This page contains a full list of calculator functions implemented in cxcalc:

cxcalc calculations

cxcalc calculations

The calculator functions are grouped based on the plugin they belong to.

Elemental Analysis

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:

-z, --atno	<atomic number>
-m, --massno	<mass number>
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc atomcount -z 7 test.mol

composition

Elemental composition calculation (w/w%).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

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:

-D, --symbolD	[true\|false] use D / T symbols for Deuterium / Tritium (default: true)

Example:

cxcalc dotdisconnectedisotopeformula test.mol

elemanal

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

Options:

-t, --type	[formula\|isotopeformula\|dotdisconnectedformula\| dotdisconnectedisotopeformula\|mass\|exactmass\|composition\| isotopecomposition\|atomcount] (default: all)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

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

elementalanalysistable

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

Options:

-t, --type	[formula\|isotopeformula\|dotdisconnectedformula\| dotdisconnectedisotopeformula\|mass\|exactmass\|composition\| isotopecomposition\|atomcount] (default: all)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: precision of the least precise atomic mass)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc exactmass test.mol

formula

Molecular formula calculation.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

 cxcalc formula -s true test.mol

icomposition

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-D, --symbolD	[true\|false] use D / T symbols for Deuterium / Tritium (default: true)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc icomposition -s true test.mol

iformula

Molecular formula calculation, isotopes included.

Options:

-D, --symbolD	[true\|false] use D / T symbols for Deuterium / Tritium (default: true)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

 cxcalc iformula -s true test.mol

isotopecomposition

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-D, --symbolD	[true\|false] use D / T symbols for Deuterium / Tritium (default: true)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc isotopecomposition -s true test.mol

isotopeformula

Molecular formula calculation, isotopes included.

Options:

-D, --symbolD	[true\|false] use D / T symbols for Deuterium / Tritium (default: true)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc isotopeformula -s true test.mol

mass

Molecule mass calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: precision of the least precise atomic mass)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc mass test.mol

sortableformula

Calculates a fixed digit sortable molecular formula.

Options:

-d, --digits	<minimum number of digits in proportionate number of atoms> (default: 5)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc sortableformula -d 4 test.mol

Charge

The following features and properties can be calculated:

atomicpolarizability

Atomic polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc atomicpolarizability test.mol

atompol

Atomic polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc atompol test.mol

averagemolecularpolarizability

Average molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc averagemolecularpolarizability test.mol

averagepol

Average molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc averagepol test.mol

avgpol

Average molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc avgpol test.mol

axxpol

Calculation of principal component of polarizability tensor axx.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc axxpol test.mol

ayypol

Calculation of principal component of polarizability tensor ayy.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc ayypol test.mol

azzpol

Calculation of principal component of polarizability tensor azz.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma\|pi\|total\|implh\| aromaticsystem\|aromaticsystemsigma\|aromaticsystempi\| aromaticring\|aromaticringsigma\|aromaticringpi] (default: total)
-i, --implh	[true\|false] implicit H charge sum shown in brackets (for sigma and total charge only) (default: false)
-r, --resonance	[true\|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

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:

f, --format	<format option for the length of the vector, or a file output parameter> (default: length)

Example:

cxcalc dipole -f sdf test.mol

formalcharge

Formal charge calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> (default: 7)
-n, --max-ions	max number of ionizable atoms to be considered (default: 9)
-m, --min-percent	<min occurrence percentage of ionic form to be considered> (optional, if omitted then only the ionic form with max percentage is considered)
-t, --charge-type	[single\|accumulated] charge type, accumulated means that charges of attached H atoms should be added (default: single)

Example:

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

molecularpolarizability

Molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc molecularpolarizability test.mol

molpol

Molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

 cxcalc molpol test.mol

oen

Orbital electronegativity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma\|pi] sigma: sigma orbital electronegativity pi: pi orbital electronegativity (default: sigma,pi)
-r, --resonance	[true\|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

 cxcalc oen -t sigma test.mol

orbitalelectronegativity

Orbital electronegativity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma\|pi] sigma: sigma orbital electronegativity pioen: pi orbital electronegativity (default: sigma,pi)
-r, --resonance	[true\|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

 cxcalc orbitalelectronegativity -p 3 test.mol

pol

Atomic and molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[molecular\|atomic] (default: both)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pol -p 3 test.mol

polarizability

Atomic and molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[molecular\|atomic] (default: both)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc polarizability -p 3 test.mol

