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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, --categorysolubility 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

 

 

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