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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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Identifies the accessible surface atoms in a given set of atoms. More...
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 () |
| Returns the radius of the probe sphere that determines the accessibility of the surface atoms. More... | |
| 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 |
| The default probe sphere radius (in Å). | |
| float | DEF_GRID_OVERSIZE = 5.0 |
| The default margin (in Å) added to each side of the bounding box for the atom lookup grid. | |
| float | DEF_GRID_STEP_SIZE = 0.75 |
| The default distance between grid points (in Å) along each axis of the atom lookup grid. | |
| float | DEF_MIN_SURFACE_ACC = 0.01 |
| The default minimum fraction of accessible test points required to classify an atom as surface-accessible. | |
Properties | |
| objectID = property(getObjectID) | |
| probeRadius = property(getProbeRadius, setProbeRadius) | |
| gridStepSize = property(getGridStepSize, setGridStepSize) | |
| gridOversize = property(getGridOversize, setGridOversize) | |
| numTestPoints = property(getNumTestPoints, setNumTestPoints) | |
| minSurfaceAccessibility = property(getMinSurfaceAccessibility, setMinSurfaceAccessibility) | |
Identifies the accessible surface atoms in a given set of atoms.
For each candidate atom, a configurable number of probe sphere test points is generated on the atom's Van der Waals surface and tested against the surrounding atoms (looked up via an internal 3D grid for efficiency). An atom is reported as surface-accessible when at least the minimum required fraction of its test points is reachable by the probe sphere. The probe radius, accessibility threshold, test point count, and grid parameters can be tuned via the provided dedicated methods. Atom 3D coordinates are obtained through an accessor function that can be customized to specific needs.
| 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 | ( | ) |
Returns the radius of the probe sphere that determines the accessibility of the surface atoms.
| 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.
| 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