cxcalc calculator functions

Elemental Analysis

Example on Windows:

"C:/Program Files/ChemAxon/MarvinBeans/bin/cxcalc" name mass -p 2 psa canonicalresonant msa -p 2 -t ASA
 msa -p 2 -t ASA_H msa -p 2 -t ASA_P refractivity 
-p 2 resonantcount molecules.sdf >_properties.molecules.txt

The following features and properties can be calculated:

atomcount
 

Number of atoms in the molecule: no atno: counts all atoms in the molecule; atno, but no massno: counts atoms of the given type in the molecule; atno, massno: counts atoms of the given isotope type in the molecule; atno, massno=0: counts atoms of the given type in the molecule, but excludes its isotopes.
 

Options:

Example:

cxcalc atomcount -z 7 test.mol

composition
 

Elemental composition calculation (w/w%).
 

Options:

Example:

cxcalc composition -s true test.mol

dotdisconnectedformula
 

Dot-disconnected molecular formula calculation.

Options: 

No options
 

Example:

cxcalc dotdisconnectedformula test.mol

dotdisconnectedisotopeformula
 

Dot-disconnected molecular formula calculation, isotopes included.
 

Options:

Example:

cxcalc dotdisconnectedisotopeformula test.mol

elemanal

Molecule data calculation: formula, isotopeformula, dotdisconnectedformula, dotdisconnectedisotopeformula, mass, exactmass, composition, isotopecomposition, atomcount.
 

Options: 

Example:

cxcalc elemanal -t "mass,composition,formula" test.mol

elementalanalysistable
 

Molecule data calculation: formula, isotopeformula, dotdisconnectedformula, dotdisconnectedisotopeformula, mass, exactmass, composition, isotopecomposition, atomcount.
 

Options:

Example:

cxcalc elementalanalysistable -t "mass,composition,formula" test.mol

exactmass
 

Exact molecule mass calculation based on the most frequent natural isotopes of the elements.
 

Options:

Example:

cxcalc exactmass test.mol

formula

Molecular formula calculation.
 

Options:

Example:

 cxcalc formula -s true test.mol

icomposition
 

Elemental composition calculation, isotopes included (w/w%).
 

Options:

Example:

cxcalc icomposition -s true test.mol

iformula

Molecular formula calculation, isotopes included.
 

Options:

Example:

 cxcalc iformula -s true test.mol

isotopecomposition
 

Elemental composition calculation, isotopes included (w/w%).

Options:

Example:

cxcalc isotopecomposition -s true test.mol

isotopeformula
 

Molecular formula calculation, isotopes included.
 

Options:

Example:

cxcalc isotopeformula -s true test.mol

mass

Molecule mass calculation.
 

Options:

Example:

cxcalc mass test.mol

massspectrum

Calculates the mass spectrum, the mass/charge values (m/z) vs. the relative abundance plot.

Options:

Example:

cxcalc massspectrum -p 4 sildenafil

sortableformula

Calculates a fixed digit sortable molecular formula.
 

Options:

Example:

cxcalc sortableformula -d 4 test.mol

Charge 

The following features and properties can be calculated:

atomicpolarizability
 

Atomic polarizability calculation.
 

Options:

Example:

cxcalc atomicpolarizability test.mol

atompol
 

Atomic polarizability calculation.
 

Options:

Example:

cxcalc atompol test.mol

averagemolecularpolarizability

Average molecular polarizability calculation.
 

Options:

Example:

cxcalc averagemolecularpolarizability test.mol

averagepol

Average molecular polarizability calculation.
 

Options:

Example:

cxcalc averagepol test.mol

avgpol
 

Average molecular polarizability calculation.

Options:

Example:

cxcalc avgpol test.mol

axxpol
 

Calculation of principal component of polarizability tensor axx.
 

Options:

Example:

cxcalc axxpol test.mol

ayypol
 

Calculation of principal component of polarizability tensor ayy.
 

