cxcalc calculations

Version 5.0.0

Elemental Analysis:	atomcount, composition, dotdisconnectedformula, dotdisconnectedisotopeformula, elemanal, elementalanalysistable, exactmass, formula, icomposition, iformula, isotopecomposition, isotopeformula, mass
Charge:	atomicpolarizability, atompol, averagemolecularpolarizability, averagepol, avgpol, axxpol, ayypol, azzpol, charge, ioncharge, molecularpolarizability, molpol, oen, orbitalelectronegativity, pol, polarizability, tholepolarizability, tpol, tpolarizability
Conformation:	conformers, hasvalidconformer, leconformer, lowestenergyconformer, moldyn, moleculardynamics
Enumerations:	enumerationcount, enumerations
Geometry:	aliphaticatom, aliphaticatomcount, aliphaticbondcount, aliphaticringcount, angle, aromaticatom, aromaticatomcount, aromaticbondcount, aromaticringcount, asa, asymmetricatom, asymmetricatomcount, balabanindex, bondcount, bondtype, carboaromaticringcount, carboringcount, chainatom, chainatomcount, chainbond, chainbondcount, chiralcenter, chiralcentercount, connected, connectedgraph, cyclomaticnumber, dihedral, distance, distancedegree, dreidingenergy, eccentricity, fusedaliphaticringcount, fusedaromaticringcount, fusedringcount, hararyindex, heteroaromaticringcount, heteroringcount, hindrance, hyperwienerindex, largestatomringsize, largestringsize, molecularsurfacearea, msa, plattindex, polarsurfacearea, psa, randicindex, ringatom, ringatomcount, ringbond, ringbondcount, ringcount, ringcountofatom, rotatablebond, rotatablebondcount, shortestpath, smallestatomringsize, smallestringsize, stericeffectindex, sterichindrance, szegedindex, topanal, topologyanalysistable, vdwsa, wateraccessiblesurfacearea, wienerindex, wienerpolarity
Isomers:	canonicalresonant, canonicaltautomer, dominanttautomerdistribution, doublebondstereoisomercount, doublebondstereoisomers, resonantcount, resonants, stereoisomercount, stereoisomers, tautomercount, tautomers, tetrahedralstereoisomercount, tetrahedralstereoisomers
Name:	name
Partitioning:	logd, logp
Protonation:	isoelectricpoint, majormicrospecies, majorms, microspeciesdistribution, msdistr, pi, pka
Other:	acc, acceptor, acceptorcount, acceptorsitecount, acceptortable, accsitecount, aromaticelectrophilicityorder, aromaticnucleophilicityorder, don, donor, donorcount, donorsitecount, donortable, donsitecount, electrophiliclocalizationenergy, energy, hbda, hbonddonoracceptor, huckel, huckeltable, msacc, msdon, nucleophiliclocalizationenergy, order, pichargedensity, pienergy, refractivity, totalchargedensity

 

---

Elemental Analysis

atomcount

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

Options:

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

Example:

cxcalc atomcount -z 7 test.mol

 

composition

Elemental composition calculation (w/w%).

Options:

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

Example:

cxcalc composition -s true test.mol

 

dotdisconnectedformula

Dot-disconnected molecular formula calculation.

Options:

No options

Example:

cxcalc dotdisconnectedformula test.mol

 

dotdisconnectedisotopeformula

Dot-disconnected molecular formula calculation, isotopes included.

Options:

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

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)
-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: false)
-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)
-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: false)
-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

 

---

Charge

atomicpolarizability

Atomic polarizability calculation.

Options:

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

Example:

cxcalc atomicpolarizability test.mol

 

atompol

Atomic polarizability calculation.

Options:

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

Example:

cxcalc atompol test.mol

 

averagemolecularpolarizability

Average molecular polarizability calculation.

Options:

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

Example:

cxcalc averagemolecularpolarizability test.mol

 

averagepol

Average molecular polarizability calculation.

Options:

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

Example:

cxcalc averagepol test.mol

 

avgpol

Average molecular polarizability calculation.

Options:

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

Example:

cxcalc avgpol test.mol

 

axxpol

Calculation of principal component of polarizability tensor axx.

