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Chemical Data Processing Library Python API - Version 1.2.3
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Chemical Data Processing Library Python API - Version 1.2.3
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Inheritance diagram for CDPL.Chem.SurfaceAtomExtractor:Public Member Functions | |
| None | __init__ () |
Constructs the SurfaceAtomExtractor instance. | |
| None | __init__ (SurfaceAtomExtractor extractor) |
| Initializes a copy of the SurfaceAtomExtractor instance extractor. More... | |
| None | __init__ (AtomContainer cntnr, MolecularGraph parent_molgraph, Fragment frag) |
| Perceives the surface accessible atoms of cntnr and adds them to the fragment frag. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setAtom3DCoordinatesFunction (Atom3DCoordinatesFunction func) |
| Specifies a function for the retrieval of atom 3D-coordinates. More... | |
| Atom3DCoordinatesFunction | getAtom3DCoordinatesFunction () |
| Returns the function that was registered for the retrieval of atom 3D-coordinates. More... | |
| None | setProbeRadius (float radius) |
| Specifies the radius of the probe sphere that determines the accessibility of the surface atoms. More... | |
| None | setGridStepSize (float size) |
| Specifies the distance between the grid-points in space which store lists of atoms with proximal positions. More... | |
| None | setGridOversize (float size) |
| Specifies the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions. More... | |
| None | setMinSurfaceAccessibility (float min_acc) |
| Specifies the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom. More... | |
| None | setNumTestPoints (int num_points) |
| Specifies the number of points on the atom surface at which a test for surface accessibility is carried out. More... | |
| float | getProbeRadius () |
| float | getGridStepSize () |
| Return the distance between the grid-points for proximal atom lookup. More... | |
| float | getGridOversize () |
| Returns the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions. More... | |
| float | getMinSurfaceAccessibility () |
| Returns the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom. More... | |
| int | getNumTestPoints () |
| Returns the number of points on the atom surface at which a test for surface accessibility is carried out. More... | |
| None | extract (AtomContainer cntr, MolecularGraph parent_molgraph, Fragment frag) |
| SurfaceAtomExtractor | assign (SurfaceAtomExtractor extractor) |
Replaces the current state of self with a copy of the state of the SurfaceAtomExtractor instance extractor. More... | |
Static Public Attributes | |
| float | DEF_PROBE_RADIUS = 1.2 |
| float | DEF_GRID_OVERSIZE = 5.0 |
| float | DEF_GRID_STEP_SIZE = 0.75 |
| float | DEF_MIN_SURFACE_ACC = 0.01 |
Properties | |
| objectID = property(getObjectID) | |
| probeRadius = property(getProbeRadius, setProbeRadius) | |
| gridStepSize = property(getGridStepSize, setGridStepSize) | |
| gridOversize = property(getGridOversize, setGridOversize) | |
| numTestPoints = property(getNumTestPoints, setNumTestPoints) | |
| minSurfaceAccessibility = property(getMinSurfaceAccessibility, setMinSurfaceAccessibility) | |
| None CDPL.Chem.SurfaceAtomExtractor.__init__ | ( | SurfaceAtomExtractor | extractor | ) |
Initializes a copy of the SurfaceAtomExtractor instance extractor.
| extractor | The SurfaceAtomExtractor instance to copy. |
| None CDPL.Chem.SurfaceAtomExtractor.__init__ | ( | AtomContainer | cntnr, |
| MolecularGraph | parent_molgraph, | ||
| Fragment | frag | ||
| ) |
Perceives the surface accessible atoms of cntnr and adds them to the fragment frag.
| cntnr | The set of atoms for which to perceive the surface accessibility. |
| parent_molgraph | The parent molecular graph which embeds the atoms in cntnr. |
| frag | The output fragment where to store the perceived surface atoms. |
| int CDPL.Chem.SurfaceAtomExtractor.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python SurfaceAtomExtractor instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two SurfaceAtomExtractor instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().
| None CDPL.Chem.SurfaceAtomExtractor.setAtom3DCoordinatesFunction | ( | Atom3DCoordinatesFunction | func | ) |
Specifies a function for the retrieval of atom 3D-coordinates.
| func | The atom 3D-coordinates function. |
| Atom3DCoordinatesFunction CDPL.Chem.SurfaceAtomExtractor.getAtom3DCoordinatesFunction | ( | ) |
Returns the function that was registered for the retrieval of atom 3D-coordinates.
| None CDPL.Chem.SurfaceAtomExtractor.setProbeRadius | ( | float | radius | ) |
Specifies the radius of the probe sphere that determines the accessibility of the surface atoms.
| radius | The radius of the probe sphere. |
| None CDPL.Chem.SurfaceAtomExtractor.setGridStepSize | ( | float | size | ) |
Specifies the distance between the grid-points in space which store lists of atoms with proximal positions.
| size | The distance between the grid-points along each axis. |
| None CDPL.Chem.SurfaceAtomExtractor.setGridOversize | ( | float | size | ) |
Specifies the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions.
| size | The margin that gets added to the molecular graph's bounding-box. |
| None CDPL.Chem.SurfaceAtomExtractor.setMinSurfaceAccessibility | ( | float | min_acc | ) |
Specifies the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom.
| min_acc | The minimum required fraction of accessible test points. |
| None CDPL.Chem.SurfaceAtomExtractor.setNumTestPoints | ( | int | num_points | ) |
Specifies the number of points on the atom surface at which a test for surface accessibility is carried out.
| num_points | The number of test points. |
| float CDPL.Chem.SurfaceAtomExtractor.getProbeRadius | ( | ) |
| float CDPL.Chem.SurfaceAtomExtractor.getGridStepSize | ( | ) |
Return the distance between the grid-points for proximal atom lookup.
| float CDPL.Chem.SurfaceAtomExtractor.getGridOversize | ( | ) |
Returns the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions.
| float CDPL.Chem.SurfaceAtomExtractor.getMinSurfaceAccessibility | ( | ) |
Returns the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom.
| int CDPL.Chem.SurfaceAtomExtractor.getNumTestPoints | ( | ) |
Returns the number of points on the atom surface at which a test for surface accessibility is carried out.
| None CDPL.Chem.SurfaceAtomExtractor.extract | ( | AtomContainer | cntr, |
| MolecularGraph | parent_molgraph, | ||
| Fragment | frag | ||
| ) |
| cntr | |
| parent_molgraph | |
| frag |
| SurfaceAtomExtractor CDPL.Chem.SurfaceAtomExtractor.assign | ( | SurfaceAtomExtractor | extractor | ) |
Replaces the current state of self with a copy of the state of the SurfaceAtomExtractor instance extractor.
| extractor | The SurfaceAtomExtractor instance to copy. |
1.9.1