Options:

Example:

cxcalc ayypol test.mol

azzpol
 

Calculation of principal component of polarizability tensor azz.
 

Options:

Example:

 cxcalc azzpol test.mol

charge
 

Partial charge calculation. Types aromaticsystem / aromaticring calculate the sum of charges in the aromatic system / aromatic ring containing the atom.
 

Options:

Example:

cxcalc -S -o result.sdf -t myCHARGE charge -t "pi,total" -p 3 test.mol

dipole

Calculates the absolute value of the dipole moment vector.

Options:

Example:

cxcalc dipole -f sdf test.mol

formalcharge
 

Formal charge calculation.
 

Options:

Example:

cxcalc formalcharge test.mol

ioncharge
 

Partial charge(s): A) on the ionic forms with distribution percentage not less than the minimum percentage specified in the min-percent parameter, or else B) on the ionic form with maximal distribution if the min-percent parameter is omitted.
 

Options:

Example:

cxcalc ioncharge -n 6 -H 8 -m 1 -t accumulated test.mol

molecularpolarizability
 

Molecular polarizability calculation.
 

Options:

Example:

cxcalc molecularpolarizability test.mol

molpol
 

Molecular polarizability calculation.
 

Options:

Example:

 cxcalc molpol test.mol

oen
 

Orbital electronegativity calculation.
 

Options:

Example:

 cxcalc oen -t sigma test.mol

orbitalelectronegativity
 

Orbital electronegativity calculation.
 

Options:

Example:

 cxcalc orbitalelectronegativity -p 3 test.mol

pol
 

Atomic and molecular polarizability calculation.
 

Options:

Example:

cxcalc pol -p 3 test.mol

polarizability
 

Atomic and molecular polarizability calculation.
 

Options:

Example:

cxcalc polarizability -p 3 test.mol

tholepolarizability
 

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
 

Options:

Example:

cxcalc tholepolarizability test.mol

tpol
 

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
 

Options:

Example:

cxcalc tpol test.mol

tpolarizability
 

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
 

Options:

Example:

cxcalc tpolarizability test.mol

Conformation
 

The following features and properties can be calculated:

conformers
 

Calculates the conformers of the molecule.
 

Options:

Example:

cxcalc conformers -m 250 -s true test.sdf

hasvalidconformer
 

Calculates if the molecule has a conformer.

Options:

No options
 

Example:

cxcalc hasvalidconformer test.sdf

leconformer
 

Calculates the lowest energy conformer of the molecule.
 

Options:

Example:

 cxcalc leconformer -f mrv test.sdf

lowestenergyconformer
 

Calculates the lowest energy conformer of the molecule.
 

Options:

Example:

cxcalc lowestenergyconformer -f mrv test.sdf

moldyn
 

Runs a molecular dynamics simulation for the molecule.
 

Options:

Example:

cxcalc moldyn -i leapfrog -n 1500 -T 400 -f sdf test.mol

moleculardynamics
 

Runs a molecular dynamics simulation for the molecule.
 

Options:

Example:

 cxcalc moleculardynamics -i positionverlet -n 1500 -T 450 -f mrv test.mol

Geometry

aliphaticatom
 

Checks if a specified atom is aliphatic.
 

Options:

Example:

cxcalc aliphaticatom test.mol

aliphaticatomcount

Counts the number of aliphatic atoms in the molecule.
 

Options:

Example:

cxcalc aliphaticatomcount test.mol

aliphaticbondcount

Aliphatic bond count.
 

Options:

Example:

 cxcalc aliphaticbondcount test.mol

aliphaticringcount

Aliphatic ring count.
 

Options:

Example:

 cxcalc aliphaticringcount test.mol

aliphaticringcountofsize
 

Aliphatic ring count of size.

Options:

Example:

 cxcalc aliphaticringcountofsize -z 5 test.mol

angle
 

Angle of three atoms.

Options:

Example:

cxcalc angle -a 2-4-6 test.mol

aromaticatom
 

Checks if a specified atom is aromatic.
 