Options:

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

Example:

cxcalc axxpol test.mol

 

ayypol

Calculation of principal component of polarizability tensor ayy.

Options:

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

Example:

cxcalc ayypol test.mol

 

azzpol

Calculation of principal component of polarizability tensor azz.

Options:

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

Example:

cxcalc azzpol test.mol

 

charge

Partial charge calculation. Types aromaticsystem / aromaticring calculate the sum of charges in the aromatic system / aromatic ring containing the atom.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma|pi|total|implh| aromaticsystem|aromaticsystemsigma|aromaticsystempi| aromaticring|aromaticringsigma|aromaticringpi] (default: total)
-i, --implh	[true|false] implicit H charge sum shown in brackets (for sigma and total charge only) (default: false)
-r, --resonance	[true|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

 

ioncharge

Partial charge(s): A) on the ionic forms with distribution percentage not less than the minimum percentage specified in the min-percent parameter, or else B) on the ionic form with maximal distribution if the min-percent parameter is omitted.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> (default: 7)
-n, --max-ions	max number of ionizable atoms to be considered (default: 9)
-m, --min-percent	<min occurrence percentage of ionic form to be considered> (optional, if omitted then only the ionic form with max percentage is considered)
-t, --charge-type	[single|accumulated] charge type, accumulated means that charges of attached H atoms should be added (default: single)

Example:

cxcalc ioncharge -n 6 -H 8 -m 1 -t accumulated test.mol

 

molecularpolarizability

Molecular polarizability calculation.

Options:

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

Example:

cxcalc molecularpolarizability test.mol

 

molpol

Molecular polarizability calculation.

Options:

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

Example:

cxcalc molpol test.mol

 

oen

Orbital electronegativity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma|pi] sigma: sigma orbital electronegativity pi: pi orbital electronegativity (default: sigma,pi)
-r, --resonance	[true|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc oen -t sigma test.mol

 

orbitalelectronegativity

Orbital electronegativity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[sigma|pi] sigma: sigma orbital electronegativity pioen: pi orbital electronegativity (default: sigma,pi)
-r, --resonance	[true|false] true: take resonant structures (default: false)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc orbitalelectronegativity -p 3 test.mol

 

pol

Atomic and molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[molecular|atomic] (default: both)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pol -p 3 test.mol

 

polarizability

Atomic and molecular polarizability calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[molecular|atomic] (default: both)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc polarizability -p 3 test.mol

 

tholepolarizability

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).

Options:

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

Example:

cxcalc tholepolarizability test.mol

 

tpol

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).

Options:

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

Example:

cxcalc tpol test.mol

 

tpolarizability

Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).

Options:

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

Example:

cxcalc tpolarizability test.mol

 

---

Conformation

conformers

Calculates the conformers of the molecule.

Options:

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

Example:

cxcalc conformers -m 250 -s true test.sdf

 

hasvalidconformer

Calculates if the molecule has a conformer.

Options:

No options

Example:

cxcalc hasvalidconformer test.sdf

 

leconformer

Calculates the lowest energy conformer of the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-e, --hyperfine	[true|false] if true hyperfine option is set (default: false)
-y, --prehydrogenize	[true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
-l, --timelimit	<timelimit for calculation in sec> (default: 900)
-O, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)

Example:

cxcalc leconformer -f mrv test.sdf

 

lowestenergyconformer

Calculates the lowest energy conformer of the molecule.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-e, --hyperfine	[true|false] if true hyperfine option is set (default: false)
-y, --prehydrogenize	[true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true)
-l, --timelimit	<timelimit for calculation in sec> (default: 900)
-O, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)

Example:

cxcalc lowestenergyconformer -f mrv test.sdf

 

moldyn

Molecular Dynamics.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	<time between steps in femtoseconds> (default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:

cxcalc moldyn test.mol   

 

moleculardynamics

Molecular Dynamics.

Options:

-f, --format	<output format> should be a 3D format (default: sdf)
-x, --forcefield	[dreiding] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	<time between steps in femtoseconds> (default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:

cxcalc moleculardynamics test.mol   

 

---

Enumerations

enumerationcount

Number of Markush enumerated structures.

