cxcalc calculator functions

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

cxcalc calculations

cxcalc calculations

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

Elemental Analysis

The following features and properties can be calculated:

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

Options :

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

Example:


cxcalc atomcount -z 7 test.mol

composition

Elemental composition calculation (w/w%).

Options:

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

Example:


cxcalc composition -s true test.mol

dotdisconnectedformula

Dot-disconnected molecular formula calculation.

Options:

No options

Example:


cxcalc dotdisconnectedformula test.mol

dotdisconnectedisotopeformula

Dot-disconnected molecular formula calculation, isotopes included.

Options:

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

Example:


cxcalc dotdisconnectedisotopeformula test.mol

elemanal

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

Options:

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

Example:


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

elementalanalysistable

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

Options:

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

Example:


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

exactmass

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

Options:

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

Example:


cxcalc exactmass test.mol

formula

Molecular formula calculation.

Options:

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

Example:

cxcalc formula -s true test.mol

icomposition

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

Options:

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

Example:


cxcalc icomposition -s true test.mol

iformula

Molecular formula calculation, isotopes included.

Options:

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

Example:

cxcalc iformula -s true test.mol

isotopecomposition

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

Options:

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

Example:


cxcalc isotopecomposition -s true test.mol

isotopeformula

Molecular formula calculation, isotopes included.

Options:

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

Example:


cxcalc isotopeformula -s true test.mol

mass

Molecule mass calculation.

Options:

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

Example:


cxcalc mass test.mol

massspectrum

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

Options:

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

Example:


cxcalc massspectrum -p 4 sildenafil

sortableformula

Calculates a fixed digit sortable molecular formula.

Options:

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

Example:


cxcalc sortableformula -d 4 test.mol

Charge

The following features and properties can be calculated:

atomicpolarizability

Atomic polarizability calculation.

Options:

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

Example:


cxcalc atomicpolarizability test.mol

atompol

Atomic polarizability calculation.

Options:

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

Example:


cxcalc atompol test.mol

averagemolecularpolarizability

Average molecular polarizability calculation.

Options:

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

Example:


cxcalc averagemolecularpolarizability test.mol

averagepol

Average molecular polarizability calculation.

Options:

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

Example:


cxcalc averagepol test.mol

avgpol

Average molecular polarizability calculation.

Options:

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

Example:


cxcalc avgpol test.mol

axxpol

Calculation of principal component of polarizability tensor axx.

Options:

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

Example:


cxcalc axxpol test.mol

ayypol

Calculation of principal component of polarizability tensor ayy.

Options:

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

Example:


cxcalc ayypol test.mol

azzpol

Calculation of principal component of polarizability tensor azz.

Options:

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

Example:

cxcalc azzpol test.mol

charge

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

Options:

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

Example:


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

dipole

Calculates the absolute value of the dipole moment vector.

Options :

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

Example:


cxcalc dipole -f sdf test.mol

formalcharge

Formal charge calculation.

Options:

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

Example:


cxcalc formalcharge test.mol

ioncharge

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

Options:

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

Example:


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

molecularpolarizability

Molecular polarizability calculation.

Options:

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

Example:


cxcalc molecularpolarizability test.mol

molpol

Molecular polarizability calculation.

Options:

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

Example:

cxcalc molpol test.mol

oen

Orbital electronegativity calculation.

Options:

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

Example:

cxcalc oen -t sigma test.mol

orbitalelectronegativity

Orbital electronegativity calculation.

Options:

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

Example:

cxcalc orbitalelectronegativity -p 3 test.mol

pol

Atomic and molecular polarizability calculation.

Options:

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

Example:


cxcalc pol -p 3 test.mol

polarizability

Atomic and molecular polarizability calculation.

Options:

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

Example:


cxcalc polarizability -p 3 test.mol

tholepolarizability

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

Options:

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

Example :


cxcalc tholepolarizability test.mol

tpol

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

Options:

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

Example:


cxcalc tpol test.mol

tpolarizability

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

Options:

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

Example:


cxcalc tpolarizability test.mol

Conformation

The following features and properties can be calculated:

conformers

Calculates the conformers of the molecule.