Options:

Example:

cxcalc aromaticatom test.mol

aromaticatomcount

Aromatic atom count.
 

Options:

Example:

cxcalc aromaticatomcount test.mol

aromaticbondcount
 

Aromatic bond count.
 

Options:

Example:

cxcalc aromaticbondcount test.mol 

aromaticringcount
 

Aromatic ring count.
 

Options:

Example:

cxcalc aromaticringcount test.mol

aromaticringcountofsize

Aromatic ring count of size.
 

Options:

Example:

 cxcalc aromaticringcountofsize -z 6 test.mol

asa

Water Accessible Surface Area calculation.
 

Options:

Example:

cxcalc asa -p 4 -r 2.2 -H 7.4 test.mol

asymmetricatom
 

Checks if a specified atom is an asymmetric atom.
 

Options:

Example:

cxcalc asymmetricatom test.mol

 asymmetricatomcount
 

The number of asymmetric atoms.
 

Options:

Example:

cxcalc asymmetricatomcount test.mol

asymmetricatoms
 

The asymmetric atoms.
 

Options:

Example:

cxcalc asymmetricatoms test.mol 

balabanindex

The Balaban index.

Options:

Example:

cxcalc balabanindex test.mol

bondcount
 

Bond count.
 

Options:

Example:

cxcalc bondcount test.mol

bondtype
 

The bond type between two atoms.
 

Options:

Example:

cxcalc bondtype -a 2-3 test.mol 

carboaliphaticringcount
 

Carboaliphatic ring count.
 

Options:

Example:

cxcalc carboaliphaticringcount test.mol 

carboaromaticringcount
 

Carboaromatic ring count.

Options:

Example:

cxcalc carboaromaticringcount test.mol

carboringcount
 

Carbo ring count.
 

Options:

Example:

cxcalc carboringcount test.mol 

chainatom
 

Checks if a specified atom is a chain atom.
 

Options:

Example:

cxcalc chainatom test.mol 

chainatomcount
 

Chain atom count.
 

Options:

Example:

cxcalc chainatomcount test.mol 

chainbond
 

Checks if the bond is a chain bond.
 

Options:

Example:

cxcalc chainbond -a 2-3 test.mol 

chainbondcount

Chain bond count.
 

Options:

Example:

cxcalc chainbondcount test.mol 

chiralcenter
 

Checks if a specified atom is a tetrahedral stereogenic center.
 

Options:

Example:

cxcalc chiralcenter test.mol 

chiralcentercount
 

The number of tetrahedral stereogenic center atoms.
 

Options:

Example:

cxcalc chiralcentercount test.mol 

chiralcenters
 

The the chiral center atoms.
 

Options:

Example:

cxcalc chiralcenters test.mol 

connected
 

Checks if two atoms are in the same connected component.
 

Options:

Example:

cxcalc connected -a 2-3 test.mol 

connectedgraph

Checks if the molecule graph is connected.
 

Options:

No options

Example:

cxcalc connectedgraph test.mol 

cyclomaticnumber
 

The cyclomatic number.
 

Options:

Example:

cxcalc cyclomaticnumber test.mol 

dihedral

Calculates the dihedral angle between four atoms.
 

Options:

Example:

cxcalc dihedral -o 2 -a 1-2-4-6 test.mol 

distance

Distance between two atoms.
 

Options:

Example:

cxcalc distance -l if2D -a 2-4 test.mol 

distancedegree
 

Distance degree of atom.

Options:

Example:

cxcalc distancedegree test.mol 

dreidingenergy

Calculates the dreiding energy of a conformer of the molecule in kcal/mol.
 

Options:

Example:

cxcalc dreidingenergy -p 1 -l always test.sdf 

eccentricity

Eccentricity of atom.

Options:

Example:

cxcalc eccentricity test.mol 

fragmentcount

Fragment count.

Options:

No options

Example:

cxcalc fragmentcount test.mol

fsp3

Fsp3 value of the molecule.