Options:

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

Example:

cxcalc enumerationcount -m true test.mol

 

enumerations

Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true|false] valence filter is on if true (default: true)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-r, --random	[true|false] random enumeration (default: false)
-f, --format	<output format> (default: concatenated smiles)

Example:

cxcalc enumerations -f sdf -a 2,3,5 -r true -m 2000 test.mol

 

---

Geometry

aliphaticatom

Checks if a specified atom is aliphatic.

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 aliphaticatom test.mol

 

aliphaticatomcount

Aliphatic 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 aliphaticatomcount test.mol

 

aliphaticbondcount

Aliphatic 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 aliphaticbondcount test.mol

 

aliphaticringcount

Aliphatic 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 aliphaticringcount test.mol

 

angle

Angle of three atoms.

Options:

-a, --atoms	[<atom1>-<atom2>-<atom3>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --leconformer	[if2D|never|always] (default: if2D)

Example:

cxcalc angle -a 2-4-6 test.mol

 

aromaticatom

Checks if a specified atom is aromatic.

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 aromaticatom test.mol

 

aromaticatomcount

Aromatic 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 aromaticatomcount test.mol

 

aromaticbondcount

Aromatic 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 aromaticbondcount test.mol

 

aromaticringcount

Aromatic 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 aromaticringcount test.mol

 

asa

Water Accessible Surface Area calculation.

Options:

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

Example:

cxcalc asa test.mol

 

asymmetricatom

Checks if a specified atom is an asymmetric atom.

Options:

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

Example:

cxcalc asymmetricatom test.mol

 

asymmetricatomcount

The number of asymmetric atoms.

Options:

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

Example:

cxcalc asymmetricatomcount test.mol

 

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, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc bondtype -a 2-3 test.mol

 

carboaromaticringcount

Carboaromatic 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 carboaromaticringcount test.mol

 

carboringcount

Carbo ring count.

Options:

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

Example:

cxcalc carboringcount test.mol

 

chainatom

Checks if a specified atom is a chain atom.

Options:

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

Example:

cxcalc chainatom test.mol

 

chainatomcount

Chain atom count.

Options:

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

Example:

cxcalc chainatomcount test.mol

 

chainbond

Checks if the bond is a chain bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc chainbond -a 2-3 test.mol

 

chainbondcount

Chain bond count.

Options:

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

Example:

cxcalc chainbondcount test.mol

 

chiralcenter

Checks if a specified atom is a tetrahedral stereogenic center.

Options:

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

Example:

cxcalc chiralcenter test.mol

 

chiralcentercount

The number of tetrahedral stereogenic center atoms.

Options:

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

Example:

cxcalc chiralcentercount test.mol

 

connected

Checks if two atoms are in the same connected component.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair

Example:

cxcalc connected -a 2-3 test.mol

 

connectedgraph

Checks if the molecule graph is connected.

Options:

No options

Example:

cxcalc connectedgraph test.mol

 

cyclomaticnumber

The cyclomatic number.

Options:

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

Example:

cxcalc cyclomaticnumber test.mol

 

dihedral

Dihedral of four atoms.

Options:

-a, --atoms	[<atom1>-<atom2>-<atom3>-<atom4>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --leconformer	[if2D|never|always] (default: if2D)

Example:

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

 

distance

Distance between two atoms.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair
-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --leconformer	[if2D|never|always] (default: if2D)

Example:

cxcalc distance -a 2-4 test.mol

 

distancedegree

Distance degree of atom.

Options:

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

Example:

cxcalc distancedegree test.mol

 

dreidingenergy

Calculates the dreiding energy of a conformer of the molecule.

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, --leconformer	[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

 

fusedaliphaticringcount

The number of fused aliphatic rings (SSSR smallest set of smallest aliphatic 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 fusedaliphaticringcount test.mol

 

fusedaromaticringcount

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

 

heteroaromaticringcount

Heteroaromatic 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 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, --leconformer	[if2D|never|always] (default: if2D)

Example:

cxcalc hindrance test.mol

 

hyperwienerindex

Hyper Wiener index.

Options:

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

Example:

cxcalc hyperwienerindex test.mol

 

largestatomringsize

Size of largest ring containing a specified atom.

Options:

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

Example:

cxcalc largestatomringsize test.mol

 

largestringsize

Largest ring size.

