cxcalc calculations

Version 14.9.29.0

Elemental Analysis:	atomcount, composition, dotdisconnectedformula, dotdisconnectedisotopeformula, elemanal, elementalanalysistable, exactmass, formula, groupeddotdisconnectedformula, icomposition, iformula, isotopecomposition, isotopeformula, mass, massspectrum, sortableformula
Charge:	atomicpolarizability, atompol, averagemolecularpolarizability, averagepol, avgpol, axxpol, ayypol, azzpol, charge, formalcharge, ioncharge, molecularpolarizability, molpol, oen, orbitalelectronegativity, pol, polarizability, tholepolarizability, tpol, tpolarizability
Conformation:	conformations, conformers, hasvalidconformer, leconformer, lowestenergyconformer, moldyn, moleculardynamics
Geometry:	aliphaticatom, aliphaticatomcount, aliphaticbondcount, aliphaticringcount, aliphaticringcountofsize, angle, aromaticatom, aromaticatomcount, aromaticbondcount, aromaticringcount, aromaticringcountofsize, asa, asymmetricatom, asymmetricatomcount, asymmetricatoms, balabanindex, bondcount, bondtype, carboaliphaticringcount, carboaromaticringcount, carboringcount, chainatom, chainatomcount, chainbond, chainbondcount, chiralcenter, chiralcentercount, chiralcenters, connected, connectedgraph, cyclomaticnumber, dihedral, distance, distancedegree, dreidingenergy, eccentricity, fragmentcount, fsp3, fusedaliphaticringcount, fusedaromaticringcount, fusedringcount, hararyindex, heteroaliphaticringcount, heteroaromaticringcount, heteroringcount, hindrance, hyperwienerindex, largestatomringsize, largestringsize, largestringsystemsize, maximalprojectionarea, maximalprojectionradius, maximalprojectionsize, minimalprojectionarea, minimalprojectionradius, minimalprojectionsize, mmff94energy, molecularsurfacearea, msa, plattindex, polarsurfacearea, psa, randicindex, ringatom, ringatomcount, ringbond, ringbondcount, ringcount, ringcountofatom, ringcountofsize, ringsystemcount, ringsystemcountofsize, rotatablebond, rotatablebondcount, shortestpath, smallestatomringsize, smallestringsize, smallestringsystemsize, stereodoublebondcount, stericeffectindex, sterichindrance, szegedindex, topanal, topologyanalysistable, vdwsa, volume, wateraccessiblesurfacearea, wienerindex, wienerpolarity
Isomers:	canonicaltautomer, dominanttautomerdistribution, doublebondstereoisomercount, doublebondstereoisomers, generictautomer, majortautomer, moststabletautomer, stereoisomercount, stereoisomers, tautomercount, tautomers, tetrahedralstereoisomercount, tetrahedralstereoisomers
Markush Enumerations:	enumerationcount, enumerations, markushenumerationcount, markushenumerations, randommarkushenumerations
Name:	name
Partitioning:	logd, logp
Protonation:	averagemicrospeciescharge, chargedistribution, isoelectricpoint, majormicrospecies, majorms, microspeciesdistribution, msdistr, pi, pka
Other:	acc, acceptor, acceptorcount, acceptormultiplicity, acceptorsitecount, acceptortable, accsitecount, aromaticelectrophilicityorder, aromaticnucleophilicityorder, canonicalresonant, chargedensity, don, donor, donorcount, donormultiplicity, donorsitecount, donortable, donsitecount, electrondensity, electrophilicityorder, electrophiliclocalizationenergy, frameworks, hbda, hbonddonoracceptor, hmochargedensity, hmoelectrondensity, hmoelectrophilicityorder, hmoelectrophiliclocalizationenergy, hmohuckel, hmohuckeleigenvalue, hmohuckeleigenvector, hmohuckelorbitals, hmohuckeltable, hmolocalizationenergy, hmonucleophilicityorder, hmonucleophiliclocalizationenergy, hmopienergy, huckel, huckeleigenvalue, huckeleigenvector, huckelorbitals, huckeltable, localizationenergy, msacc, msdon, nucleophilicityorder, nucleophiliclocalizationenergy, pichargedensity, pienergy, refractivity, resonantcount, resonants, totalchargedensity

 

---

Elemental Analysis

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

 

groupeddotdisconnectedformula

Grouped dot-disconnected molecular formula calculation.

Options:

No options

Example:

cxcalc groupeddotdisconnectedformula 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

Mass spectrum 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 massspectrum test.mol

 

sortableformula

Calculates a fixed digit sortable molecular formula.

Options:

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

Example:

cxcalc sortableformula -d 4 test.mol

 

---

Charge

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

 

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

conformations

Calculates conformations for the molecule via cool dynamics.

Options:

-f, --format	<output format> should be a 3D format [mrv|sdf] (default: sdf)
-a, --auto	<true|false> if true, adjust simulation count automatically, (default:true)
-g, --log	<filename> store short summary in a logfile (default:confp.log)
-x, --forcefield	[dreiding|mmff94|Gaussian] forcefield used for calculation (default: mmff94)
-m, --maxconformations	<maximum number of conformations to be generated> (default: 400)
-d, --diversity	<diversity limit> (default: 0.5)
-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: 120)
-O, --optimization	[0|1|2|3] conformer generation optimizaion 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 behavior is no optimization (default: -1)
-e, --energyWindow	<value> the limit of energy from the lowest found value
-v, --verbose	<value> the level of verbosity
-r,--raw	[true:false] use fast diversity calculation or not (default:true)

Example:

cxcalc conformations -m 250 test.sdf

 

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)
-m, --maxconformers	<maximum number of conformers to be generated> (default: 10)
-d, --diversity	<diversity limit> (default: 0.1)
-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)
-m, --maxconformers	<maximum number of conformers to be generated> (default: 10)
-d, --diversity	<diversity limit> (default: 0.1)
-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

Molecular Dynamics.

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 test.mol

 

moleculardynamics

Molecular Dynamics.

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 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

Aliphatic 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 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 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

Dihedral of 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 -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 -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 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 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)
-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 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)
-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 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 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)
-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 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)
-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 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 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 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 -t myPSA 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 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 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 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 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 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 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 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 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 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 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

 

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 Enumerations

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

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

 

---

Name

name

Generates the IUPAC name of 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

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	[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 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 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 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

 

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