Options:

No options

Example:

cxcalc fsp3 test.mol 

fusedaliphaticringcount

The number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings).

Options:

Example:

cxcalc fusedaliphaticringcount test.mol

fusedaromaticringcount

The number of fused aromatic rings (SSSR smallest set of smallest aromatic rings).

Options:

Example:

cxcalc fusedaromaticringcount test.mol 

fusedringcount
 

The number of fused rings (SSSR smallest set of smallest rings).

Options:

Example:

cxcalc fusedringcount test.mol 

hararyindex
 

Harary index.

Options:

Example:

 cxcalc hararyindex test.mol

heteroaliphaticringcount

Heteroaliphatic ring count.
 

Options:

Example:

cxcalc heteroaliphaticringcount test.mol 

heteroaromaticringcount
 

Heteroaromatic ring count.
 

Options:

Example:

cxcalc heteroaromaticringcount test.mol 

heteroringcount

Hetero ring count.
 

Options:

Example:

cxcalc heteroringcount test.mol 

hindrance

Steric hindrance.
 

Options:

Example:

cxcalc hindrance -p 3 -o 2 -l always test.mol 

hyperwienerindex

Hyper Wiener index.
 

Options:

Example:

cxcalc hyperwienerindex test.mol 

largestatomringsize
 

Size of largest ring containing a specified atom.
 

Options:

Example:

cxcalc largestatomringsize -s true test.mol 

largestringsize

Largest ring size.

Options:

Example:

cxcalc largestringsize test.mol 

largestringsystemsize
 

Largest ring system size.
 

Options:

Example:

cxcalc largestringsystemsize test.mol 

maximalprojectionarea

Calculates the maximal projection area.

Options:

Example:

cxcalc maximalprojectionarea -p 4 -o true -l never test.sdf 

maximalprojectionradius
 

Calculates the maximal projection radius.
 

Options:

Example:

cxcalc maximalprojectionradius -s 1.2 -o 3 test.sdf 

maximalprojectionsize
 

Calculates the size of the molecule perpendicular to the maximal projection area surface.
 

Options:

Example:

cxcalc maximalprojectionsize -p 3 -o 2 -o true -l always test.sdf 

minimalprojectionarea
 

Calculates the minimal projection area.
 

Options:

Example:

cxcalc minimalprojectionarea -s 1.5 -l never -o 0 test.sdf 

minimalprojectionradius
 

Calculates the minimal projection radius.
 

Options:

Example:

cxcalc minimalprojectionradius -s 1.3 -o true test.sdf 

minimalprojectionsize
 

Calculates the size of the molecule perpendicular to the minimal projection area surface.
 

Options:

Example:

cxcalc minimalprojectionsize -p 3 -o 2 -O true -l always test.sdf 

mmff94energy
 

Calculates the MMFF94 energy of the molecule in kcal/mol.
 

Options:

Example:

cxcalc mmff94energy --mmff94optimization true -p 3 test.sdf 

molecularsurfacearea

Molecular Surface Area calculation (3D).
 

Options:

Example:

cxcalc molecularsurfacearea -t ASA+ -i true -H 7.4 test.mol 

msa

Molecular Surface Area calculation (3D).
 

Options:

Example:

cxcalc msa -t ASA+ -i true -H 7.4 test.mol 

plattindex

The Platt index.
 

Options:

Example:

cxcalc plattindex test.mol 

polarsurfacearea
 

Topological Polar Surface Area calculation (2D).
 

Options:

Example:

cxcalc -S -t myPSA polarsurfacearea test.mol 

psa

Topological Polar Surface Area calculation (2D).
 

Options:

Example:

cxcalc -S false -p 3 psa test.mol

randicindex
 

The Randic index.
 

Options:

Example:

cxcalc randicindex test.mol 

ringatom
 

Checks if a specified atom is a ring atom.
 

Options:

Example:

cxcalc ringatom test.mol 

ringatomcount
 

Ring atom count.
 

Options:

Example:

cxcalc ringatomcount test.mol 

ringbond

Checks if the bond is a ring bond.
 

