cxcalc calculations

    Version 6.2.2

     Elemental Analysis:    atomcount, composition, dotdisconnectedformula, dotdisconnectedisotopeformula, elemanal, elementalanalysistable, exactmass, formula, icomposition, iformula, isotopecomposition, isotopeformula, mass, sortableformula
     Charge:    atomicpolarizability, atompol, averagemolecularpolarizability, averagepol, avgpol, axxpol, ayypol, azzpol, charge, formalcharge, ioncharge, molecularpolarizability, molpol, oen, orbitalelectronegativity, pol, polarizability, tholepolarizability, tpol, tpolarizability
     Conformation:    conformers, hasvalidconformer, leconformer, lowestenergyconformer, moldyn, moleculardynamics
     Geometry:    aliphaticatom, aliphaticatomcount, aliphaticbondcount, aliphaticringcount, aliphaticringcountofsize, angle, aromaticatom, aromaticatomcount, aromaticbondcount, aromaticringcount, aromaticringcountofsize, asa, asymmetricatom, asymmetricatomcount, asymmetricatoms, balabanindex, bondcount, bondtype, carboaliphaticringcount, carboaromaticringcount, carboringcount, chainatom, chainatomcount, chainbond, chainbondcount, chiralcenter, chiralcentercount, chiralcenters, connected, connectedgraph, cyclomaticnumber, dihedral, distance, 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
     Predictor:    predict, predictor
     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

     

    icomposition

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

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

     

    iformula

    Molecular formula calculation, isotopes included.

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

     

    isotopecomposition

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

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

     

    isotopeformula

    Molecular formula calculation, isotopes included.

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

     

    mass

    Molecule mass calculation.

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

     

    sortableformula

    Calculates a fixed digit sortable molecular formula.

    Options:
    -d, --digits    <minimum number of digits in proportionate number of atoms> (default: 5)
    -s, --single    [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
    Example:
    cxcalc sortableformula -d 4 test.mol

     


    Charge

    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

    conformers

    Calculates the conformers of the molecule.

    Options:
    -f, --format    <output format> should be a 3D format (default: sdf)
    -x, --forcefield    [dreiding|mmff94] forcefield used for calculation (default: dreiding)
    -m, --maxconformers    <maximum number of conformers to be generated> (default: 100)
    -d, --diversity    <diversity limit> (default: 0.1)
    -s, --saveconfdesc    [true|false] if true a single conformer is saved with a property containing conformer information (default: false)
    -e, --hyperfine    [true|false] if true hyperfine option is set (default: false)
    -y, --prehydrogenize    [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
    -l, --timelimit    <timelimit for calculation in sec> (default: 900)
    -O, --optimization    [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
    Example:
    cxcalc conformers -m 250 -s true test.sdf

     

    hasvalidconformer

    Calculates if the molecule has a conformer.

    Options:
    No options
    Example:
    cxcalc hasvalidconformer test.sdf

     

    leconformer

    Calculates the lowest energy conformer of the molecule.

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

     

    lowestenergyconformer

    Calculates the lowest energy conformer of the molecule.

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

     

    moldyn

    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)
    -s, --scalefactor    <radius scale factor>
    -o, --optimization    [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
    -O, --optimizeprojection    [true|false] sets projection optimization (default: false)
    -l, --calcforleconformer    [if2D|never|always] (default: if2D)
    Example:
    cxcalc maximalprojectionarea test.sdf

     

    maximalprojectionradius

    Calculates the maximal projection radius.

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

     

    minimalprojectionradius

    Calculates the minimal projection radius.

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

     


    Predictor

    predict

    Predicts molecular properties.

    Options:
    -p, --precision    <floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
    -I, --trainingid    <training id> sets the training
    Example:
    cxcalc predict --trainingid pampa test.mol

     

    predictor

    Predicts molecular properties.

    Options:
    -p, --precision    <floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
    -I, --trainingid    <training id> sets the training
    Example:
    cxcalc predictor --trainingid pampa 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

     

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