tholepolarizability

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc tholepolarizability test.mol

tpol

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc tpol test.mol

tpolarizability

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc tpolarizability test.mol

Conformation

The following features and properties can be calculated:

conformers

Calculates the conformers of the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding\|mmff94] forcefield used for calculation (default: dreiding)
-m, --maxconformers	<maximum number of conformers to be generated> (default: 100)
-d, --diversity	<diversity limit> (default: 0.1)
-s, --saveconfdesc	[true\|false] if true a single conformer is saved with a property containing conformer information (default: false)
-e, --hyperfine	[true\|false] if true hyperfine option is set (default: false)
-y, --prehydrogenize	[true\|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
-l, --timelimit	<timelimit for calculation in sec> (default: 900)
-O, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)

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:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding\|mmff94] forcefield used for calculation (default: dreiding)
-e, --hyperfine	[true\|false] if true hyperfine option is set (default: false)
-y, --prehydrogenize	[true\|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
-l, --timelimit	<timelimit for calculation in sec> (default: 900)
-O, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-m, --multifrag	[true\|false] in case of multi-fragment molecules and if mmff94 forcefield selected: takes largest fragment if false, takes whole molecule if true (default: false)

Example:

 cxcalc leconformer -f mrv test.sdf

lowestenergyconformer

Calculates the lowest energy conformer of the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding\|mmff94] forcefield used for calculation (default: dreiding)
-e, --hyperfine	[true\|false] if true hyperfine option is set (default: false)
-y, --prehydrogenize	[true\|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
-l, --timelimit	<timelimit for calculation in sec> (default: 900)
-O, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-m, --multifrag	[true\|false] in case of multi-fragment molecules and if mmff94 forcefield selected: takes largest fragment if false, takes whole molecule if true (default: false)

Example:

cxcalc lowestenergyconformer -f mrv test.sdf

moldyn

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding\|mmff94] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet\|velocityverlet\|leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	<time between steps in femtoseconds> (default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:

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

moleculardynamics

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding\|mmff94] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet\|velocityverlet\|leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	<time between steps in femtoseconds> (default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:

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

Geometry

aliphaticatom

Checks if a specified atom is aliphatic.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aliphaticatom test.mol

aliphaticatomcount

Counts the number of aliphatic atoms in the molecule.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aliphaticatomcount test.mol

aliphaticbondcount

Aliphatic bond count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

 cxcalc aliphaticbondcount test.mol

aliphaticringcount

Aliphatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

 cxcalc aliphaticringcount test.mol

aliphaticringcountofsize

Aliphatic ring count of size.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
-z, --size	<ring size> size of rings to count

Example:

 cxcalc aliphaticringcountofsize -z 5 test.mol

angle

Angle of three atoms.

Options:

-a, --atoms	[<atom1>-<atom2>-<atom3>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

aromaticatom

Checks if a specified atom is aromatic.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aromaticatom test.mol

aromaticatomcount

Aromatic atom count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aromaticatomcount test.mol

aromaticbondcount

Aromatic bond count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aromaticbondcount test.mol

aromaticringcount

Aromatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc aromaticringcount test.mol

aromaticringcountofsize

Aromatic ring count of size.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
-z, --size	<ring size> size of rings to count

Example:

 cxcalc aromaticringcountofsize -z 6 test.mol

asa

Water Accessible Surface Area calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-r, --solventradius	<solvent radius: 0.0-5.0> (default: 1.4)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true\|false] show incremental surface area on atoms (default: false)

Example:

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

asymmetricatom

Checks if a specified atom is an asymmetric atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc asymmetricatom test.mol

asymmetricatomcount

The number of asymmetric atoms.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc asymmetricatomcount test.mol

asymmetricatoms

The asymmetric atoms.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc asymmetricatoms test.mol

balabanindex

The Balaban index.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc balabanindex test.mol

bondcount

Bond count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc bondcount test.mol

bondtype

The bond type between two atoms.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc bondtype -a 2-3 test.mol

carboaliphaticringcount

Carboaliphatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc carboaliphaticringcount test.mol

carboaromaticringcount

Carboaromatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc carboaromaticringcount test.mol

carboringcount

Carbo ring count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc carboringcount test.mol

chainatom

Checks if a specified atom is a chain atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chainatom test.mol

chainatomcount

Chain atom count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chainatomcount test.mol

chainbond

Checks if the bond is a chain bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc chainbond -a 2-3 test.mol

chainbondcount

Chain bond count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chainbondcount test.mol

chiralcenter

Checks if a specified atom is a tetrahedral stereogenic center.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chiralcenter test.mol

chiralcentercount

The number of tetrahedral stereogenic center atoms.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chiralcentercount test.mol

chiralcenters

The the chiral center atoms.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc chiralcenters test.mol

connected

Checks if two atoms are in the same connected component.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair

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:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc cyclomaticnumber test.mol

dihedral

Calculates the dihedral angle between four atoms.

