This is the latest version of the ChemAxon Documentation.
This page contains a full list of calculator functions implemented in cxcalc:
cxcalc calculations
The calculator functions are grouped based on the plugin they belong to.
Elemental Analysis
The following features and properties can be calculated:
atomcount
Number of atoms in the molecule: no atno: counts all atoms in the molecule; atno, but no massno: counts atoms of the given type in the molecule; atno, massno: counts atoms of the given isotope type in the molecule; atno, massno=0: counts atoms of the given type in the molecule, but excludes its isotopes.
Options:
| -z, --atno | <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 | <output format> should be a 3D format (default: sdf) |
| -x, --forcefield | [dreiding|mmff94] forcefield used for calculation (default: dreiding) |
| -m, --maxconformers | <maximum number of conformers to be generated> (default: 100) |
| -d, --diversity | <diversity limit> (default: 0.1) |
| -s, --saveconfdesc | [true|false] if true a single conformer is saved with a property containing conformer information (default: false) |
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
Example:
cxcalc conformers -m 250 -s true test.sdf
hasvalidconformer
Calculates if the molecule has a conformer.
Options:
No options
Example:
cxcalc hasvalidconformer test.sdf
leconformer
Calculates the lowest energy conformer of the molecule.
Options:
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding|mmff94] forcefield used for calculation (default: dreiding) |
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -m, --multifrag | [true|false] in case of multi-fragment molecules and if mmff94 forcefield selected: takes largest fragment if false, takes whole molecule if true (default: false) |
Example:
cxcalc leconformer -f mrv test.sdf
lowestenergyconformer
Calculates the lowest energy conformer of the molecule.
Options:
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding|mmff94] forcefield used for calculation (default: dreiding) |
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -m, --multifrag | [true|false] in case of multi-fragment molecules and if mmff94 forcefield selected: takes largest fragment if false, takes whole molecule if true (default: false) |
Example:
cxcalc lowestenergyconformer -f mrv test.sdf
moldyn
Runs a molecular dynamics simulation for the molecule.
Options:
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding|mmff94] forcefield used for calculation (default: dreiding) |
| -i, --integrator | [positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet) |
| -n, --stepno | <number of simulation steps> (default: 1000) |
| -m, --steptime | <time between steps in femtoseconds> (default: 0.1) |
| -T, --temperature | <temperature in Kelvin> (default: 300 K) |
| -s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
Example:
cxcalc moldyn -i leapfrog -n 1500 -T 400 -f sdf test.mol
moleculardynamics
Runs a molecular dynamics simulation for the molecule.
Options:
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding|mmff94] forcefield used for calculation (default: dreiding) |
| -i, --integrator | [positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet) |
| -n, --stepno | <number of simulation steps> (default: 1000) |
| -m, --steptime | <time between steps in femtoseconds> (default: 0.1) |
| -T, --temperature | <temperature in Kelvin> (default: 300 K) |
| -s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
Example:
cxcalc moleculardynamics -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
Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize,fsp3.
Options:
| -a --arom | [general|basic|loose] sets aromatization method |
|---|---|
| -t, --type | [atomcount|aliphaticatomcount|aromaticatomcount| bondcount|aliphaticbondcount|aromaticbondcount| rotatablebondcount|ringcount|aliphaticringcount| aromaticringcount|heteroringcount|heteroaliphaticringcount| heteroaromaticringcount|ringatomcount|ringbondcount| chainatomcount|chainbondcount| smallestringsize|largestringsize|fsp3] (default: all) |
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
Example:
cxcalc topologyanalysistable -a basic -s true test.mol
vdwsa
Van der Waals Surface Area calculation.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <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 | <output format> (default: smiles table, multiple molecule output if specified) |
|---|---|
| -R, --rational | [true|false] true: generates only rational tautomers (default: false) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
Example:
cxcalc canonicaltautomer -f sdf -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 | <output format> (default: sdf:-a) |
| -t, --tag | <SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION) |
Example:
cxcalc dominanttautomerdistribution test.mol
doublebondstereoisomercount
The number of double-bond stereoisomers of the molecule.