Options:

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

Example:

cxcalc largestringsize test.mol

 

molecularsurfacearea

Molecular Surface Area calculation (3D).

Options:

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

Example:

cxcalc molecularsurfacearea -t ASA+ -i true -H 7.4 test.mol

 

msa

Molecular Surface Area calculation (3D).

Options:

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

Example:

cxcalc msa -t ASA+ -i true -H 7.4 test.mol

 

plattindex

The Platt index.

Options:

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

Example:

cxcalc plattindex test.mol

 

polarsurfacearea

Topological Polar Surface Area calculation (2D).

Options:

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

Example:

cxcalc -S -t myPSA polarsurfacearea test.mol

 

psa

Topological Polar Surface Area calculation (2D).

Options:

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

Example:

cxcalc -S -t myPSA psa test.mol

 

randicindex

The Randic index.

Options:

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

Example:

cxcalc randicindex test.mol

 

ringatom

Checks if a specified atom is a ring atom.

Options:

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

Example:

cxcalc ringatom test.mol

 

ringatomcount

Ring atom count.

Options:

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

Example:

cxcalc ringatomcount test.mol

 

ringbond

Checks if the bond is a ring bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc ringbond -a 2-3 test.mol

 

ringbondcount

Ring bond count.

Options:

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

Example:

cxcalc ringbondcount test.mol

 

ringcount

Ring count.

Options:

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

Example:

cxcalc ringcount test.mol

 

ringcountofatom

Ring counts of atoms.

Options:

No options

Example:

cxcalc ringcountofatoms -a 2-3 test.mol

 

rotatablebond

Checks if the bond is a rotatable bond.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc rotatablebond -a 2-3 test.mol

 

rotatablebondcount

Rotatable bond count.

Options:

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

Example:

cxcalc rotatablebondcount test.mol

 

shortestpath

Length of shortest path between two atoms.

Options:

-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the atom pair

Example:

cxcalc shortestpath -a 2-3 test.mol

 

smallestatomringsize

Size of smallest ring containing a specified atom.

Options:

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

Example:

cxcalc smallestatomringsize test.mol

 

smallestringsize

Smallest ring size.

Options:

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

Example:

cxcalc smallestringsize test.mol

 

stericeffectindex

Steric effect index.

Options:

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

Example:

cxcalc stericeffectindex test.mol

 

sterichindrance

Steric hindrance.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-o, --optimization	[0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1)
-l, --leconformer	[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,aromaticheteroringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize.

Options:

-t, --type	[atomcount|aliphaticatomcount|aromaticatomcount| bondcount|aliphaticbondcount|aromaticbondcount|rotatablebondcount| ringcount|aliphaticringcount|aromaticringcount|heteroringcount|aromaticheteroringcount| ringatomcount|ringbondcount|chainatomcount|chainbondcount| smallestringsize|largestringsize] (default: all)
-s, --single	[true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc topanal test.mol

 

topologyanalysistable

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

Options:

-t, --type	[atomcount|aliphaticatomcount|aromaticatomcount| bondcount|aliphaticbondcount|aromaticbondcount|rotatablebondcount| ringcount|aliphaticringcount|aromaticringcount|heteroringcount|aromaticheteroringcount| ringatomcount|ringbondcount|chainatomcount|chainbondcount| smallestringsize|largestringsize] (default: all)
-s, --single	[true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)

Example:

cxcalc topologyanalysistable test.mol

 

vdwsa

Van der Waals Surface Area calculation.

Options:

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

Example:

cxcalc vdwsa -H 7.4 test.mol

 

wateraccessiblesurfacearea

Water Accessible Surface Area calculation.

Options:

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

Example:

cxcalc wateraccessiblesurfacearea test.mol

 

wienerindex

Wiener index.

Options:

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

Example:

cxcalc wienerindex test.mol

 

wienerpolarity

Wiener polarity.

Options:

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

Example:

cxcalc wienerpolarity test.mol

 

---

Isomers

canonicalresonant

Canonical resonant structure.

Options:

-f, --format	<output format> (default: smiles)

Example:

cxcalc canonicalResonant -f sdf test.mol

 

canonicaltautomer

Canonical tautomer.

