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object --+
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TopologicalDescriptors
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| structure.Structure |
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| str |
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| structure.Structure |
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| Descriptor |
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| str |
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| one of {float, int, bool, str} |
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Inherited from |
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Initializes valid topological descriptors, and creates an empty cached property dictionary.
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Calculates a set of topological descriptors for a given structure.
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Create descriptor m2io property name for a Descriptor.
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Creates a copy of the structure with all hydrogens removed; such heavy atom only structures are required for certain properties.
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Locates the corresponding Descriptor in the class tuple of Descriptors. Looks for Descriptor based on matching the passed string to any of the key, label, or "label (key)" strings.
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Create complete descriptor label-key string
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Evalulates a descriptor for a given structure. If successful, the value is cast to the expected type before returning.
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Returns set of valid descriptor tuples in the form of: (descriptor key, descriptor label, function mapping) @return: set of available topological descriptor mappings @rtype: set of tuples |
Collect the number of hydrogens connected to each heavy atom
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Build adjacency matrix for structure
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Build distance matrix for structure
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Laplacian eigenvalues
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Sum of topological distance between atom pairs of atom types
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Get number of chiral atoms -- R or S for chiral category
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Van der Waals surface area of each atom, i, given as:
4*pi*ri*ri - pi*ri*sigma((rj*rj-(ri-dij)*(ri-dij))/dij)
for j running for each bond of atom i and
ri, rj -> van der waals radius of respective atoms
dij -> min(max(|ri-rj|,bij),ri+rj)
bij -> ideal bond length, bij = sij - oij
sij -> bond length of atom i and j calculated using MMFF94
oij -> correction in bond length (0 for single, 0.1 for aromatic,
0.2 for double, 0.3 for triple)
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Return van der waals surface area of a molecule vsa = sigma(vsa of each atom i)
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Return atomic contribution based on MR values. This will help to capture polarizability.
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Return atomic contributions based on Alpgp values. This is useful to capture hydrophobic and hydrophillic effect.
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Return atomic contribution based on Gasteiger charges. This is useful to capture direct electrostatic interactions.
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