Options:

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

Example:


cxcalc conformers -m 250 -s true test.sdf

hasvalidconformer

Calculates if the molecule has a conformer.

Options:

No options

Example:


cxcalc hasvalidconformer test.sdf

leconformer

Calculates the lowest energy conformer of the molecule.

Options:

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

Example:

cxcalc leconformer -f mrv test.sdf

lowestenergyconformer

Calculates the lowest energy conformer of the molecule.

Options:

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

Example:


cxcalc lowestenergyconformer -f mrv test.sdf

moldyn

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding	mmff94] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet	velocityverlet	leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	(default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:


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

moleculardynamics

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding	mmff94] forcefield used for calculation (default: dreiding)
-i, --integrator	[positionverlet	velocityverlet	leapfrog] integrator type used for calculation (default: velocityverlet)
-n, --stepno	<number of simulation steps> (default: 1000)
-m, --steptime	(default: 0.1)
-T, --temperature	<temperature in Kelvin> (default: 300 K)
-s, --samplinginterval	<sampling interval in femtoseconds> (default: 10)

Example:

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

Geometry

aliphaticatom

Checks if a specified atom is aliphatic.

Options:

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

Example:


cxcalc aliphaticatom test.mol

aliphaticatomcount

Counts the number of aliphatic atoms in the molecule.

Options:

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

Example:


cxcalc aliphaticatomcount test.mol

aliphaticbondcount

Aliphatic bond count.

Options:

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

Example:

cxcalc aliphaticbondcount test.mol

aliphaticringcount

Aliphatic ring count.

Options:

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

Example:

cxcalc aliphaticringcount test.mol

aliphaticringcountofsize

Aliphatic ring count of size.

Options:

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

Example:

cxcalc aliphaticringcountofsize -z 5 test.mol

angle

Angle of three atoms.

Options:

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

Example:


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

aromaticatom

Checks if a specified atom is aromatic.

Options:

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

Example:


cxcalc aromaticatom test.mol

aromaticatomcount

Aromatic atom count.

Options:

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

Example:


cxcalc aromaticatomcount test.mol

aromaticbondcount

Aromatic bond count.

Options:

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

Example:

cxcalc aromaticbondcount test.mol

aromaticringcount

Aromatic ring count.

Options:

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

Example:


cxcalc aromaticringcount test.mol

aromaticringcountofsize

Aromatic ring count of size.

Options:

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

Example:

cxcalc aromaticringcountofsize -z 6 test.mol

asa

Water Accessible Surface Area calculation.

Options:

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

Example:


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

asymmetricatom

Checks if a specified atom is an asymmetric atom.

Options:

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

Example:


cxcalc asymmetricatom test.mol

asymmetricatomcount

The number of asymmetric atoms.

Options:

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

Example:


cxcalc asymmetricatomcount test.mol

asymmetricatoms

The asymmetric atoms.

Options:

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

Example:

cxcalc asymmetricatoms test.mol

balabanindex

The Balaban index.

Options:

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

Example:


cxcalc balabanindex test.mol

bondcount

Bond count.

Options:

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

Example:


cxcalc bondcount test.mol

bondtype

The bond type between two atoms.

Options:

-a --arom	[general	basic	loose] sets aromatization method
-a, --atoms	[<atom1>-<atom2>] (1-based) atom indexes of the bond atoms

Example:

cxcalc bondtype -a 2-3 test.mol

carboaliphaticringcount

Carboaliphatic ring count.

Options:

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

Example:

cxcalc carboaliphaticringcount test.mol

carboaromaticringcount

Carboaromatic ring count.

Options:

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

Example:


cxcalc carboaromaticringcount test.mol

carboringcount

Carbo ring count.

Options:

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

Example:

cxcalc carboringcount test.mol

chainatom

Checks if a specified atom is a chain atom.

Options:

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

Example:

cxcalc chainatom test.mol

chainatomcount

Chain atom count.

Options:

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

Example:

cxcalc chainatomcount test.mol

chainbond

Checks if the bond is a chain bond.