Options:

-a, --atoms	[<atom1>-<atom2>-<atom3>-<atom4>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

distance

Distance between two atoms.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

distancedegree

Distance degree of atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc distancedegree test.mol

dreidingenergy

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

cxcalc dreidingenergy -p 1 -l always test.sdf

eccentricity

Eccentricity of atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

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:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc fusedaliphaticringcount test.mol

fusedaromaticringcount

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

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc fusedaromaticringcount test.mol

fusedringcount

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

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc fusedringcount test.mol

hararyindex

Harary index.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

 cxcalc hararyindex test.mol

heteroaliphaticringcount

Heteroaliphatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc heteroaliphaticringcount test.mol

heteroaromaticringcount

Heteroaromatic ring count.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc heteroaromaticringcount test.mol

heteroringcount

Hetero ring count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc heteroringcount test.mol

hindrance

Steric hindrance.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

hyperwienerindex

Hyper Wiener index.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc hyperwienerindex test.mol

largestatomringsize

Size of largest ring containing a specified atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc largestatomringsize -s true test.mol

largestringsize

Largest ring size.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc largestringsize test.mol

largestringsystemsize

Largest ring system size.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc largestringsystemsize test.mol

maximalprojectionarea

Calculates the maximal projection area.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --scalefactor	<radius scale factor>
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

maximalprojectionradius

Calculates the maximal projection radius.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --scalefactor	<radius scale factor>
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

minimalprojectionarea

Calculates the minimal projection area.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --scalefactor	<radius scale factor>
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

minimalprojectionradius

Calculates the minimal projection radius.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --scalefactor	<radius scale factor>
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-O, --optimizeprojection	[true\|false] sets projection optimization (default: false)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)
--mmff94optimization	[true\|false] sets MFF94 optimization (default: false)

Example:

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

molecularsurfacearea

Molecular Surface Area calculation (3D).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-t, --type	[vanderwaals\|ASA\|ASA+\|ASA-\|ASA_H\|ASA_P] (default: vanderwaals)
-i, --increments	[true\|false] show incremental surface area on atoms (default: false)

Example:

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

msa

Molecular Surface Area calculation (3D).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-t, --type	[vanderwaals\|ASA\|ASA+\|ASA-\|ASA_H\|ASA_P] (default: vanderwaals)
-i, --increments	[true\|false] show incremental surface area on atoms (default: false)

Example:

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

plattindex

The Platt index.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc plattindex test.mol

polarsurfacearea

Topological Polar Surface Area calculation (2D).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-S, --excludesulfur	[true\|false] exclude sulfur atom from calculation (default: true)
-P, --excludephosphorus	[true\|false] exclude phosphorus atom from calculation (default: true)

Example:

cxcalc -S -t myPSA polarsurfacearea test.mol

psa

Topological Polar Surface Area calculation (2D).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-S, --excludesulfur	[true\|false] exclude sulfur atom from calculation (default: true)
-P, --excludephosphorus	[true\|false] exclude phosphorus atom from calculation (default: true)

Example:

cxcalc -S false -p 3 psa test.mol

randicindex

The Randic index.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc randicindex test.mol

ringatom

Checks if a specified atom is a ring atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc ringatom test.mol

ringatomcount

Ring atom count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc ringatomcount test.mol

ringbond

Checks if the bond is a ring bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc ringbond -a 2-3 test.mol

ringbondcount

Ring bond count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc ringbondcount test.mol

ringcount

Ring count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc ringcount test.mol

ringcountofatom

Ring counts of atoms.

Options:

No options

Example:

cxcalc ringcountofatom test.mol

ringcountofsize

Ring count of size.

