cxcalc calculator functions

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

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
 

massspectrum

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

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 massspectrum -p 4 sildenafil

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