cxcalc calculator functions

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

    cxcalc calculations

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

    Elemental Analysis

    The following features and properties can be calculated:

    atomcount

    Number of atoms in the molecule: no atno: counts all atoms in the molecule; atno, but no massno: counts atoms of the given type in the molecule; atno, massno: counts atoms of the given isotope type in the molecule; atno, massno=0: counts atoms of the given type in the molecule, but excludes its isotopes.

    Options :

    -z, --atno
    -m, --massno
    -s, --single [true false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

    Example:

    
    cxcalc atomcount -z 7 test.mol

    composition

    Elemental composition calculation (w/w%).

    Options:

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

    Example:

    
    cxcalc composition -s true test.mol

    dotdisconnectedformula

    Dot-disconnected molecular formula calculation.

    Options:

    No options

    Example:

    
    cxcalc dotdisconnectedformula test.mol

    dotdisconnectedisotopeformula

    Dot-disconnected molecular formula calculation, isotopes included.

    Options:

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

    Example:

    
    cxcalc dotdisconnectedisotopeformula test.mol

    elemanal

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

    Options:

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

    Example:

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

    elementalanalysistable

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

    Options:

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

    Example:

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

    exactmass

    Exact molecule mass calculation based on the most frequent natural isotopes of the elements.

    Options:

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

    Example:

    
    cxcalc exactmass test.mol

    formula

    Molecular formula calculation.

    Options:

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

    Example:

    
     cxcalc formula -s true test.mol

    icomposition

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

    Options:

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

    Example:

    
    cxcalc icomposition -s true test.mol

    iformula

    Molecular formula calculation, isotopes included.

    Options:

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

    Example:

    
     cxcalc iformula -s true test.mol

    isotopecomposition

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

    Options:

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

    Example:

    
    cxcalc isotopecomposition -s true test.mol

    isotopeformula

    Molecular formula calculation, isotopes included.

    Options:

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

    Example:

    
    cxcalc isotopeformula -s true test.mol

    mass

    Molecule mass calculation.

    Options:

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

    Example:

    
    cxcalc mass test.mol

    massspectrum

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

    Options:

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

    Example:

    
    cxcalc massspectrum -p 4 sildenafil

    sortableformula

    Calculates a fixed digit sortable molecular formula.

    Options:

    -d, --digits (default: 5)
    -s, --single [true false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

    Example:

    
    cxcalc sortableformula -d 4 test.mol

    Charge

    The following features and properties can be calculated:

    atomicpolarizability

    Atomic polarizability calculation.

    Options:

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

    Example:

    
    cxcalc -S -o result.sdf -t myCHARGE charge -t "pi,total" -p 3 test.mol

    dipole

    Calculates the absolute value of the dipole moment vector.

    Options :

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

    Example:

    
    cxcalc dipole -f sdf test.mol

    formalcharge

    Formal charge calculation.

    Options:

    -H, --pH 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 (default: 7)
    -n, --max-ions max number of ionizable atoms to be considered (default: 9)
    -m, --min-percent (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 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 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 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 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 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 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 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 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 takes major microspecies at this pH (default: no pH, takes the input molecule)

    Example:

    
    cxcalc tpolarizability test.mol

    Conformation

    The following features and properties can be calculated:

    conformers

    Calculates the conformers of the molecule.

    Options:

    -f, --format should be a 3D format (default: sdf)
    -x, --forcefield [dreiding mmff94] forcefield used for calculation (default: dreiding)
    -m, --maxconformers (default: 100)
    -d, --diversity (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 (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 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 (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 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 (default: 900)
    -O, --optimization [0 1 2 3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
    -m, --multifrag [true false] in case of multi-fragment molecules and if mmff94 forcefield selected: takes largest fragment if false, takes whole molecule if true (default: false)

    Example:

    
    cxcalc lowestenergyconformer -f mrv test.sdf

    moldyn

    Runs a molecular dynamics simulation for the molecule.