Options:

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

Example:

cxcalc chainbond -a 2-3 test.mol

chainbondcount

Chain bond count.

Options:

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

Example:

cxcalc chainbondcount test.mol

chiralcenter

Checks if a specified atom is a tetrahedral stereogenic center.

Options:

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

Example:

cxcalc chiralcenter test.mol

chiralcentercount

The number of tetrahedral stereogenic center atoms.

Options:

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

Example:

cxcalc chiralcentercount test.mol

chiralcenters

The the chiral center atoms.

Options:

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

Example:

cxcalc chiralcenters test.mol

connected

Checks if two atoms are in the same connected component.

Options:

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

Example:

cxcalc connected -a 2-3 test.mol

connectedgraph

Checks if the molecule graph is connected.

Options: No options

Example:

cxcalc connectedgraph test.mol

cyclomaticnumber

The cyclomatic number.

Options:

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

Example:

cxcalc cyclomaticnumber test.mol

dihedral

Calculates the dihedral angle between four atoms.

Options:

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

Example:

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

distance

Distance between two atoms.

Options:

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

Example:

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

distancedegree

Distance degree of atom.

Options:

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

Example:

cxcalc distancedegree test.mol

dreidingenergy

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

Options:

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

Example:

cxcalc dreidingenergy -p 1 -l always test.sdf

eccentricity

Eccentricity of atom.

Options:

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

Example:

cxcalc eccentricity test.mol

fragmentcount

Fragment count.

Options:

No options

Example:


cxcalc fragmentcount test.mol

fsp3

Fsp3 value of the molecule.

Options:

No options

Example:

cxcalc fsp3 test.mol

fusedaliphaticringcount

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

Options:

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

Example:


cxcalc fusedaliphaticringcount test.mol

fusedaromaticringcount

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

Options:

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

Example:

cxcalc fusedaromaticringcount test.mol

fusedringcount

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

Options:

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

Example:

cxcalc fusedringcount test.mol

hararyindex

Harary index.

Options:

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

Example:

cxcalc hararyindex test.mol

heteroaliphaticringcount

Heteroaliphatic ring count.

Options:

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

Example:

cxcalc heteroaliphaticringcount test.mol

heteroaromaticringcount

Heteroaromatic ring count.

Options:

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

Example:

cxcalc heteroaromaticringcount test.mol

heteroringcount

Hetero ring count.

Options:

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

Example:

cxcalc heteroringcount test.mol

hindrance

Steric hindrance.

Options:

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

Example:

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

hyperwienerindex

Hyper Wiener index.

Options:

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

Example:

cxcalc hyperwienerindex test.mol

largestatomringsize

Size of largest ring containing a specified atom.

Options:

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

Example:

cxcalc largestatomringsize -s true test.mol

largestringsize

Largest ring size.

Options:

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

Example:

cxcalc largestringsize test.mol

largestringsystemsize

Largest ring system size.

Options:

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

Example:

cxcalc largestringsystemsize test.mol

maximalprojectionarea

Calculates the maximal projection area.

Options:

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

Example:

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

maximalprojectionradius

Calculates the maximal projection radius.

Options:

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

Example:

cxcalc maximalprojectionradius -s 1.2 -o 3 test.sdf

maximalprojectionsize

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

Options:

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

Example:

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

minimalprojectionarea

Calculates the minimal projection area.

Options:

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

Example:

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

minimalprojectionradius

Calculates the minimal projection radius.

Options:

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

Example:

cxcalc minimalprojectionradius -s 1.3 -o true test.sdf

minimalprojectionsize

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

Options:

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

Example:

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

mmff94energy

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

Options:

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

Example:

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

molecularsurfacearea

Molecular Surface Area calculation (3D).

Options:

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

Example:

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

msa

Molecular Surface Area calculation (3D).

Options:

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

Example:

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

plattindex

The Platt index.

Options:

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

Example:

cxcalc plattindex test.mol

polarsurfacearea

Topological Polar Surface Area calculation (2D).

Options:

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

Example:

cxcalc -S -t myPSA polarsurfacearea test.mol

psa

Topological Polar Surface Area calculation (2D).

