Physical and chemical properties#
Classifying a full explicit graph under auditable named AutoDock rules |
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Perceiving detached source-indexed atom and bond flags |
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Calculating named models with charge conservation, coverage and producer provenance |
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Separating indexed H neighbors from stored virtual H counts |
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Transferring missing assignments through an exhaustive declared atom map |
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Constructing declared residue, terminal and disulfide chemistry without coordinates |
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Canonicalizing already declared aromatic bonds while retaining original orders in a report |
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Preparing rings from declared aromatic bonds |
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Getting the buried surface area of elements in a molecular system |
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Getting the atomic radius of a molecular system (supports vdw and protor definitions) |
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Getting the fraction of buried surface area for elements in a molecular system |
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Getting absolute CIP labels from declared stereo or one structure |
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Getting the formal, tabulated, or partial force field charge of elements |
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Recognizing sparse formal-charge centers in one chemical state |
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Inspecting stored field coverage before explicit chemical preparation |
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Getting Pauling electronegativities for constituent atoms |
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Recognizing ordered donor–halogen and acceptor–reference pairs |
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Recognizing attributed donor–hydrogen pairs and acceptors |
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Recognizing declared chemical atom sites independently of geometry |
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Getting hydrophobicity values for residues from standard biochemical scales |
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Recognizing metal and ligand chemistry independently of geometry |
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Recognizing neutral explicit O-H-H molecular components |
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Getting atomic, residue, or total molecular system mass |
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Getting polarity descriptors for residues from reference scales |
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Getting the solvent accessible surface area of a molecular system |
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Getting reference surface areas of amino acid residues |
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Getting transmembrane insertion scores for residues in a molecular system |
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Getting residue sidechain volumes from reference scales |