Options:
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
|---|---|
| -D, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
Example:
cxcalc doublebondstereoisomercount test.sdf
doublebondstereoisomers
Generates double-bond stereoisomers of the molecule.
Options:
| -f, --format | <output format> (default: sdf) |
|---|---|
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
| -D, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -v, --verify3d | [true|false] if true invalid 3D structures of genereated stereoisomers are filtered |
| -3, --in3d | [true|false] if true 3D structures are generated (invalid 3D structures are filtered) |
Example:
cxcalc doublebondstereoisomers -f mrv test.sdf
generictautomer
Generic tautomer.
Options:
| -f, --format | <output format> (default: smiles table, multiple molecule output if specified) |
|---|---|
| -l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds (default: 4) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
Example:
cxcalc generictautomer -f sdf test.mol
majortautomer
Major tautomer.
Options:
| -f, --format | <output format> (default: smiles table, multiple molecule output if specified) |
|---|---|
| -l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds (default: 4) |
| -H, --pH | <pH value> considers pH effect at this pH. (default: do not consider pH effect) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
Example:
cxcalc majortautomer -H 7.4 -f sdf test.mol
moststabletautomer
Most stable tautomer. Depreacated, use "majortautomer" instead.
Options:
| -f, --format | <output format> (default: smiles table, multiple molecule output if specified) |
|---|---|
| -l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds (default: 4) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
Example:
cxcalc moststabletautomer -f sdf test.mol
stereoisomercount
The number of stereoisomers of the molecule.
Options:
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
|---|---|
| -D, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protecttetrahedralstereo | [true|false] true: protect tetrahedral stereo centers (default: false) |
Example:
cxcalc stereoisomercount -m 100 test.sdf
stereoisomers
Generates stereoisomers of the molecule.
Options:
| -f, --format | <output format> (default: sdf) |
|---|---|
| -m, --maxstereoisomers | <maximum number of stereoisomers to be generated> (default: 1000) |
| -D, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protecttetrahedralstereo | [true|false] true: protect tetrahedral stereo centers (default: false) |
| -v, --verify3d | [true|false] if true invalid 3D structures of genereated stereoisomers are filtered |
| -3, --in3d | [true|false] if true 3D structures are generated (invalid 3D structures are filtered) |
Example:
cxcalc stereoisomers -v true test.sdf
stereoanalysis
Calculate stereo descriptors.
Options:
| -T --type | stereo descriptor type [tetrahedral | cistrans | |
|---|
Example:
cxcalc stereoanalysis test.mol
tautomercount
The number of tautomers.
Options:
| -d, --dominants | [true|false] true: take dominant tautomers (default: true) |
|---|---|
| -R, --rational | [true|false] true: takes only rational tautomers (default: false) |
| -m, --max | <count> max. number of structures to be generated (default: 200) |
| -l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds |
| -H, --pH | <pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -s, --symfilter | [true|false] true: filter out symmetrical structures false: allow duplicates (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
Example:
cxcalc tautomerCount -s false test.mol
tautomers
Tautomers.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 0) |
|---|---|
| -c, --canonical | [true|false] true: take canonical tautomer (default: false) |
| -R, --rational | [true|false] true: generates only rational tautomers (default: false) |
| -g, --generic | [true|false] true: take generic tautomer (default: false) |
| -M, --major | [true|false] true: take major tautomer (default: false) |
| -d, --dominants | [true|false] true: take dominant tautomers (default: true) |
| -D, --distribution | [true|false] true: calculate dominant tautomer distribution (default: false) |
| -m, --max | <count> maximum number of structures to be generated (default: 200) |
| -l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds (default: 4) |
| -H, --pH | <pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect) |
| -a, --protectaromaticity | [true|false] true: protect aromaticity (default: true) |
| -C, --protectcharge | [true|false] true: protect charge (default: true) |
| -e, --excludeantiaroma | [true|false] true: exclude antiaromatic compounds (default: true) |
| -P, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
| -T, --protectalltetrahedralcenters | [true|false] true: protect all tetrahedral stereo centers (default: false) |
| -L, --protectlabeledtetrahedralcenters | [true|false] true: protect labeled tetrahedral stereo centers (default: false) |
| -E, --protectestergroups | [true|false] true: protect ester groups (default: true) |
| -s, --symfilter | [true|false] true: filter out symmetrical structures false: allow duplicates (default: true) |
| -f, --format | <output format> (default: fused smiles, multiple molecule output if specified) |
| -t, --tag | <SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION) |
| -r, --ring | [true|false] Enable/disable ring tautomers. Default false. |
Example:
cxcalc tautomers -f sdf test.mol cxcalc tautomers --dominants false --rational true test.mol --format smiles
tetrahedralstereoisomercount
The number of tetrahedral stereoisomers of the molecule.