Options:

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

Example:


cxcalc -S false -p 3 psa test.mol

randicindex

The Randic index.

Options:

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

Example:

cxcalc randicindex test.mol

ringatom

Checks if a specified atom is a ring atom.

Options:

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

Example:

cxcalc ringatom test.mol

ringatomcount

Ring atom count.

Options:

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

Example:

cxcalc ringatomcount test.mol

ringbond

Checks if the bond is a ring bond.

Options:

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

Example:

cxcalc ringbond -a 2-3 test.mol

ringbondcount

Ring bond count.

Options:

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

Example:

cxcalc ringbondcount test.mol

ringcount

Ring count.

Options:

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

Example:

cxcalc ringcount test.mol

ringcountofatom

Ring counts of atoms.

Options:

No options

Example:

cxcalc ringcountofatom test.mol

ringcountofsize

Ring count of size.

Options:

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

Example:

cxcalc ringcountofsize -z 5 test.mol

ringsystemcount

The number of ring systems.

Options:

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

Example:

cxcalc ringsystemcount test.mol

ringsystemcountofsize

Ring system count of size.

Options:

-s, --single	[true	false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false)
-z, --size	<size> size of ring systems to count

Example:

cxcalc ringsystemcountofsize -z 3 test.mol

rotatablebond

Checks if the bond is a rotatable bond.

Options:

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

Example:

cxcalc rotatablebond -a 2-3 test.mol

rotatablebondcount

Rotatable bond count.

Options:

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

Example:

cxcalc rotatablebondcount test.mol

shortestpath

Length of shortest path between two atoms.

Options:

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

Example:

cxcalc shortestpath -a 2-3 test.mol

smallestatomringsize

Size of smallest ring containing a specified atom.

Options:

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

Example:

cxcalc smallestatomringsize test.mol

smallestringsize

Smallest ring size.

Options:

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

Example:

cxcalc smallestringsize test.mol

smallestringsystemsize

Smallest ring system size.

Options:

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

Example:

cxcalc smallestringsystemsize -s true test.mol

stereodoublebondcount

The number of stereo double bonds.

Options:

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

Example:

cxcalc stereodoublebondcount -s true test.mol

stericeffectindex

Steric effect index.

Options:

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

Example:

cxcalc stericeffectindex -p 3 -s true test.mol

sterichindrance

Steric hindrance.

Options:

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

Example:

cxcalc sterichindrance test.mol

szegedindex

Szeged index.

Options:

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

Example:

cxcalc szegedindex test.mol

topanal

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

Options:

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

Example:

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

topologyanalysistable

Options:

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

Example:

cxcalc topologyanalysistable -a basic -s true test.mol

vdwsa

Van der Waals Surface Area calculation.

Options:

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

Example:

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

volume

Calculates the van der Waals volume of the molecule.

Options:

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

Example:

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

wateraccessiblesurfacearea

Water Accessible Surface Area calculation.

Options:

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

Example:

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

wienerindex

Wiener index.

Options:

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

Example:

cxcalc wienerindex test.mol

wienerpolarity

Wiener polarity.

Options:

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

Example:

cxcalc wienerpolarity test.mol

Isomers

canonicaltautomer

Canonical tautomer.

Options:

-f, --format	(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	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)
-f, --format	(default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION)

Example:

cxcalc dominanttautomerdistribution test.mol

doublebondstereoisomercount

The number of double-bond stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)

Example:


cxcalc doublebondstereoisomercount test.sdf

doublebondstereoisomers

Generates double-bond stereoisomers of the molecule.

Options:

-f, --format	(default: sdf)
-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-v, --verify3d	[true	false] if true invalid 3D structures of genereated stereoisomers are filtered
-3, --in3d	[true	false] if true 3D structures are generated (invalid 3D structures are filtered)

Example:

cxcalc doublebondstereoisomers -f mrv test.sdf

generictautomer

Generic tautomer.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)

Example:

cxcalc generictautomer -f sdf test.mol

majortautomer

Major tautomer.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)

Example:


cxcalc majortautomer -H 7.4 -f sdf test.mol

moststabletautomer

Most stable tautomer. Depreacated, use "majortautomer" instead.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)

Example:

cxcalc moststabletautomer -f sdf test.mol

stereoisomercount

The number of stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-D, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protecttetrahedralstereo	[true	false] true: protect tetrahedral stereo centers (default: false)

Example:

cxcalc stereoisomercount -m 100 test.sdf

stereoisomers

Generates stereoisomers of the molecule.