Options:

Example:

cxcalc ringbond -a 2-3 test.mol 

ringbondcount
 

Ring bond count.

Options:

Example:

cxcalc ringbondcount test.mol 

ringcount
 

Ring count.
 

Options:

Example:

cxcalc ringcount test.mol 

ringcountofatom
 

Ring counts of atoms.
 

Options:

No options

Example:

cxcalc ringcountofatom test.mol 

ringcountofsize
 

Ring count of size.

Options:

Example:

cxcalc ringcountofsize -z 5 test.mol 

ringsystemcount
 

The number of ring systems.
 

Options:

Example:

cxcalc ringsystemcount test.mol 

ringsystemcountofsize

Ring system count of size.

Options:

Example:

cxcalc ringsystemcountofsize -z 3 test.mol 

rotatablebond
 

Checks if the bond is a rotatable bond.

Options:

Example:

cxcalc rotatablebond -a 2-3 test.mol 

rotatablebondcount
 

Rotatable bond count.
 

Options:

Example:

cxcalc rotatablebondcount test.mol 

shortestpath
 

Length of shortest path between two atoms.
 

Options:

Example:

cxcalc shortestpath -a 2-3 test.mol 

smallestatomringsize
 

Size of smallest ring containing a specified atom.
 

Options:

Example:

cxcalc smallestatomringsize test.mol 

smallestringsize
 

Smallest ring size.

Options:

Example:

cxcalc smallestringsize test.mol 

smallestringsystemsize
 

Smallest ring system size.
 

Options:

Example:

cxcalc smallestringsystemsize -s true test.mol 

stereodoublebondcount
 

The number of stereo double bonds.
 

Options:

Example:

cxcalc stereodoublebondcount -s true test.mol 

stericeffectindex
 

Steric effect index.
 

Options:

Example:

cxcalc stericeffectindex -p 3 -s true test.mol 

sterichindrance
 

Steric hindrance.
 

Options:

Example:

cxcalc sterichindrance test.mol 

szegedindex
 

Szeged index.

Options:

Example:

cxcalc szegedindex test.mol 

topanal
 

Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize,fsp3.
 

Options:

Example:

cxcalc topanal -a loose -t largestringsize -s true test.mol 

topologyanalysistable
 

Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize,fsp3.
 

Options:

Example:

cxcalc topologyanalysistable -a basic -s true test.mol 

vdwsa
 

Van der Waals Surface Area calculation.
 

Options:

Example:

cxcalc vdwsa -H 7.4 -i true -p 4 test.mol 

volume

Calculates the van der Waals volume of the molecule.
 

Options:

Example:

cxcalc volume -p 3 -o 3 -l never test.sdf 

wateraccessiblesurfacearea
 

Water Accessible Surface Area calculation.
 

Options:

Example:

cxcalc -p 4 -r 1.5 -H 7.4 wateraccessiblesurfacearea test.mol 

wienerindex
 

Wiener index.
 

Options:

Example:

cxcalc wienerindex test.mol 

wienerpolarity
 

Wiener polarity.
 

Options:

Example:

cxcalc wienerpolarity test.mol 

Isomers

canonicaltautomer

Canonical tautomer.

Options:

Example:

cxcalc canonicaltautomer -f sdf -a false -C false test.mol 

dominanttautomerdistribution

Dominant tautomer distribution.
 

Options:

Example:

cxcalc dominanttautomerdistribution test.mol 

doublebondstereoisomercount
 

The number of double-bond stereoisomers of the molecule.
 

Options:

Example:

cxcalc doublebondstereoisomercount test.sdf

doublebondstereoisomers
 

Generates double-bond stereoisomers of the molecule.
 

Options:

Example:

cxcalc doublebondstereoisomers -f mrv test.sdf 

generictautomer
 

Generic tautomer.
 

Options:

Example:

cxcalc generictautomer -f sdf test.mol 

majortautomer
 

Major tautomer.

