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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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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 molecular graph 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 Vis.FontMetrics instance used for measuring the dimension of text labels. 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 Vis.FontMetrics instance that will be used to measure the dimension of text labels. More... | |
| None | getModelBounds (Rectangle2D bounds) |
| Calculates the axis-aligned 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 key) |
| bool | __contains__ (LookupKey key) |
Returns the result of the membership test operation key in self. 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_BRUSH | Specifies the brush for filling the background 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 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 molecular graph 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 structure or any properties of molgraph have changed after this method has been called then the method needs to be invoked 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.
None if none was specified. | FontMetrics CDPL.Vis.StructureView2D.getFontMetrics | ( | ) |
Returns a reference to the Vis.FontMetrics instance used for measuring the dimension of text labels.
None if none was specified. 
1.9.1