Options:

-a --arom	[general\|basic\|loose] sets aromatization method
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
-z, --size	<ring size> size of rings to count

Example:

cxcalc ringcountofsize -z 5 test.mol

ringsystemcount

The number of ring systems.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc ringsystemcount test.mol

ringsystemcountofsize

Ring system count of size.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
-z, --size	<size> size of ring systems to count

Example:

cxcalc ringsystemcountofsize -z 3 test.mol

rotatablebond

Checks if the bond is a rotatable bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc rotatablebond -a 2-3 test.mol

rotatablebondcount

Rotatable bond count.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc rotatablebondcount test.mol

shortestpath

Length of shortest path between two atoms.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair

Example:

cxcalc shortestpath -a 2-3 test.mol

smallestatomringsize

Size of smallest ring containing a specified atom.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc smallestatomringsize test.mol

smallestringsize

Smallest ring size.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc smallestringsize test.mol

smallestringsystemsize

Smallest ring system size.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes smallest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc smallestringsystemsize -s true test.mol

stereodoublebondcount

The number of stereo double bonds.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc stereodoublebondcount -s true test.mol

stericeffectindex

Steric effect index.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc stericeffectindex -p 3 -s true test.mol

sterichindrance

Steric hindrance.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

cxcalc sterichindrance test.mol

szegedindex

Szeged index.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

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:

-a --arom	[general\|basic\|loose] sets aromatization method
-t, --type	[atomcount\|aliphaticatomcount\|aromaticatomcount\| bondcount\|aliphaticbondcount\|aromaticbondcount\| rotatablebondcount\|ringcount\|aliphaticringcount\| aromaticringcount\|heteroringcount\|heteroaliphaticringcount\| heteroaromaticringcount\|ringatomcount\|ringbondcount\| chainatomcount\|chainbondcount\| smallestringsize\|largestringsize\|fsp3] (default: all)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

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:

-a --arom	[general\|basic\|loose] sets aromatization method
-t, --type	[atomcount\|aliphaticatomcount\|aromaticatomcount\| bondcount\|aliphaticbondcount\|aromaticbondcount\| rotatablebondcount\|ringcount\|aliphaticringcount\| aromaticringcount\|heteroringcount\|heteroaliphaticringcount\| heteroaromaticringcount\|ringatomcount\|ringbondcount\| chainatomcount\|chainbondcount\| smallestringsize\|largestringsize\|fsp3] (default: all)
-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc topologyanalysistable -a basic -s true test.mol

vdwsa

Van der Waals Surface Area calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true\|false] show incremental surface area on atoms (default: false)

Example:

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

volume

Calculates the van der Waals volume of the molecule.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0\|1\|2\|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --calcforleconformer	[if2D\|never\|always] (default: if2D)

Example:

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

wateraccessiblesurfacearea

Water Accessible Surface Area calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-r, --solventradius	<solvent radius: 0.0-5.0> (default: 1.4)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true\|false] show incremental surface area on atoms (default: false)

Example:

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

wienerindex

Wiener index.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc wienerindex test.mol

wienerpolarity

Wiener polarity.

Options:

-s, --single	[true\|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc wienerpolarity test.mol

Isomers

canonicaltautomer

Canonical tautomer.

Options:

-f, --format	<output format> (default: smiles table, multiple molecule output if specified)
-R, --rational	[true\|false] true: generates only rational tautomers (default: false)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)

Example:

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

dominanttautomerdistribution

Dominant tautomer distribution.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 0)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION)

Example:

cxcalc dominanttautomerdistribution test.mol

doublebondstereoisomercount

The number of double-bond stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)

Example:

cxcalc doublebondstereoisomercount test.sdf

doublebondstereoisomers

Generates double-bond stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-v, --verify3d	[true\|false] if true invalid 3D structures of genereated stereoisomers are filtered
-3, --in3d	[true\|false] if true 3D structures are generated (invalid 3D structures are filtered)

Example:

cxcalc doublebondstereoisomers -f mrv test.sdf

generictautomer

Generic tautomer.

Options:

-f, --format	<output format> (default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)

Example:

cxcalc generictautomer -f sdf test.mol

majortautomer

Major tautomer.

Options:

-f, --format	<output format> (default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)

Example:

cxcalc majortautomer -H 7.4 -f sdf test.mol

moststabletautomer

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

Options:

-f, --format	<output format> (default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)

Example:

cxcalc moststabletautomer -f sdf test.mol

stereoisomercount

The number of stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protecttetrahedralstereo	[true\|false] true: protect tetrahedral stereo centers (default: false)

Example:

cxcalc stereoisomercount -m 100 test.sdf

stereoisomers

Generates stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protecttetrahedralstereo	[true\|false] true: protect tetrahedral stereo centers (default: false)
-v, --verify3d	[true\|false] if true invalid 3D structures of genereated stereoisomers are filtered
-3, --in3d	[true\|false] if true 3D structures are generated (invalid 3D structures are filtered)

Example:

cxcalc stereoisomers -v true test.sdf

stereoanalysis

Calculate stereo descriptors.

