Hi,
just for reference and hitback from other users:
Actually the functions are all well defined in the online Help and also the Help File:
http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html
These functions are from the helpfile:
JChem for Excel Reference v1.1.2
Elemental Analysis The following sub-topics provide a summary of structure based calculations.
JCAtomCount
Returns the number of atoms in the molecule including hydrogens.
JCComposition
Returns the elemental composition given in weight percentage (w/w %) calculated from the atomic masses.
JCDotDisconnectedFormula
Returns the chemical formula of the molecule(s) separating fragment formulas by dots (e.g. salts, counterions, solvent molecules etc. are present).
JCDotDisconnectedIsotopeFormula
Returns the chemical formula of the molecule separating fragment formulas by dots and listingisotopes separately.
JCExactMass
Returns the monoisotopic mass calculated from the weights of the most abundant natural isotopes of the elements.
JCIsotopeComposition
Returns the elemental composition, listing isotopes separately (w/w %).
JCIsotopeFormula
Returns the chemical formula of the molecule listing isotopes separately according to the Hill system.
JCMass
Returns the average molecular mass calculated from the standard atomic weights.
JCMolFormula
Returns the chemical formula of the molecule according to the Hill system: the number of carbon atoms is indicated first, the number of hydrogen atoms next (including deuterium and tritium whenusing D and T symbols), and then the number of all other chemical elements subsequently, in alphabetical order. When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically.
Structures can be quickly and accurately named using either traditional names or International Union of Pure and Applied Chemistry (IUPAC) nomenclature recommendations (2004).
JCIUPACName
Returns the IUPAC Name.
Returns the traditional IUPAC name.
Most molecules contain some specific functional groups likely to loose or gain a proton under specific circumstances. Each ionization equilibrium between the protonated or deprotonated forms of the molecule can be described with a constant value called pKa. The pKa function calculates the pKa values of all proton gaining or loosing atoms on the basis of the partial charge distribution.
There is no upper limit for the number of ionizable atoms in the molecule and so the pKa function can also be used for proteins.
JCAcidicpKa
Returns the acidic pKa value for the specified strongness index.
JCBasicpKa
Returns the basic pKa value for the specified strongness index.
JCAcidicpKaLargeModel
Returns the acidic pKa value for the specified strongness index using large model (this model is optimized for a large number of ionizable atoms)
JCBasicpKaLargeModel
Returns the basic pKa value for the specified strongness index using large model (this model is optimized for a large number of ionizable atoms)
The Major microspecies Plugin calculates the dominant protonation state of a molecule at a specified pH.
JCMicrospeciesCount
Returns the number of microspecies.
The isoelectric point (pI) is the pH at which a molecule carries no net electrical charge. The Isoelectric Point Plugin calculation considers all macro ionization states of an ionizable molecule across the pHrange. The net charge at given pH is calculated from the weighted sum of the macro distribution.
Proteins have minimal solubility at their isoelectric point. The mobility of molecule is minimal at pI and so an important parameter for electroanalytical separation techniques.
JClogP
Returns the octanol/water partition coefficient, which is used in QSAR analysis and rational drug design as a measure of molecular hydrophobicity. The calculation method is based on the publicationof Viswanadhan at al. The logP value of a molecule is composed of the increment values of its atoms. Though, logP is generally calculated for the neutral molecule forms only, this function is able to handle ionic species as well, owing to the improved algorithm.
JClogD
Returns the octanol-water distribution coefficient, of the compound at any pH value. Compounds having ionizable groups exist in solution as a mixture of different ionic forms. The ionization of those groups and so the ratio of the ionic forms depends on the pH. Since logP describes the hydrophobicity of one form only, the apparent logP value can be different.
The electric field generated by partial charges of a molecule spread through intermolecular cavities and the solvent that the molecule is solved within. The induced partial charge (induced dipole) has a tendency to diminish the external electric field and this is termed polarizability. Our calculation takes into account the effect of partial charges upon atomic polarizability as well as 2D and 3D geometries. The electric field generated by partial charges of a molecule spread through intermolecular cavities and the solvent that the molecule is solved within. The induced partial charge (induced dipole) has a tendency to diminish the external electric field and this is termed polarizability.
The more stable each ionized site is the more its vicinity is polarizable. This is why atomic polarizability is an important factor in the determination of pK and why it is considered in our pK calculation plugin.
Atomic polarizability is altered by partial charges of atoms. Our calculation takes into account the effect of partial charge upon atomic polarizability as well as the the 2D and 3D geometries.
JCMolecularPolarizability
Returns the molecular polarizability value.
Tautomers are structural isomers which are in dynamic equilibrium due to the migration of a proton.
JCDominantTautomerCount
Returns the number of dominant tautomers.
JCTautomerCount
Returns the number of tautomers.
Lone pair, radical electron or formal charge of certain atoms in a molecule can migrate within a delocalized system. Some resonance structures are stable, these structures are called mesomer structures. Our resonance structure generator creates all resonance forms of a molecule.
JCResonantCount
Returns the number of resonant structures.
JCStereoIsomerCount
The Stereoisomer Plugin produces all possible stereoisomers of a given compound. The plugin handles both tetrahedral and double bond stereogenic centers. Identical stereo-isomers of a molecule are filtered out; energetically impossible conformations can be also be filtered.
JCDoubleBondStereoisomerCount
Number of DB Stereosiomers
JCTetrahedralStereoisomerCount
The calculation generates the stable 3D structures, conformers, of a given molecule. The stability of the conformers is estimated through comparing their energy content, calculated in the framework of a molecular mechanics force-field. The 3D structure (conformation) strongly affects the properties and the reactions of molecules.