Options:

-f, --format	<output format> (default: fused smiles, multiple molecule output if specified)

Example:

cxcalc canonicalTautomer -f sdf test.mol

 

dominanttautomerdistribution

Dominant tautomer distribution.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 0)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. (default: do not consider pH effect)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION)

Example:

cxcalc dominanttautomerdistribution test.mol	

 

doublebondstereoisomercount

The number of double-bond stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 200)

Example:

cxcalc doublebondstereoisomercount test.sdf

 

doublebondstereoisomers

Generates double-bond stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 200)
-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

 

resonantcount

The number of resonant structures.

Options:

-r, --mcontrib	[true|false] true: take major contributors (default: true)
-m, --max	<count> max. number of structures to be generated (default: 200)
-s, --symfilter	[true|false] true: filter out symmetrical structures false: allow duplicates (default: true)

Example:

cxcalc resonantCount test.mol

 

resonants

Resonant structures.

Options:

-c, --canonical	[true|false] true: take canonical resonant form (default: false)
-r, --mcontrib	[true|false] true: take major contributors (default: true)
-m, --max	<count> max. number of structures to be generated (default: 200)
-f, --format	<output format> (default: fused smiles, multiple molecule output if specified)
-s, --symfilter	[true|false] true: filter out symmetrical structures false: allow duplicates (default: true)

Example:

cxcalc resonants -f sdf test.mol

 

stereoisomercount

The number of stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 200)

Example:

cxcalc stereoisomercount test.sdf

 

stereoisomers

Generates stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of stereoisomers to be generated> (default: 200)
-v, --verify3d	[true|false] if true invalid 3D structures of genereated stereoisomers are filtered
-3, --in3d	[true|false] if true 3D structures are generated (invalid 3D structures are filtered)

Example:

cxcalc stereoisomers -v true test.sdf

 

tautomercount

The number of tautomers.

Options:

-d, --dominants	[true|false] true: take dominant tautomers (default: false)
-m, --max	<count> max. number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-s, --symfilter	[true|false] true: filter out symmetrical structures false: allow duplicates (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)
-d, --dominants	[true|false] true: take dominant tautomers (default: false)
-D, --distribution	[true|false] true: calculate dominant tautomer distribution (default: false)
-m, --max	<count> maximum number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-s, --symfilter	[true|false] true: filter out symmetrical structures false: allow duplicates (default: true)
-f, --format	<output format> (default: fused smiles, multiple molecule output if specified)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION)

Example:

cxcalc tautomers -f sdf test.mol

 

tetrahedralstereoisomercount

The number of tetrahedral stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 200)

Example:

cxcalc tetrahedralstereoisomercount test.sdf

 

tetrahedralstereoisomers

Generates tetrahedral stereoisomers of the molecule.

Options:

-f, --format	<output format> (default: sdf)
-m, --maxstereoisomers	<maximum number of tetrahedral stereoisomers to be generated> (default: 200)
-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

 

---

Name

name

Generates the IUPAC name of the molecule.

Options:

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

Example:

cxcalc name test.sdf

 

---

Partitioning

logd

logD calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-H, --pH	<pH value> takes logD at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-1, --ref1	<pH reference 1> (default: none)
-2, --ref2	<pH reference 2> (default: none)
-3, --ref3	<pH reference 3> (default: none)
-4, --ref4	<pH reference 4> (default: none)
-c, --considertautomerization	[true|false] consider tautomerization (default: false)

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)
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-t, --type	[increments|inch|logPMicro|logPTrue] (default: logPTrue)
-i, --inch	[true|false] incremental logP on H atoms shown in brackets (for incremental logP only) (default: false)
-M, --majortautomer	[true|false] take major tautomeric form (default: false)

Example:

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

 

---

Protonation

isoelectricpoint

Isoelectric point calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)

Example:

cxcalc isoelectricpoint test.mol

 

majormicrospecies

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	<output format> (default: smiles)

Example:

cxcalc majormicrospecies -H 3.5 -f mol test.mol

 

majorms

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	<output format> (default: smiles)

Example:

cxcalc majorms -H 3.5 -f mol test.mol

 

microspeciesdistribution

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])