Options:

-T --type	stereo descriptor type [tetrahedral \| cistrans \| axial \| atrop] (default: not set)

Example:

cxcalc stereoanalysis test.mol

tautomercount

The number of tautomers.

Options:

-d, --dominants	[true\|false] true: take dominant tautomers (default: true)
-R, --rational	[true\|false] true: takes only rational tautomers (default: false)
-m, --max	<count> max. number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-s, --symfilter	[true\|false] true: filter out symmetrical structures false: allow duplicates (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)

Example:

cxcalc tautomerCount -s false test.mol

tautomers

Tautomers.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 0)
-c, --canonical	[true\|false] true: take canonical tautomer (default: false)
-R, --rational	[true\|false] true: generates only rational tautomers (default: false)
-g, --generic	[true\|false] true: take generic tautomer (default: false)
-M, --major	[true\|false] true: take major tautomer (default: false)
-d, --dominants	[true\|false] true: take dominant tautomers (default: true)
-D, --distribution	[true\|false] true: calculate dominant tautomer distribution (default: false)
-m, --max	<count> maximum number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true\|false] true: protect aromaticity (default: true)
-C, --protectcharge	[true\|false] true: protect charge (default: true)
-e, --excludeantiaroma	[true\|false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true\|false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true\|false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true\|false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true\|false] true: protect ester groups (default: true)
-s, --symfilter	[true\|false] true: filter out symmetrical structures false: allow duplicates (default: true)
-f, --format	<output format> (default: fused smiles, multiple molecule output if specified)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION)
-r, --ring	[true\|false] Enable/disable ring tautomers. Default false.

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:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-T, --protecttetrahedralstereo	[true\|false] true: protect tetrahedral stereo centers (default: false)

Example:

cxcalc tetrahedralstereoisomercount test.sdf

tetrahedralstereoisomers

Generates tetrahedral stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of tetrahedral stereoisomers to be generated> (default: 1000)
-T, --protecttetrahedralstereo	[true\|false] true: protect tetrahedral stereo centers (default: false)
-v, --verify3d	[true\|false] if true invalid 3D structures of genereated stereoisomers are filtered
-3, --in3d	[true\|false] if true 3D structures are generated (invalid 3D structures are filtered)

Example:

cxcalc tetrahedralstereoisomers -3 true test.sdf

Markush enumeration

enumerationcount

Number of Markush enumerated structures.

Options:

-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-m, --magnitude	[true\|false] display magnitude if >= 100 000 (default: false)
-g, --enumhomology	[true\|false] enumerate homology groups (default: false)

Example:

cxcalc enumerationcount -m true test.mol

enumerations

Generates Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true\|false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true\|false] align scaffold (default: false)
-c, --coloring	[none\|all\|scaffold\|rgroups] structure coloring (default: none)
-r, --random	[true\|false] random enumeration (default: false)
-g, --enumhomology	[true\|false] enumerate homology groups (default: false)
-o, --code	[true\|false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	<output format> (default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:

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

markushenumerationcount

Number of Markush enumerated structures.

Options:

-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-m, --magnitude	[true\|false] display magnitude if >= 100 000 (default: false)
-g, --enumhomology	[true\|false] enumerate homology groups (default: false)

Example:

cxcalc markushenumerationcount -m true test.mol

markushenumerations

Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true\|false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true\|false] align scaffold (default: false)
-c, --coloring	[none\|all\|scaffold\|rgroups] structure coloring (default: none)
-r, --random	[true\|false] random enumeration (default: false)
-g, --enumhomology	[true\|false] enumerate homology groups (default: false)
-o, --code	[true\|false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	<output format> (default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:

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

randommarkushenumerations

Randomly constructed Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true\|false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true\|false] align scaffold (default: false)
-c, --coloring	[none\|all\|scaffold\|rgroups] structure coloring (default: none)
-g, --enumhomology	[true\|false] enumerate homology groups (default: false)
-o, --code	[true\|false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	<output format> (default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:

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

Naming

name

Generates the IUPAC name for the molecule.

