the lines of double and triple bonds | ||
| Vis.MolecularGraphProperty.STEREO_BOND_WEDGE_WIDTH | Specifies the width of wedge-shaped stereo bonds | ||
| Vis.MolecularGraphProperty.STEREO_BOND_HASH_SPACING | Specifies the distance between the hashes of down stereo bonds | ||
| Vis.MolecularGraphProperty.REACTION_CENTER_LINE_LENGTH | Specifies the length of the lines in reaction center marks | ||
| Vis.MolecularGraphProperty.REACTION_CENTER_LINE_SPACING | Specifies the distance between the lines in reaction center marks | ||
| Vis.MolecularGraphProperty.DOUBLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of asymmetric double bonds have to be trimmed at each line end | ||
| Vis.MolecularGraphProperty.TRIPLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of triple bonds have to be trimmed at each line end | ||
| Vis.MolecularGraphProperty.BOND_LABEL_FONT | Specifies the font for bond labels | ||
| Vis.MolecularGraphProperty.BOND_LABEL_SIZE | Specifies the size of bond labels | ||
| Vis.MolecularGraphProperty.BOND_CONFIGURATION_LABEL_FONT | Specifies the font for bond configuration labels | ||
| Vis.MolecularGraphProperty.BOND_CONFIGURATION_LABEL_SIZE | Specifies the size of bond configuration labels | Vis.MolecularGraphProperty.BOND_CONFIGURATION_LABEL_COLOR | Specifies the color of bond configuration labels |
| Vis.MolecularGraphProperty.BOND_CUSTOM_LABEL_FONT | Specifies the font for bond custom labels | ||
| Vis.MolecularGraphProperty.BOND_CUSTOM_LABEL_SIZE | Specifies the size of bond custom labels | Vis.MolecularGraphProperty.BOND_CUSTOM_LABEL_COLOR | Specifies the color of bond custom labels |
| Vis.MolecularGraphProperty.BOND_LABEL_MARGIN | Specifies the margin of free space around bond labels | ||
| Vis.MolecularGraphProperty.BOND_HIGHLIGHT_AREA_WIDTH | Specifies the width of bond highlighting areas | ||
| Vis.MolecularGraphProperty.BOND_HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling bond highlighting areas | ||
| Vis.MolecularGraphProperty.BOND_HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing bond highlighting area outlines |
Supported Chem.Atom properties:
| Chem.Atom Property | Description |
|---|---|
| Vis.AtomProperty.COLOR | Specifies the color of text labels |
| Vis.AtomProperty.LABEL_FONT | Specifies the font for atom element and query match expression labels |
| Vis.AtomProperty.LABEL_SIZE | Specifies the size of atom element and query match expression labels |
| Vis.AtomProperty.SECONDARY_LABEL_FONT | Specifies the font for text labels that show the value of various atomic properties |
| Vis.AtomProperty.SECONDARY_LABEL_SIZE | Specifies the size of text labels that show the value of various atomic properties |
| Vis.AtomProperty.LABEL_MARGIN | Specifies the margin of free space around atom labels |
| Vis.AtomProperty.CONFIGURATION_LABEL_FONT | Specifies the font for atom configuration labels |
| Vis.AtomProperty.CONFIGURATION_LABEL_SIZE | Specifies the size of atom configuration labels |
| Vis.AtomProperty.CONFIGURATION_LABEL_COLOR | Specifies the color of atom configuration labels |
| Vis.AtomProperty.CUSTOM_LABEL_FONT | Specifies the font for atom custom labels |
| Vis.AtomProperty.CUSTOM_LABEL_SIZE | Specifies the size of atom custom labels |
| Vis.AtomProperty.CUSTOM_LABEL_COLOR | Specifies the color of atom custom labels |
| Vis.AtomProperty.RADICAL_ELECTRON_DOT_SIZE | Specifies the size of radical electron dots |
| Vis.AtomProperty.HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling highlighting areas |
| Vis.AtomProperty.HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing highlighting area outlines |
Supported Chem.Bond properties:
| Chem.Bond Property | Description |
|---|---|
| Vis.BondProperty.COLOR | Specifies the color of the bond |
| Vis.BondProperty.LINE_WIDTH | Specifies the width of bond lines |
| Vis.BondProperty.LINE_SPACING | Specifies the distance between the lines of double and triple bonds |
| Vis.BondProperty.STEREO_BOND_WEDGE_WIDTH | Specifies the width of wedge-shaped stereo bonds |
| Vis.BondProperty.STEREO_BOND_HASH_SPACING | Specifies the distance between the hashes of down stereo bonds |
| Vis.BondProperty.REACTION_CENTER_LINE_LENGTH | Specifies the length of the lines in reaction center marks |
| Vis.BondProperty.REACTION_CENTER_LINE_SPACING | Specifies the distance between the lines in reaction center marks |
| Vis.BondProperty.DOUBLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of asymmetric double bonds have to be trimmed at each line end |
| Vis.BondProperty.TRIPLE_BOND_TRIM_LENGTH | Specifies the amount by which the non-central lines of triple bonds have to be trimmed at each line end |
| Vis.BondProperty.LABEL_FONT | Specifies the font for bond labels |
| Vis.BondProperty.LABEL_SIZE | Specifies the size of bond labels |
| Vis.BondProperty.LABEL_MARGIN | Specifies the margin of free space around bond labels |
| Vis.BondProperty.CONFIGURATION_LABEL_FONT | Specifies the font for bond configuration labels |
| Vis.BondProperty.CONFIGURATION_LABEL_SIZE | Specifies the size of bond configuration labels |
| Vis.BondProperty.CONFIGURATION_LABEL_COLOR | Specifies the color of bond configuration labels |
| Vis.BondProperty.CUSTOM_LABEL_FONT | Specifies the font for bond custom labels |
| Vis.BondProperty.CUSTOM_LABEL_SIZE | Specifies the size of bond custom labels |
| Vis.BondProperty.CUSTOM_LABEL_COLOR | Specifies the color of bond custom labels |
| Vis.BondProperty.HIGHLIGHT_AREA_BRUSH | Specifies the brush to use for filling highlighting areas |
| Vis.BondProperty.HIGHLIGHT_AREA_OUTLINE_PEN | Specifies the pen to use for drawing highlighting area outlines |
| None CDPL.Vis.StructureView2D.__init__ | ( | Chem.MolecularGraph | molgraph | ) |
Constructs and initializes a StructureView2D instance for the visualization of the chemical structure specified by molgraph.
| molgraph | A reference to the Chem.MolecularGraph object to visualize. |
| None CDPL.Vis.StructureView2D.setStructure | ( | Chem.MolecularGraph | molgraph | ) |
Specifies the chemical structure to visualize.
If the chemical structure or a property has changed after this method has been called for a Chem.MolecularGraph object, the method needs to be called again for the object to make the changes visible.
| molgraph | A reference to the Chem.MolecularGraph object to visualize, or None. |
| Chem.MolecularGraph CDPL.Vis.StructureView2D.getStructure | ( | ) |
Returns a reference to the visualized chemical structure.
| FontMetrics CDPL.Vis.StructureView2D.getFontMetrics | ( | ) |
Returns a reference to the used font metrics object.
1.9.1