Options:

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

Example:

cxcalc stereoisomers -v true test.sdf

stereoanalysis

Calculate stereo descriptors.

Options:

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

Example:


cxcalc stereoanalysis test.mol

tautomercount

The number of tautomers.

Options:

-d, --dominants	[true	false] true: take dominant tautomers (default: true)
-n, --normal	[true	false] true: takes only normal tautomers (default: false)
-m, --max	<count> max. number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-s, --symfilter	[true	false] true: filter out symmetrical structures false: allow duplicates (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)

Example:

cxcalc tautomerCount -s false test.mol

tautomers

Tautomers.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 0)
-c, --canonical	[true	false] true: take canonical tautomer (default: false)
-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	<count> maximum number of structures to be generated (default: 200)
-l, --pathlength	<length> maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	<pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true	false] true: protect aromaticity (default: true)
-C, --protectcharge	[true	false] true: protect charge (default: true)
-e, --excludeantiaroma	[true	false] true: exclude antiaromatic compounds (default: true)
-P, --protectdoublebondstereo	[true	false] true: protect double bond stereo (default: false)
-T, --protectalltetrahedralcenters	[true	false] true: protect all tetrahedral stereo centers (default: false)
-L, --protectlabeledtetrahedralcenters	[true	false] true: protect labeled tetrahedral stereo centers (default: false)
-E, --protectestergroups	[true	false] true: protect ester groups (default: true)
-s, --symfilter	[true	false] true: filter out symmetrical structures false: allow duplicates (default: true)
-f, --format	(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	<maximum number of double bond stereoisomers to be generated> (default: 1000)
-T, --protecttetrahedralstereo	[true	false] true: protect tetrahedral stereo centers (default: false)

Example:

cxcalc tetrahedralstereoisomercount test.sdf

tetrahedralstereoisomers

Generates tetrahedral stereoisomers of the molecule.

Options:

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

Example:

cxcalc tetrahedralstereoisomers -3 true test.sdf

Markush enumeration

enumerationcount

Number of Markush enumerated structures.

Options:

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

Example:

cxcalc enumerationcount -m true test.mol

enumerations

Generates Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true	false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true	false] align scaffold (default: false)
-c, --coloring	[none	all	scaffold	rgroups] structure coloring (default: none)
-r, --random	[true	false] random enumeration (default: false)
-g, --enumhomology	[true	false] enumerate homology groups (default: false)
-o, --code	[true	false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:

cxcalc enumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol

markushenumerationcount

Number of Markush enumerated structures.

Options:

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

Example:


cxcalc markushenumerationcount -m true test.mol

markushenumerations

Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true	false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true	false] align scaffold (default: false)
-c, --coloring	[none	all	scaffold	rgroups] structure coloring (default: none)
-r, --random	[true	false] random enumeration (default: false)
-g, --enumhomology	[true	false] enumerate homology groups (default: false)
-o, --code	[true	false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:


cxcalc markushenumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol

randommarkushenumerations

Randomly constructed Markush enumerated structures.

Options:

-m, --max	<count> max. number of structures to be generated (default: all)
-v, --valencecheck	[true	false] valence filter is on if true (default: false)
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true	false] align scaffold (default: false)
-c, --coloring	[none	all	scaffold	rgroups] structure coloring (default: none)
-g, --enumhomology	[true	false] enumerate homology groups (default: false)
-o, --code	[true	false] generate Markush code (default: false)
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	<dim[:opts]> clean dimension with options (default: no clean)

Example:


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

Naming

name

Generates the IUPAC name for the molecule.