Options:

-t, --type	[preferred\|traditional] (default: preferred) preferred: Preferred IUPAC Name traditional: traditional name

Example:

cxcalc name test.sdf

Partitioning

logd

logD calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-m, --method	[vg\|klop\|phys\|user\|weighted] (default: weighted)
--logptrainingid	<logP training id>
-w, --weights	<wVG:wKLOP:wPHYS:wUSER> method weights (default: 1:1:1:0) wVG: weight of the VG method wKLOP: weight of the KLOP method wPHYS: weight of the PHYS method wUSER: weight of the user defined method
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-H, --pH	<pH value> takes logD at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-1, --ref1	<pH reference 1> (default: none)
-2, --ref2	<pH reference 2> (default: none)
-3, --ref3	<pH reference 3> (default: none)
-4, --ref4	<pH reference 4> (default: none)
--considertautomerization	[true\|false] consider tautomerization and resonance(default: false)
--pkacorrectionlibrary	<pKa correction library ID>

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:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-m, --method	[vg\|klop\|phys\|user\|weighted] (default: weighted)
--trainingid	<training id>
-w, --weights	<wVG:wKLOP:wPHYS:wUSER> method weights (default: 1:1:1:0) wVG: weight of the VG method wKLOP: weight of the KLOP method wPHYS: weight of the PHYS method wUSER: weight of the user defined method
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-t, --type	[increments\|logPMicro\|logPTrue] (default: logPTrue)
-i, --increments	[true\|false] show atomic increments (default: false)
--considertautomerization	[true\|false] consider tautomerization and resonance (default: false)
-H, --pH	<pH value> gets logp of the major microspecies at this pH (default: no pH, use given protonation state)

Example:

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

Protonation

averagemicrospeciescharge

Average microspecies charge calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> calculates average charge at this pH (default: 7.4)

Example:

 cxcalc averagemicrospeciescharge test.mol

chargedistribution

Charge distribution calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> calculates average charge at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)

Example:

cxcalc chargedistribution test.mol

isoelectricpoint

Isoelectric point calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)

Example:

cxcalc isoelectricpoint test.mol

majormicrospecies

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	<output format> (default: smiles)
-M, --majortautomer	[true\|false] take major tautomeric form (default: false)
-K, --keephydrogens	[true\|false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc majormicrospecies -H 3.5 -f mol test.mol

majorms

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	<output format> (default: smiles)
-M, --majortautomer	[true\|false] take major tautomeric form (default: false)
-K, --keephydrogens	[true\|false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc majorms -H 3.5 -f mol test.mol

microspeciesdistribution

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])
-M, --majortautomer	[true\|false] take major tautomeric form (default: false)
-K, --keephydrogens	[true\|false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc microspeciesdistribution -H 3.5 test.mol

msdistr

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])
-M, --majortautomer	[true\|false] take major tautomeric form (default: false)
-K, --keephydrogens	[true\|false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc msdistr -H 3.5 test.mol

pi

Isoelectric point calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)

Example:

cxcalc pI test.mol

pka

pKa calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[pKa\|acidic\|basic] (default: pKa)
-m, --mode	[macro\|micro] (default: macro)
-P, --prefix	[static\|dynamic] (default: static)
-d, --model	[small\|large] calculation model small: optimized for at most 8 ionizable atoms large: optimized for a large number of ionizable atoms (default: small)
-i, --min	<min basic pKa> (default: -10)
-x, --max	<max acidic pKa> (default: 20)
-T, --temperature	<temperature in Kelvin> (default: 298 K)
-a, --na	<number of acidic pKa values displayed> (default: 2)
-b, --nb	<number of basic pKa values displayed> (default: 2)
--considertautomerization	[true\|false] consider tautomerization and resonance (default: false)
-L, --correctionlibrary	<correction library ID>
-P, --correctionlibrarypath	<path of the correction library> use this parameter when the correction library not stored on the default location

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:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acc test.sdf

acceptor

Hydrogen bond acceptor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptor test.sdf

acceptorcount

Hydrogen bond acceptor atom count in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptorcount -H 7.4 test.sdf

acceptormultiplicity

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptormultiplicity test.sdf

acceptorsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptorsitecount test.sdf

acceptortable

Hydrogen bond acceptor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptortable test.sdf

accsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc accsitecount test.sdf

aromaticelectrophilicityorder

Order in E(+) attack. Deprecated.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc aromaticelectrophilicityorder -H 7.4 test.mol

aromaticnucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc aromaticnucleophilicityorder -H 7.4 test.mol

canonicalresonant

Canonical resonant structure.