Example:

cxcalc microspeciesdistribution -H 3.5 test.mol

 

msdistr

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	<output format> (default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])

Example:

cxcalc msdistr -H 3.5 test.mol

 

pi

Isoelectric point calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)

Example:

cxcalc pI test.mol

 

pka

pKa calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[pKa|acidic|basic] (default: pKa)
-m, --mode	[macro|micro] (default: macro)
-P, --prefix	[static|dynamic] (default: static)
-d, --model	[small|large] calculation model small: optimized for at most 8 ionizable atoms large: optimized for a large number of ionizable atoms (default: small)
-i, --min	<min basic pKa> (default: -10)
-x, --max	<max acidic pKa> (default: 20)
-T, --temperature	<temperature in Kelvin> (default: 298 K)
-a, --na	<number of acidic pKa values displayed> (default: 2)
-b, --nb	<number of basic pKa values displayed> (default: 2)
-M, --majortautomer	[true|false] take major tautomeric form (default: false)

Example:

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

 

---

Other

acc

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc acc test.sdf 

 

acceptor

Hydrogen bond acceptor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc acceptor -l 2 -u 12 -s 0.5 test.sdf 

 

acceptorcount

Hydrogen bond acceptor atom count in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc acceptorcount -H 7.4 test.sdf 

 

acceptorsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc accsitecount test.sdf 

 

acceptortable

Hydrogen bond acceptor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc acceptortable -l 2 -u 12 -s 0.5 test.sdf 

 

accsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc acceptorsitecount test.sdf 

 

aromaticelectrophilicityorder

Order in E(+) attack.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc aromaticelectrophilicityorder -H 7.4 test.mol

 

aromaticnucleophilicityorder

Order in Nu(-) attack.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc aromaticnucleophilicityorder -H 7.4 test.mol

 

don

Hydrogen bond donor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc don test.sdf

 

donor

Hydrogen bond donor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donor -l 2 -u 12 -s 0.5 test.sdf 

 

donorcount

Hydrogen bond donor atom count in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donorcount -H 7.4 test.sdf 

 

donorsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donorsitecount test.sdf 

 

donortable

Hydrogen bond donor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donortable -l 2 -u 12 -s 0.5 test.sdf

 

donsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc donsitecount test.sdf 

 

electrophiliclocalizationenergy

Electrophilic localization energy L(+).

Options:

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

Example:

cxcalc electrophiliclocalizationenergy test.mol

 

energy

Localization energy L(+)/L(-).

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-s, --subtype	[e|n|en] e: electrophilic, n: nucleophilic, en: both (default: en)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc energy 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: acc,don,accsitecount,donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

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: acc,don,accsitecount,donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hbonddonoracceptor -t msacc,msdon -l 2 -u 12 -s 0.5 test.sdf 

 

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|pichargedensity|totalchargedensity] (default: order,localizationenergy, pienergy,pichargedensity,totalchargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc -S -o result.sdf huckel -H 7.4 -p 3 test.mol

 

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|pichargedensity|totalchargedensity] (default: order,localizationenergy, pienergy,pichargedensity,totalchargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc -S -o result.sdf huckeltable -H 7.4 -p 3 test.mol

 

msacc

Hydrogen bond acceptor average multiplicity over microspecies by pH.

Options:

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

Example:

cxcalc msacc test.sdf 

 

msdon

Hydrogen bond donor average multiplicity over microspecies by pH.

Options:

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

Example:

cxcalc msdon test.sdf 

 

nucleophiliclocalizationenergy

Nucleophilic localization energy L(-).

Options:

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

Example:

cxcalc nucleophiliclocalizationenergy test.mol

 

order

Order in E(+)/Nu(-) attack.

Options:

-s, --subtype	[e|n|en] e: electrophilic, n: nucleophilic, en: both (default: en)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc order -t order:e -H 7.4 test.mol

 

pichargedensity

Pi charge density.

Options:

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

Example:

cxcalc pichargedensity -p 4 -H 6.5 test.mol

 

pienergy

Pi energy.

Options:

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

Example:

cxcalc 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

 

totalchargedensity

Total charge density.

Options:

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

Example:

cxcalc totalchargedensity -p 4 -H 6.5 test.mol