Physical-Chemical Data

MolSysMT standardizes physical-chemical properties, atomic attributes, element classifications, biophysical scales, and volumetric observables across diverse structural chemistry models and software packages.

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Atomic Properties

Properties describing individual atoms, elements, isotopes, and core physical invariants:

Attribute / Property	Target Scope	Description	Canonical Unit
atom_name	Atom	IUPAC/PDB atom identifier string (e.g., "CA", "N", "OG").	N/A
atom_type	Atom	Forcefield-specific or ProTor atom type code.	N/A
element_symbol	Atom	Chemical element symbol (e.g., "C", "N", "O", "Fe").	N/A
atomic_number	Atom	Nuclear proton count (\(Z\)).	N/A
mass	Atom / Group / System	Atomic, residue, or total molecular system mass.	dalton (Da)
isotope	Atom	Isotope mass number (\(A\)).	N/A
atomic_radius	Atom	Van der Waals radius, covalent radius, or ProTor VdW radius.	nanometer (nm)

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Chemical State and Charges

Properties defining electronic states, formal/partial charges, and protonation:

Attribute / Property	Target Scope	Description	Canonical Unit
charge	Atom / Group / System	Formal or net electric charge calculated across elements.	elementary_charge (e)
partial_charge	Atom	Forcefield-assigned fractional point charge.	elementary_charge (e)
formal_charge	Atom / Group	Integer electronic formal charge state.	elementary_charge (e)
electronegativity	Atom	Pauling or Mulliken atomic electronegativity scale value.	N/A
aromaticity	Atom / Bond	Huckel aromaticity classification flag.	Boolean
n_implicit_hydrogens	Atom / Group	Count of non-explicitly modeled hydrogen atoms.	Integer
n_unpaired_electrons	Atom	Radical or free electron count.	Integer
pka	Group	Acid dissociation constant value for ionizable groups.	N/A

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Biophysical and Residue Scales

Properties defining residue-level hydrophobicity, polarity, and structural classification:

Attribute / Property	Target Scope	Description	Canonical Unit
group_type	Group	Residue classification (amino_acid, nucleic_acid, water, ion, small_molecule, saccharide, lipid).	N/A
amino_acid_type	Group	Standard 3-letter or 1-letter amino acid code.	N/A
nucleic_acid_type	Group	Standard nucleotide base classification code (A, C, G, T, U).	N/A
hydrophobicity	Group	Hydrophobicity score (Kyte-Doolittle, Eisenberg, or Wimley-White scales).	N/A
polarity	Group	Amino acid sidechain polarity index.	N/A
transmembrane_tendency	Group	Free energy scale of insertion into lipid bilayers.	kilojoule_per_mole (kJ/mol)

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Surface Accessibility and Volumetric Observables

Observables describing spatial extent, solvent exposure, and molecular volume:

Attribute / Property	Target Scope	Description	Canonical Unit
sasa / surface_area	Atom / Group / System	Solvent Accessible Surface Area (Lee-Richards or Shrake-Rupley algorithms).	nanometer ** 2 (nm²)
volume	Group / System	Molecular or atomic volume via Voronoi tessellation or solvent envelope.	nanometer ** 3 (nm³)
area_buried	Group / Interface	Surface area buried upon interface formation or folding.	nanometer ** 2 (nm²)
buried_fraction	Atom / Group	Fractional extent of surface burial (\(0.0 \dots 1.0\)).	N/A