Options:

Example:

cxcalc majortautomer -H 7.4 -f sdf test.mol

moststabletautomer
 

Most stable tautomer. Depreacated, use "majortautomer" instead.
 

Options:

Example:

cxcalc moststabletautomer -f sdf test.mol 

stereoisomercount

The number of stereoisomers of the molecule.

Options:

Example:

cxcalc stereoisomercount -m 100 test.sdf 

stereoisomers
 

Generates stereoisomers of the molecule.

Options:

Example:

cxcalc stereoisomers -v true test.sdf 

stereoanalysis

Calculate stereo descriptors.

Options:

Example:

cxcalc stereoanalysis test.mol

tautomercount
 

The number of tautomers.

Options:

Example:

cxcalc tautomerCount -s false test.mol 

tautomers
 

Tautomers.

Options:

Example:

cxcalc tautomers -f sdf test.mol
cxcalc tautomers --dominants false --rational true test.mol --format smiles

tetrahedralstereoisomercount
 

The number of tetrahedral stereoisomers of the molecule.

Options:

Example:

cxcalc tetrahedralstereoisomercount test.sdf 

tetrahedralstereoisomers
 

Generates tetrahedral stereoisomers of the molecule.

Options:

Example:

cxcalc tetrahedralstereoisomers -3 true test.sdf 

Markush enumeration
 

enumerationcount
 

Number of Markush enumerated structures.
 

Options:

Example: 

cxcalc enumerationcount -m true test.mol 

enumerations
 

Generates Markush enumerated structures.
 

Options:

Example:

cxcalc enumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol 

markushenumerationcount
 

Number of Markush enumerated structures.

Options:

Example:

cxcalc markushenumerationcount -m true test.mol

markushenumerations

Markush enumerated structures.

Options:

Example:

cxcalc markushenumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol

randommarkushenumerations

Randomly constructed Markush enumerated structures.

Options:

Example:

cxcalc randommarkushenumerations -f sdf -C 2:t5000 test.mol

Naming
 

name
 

Generates the IUPAC name for the molecule.
 

Options:

Example:

cxcalc name test.sdf 

Partitioning

logd
 

logD calculation.
 

Options:

Example:

cxcalc -i ID logd -l 2 -u 3 -s 0.5 test.sdf 

logp

logP calculation: for type logPTrue: logP of uncharged species, or, in the case of zwitterions, logD at pI; for type logPMicro: logP of the input species.

Options:

Example:

cxcalc -S -t myLOGP logp -a 0.15 -k 0.05 test.mol 

Protonation

averagemicrospeciescharge
 

Average microspecies charge calculation.
 

Options:

Example:

 cxcalc averagemicrospeciescharge test.mol

chargedistribution
 

Charge distribution calculation.
 

Options: 

Example:

cxcalc chargedistribution test.mol 

isoelectricpoint
 

Isoelectric point calculation.

Options:

Example:

cxcalc isoelectricpoint test.mol 

majormicrospecies
 

Major microspecies at given pH.
 

Options: 

Example:

cxcalc majormicrospecies -H 3.5 -f mol test.mol 

majorms

Major microspecies at given pH.

Options:

Example:

cxcalc majorms -H 3.5 -f mol test.mol 

microspeciesdistribution

Microspecies list with distributions at given pH.

Options:

Example:

cxcalc microspeciesdistribution -H 3.5 test.mol 

msdistr
 

Microspecies list with distributions at given pH.
 

Options:

Example:

cxcalc msdistr -H 3.5 test.mol 

pi

Isoelectric point calculation.

Options:

Example:

cxcalc pI test.mol 

pka

pKa calculation.

Options:

Example:

cxcalc pka -i -15 -x 25 -a 3 -b 3 -d large test.mol 

Other calculator functions

acc
 

Hydrogen bond acceptor multiplicity calculation on atoms.
 

Options:

Example:

cxcalc acc test.sdf 

acceptor
 

Hydrogen bond acceptor calculation.
 