Options:

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

Example:

cxcalc name test.sdf

Partitioning

logd

logD calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-m, --method	[vg	klop	phys	user	weighted] (default: weighted)
--logptrainingid	<logP training id>
-w, --weights	<wVG:wKLOP:wPHYS:wUSER> method weights (default: 1:1:1:0) wVG: weight of the VG method wKLOP: weight of the KLOP method wPHYS: weight of the PHYS method wUSER: weight of the user defined method
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-H, --pH	<pH value> takes logD at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-1, --ref1	<pH reference 1> (default: none)
-2, --ref2	<pH reference 2> (default: none)
-3, --ref3	<pH reference 3> (default: none)
-4, --ref4	<pH reference 4> (default: none)
--considertautomerization	[true	false] consider tautomerization and resonance(default: false)
--pkacorrectionlibrary	<pKa correction library ID>

Example:

cxcalc -i ID logd -l 2 -u 3 -s 0.5 test.sdf

logp

logP calculation: for type logPTrue: logP of uncharged species, or, in the case of zwitterions, logD at pI; for type logPMicro: logP of the input species.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-m, --method	[vg	klop	phys	user	weighted] (default: weighted)
--trainingid	<training id>
-w, --weights	<wVG:wKLOP:wPHYS:wUSER> method weights (default: 1:1:1:0) wVG: weight of the VG method wKLOP: weight of the KLOP method wPHYS: weight of the PHYS method wUSER: weight of the user defined method
-a, --anion	<Cl- concentration> (default: 0.1, range: [0.0, 0.25])
-k, --kation	<Na+ K+ concentration> (default: 0.1, range: [0.0, 0.25])
-t, --type	[increments	logPMicro	logPTrue] (default: logPTrue)
-i, --increments	[true	false] show atomic increments (default: false)
--considertautomerization	[true	false] consider tautomerization and resonance (default: false)
-H, --pH	<pH value> gets logp of the major microspecies at this pH (default: no pH, use given protonation state)

Example:

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

Protonation

averagemicrospeciescharge

Average microspecies charge calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> calculates average charge at this pH (default: 7.4)

Example:

cxcalc averagemicrospeciescharge test.mol

chargedistribution

Charge distribution calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-H, --pH	<pH value> calculates average charge at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)

Example:

cxcalc chargedistribution test.mol

isoelectricpoint

Isoelectric point calculation.

Options:

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

Example:

cxcalc isoelectricpoint test.mol

majormicrospecies

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	(default: smiles)
-M, --majortautomer	[true	false] take major tautomeric form (default: false)
-K, --keephydrogens	[true	false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc majormicrospecies -H 3.5 -f mol test.mol

majorms

Major microspecies at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	(default: smiles)
-M, --majortautomer	[true	false] take major tautomeric form (default: false)
-K, --keephydrogens	[true	false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc majorms -H 3.5 -f mol test.mol

microspeciesdistribution

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	(default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])
-M, --majortautomer	[true	false] take major tautomeric form (default: false)
-K, --keephydrogens	[true	false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc microspeciesdistribution -H 3.5 test.mol

msdistr

Microspecies list with distributions at given pH.

Options:

-H, --pH	<pH value> gets major microspecies at this pH (default: 7.4)
-f, --format	(default: sdf:-a)
-t, --tag	<SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...])
-M, --majortautomer	[true	false] take major tautomeric form (default: false)
-K, --keephydrogens	[true	false] keep explicit hydrogen on result molecule (default: false)

Example:

cxcalc msdistr -H 3.5 test.mol

pi

Isoelectric point calculation.

