2D 2D coordinates 2D-coordinates 3D 3D coordinates 3D isomorphism 3D model 3D-coordinates adjacency matrix amino acid amino acids animation aromatic ring aromaticity detector ASN association atom atom coloring atom mapping atom parity atom type atom types atomic AtomPlacer3D BCUT Binary Space Partitioning Tree biopolymer bond bond count bond creation bond order bond order adjustment calculation canonicalization CAS number CDK source code center of mass charge distribution chemical identifier chemical validation chi chain index chi cluster index chi path cluster index chi path index CIF class convertor classification CML conformer conformation connection matrix connectivity coordinate calculation coordinate generation CPK creation crystal DBE descriptor diagonalization dictionary double bond equivalent E-state EAID number electron electronegativities electronegativity element estate file format file format SDF fingerprint force field fractional coordinates fragment free valence Gamess Gauss elimination Gaussian (tm) Gaussian basis set generator geometry Gram-Schmidt algorithm graph graph matrix gravitational index HIN HOSE code hydrogen id implicit CDK references INChI input file ionization potential isomorphism isotope isotope pattern IUPAC name jaccard Jacobi algorithm join-the-dots JRI Kappe shape index layout line search linear linear regression Lipinski lipophilicity log file logP lone-pair mass MDL molfile MDL molfile V3000 MDL RXN MDL RXN file MDL V3000 MM2 mmCIF mmff94 Mol2 molecular molecular formula molecule moment of inertia monomer Morgan number Murcko fragments neural network Newton-Raphson notional coordinates number orbital orthonormalization output parser partial atomic charges partial charges partial equalization of orbital partial least squares path PDB pdbpolymer PEOE PEPE periodic table permutation Petit-Jean pharmacophore physical properties PLS pocket polarizability polymer Polymorph Predictor (tm) prime numbers projection in 2D protein PubChem PubChem Compound ASN PubChem Compound XML R radial distribution function radical radius RDF reaction rebonding recalculation refractivity regression removal ring ring finding ring search rotatable RSS rule-of-five saturation SDF set of shape index ShelX ShelXL similarity smallest-set-of-rings SMARTS SMARTS AST SMILES sorting spanning tree spherical atom search stabilization charge stack steepest descent stereochemistry structure diagram generation Structure Diagram Generation (SDG) structure generator stuctures substructure search Sybyl tanimoto templates topological bond order ctypes total polar surface area TPSA type unpaired valency validation vanderwaals WHIM Wiener number XLogP XYZ Z Matrix Z-matrix Zagreb index