    Options:

    -f, --format 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 (default: 1000)
    -m, --steptime
    -T, --temperature (default: 300 K)
    -s, --samplinginterval (default: 10)

    Example:

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

    moleculardynamics

    Runs a molecular dynamics simulation for the molecule.

    Options:

    -f, --format 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 (default: 1000)
    -m, --steptime
    -T, --temperature (default: 300 K)
    -s, --samplinginterval (default: 10)

    Example:

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

    Geometry

    aliphaticatom

    Checks if a specified atom is aliphatic.

    Options:

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

    Example:

    
    cxcalc aliphaticatom test.mol

    aliphaticatomcount

    Counts the number of aliphatic atoms in the molecule.

    Options:

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

    Example:

    
    cxcalc aliphaticatomcount test.mol

    aliphaticbondcount

    Aliphatic bond count.

    Options:

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

    Example:

    
     cxcalc aliphaticbondcount test.mol

    aliphaticringcount

    Aliphatic ring count.

    Options:

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

    Example:

    
     cxcalc aliphaticringcount test.mol

    aliphaticringcountofsize

    Aliphatic ring count of size.

    Options:

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

    Example:

    
     cxcalc aliphaticringcountofsize -z 5 test.mol

    angle

    Angle of three atoms.

    Options:

    -a, --atoms [--] (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 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 takes major microspecies at this pH (default: no pH, takes the input molecule)
    -i, --increments [true false] show incremental surface area on atoms (default: false)

    Example:

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

    asymmetricatom

    Checks if a specified atom is an asymmetric atom.

    Options:

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

    Example:

    
    cxcalc asymmetricatom test.mol

    asymmetricatomcount

    The number of asymmetric atoms.

    Options:

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

    Example:

    
    cxcalc asymmetricatomcount test.mol

    asymmetricatoms

    The asymmetric atoms.

    Options:

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

    Example:

    
    cxcalc asymmetricatoms test.mol 

    balabanindex

    The Balaban index.

    Options:

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

    Example:

    
    cxcalc balabanindex test.mol

    bondcount

    Bond count.

    Options:

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

    Example:

    
    cxcalc bondcount test.mol

    bondtype

    The bond type between two atoms.

    Options:

    -a --arom [general basic loose] sets aromatization method
    -a, --atoms [-] (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 [-] (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 [-] (1-based) atom indexes of the atom pair

    Example:

    
    cxcalc connected -a 2-3 test.mol 

    connectedgraph

    Checks if the molecule graph is connected.

    Options: No options

    Example:

    
    cxcalc connectedgraph test.mol 

    cyclomaticnumber

    The cyclomatic number.

    Options:

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

    Example:

    
    cxcalc cyclomaticnumber test.mol 

    dihedral

    Calculates the dihedral angle between four atoms.

    Options:

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

    Example:

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

    distance

    Distance between two atoms.

    Options:

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

    Example:

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

    distancedegree

    Distance degree of atom.

    Options:

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

    Example:

    
    cxcalc distancedegree test.mol 

    dreidingenergy

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

    Options:

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

    Example:

    
    cxcalc dreidingenergy -p 1 -l always test.sdf 

    eccentricity

    Eccentricity of atom.

    Options:

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

    Example:

    
    cxcalc eccentricity test.mol 

    fragmentcount

    Fragment count.

    Options:

    No options

    Example:

    
    cxcalc fragmentcount test.mol

    fsp3

    Fsp3 value of the molecule.

    Options:

    No options

    Example:

    
    cxcalc fsp3 test.mol 

    fusedaliphaticringcount

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

    Options:

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

    Example:

    
    cxcalc fusedaliphaticringcount test.mol

    fusedaromaticringcount

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

    Options:

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

    Example:

    
    cxcalc fusedaromaticringcount test.mol 

    fusedringcount

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

    Options:

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

    Example:

    
    cxcalc fusedringcount test.mol 

    hararyindex

    Harary index.