Options:

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

Example:

cxcalc pI test.mol

pka

pKa calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[pKa	acidic	basic] (default: pKa)
-m, --mode	[macro	micro] (default: macro)
-P, --prefix	[static	dynamic] (default: static)
-d, --model	[small	large] calculation model small: optimized for at most 8 ionizable atoms large: optimized for a large number of ionizable atoms (default: small)
-i, --min	<min basic pKa> (default: -10)
-x, --max	<max acidic pKa> (default: 20)
-T, --temperature	<temperature in Kelvin> (default: 298 K)
-a, --na	<number of acidic pKa values displayed> (default: 2)
-b, --nb	<number of basic pKa values displayed> (default: 2)
--considertautomerization	[true	false] consider tautomerization and resonance (default: false)
-L, --correctionlibrary	<correction library ID>
-P, --correctionlibrarypath	<path of the correction library> use this parameter when the correction library not stored on the default location

Example:

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

Other calculator functions

acc

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc acc test.sdf

acceptor

Hydrogen bond acceptor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptor test.sdf

acceptorcount

Hydrogen bond acceptor atom count in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:


cxcalc acceptorcount -H 7.4 test.sdf

acceptormultiplicity

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptormultiplicity test.sdf

acceptorsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptorsitecount test.sdf

acceptortable

Hydrogen bond acceptor calculation.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc acceptortable test.sdf

accsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc accsitecount test.sdf

aromaticelectrophilicityorder

Order in E(+) attack. Deprecated.

Options:

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

Example:

cxcalc aromaticelectrophilicityorder -H 7.4 test.mol

aromaticnucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

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

Example:

cxcalc aromaticnucleophilicityorder -H 7.4 test.mol

canonicalresonant

Canonical resonant structure.

Options:

-f, --format	(default: smiles)

Example:

cxcalc canonicalResonant -f sdf test.mol

chargedensity

Charge density.

Options:

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

Example:

cxcalc chargedensity -p 4 -H 6.5 test.mol

don

Hydrogen bond donor multiplicity calculation on atoms.

Options:

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

Example:

cxcalc don test.sdf

donor

Hydrogen bond donor calculation.

Options:

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

Example:

cxcalc donor test.sdf

donorcount

Hydrogen bond donor atom count in molecule.

Options:

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

Example:

cxcalc donorcount -H 7.4 test.sdf

donormultiplicity

Hydrogen bond donor multiplicity calculation on atoms.

Options:

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

Example:

cxcalc don test.sdf

donorsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

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

Example:

cxcalc donorsitecount test.sdf

donortable

Hydrogen bond donor calculation.

Options:

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

Example:


cxcalc donortable test.sdf

donsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

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

Example:

cxcalc donsitecount test.sdf

electrondensity

Electron density.

Options:

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

Example:

cxcalc electrondensity -p 4 -H 6.5 test.mol

electrophilicityorder

Order in E(+) attack. Deprecated.

Options:

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

Example:

cxcalc electrophilicityorder -H 7.4 test.mol

electrophiliclocalizationenergy

Electrophilic localization energy L(+).

Options:

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

Example:

cxcalc electrophiliclocalizationenergy test.mol

frameworks

Calculates different structural frameworks (Bemis-Murcko, MCS, etc) of the molecule

Options:

-t, --type	[bmf	bmfl
-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	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

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

hbonddonoracceptor

Hydrogen bond acceptor-donor calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[acc	don	accsitecount	donsitecount	acceptorcount	donorcount	msacc	msdon] (default: acceptorcount,donorcount,accsitecount, donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

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

hmochargedensity

HMO Charge density.

Options:

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

Example:

cxcalc hmochargedensity -p 4 -H 6.5 test.mol

hmoelectrondensity

HMO Electron density.

Options:

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

Example:

cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol

hmoelectrophilicityorder

Order in E(+) attack (HMO).

Options:

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

Example:

cxcalc hmoelectrophilicityorder -H 7.4 test.mol

hmoelectrophiliclocalizationenergy

HMO Electrophilic localization energy L(+).

Options:

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

Example:

cxcalc hmoelectrophiliclocalizationenergy test.mol

hmohuckel

HMO Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order	order:e	order:n	localizationenergy	localizationenergy:e	localizationenergy:n	pienergy	electrondensity	chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:


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

hmohuckeleigenvalue

HMO Huckel eigenvalue.

Options:

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

Example:

cxcalc hmohuckeleigenvalue test.mol

hmohuckeleigenvector

HMO Huckel eigenvector.

Options:

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

Example:

cxcalc hmohuckeleigenvector test.mol

hmohuckelorbitals

HMO Huckel orbital coefficients.