Options:

-f, --format	<output format> (default: smiles)

Example:

cxcalc canonicalResonant -f sdf test.mol

chargedensity

Charge density.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc chargedensity -p 4 -H 6.5 test.mol

don

Hydrogen bond donor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc don test.sdf

donor

Hydrogen bond donor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donor test.sdf

donorcount

Hydrogen bond donor atom count in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donorcount -H 7.4 test.sdf

donormultiplicity

Hydrogen bond donor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc don test.sdf

donorsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donorsitecount test.sdf

donortable

Hydrogen bond donor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donortable test.sdf

donsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donsitecount test.sdf

electrondensity

Electron density.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc electrondensity -p 4 -H 6.5 test.mol

electrophilicityorder

Order in E(+) attack. Deprecated.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc electrophilicityorder -H 7.4 test.mol

electrophiliclocalizationenergy

Electrophilic localization energy L(+).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc electrophiliclocalizationenergy test.mol

frameworks

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

Options:

-t, --type	[bmf\|bmfl\|mcs\|largestring\|allringsystems\| largestringsystem\|sssr\|cssr\|keep] Framework type to calculate
-i, --lfin	[true\|false] Process only the largest fragment of input structure (default: false)
-p, --prunein	[true\|false] Prune input: generalize input atom and bond types (default: false)
-h, --hydrogenize	[true\|fase] Add explicit hydrogens to the input structure (default: false)
-d, --dehydrogenize	[true\|false] Remove explicit hydrogens from the input structure (default: false)
-r, --pruneout	[true\|false] Prune results: generalize result atom and bond types (default: false)
-o, --lfout	[true\|false] Return only the largest fragment of the result (default: false)
-q, --oeqcheck	[true\|false] Remove topologically equivalent output fragments (default: false)
-s, --keepsingleatom	[true\|false] Return a single atom for non-empty acyclic input structures (default: true)
-f, --format	<output format> (default: sdf)

Example:

cxcalc frameworks -t bmf -s true test.mol

hbda

Hydrogen bond acceptor-donor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[acc\|don\|accsitecount\|donsitecount\| acceptorcount\|donorcount\|msacc\|msdon] (default: acceptorcount,donorcount,accsitecount, donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

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

hbonddonoracceptor

Hydrogen bond acceptor-donor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[acc\|don\|accsitecount\|donsitecount\| acceptorcount\|donorcount\|msacc\|msdon] (default: acceptorcount,donorcount,accsitecount, donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

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

hmochargedensity

HMO Charge density.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

 cxcalc hmochargedensity -p 4 -H 6.5 test.mol

hmoelectrondensity

HMO Electron density.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol

hmoelectrophilicityorder

Order in E(+) attack (HMO).

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmoelectrophilicityorder -H 7.4 test.mol

hmoelectrophiliclocalizationenergy

HMO Electrophilic localization energy L(+).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmoelectrophiliclocalizationenergy test.mol

hmohuckel

HMO Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order\|order:e\|order:n\| localizationenergy\| localizationenergy:e\|localizationenergy:n\| pienergy\|electrondensity\|chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

hmohuckeleigenvalue

HMO Huckel eigenvalue.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckeleigenvalue test.mol

hmohuckeleigenvector

HMO Huckel eigenvector.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckeleigenvector test.mol

hmohuckelorbitals

HMO Huckel orbital coefficients.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckelorbitals test.mol

hmohuckeltable

HMO Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[hmoorder\|hmoorder:e\|hmoorder:n\| hmolocalizationenergy\| hmolocalizationenergy:e\|hmolocalizationenergy:n\| hmopienergy\|hmoelectrondensity\|hmochargedensity] (default: hmoorder,hmolocalizationenergy, hmopienergy,hmoelectrondensity,hmochargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

hmolocalizationenergy

HMO Localization energy L(+)/L(-).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --subtype	[e\|n\|en] e: electrophilic, n: nucleophilic, en: both (default: en)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmolocalizationenergy test.mol

hmonucleophilicityorder

Order in Nu(-) attack (HMO).