    Options:

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

    Example:

    
     cxcalc hararyindex test.mol

    heteroaliphaticringcount

    Heteroaliphatic ring count.

    Options:

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

    Example:

    
    cxcalc heteroaliphaticringcount test.mol 

    heteroaromaticringcount

    Heteroaromatic ring count.

    Options:

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

    Example:

    
    cxcalc heteroaromaticringcount test.mol 

    heteroringcount

    Hetero ring count.

    Options:

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

    Example:

    
    cxcalc heteroringcount test.mol 

    hindrance

    Steric hindrance.

    Options:

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

    Example:

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

    hyperwienerindex

    Hyper Wiener index.

    Options:

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

    Example:

    
    cxcalc hyperwienerindex test.mol 

    largestatomringsize

    Size of largest ring containing a specified atom.

    Options:

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

    Example:

    
    cxcalc largestatomringsize -s true test.mol 

    largestringsize

    Largest ring size.

    Options:

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

    Example:

    
    cxcalc largestringsize test.mol 

    largestringsystemsize

    Largest ring system size.

    Options:

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

    Example:

    
    cxcalc largestringsystemsize test.mol 

    maximalprojectionarea

    Calculates the maximal projection area.

    Options:

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

    Example:

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

    maximalprojectionradius

    Calculates the maximal projection radius.

    Options:

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

    Example:

    
    cxcalc maximalprojectionradius -s 1.2 -o 3 test.sdf 

    maximalprojectionsize

    Calculates the size of the molecule perpendicular to the maximal projection area surface.

    Options:

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

    Example:

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

    minimalprojectionarea

    Calculates the minimal projection area.

    Options:

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

    Example:

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

    minimalprojectionradius

    Calculates the minimal projection radius.

    Options:

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

    Example:

    
    cxcalc minimalprojectionradius -s 1.3 -o true test.sdf 

    minimalprojectionsize

    Calculates the size of the molecule perpendicular to the minimal projection area surface.

    Options:

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

    Example:

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

    mmff94energy

    Calculates the MMFF94 energy of the molecule in kcal/mol.

    Options:

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

    Example:

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

    molecularsurfacearea

    Molecular Surface Area calculation (3D).

    Options:

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

    Example:

    
    cxcalc -S false -p 3 psa test.mol

    randicindex

    The Randic index.

    Options:

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

    Example:

    
    cxcalc randicindex test.mol 

    ringatom

    Checks if a specified atom is a ring atom.

    Options:

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

    Example:

    
    cxcalc ringatom test.mol 

    ringatomcount

    Ring atom count.

    Options:

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

    Example:

    
    cxcalc ringatomcount test.mol 

    ringbond

    Checks if the bond is a ring bond.

    Options:

    -a, --atoms [-] (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 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 of ring systems to count

    Example:

    
    cxcalc ringsystemcountofsize -z 3 test.mol 

    rotatablebond

    Checks if the bond is a rotatable bond.

    Options:

    -a, --atoms [-] (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 [-] (1-based) atom indexes of the atom pair

    Example:

    
    cxcalc shortestpath -a 2-3 test.mol 

    smallestatomringsize

    Size of smallest ring containing a specified atom.

    Options:

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

    Example:

    
    cxcalc smallestatomringsize test.mol 

    smallestringsize

    Smallest ring size.

    Options:

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

    Example:

    
    cxcalc smallestringsize test.mol 

    smallestringsystemsize

    Smallest ring system size.

    Options:

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

    Example:

    
    cxcalc smallestringsystemsize -s true test.mol 

    stereodoublebondcount

    The number of stereo double bonds.

    Options:

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

    Example:

    
    cxcalc stereodoublebondcount -s true test.mol 

    stericeffectindex

    Steric effect index.

    Options:

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

    Example:

    
    cxcalc stericeffectindex -p 3 -s true test.mol 

    sterichindrance

    Steric hindrance.