Options:

Example:

cxcalc acceptor test.sdf 

acceptorcount
 

Hydrogen bond acceptor atom count in molecule.
 

Options:

Example:

cxcalc acceptorcount -H 7.4 test.sdf

acceptormultiplicity
 

Hydrogen bond acceptor multiplicity calculation on atoms.
 

Options:

Example:

cxcalc acceptormultiplicity test.sdf 

acceptorsitecount
 

Hydrogen bond acceptor multiplicity in molecule.
 

Options:

Example:

cxcalc acceptorsitecount test.sdf 

acceptortable
 

Hydrogen bond acceptor calculation.
 

Options:

Example:

cxcalc acceptortable test.sdf 

accsitecount
 

Hydrogen bond acceptor multiplicity in molecule.
 

Options:

Example:

cxcalc accsitecount test.sdf 

aromaticelectrophilicityorder
 

Order in E(+) attack. Deprecated.
 

Options:

Example:

cxcalc aromaticelectrophilicityorder -H 7.4 test.mol 

aromaticnucleophilicityorder
 

Order in Nu(-) attack. Deprecated.
 

Options:

Example:

cxcalc aromaticnucleophilicityorder -H 7.4 test.mol 

canonicalresonant
 

Canonical resonant structure.
 

Options:

Example:

cxcalc canonicalResonant -f sdf test.mol 

chargedensity
 

Charge density.
 

Options:

Example:

cxcalc chargedensity -p 4 -H 6.5 test.mol 

don
 

Hydrogen bond donor multiplicity calculation on atoms.
 

Options:

Example:

cxcalc don test.sdf 

donor
 

Hydrogen bond donor calculation.
 

Options:

Example:

cxcalc donor test.sdf 

donorcount
 

Hydrogen bond donor atom count in molecule.
 

Options:

Example:

cxcalc donorcount -H 7.4 test.sdf 

donormultiplicity
 

Hydrogen bond donor multiplicity calculation on atoms.
 

Options:

Example:

cxcalc don test.sdf 

donorsitecount
 

Hydrogen bond donor multiplicity in molecule.
 

Options:

Example:

cxcalc donorsitecount test.sdf 

donortable
 

Hydrogen bond donor calculation.

Options:

Example:

cxcalc donortable test.sdf

donsitecount
 

Hydrogen bond donor multiplicity in molecule.
 

Options:

Example:

cxcalc donsitecount test.sdf 

electrondensity
 

Electron density.
 

Options:

Example:

cxcalc electrondensity -p 4 -H 6.5 test.mol 

electrophilicityorder
 

Order in E(+) attack. Deprecated.
 

Options:

Example:

cxcalc electrophilicityorder -H 7.4 test.mol 

electrophiliclocalizationenergy
 

Electrophilic localization energy L(+).
 

Options:

Example:

cxcalc electrophiliclocalizationenergy test.mol 

frameworks
 

Calculates different structural frameworks (Bemis-Murcko, MCS, etc) of the molecule
 

Options:

Example:

cxcalc frameworks -t bmf -s true test.mol 

hbda
 

Hydrogen bond acceptor-donor calculation.
 

Options:

Example:

cxcalc hbda -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf 

hbonddonoracceptor
 

Hydrogen bond acceptor-donor calculation.
 

Options:

Example:

cxcalc hbonddonoracceptor -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf 

hmochargedensity
 

HMO Charge density.
 

Options:

Example:

 cxcalc hmochargedensity -p 4 -H 6.5 test.mol

hmoelectrondensity
 

HMO Electron density.
 

Options:

Example:

cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol 

hmoelectrophilicityorder
 

Order in E(+) attack (HMO).
 

Options:

Example:

cxcalc hmoelectrophilicityorder -H 7.4 test.mol 

hmoelectrophiliclocalizationenergy
 

HMO Electrophilic localization energy L(+).

Options:

Example:

cxcalc hmoelectrophiliclocalizationenergy test.mol 

hmohuckel

HMO Huckel analysis parameters.
 