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmonucleophilicityorder -H 7.4 test.mol

hmonucleophiliclocalizationenergy

HMO Nucleophilic localization energy L(-).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmonucleophiliclocalizationenergy test.mol

hmopienergy

HMO Pi energy.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmopienergy test.mol

huckel

Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order\|order:e\|order:n\| localizationenergy\| localizationenergy:e\|localizationenergy:n\| pienergy\|electrondensity\|chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

huckeleigenvalue

Huckel eigenvalue. Deprecated.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckeleigenvalue test.mol

huckeleigenvector

Huckel eigenvector. Deprecated.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckeleigenvector test.mol

huckelorbitals

Huckel orbital coefficients. Deprecated.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckelorbitals test.mol

huckeltable

Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order\|order:e\|order:n\| localizationenergy\| localizationenergy:e\|localizationenergy:n\| pienergy\|electrondensity\|chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

localizationenergy

Localization energy L(+)/L(-).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --subtype	[e\|n\|en] e: electrophilic, n: nucleophilic, en: both (default: en)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc localizationenergy test.mol

msacc

Hydrogen bond acceptor average multiplicity over microspecies by pH.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-e, --excludesulfur	[true\|false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true\|false] exclude halogens from acceptors (default: true)

Example:

cxcalc msacc -l 2.0 -u 12.0 test.sdf

msdon

Hydrogen bond donor average multiplicity over microspecies by pH.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)

Example:

cxcalc msdon -l 2.0 -u 12.0 test.sdf

nucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc nucleophilicityorder -H 7.4 test.mol

nucleophiliclocalizationenergy

Nucleophilic localization energy L(-).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc nucleophiliclocalizationenergy test.mol

pichargedensity

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pichargedensity -p 4 -H 6.5 test.mol

pienergy

Pi energy. Deprecated.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pienergy test.mol

refractivity

Refractivity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[increments\|inch\|refractivity] (default: refractivity)
-i, --inch	[true\|false] refractivity on H atoms shown in brackets (for incremental refractivity only) (default: false)

Example:

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

resonantcount

The number of resonant structures.

Options:

-r, --mcontrib	[true\|false] true: take major contributors (default: true)
-m, --max	<count> max. number of structures to be generated (default: 200)
-s, --symfilter	[true\|false] true: filter out symmetrical structures false: allow duplicates (default: true)

Example:

cxcalc resonantCount test.mol

resonants

Resonant structures.

Options:

-c, --canonical	[true\|false] true: take canonical resonant form (default: false)
-r, --mcontrib	[true\|false] true: take major contributors (default: true)
-m, --max	<count> max. number of structures to be generated (default: 200)
-f, --format	<output format> (default: fused smiles, multiple molecule output if specified)
-s, --symfilter	[true\|false] true: filter out symmetrical structures false: allow duplicates (default: true)

Example:

cxcalc resonants -f sdf test.mol

solubility

Calculates aqueous solubility.

Options:

U, --unit	measurement unit [mg/ml \| mol/l \| logS] (default: logS)
-i, --intrinsic	intrinsic solubility (default: false)
-c, --category	solubility category (default: false)
-H, --pH	<pH value> solubility at this pH (default: not set)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)

Example:

 cxcalc logs -i true -H 7.4 test.mol

totalchargedensity

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

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

 cxcalc totalchargedensity -p 4 -H 6.5 test.mol

Calculator Plugins : cxcalc calculator functions

cxcalc calculations

Elemental Analysis

atomcount

composition

dotdisconnectedformula

dotdisconnectedisotopeformula

elemanal

elementalanalysistable

exactmass

formula

icomposition

iformula

isotopecomposition

isotopeformula

mass

sortableformula

Charge

atomicpolarizability

atompol

averagemolecularpolarizability

averagepol

avgpol

axxpol

ayypol

azzpol

charge

dipole

formalcharge

ioncharge

molecularpolarizability

molpol

oen

orbitalelectronegativity

pol

polarizability

tholepolarizability

tpol

tpolarizability

Conformation

conformers

hasvalidconformer

leconformer

lowestenergyconformer

moldyn

moleculardynamics

Geometry

aliphaticatom

aliphaticatomcount

aliphaticbondcount

aliphaticringcount

aliphaticringcountofsize

angle

aromaticatom

aromaticatomcount

aromaticbondcount

aromaticringcount

aromaticringcountofsize

asa

asymmetricatom

asymmetricatomcount

asymmetricatoms

balabanindex

bondcount

bondtype

carboaliphaticringcount

carboaromaticringcount

carboringcount

chainatom

chainatomcount

chainbond

chainbondcount

chiralcenter

chiralcentercount

chiralcenters

connected

connectedgraph

cyclomaticnumber

dihedral

distance