    Options:

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

    Example:

    
    cxcalc sterichindrance test.mol 

    szegedindex

    Szeged index.

    Options:

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

    Example:

    
    cxcalc szegedindex test.mol 

    topanal

    Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize,fsp3.

    Options:

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

    Example:

    
    cxcalc topanal -a loose -t largestringsize -s true test.mol 

    topologyanalysistable

    Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize,fsp3.

    Options:

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

    Example:

    
    cxcalc topologyanalysistable -a basic -s true test.mol 

    vdwsa

    Van der Waals Surface Area calculation.

    Options:

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

    Example:

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

    volume

    Calculates the van der Waals volume of the molecule.

    Options:

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

    Example:

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

    wateraccessiblesurfacearea

    Water Accessible Surface Area calculation.

    Options:

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

    Example:

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

    wienerindex

    Wiener index.

    Options:

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

    Example:

    
    cxcalc wienerindex test.mol 

    wienerpolarity

    Wiener polarity.

    Options:

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

    Example:

    
    cxcalc wienerpolarity test.mol 

    Isomers

    canonicaltautomer

    Canonical tautomer.

    Options:

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

    Example:

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

    dominanttautomerdistribution

    Dominant tautomer distribution.

    Options:

    -p, --precision <floating point precision as number of fractional digits: 0-8 or inf> (default: 0)
    -l, --pathlength maximum allowed length of the tautomerization path in chemical bonds (default: 4)
    -H, --pH 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 (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 (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 (default: sdf)
    -m, --maxstereoisomers (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 (default: smiles table, multiple molecule output if specified)
    -l, --pathlength 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 (default: smiles table, multiple molecule output if specified)
    -l, --pathlength maximum allowed length of the tautomerization path in chemical bonds (default: 4)
    -H, --pH 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 (default: smiles table, multiple molecule output if specified)
    -l, --pathlength 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 (default: 1000)
    -D, --protectdoublebondstereo [true false] true: protect double bond stereo (default: false)
    -T, --protecttetrahedralstereo [true false] true: protect tetrahedral stereo centers (default: false)

    Example:

    
    cxcalc stereoisomercount -m 100 test.sdf 

    stereoisomers

    Generates stereoisomers of the molecule.

    Options:

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

    Example:

    
    cxcalc stereoisomers -v true test.sdf 

    stereoanalysis

    Calculate stereo descriptors.

    Options:

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

    Example:

    
    cxcalc stereoanalysis test.mol

    tautomercount

    The number of tautomers.

    Options:

    -d, --dominants [true false] true: take dominant tautomers (default: true)
    -n, --normal [true false] true: takes only normal tautomers (default: false)
    -m, --max max. number of structures to be generated (default: 200)
    -l, --pathlength maximum allowed length of the tautomerization path in chemical bonds
    -H, --pH 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)
    -n, --normal [true false] true: generates only normal 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 maximum number of structures to be generated (default: 200)
    -l, --pathlength maximum allowed length of the tautomerization path in chemical bonds (default: 4)
    -H, --pH 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 (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 --normal true test.mol --format smiles

    tetrahedralstereoisomercount

    The number of tetrahedral stereoisomers of the molecule.

    Options:

    -m, --maxstereoisomers (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 (default: sdf)
    -m, --maxstereoisomers (default: 1000)
    -T, --protecttetrahedralstereo [true false] true: protect tetrahedral stereo centers (default: false)
    -v, --verify3d [true false] if true invalid 3D structures of genereated stereoisomers are filtered
    -3, --in3d [true false] if true 3D structures are generated (invalid 3D structures are filtered)

    Example:

    
    cxcalc tetrahedralstereoisomers -3 true test.sdf 

    Markush enumeration

    enumerationcount

    Number of Markush enumerated structures.

    Options:

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

    Example:

    
    cxcalc enumerationcount -m true test.mol 

    enumerations

    Generates Markush enumerated structures.