Options:

Example:

cxcalc -S -o result.sdf hmohuckel -H 7.4 -p 3 test.mol

hmohuckeleigenvalue
 

HMO Huckel eigenvalue.
 

Options:

Example:

cxcalc hmohuckeleigenvalue test.mol 

hmohuckeleigenvector

HMO Huckel eigenvector.
 

Options:

Example:

cxcalc hmohuckeleigenvector test.mol 

hmohuckelorbitals
 

HMO Huckel orbital coefficients.
 

Options:

Example:

cxcalc hmohuckelorbitals test.mol 

hmohuckeltable
 

HMO Huckel analysis parameters.
 

Options:

Example:

cxcalc -S -o result.sdf hmohuckeltable -H 7.4 -p 3 test.mol 

hmolocalizationenergy
 

HMO Localization energy L(+)/L(-).
 

Options:

Example:

cxcalc hmolocalizationenergy test.mol 

hmonucleophilicityorder
 

Order in Nu(-) attack (HMO).

Options:

Example:

cxcalc hmonucleophilicityorder -H 7.4 test.mol 

hmonucleophiliclocalizationenergy
 

HMO Nucleophilic localization energy L(-).
 

Options:

Example:

cxcalc hmonucleophiliclocalizationenergy test.mol 

hmopienergy
 

HMO Pi energy.
 

Options:

Example:

cxcalc hmopienergy test.mol 

huckel
 

Huckel analysis parameters.
 

Options:

Example:

cxcalc -S -o result.sdf huckel -H 7.4 -p 3 test.mol 

huckeleigenvalue
 

Huckel eigenvalue. Deprecated.
 

Options:

Example:

cxcalc huckeleigenvalue test.mol 

huckeleigenvector
 

Huckel eigenvector. Deprecated.

Options:

Example:

cxcalc huckeleigenvector test.mol 

huckelorbitals
 

Huckel orbital coefficients. Deprecated.
 

Options:

Example:

cxcalc huckelorbitals test.mol 

huckeltable
 

Huckel analysis parameters.
 

Options:

Example:

cxcalc -S -o result.sdf huckeltable -H 7.4 -p 3 test.mol

localizationenergy
 

Localization energy L(+)/L(-).
 

Options:

Example:

cxcalc localizationenergy test.mol

msacc
 

Hydrogen bond acceptor average multiplicity over microspecies by pH.
 

Options:

Example:

cxcalc msacc -l 2.0 -u 12.0 test.sdf 

msdon
 

Hydrogen bond donor average multiplicity over microspecies by pH.
 

Options:

Example:

cxcalc msdon -l 2.0 -u 12.0 test.sdf 

nucleophilicityorder
 

Order in Nu(-) attack. Deprecated.
 

Options:

Example:

cxcalc nucleophilicityorder -H 7.4 test.mol 

nucleophiliclocalizationenergy
 

Nucleophilic localization energy L(-).
 

Options:

Example:

cxcalc nucleophiliclocalizationenergy test.mol 

pichargedensity
 

Pi charge density. Deprecated, use "electrondensity" calculation.
 

Options:

Example:

cxcalc pichargedensity -p 4 -H 6.5 test.mol

pienergy
 

Pi energy. Deprecated.
 

Options:

Example:

cxcalc pienergy test.mol 

refractivity
 

Refractivity calculation.
 

Options:

Example:

 cxcalc refractivity -p 3 -t refractivity,increments test.mol

resonantcount
 

The number of resonant structures.
 

Options:

Example:

cxcalc resonantCount test.mol

resonants
 

Resonant structures.
 

Options:

Example:

cxcalc resonants -f sdf test.mol

solubility

Calculates aqueous solubility.

Options:

Example:

 cxcalc logs -i true -H 7.4 test.mol

totalchargedensity
 

Total charge density. Deprecated, use "chargedensity" calculation.
 

Options:

Example:

 cxcalc totalchargedensity -p 4 -H 6.5 test.mol