Options:

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

Example:

cxcalc hmohuckelorbitals test.mol

hmohuckeltable

HMO Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[hmoorder	hmoorder:e	hmoorder:n	hmolocalizationenergy	hmolocalizationenergy:e	hmolocalizationenergy:n	hmopienergy	hmoelectrondensity	hmochargedensity] (default: hmoorder,hmolocalizationenergy, hmopienergy,hmoelectrondensity,hmochargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

hmolocalizationenergy

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

Options:

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

Example:

cxcalc hmolocalizationenergy test.mol

hmonucleophilicityorder

Order in Nu(-) attack (HMO).

Options:

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

Example:

cxcalc hmonucleophilicityorder -H 7.4 test.mol

hmonucleophiliclocalizationenergy

HMO Nucleophilic localization energy L(-).

Options:

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

Example:

cxcalc hmonucleophiliclocalizationenergy test.mol

hmopienergy

HMO Pi energy.

Options:

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

Example:

cxcalc hmopienergy test.mol

huckel

Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order	order:e	order:n	localizationenergy	localizationenergy:e	localizationenergy:n	pienergy	electrondensity	chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

huckeleigenvalue

Huckel eigenvalue. Deprecated.

Options:

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

Example:

cxcalc huckeleigenvalue test.mol

huckeleigenvector

Huckel eigenvector. Deprecated.

Options:

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

Example:

cxcalc huckeleigenvector test.mol

huckelorbitals

Huckel orbital coefficients. Deprecated.

Options:

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

Example:

cxcalc huckelorbitals test.mol

huckeltable

Huckel analysis parameters.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[order	order:e	order:n	localizationenergy	localizationenergy:e	localizationenergy:n	pienergy	electrondensity	chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity)
-H, --pH	<pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:


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

localizationenergy

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

Options:

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

Example:


cxcalc localizationenergy test.mol

msacc

Hydrogen bond acceptor average multiplicity over microspecies by pH.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)
-e, --excludesulfur	[true	false] exclude sulfur atom from acceptors (default: true)
-x, --excludehalogens	[true	false] exclude halogens from acceptors (default: true)

Example:

cxcalc msacc -l 2.0 -u 12.0 test.sdf

msdon

Hydrogen bond donor average multiplicity over microspecies by pH.

Options:

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

Example:

cxcalc msdon -l 2.0 -u 12.0 test.sdf

nucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

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

Example:

cxcalc nucleophilicityorder -H 7.4 test.mol

nucleophiliclocalizationenergy

Nucleophilic localization energy L(-).

Options:

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

Example:

cxcalc nucleophiliclocalizationenergy test.mol

pichargedensity

Pi charge density. Deprecated, use "electrondensity" calculation.

Options:

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

Example:


cxcalc pichargedensity -p 4 -H 6.5 test.mol

pienergy

Pi energy. Deprecated.

Options:

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

Example:

cxcalc pienergy test.mol

refractivity

Refractivity calculation.

Options:

-p, --precision	<floating point precision as number of fractional digits: 0-8 or inf> (default: 2)
-t, --type	[increments	inch	refractivity] (default: refractivity)
-i, --inch	[true	false] refractivity on H atoms shown in brackets (for incremental refractivity only) (default: false)

Example:

cxcalc refractivity -p 3 -t refractivity,increments test.mol

resonantcount

The number of resonant structures.

Options:

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

Example:

cxcalc resonantCount test.mol

resonants

Resonant structures.

Options:

-c, --canonical	[true	false] true: take canonical resonant form (default: false)
-r, --mcontrib	[true	false] true: take major contributors (default: true)
-m, --max	<count> max. number of structures to be generated (default: 200)
-f, --format	(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	<pH value> solubility at this pH (default: not set)
-l, --lower	<pH lower limit> (default: 0)
-u, --upper	<pH upper limit> (default: 14)
-s, --step	<pH step size> (default: 1)

Example :

 cxcalc logs -i true -H 7.4 test.mol

totalchargedensity

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

Options:

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

Example:

cxcalc totalchargedensity -p 4 -H 6.5 test.mol