    Options:

    -m, --max 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 (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 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 (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 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 (default: concatenated smiles)
    -C, --clean <dim[:opts]> clean dimension with options (default: no clean)

    Example:

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

    Naming

    name

    Generates the IUPAC name for the molecule.

    Options:

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

    Example:

    
    cxcalc name test.sdf 

    Partitioning

    logd

    logD calculation.

    Options:

    -p, --precision <floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
    -m, --method [vg klop phys user weighted] (default: weighted)
    --logptrainingid
    -w, --weights 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 (default: 0.1, range: [0.0, 0.25])
    -k, --kation <Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
    -H, --pH takes logD at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
    -l, --lower (default: 0)
    -u, --upper (default: 14)
    -s, --step (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

    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
    -w, --weights 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 (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 gets logp of the major microspecies at this pH (default: no pH, use given protonation state)

    Example:

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

    Protonation

    averagemicrospeciescharge

    Average microspecies charge calculation.

    Options:

    -p, --precision <floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
    -H, --pH 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 calculates average charge at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
    -l, --lower (default: 0)
    -u, --upper (default: 14)
    -s, --step (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 gets major microspecies at this pH (default: no pH, all microspecies)
    -f, --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 gets major microspecies at this pH (default: no pH, all microspecies)
    -f, --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 gets major microspecies at this pH (default: 7.4)
    -f, --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 gets major microspecies at this pH (default: 7.4)
    -f, --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 (default: -10)
    -x, --max (default: 20)
    -T, --temperature (default: 298 K)
    -a, --na (default: 2)
    -b, --nb (default: 2)
    --considertautomerization [true false] consider tautomerization and resonance (default: false)
    -L, --correctionlibrary
    -P, --correctionlibrarypath use this parameter when the correction library not stored on the default location

    Example:

    
    cxcalc pka -i -15 -x 25 -a 3 -b 3 -d large test.mol 

    Other calculator functions

    acc

    Hydrogen bond acceptor multiplicity calculation on atoms.

    Options:

    -H, --pH 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 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 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 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 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 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 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 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 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 (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 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 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 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 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 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 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 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 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 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 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 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 (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 (default: 0)
    -u, --upper (default: 14)
    -s, --step (default: 1)
    -H, --pH 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 (default: 0)
    -u, --upper (default: 14)
    -s, --step (default: 1)
    -H, --pH 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 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 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 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 takes major microspecies at this pH (default: no pH, takes the input molecule)

    Example:

    
    cxcalc hmoelectrophiliclocalizationenergy test.mol 

    hmohuckel

    HMO Huckel analysis parameters.

    Options:

    -p, --precision <floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
    -t, --type [order order:e order:n localizationenergy localizationenergy:e localizationenergy:n pienergy electrondensity chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
    -H, --pH 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 (default: 0)
    -u, --upper (default: 14)
    -s, --step (default: 1)
    -e, --excludesulfur [true false] exclude sulfur atom from acceptors (default: true)
    -x, --excludehalogens [true false] exclude halogens from acceptors (default: true)

    Example:

    
    cxcalc msacc -l 2.0 -u 12.0 test.sdf 

    msdon

    Hydrogen bond donor average multiplicity over microspecies by pH.

    Options:

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

    Example:

    
    cxcalc msdon -l 2.0 -u 12.0 test.sdf 

    nucleophilicityorder

    Order in Nu(-) attack. Deprecated.

    Options:

    -H, --pH 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 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 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 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 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 max. number of structures to be generated (default: 200)
    -f, --format (default: fused smiles, multiple molecule output if specified)
    -s, --symfilter [true false] true: filter out symmetrical structures false: allow duplicates (default: true)

    Example:

    
    cxcalc resonants -f sdf test.mol

    solubility

    Calculates aqueous solubility.

    Options :

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

    Example :

    
     cxcalc logs -i true -H 7.4 test.mol

    totalchargedensity

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

    Options:

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

    Example:

    
     cxcalc totalchargedensity -p 4 -H 6.5 test.mol