JCConformerCount
Number of conformers
JCHasValidConformer
Test if conformer exists
JCAtomCount
Returns number of atoms in the molecule including hydrogens.
JCBondCount
Returns the number of bonds in the molecule including hydrogens.
JCCyclomaticNumber
Returns the smallest number of bonds which must be removed such that no circuit remains. Also known as circuit rank.
JCRingCount
Returns the number of rings in the molecule. This calculation is based on SSSR (Smallest Set of Smallest Rings).
JCRingAtomCount
Returns number of ring atoms.
JCRingBondCount
Returns the number of ring bonds.
JCChainAtomCount
Returns the number of chain atoms (non-ring atoms excluding hydrogens).
JCChainBondCount
Returns the number of chain bonds (non-ring bonds excluding bonds of hydrogen atoms).
JCAliphaticRingCount
Returns the number of those rings in the molecule, which have non-aromatic bonds (SSSR based).
JCAromaticRingCount
Returns the number of aromatic rings in the molecule. This number is calculated from the smallest setof smallest aromatic rings (SSSAR), which might contain rings which are not part of the standard SSSR ring set. As a consequence, the sum of the aliphatic ring count and the aromatic ring count can sometimes be greater the the ring count value. The difference is the sign of a macroaromatic ring system.
JCAliphaticAtomCount
Returns the number of atoms in the molecule having no aromatic bond (excluding hydrogens).
Returns the number of non-aromatic bonds in the molecule (excluding bonds of hydrogen atoms).
JCAromaticAtomCount
Returns number of atoms in the molecule having aromatic bonds.
JCAromaticBondCount
Returns the number of aromatic bonds in the molecule.
JCCarboRingCount
Returns the number of those rings in the molecule, which contain carbon atoms only.
JCHeteroRingCount
Returns the number of those rings in the molecule, which contain hetero atoms.
JCHeteroAromaticRingCount
Returns number of aromatic heterocycles in the molecule.
JCCarboAromaticRingCount
Returns the number of heterocycles in the molecule containing carbon atoms only (SSSAR based).
JCFusedRingCount
Returns the number of fused rings in the molecule (having common bonds).
JCFusedAliphaticRingCount
Returns the number of aliphatic rings having common bonds with other rings.
JCFusedAromaticRingCount
Returns the number of aromatic rings having common bonds with other rings.
JCLargestRingSize
Returns the size of the largest ring in the molecule.
JCSmallestRingSize
Returns the size of the smallest ring in the molecule.
JCPlattIndex
Returns the sum of the edge degrees of a molecular graph.
JCRandicIndex
Returns the harmonic sum of the geometric means of the node degrees for each edge.
JCBalabanIndex
Returns the Balaban distance connectivity of the molecule, which is the average distance sum
connectivity.
JCHararyIndex
Returns the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the
molecule.
JCHyperWienerIndex
Returns a variant of the Wiener index.
JCSzegedIndex
The Szeged index extends the Wiener index for cyclic graphs by counting the number of atoms on both sides of each bond (those atoms only which are nearer to the given side of the bond than to the other), and sum these counts.
JCWienerIndex
Returns the average topological atom distance (half of the sumof all atom distances) in the molecule.
JCAsymmetricAtomCount
Returns the number of asymmetric atoms (having four different ligands).
JCRotatableBondCount
Returns the number of rotatable bonds in the molecule. Unsaturated bonds, and single bonds connected to hydrogens or terminal atoms, single bonds of amides, sulphonamides and those connecting two hindered aromatic rings (having at least three ortho substituents) are considered non-rotatable.
JCDreidingEnergy
Returns the energy related to the stability of the actual 3D structure (conformation) of the molecule.
JCPSA
Returns the polar surface area (PSA) is formed by polar atoms of a molecule. It is a descriptor that
of transport properties of drugs.
A Markush structure is a description of a compound class by generic notations, primarily used in
patent claims and the description of combinatorial libraries. The library of a Markush structure is the
total set of specific molecules that are described by the Markush structure.
The Markush enumeration plugin can be used to generate a whole or a subset of the library of a generic
Markush structure. It is also capable of calculating the total number of specific structures present in a
Markush library.
JCMarkushEnumerationCount
Returns the number of Markush enumerations.
Hydrogen Bond Donor-Acceptor (HBDA) calculates atomic hydrogen bond donor and acceptor
inclination. HDBA is a useful characteristic in defining ´drug likeness´.
Atomic data and overall hydrogen bond donor and acceptor multiplicity are displayed for the input
molecule (or its physiological microspecies at a given pH). The weighted average hydrogen bond
donor and acceptor multiplicities, taken over all microspecies, with proportions of their presence, are
presented over pH's and charted.
JCAcceptorCount
Hydrogen bond acceptor atom count in molecule
JCDonorCount
Hydrogen bond donor atom count in molecule
JCAcceptorSiteCount
JCDonorSiteCount
Molar refractivity is strongly related to the volume of the molecules and to London dispersive forces
that has important effect in drug-receptor interaction.
JCRefractivity
Refractivity calculation
Following functions compute the dissimilarity value between two molecules.
JCDissimilarityCFEuclidean
JCDissimilarityCFTanimoto
JCDissimilarityPFEuclidean
JCDissimilarityPFTanimoto
JCDissimilarityBCUTEuclidean