Options:
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
|---|---|
| -T, --protecttetrahedralstereo | [true|false] true: protect tetrahedral stereo centers (default: false) |
Example:
cxcalc tetrahedralstereoisomercount test.sdf
tetrahedralstereoisomers
Generates tetrahedral stereoisomers of the molecule.
Options:
| -f, --format | <output format> (default: sdf) |
|---|---|
| -m, --maxstereoisomers | <maximum number of tetrahedral stereoisomers to be generated> (default: 1000) |
| -T, --protecttetrahedralstereo | [true|false] true: protect tetrahedral stereo centers (default: false) |
| -v, --verify3d | [true|false] if true invalid 3D structures of genereated stereoisomers are filtered |
| -3, --in3d | [true|false] if true 3D structures are generated (invalid 3D structures are filtered) |
Example:
cxcalc tetrahedralstereoisomers -3 true test.sdf
Markush 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 | <output format> (default: concatenated smiles) |
| -C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
cxcalc enumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol
markushenumerationcount
Number of Markush enumerated structures.
Options:
| -a, --atoms | [atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all) |
|---|---|
| -m, --magnitude | [true|false] display magnitude if >= 100 000 (default: false) |
| -g, --enumhomology | [true|false] enumerate homology groups (default: false) |
Example:
cxcalc markushenumerationcount -m true test.mol
markushenumerations
Markush enumerated structures.
Options:
| -m, --max | <count> max. number of structures to be generated (default: all) |
|---|---|
| -v, --valencecheck | [true|false] valence filter is on if true (default: false) |
| -a, --atoms | [atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all) |
| -s, --alignscaffold | [true|false] align scaffold (default: false) |
| -c, --coloring | [none|all|scaffold|rgroups] structure coloring (default: none) |
| -r, --random | [true|false] random enumeration (default: false) |
| -g, --enumhomology | [true|false] enumerate homology groups (default: false) |
| -o, --code | [true|false] generate Markush code (default: false) |
| -i, --structureid | [id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID) |
| -f, --format | <output format> (default: concatenated smiles) |
| -C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
cxcalc markushenumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol
randommarkushenumerations
Randomly constructed Markush enumerated structures.
Options:
| -m, --max | <count> max. number of structures to be generated (default: all) |
|---|---|
| -v, --valencecheck | [true|false] valence filter is on if true (default: false) |
| -a, --atoms | [atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all) |
| -s, --alignscaffold | [true|false] align scaffold (default: false) |
| -c, --coloring | [none|all|scaffold|rgroups] structure coloring (default: none) |
| -g, --enumhomology | [true|false] enumerate homology groups (default: false) |
| -o, --code | [true|false] generate Markush code (default: false) |
| -i, --structureid | [id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID) |
| -f, --format | <output format> (default: concatenated smiles) |
| -C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
cxcalc randommarkushenumerations -f sdf -C 2:t5000 test.mol
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 | <output format> (default: smiles) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
| -K, --keephydrogens | [true|false] keep explicit hydrogen on result molecule (default: false) |
Example:
cxcalc majormicrospecies -H 3.5 -f mol test.mol
majorms
Major microspecies at given pH.
Options:
| -H, --pH | <pH value> gets major microspecies at this pH (default: no pH, all microspecies) |
|---|---|
| -f, --format | <output format> (default: smiles) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
| -K, --keephydrogens | [true|false] keep explicit hydrogen on result molecule (default: false) |
Example:
cxcalc majorms -H 3.5 -f mol test.mol
microspeciesdistribution
Microspecies list with distributions at given pH.
Options:
| -H, --pH | <pH value> gets major microspecies at this pH (default: 7.4) |
|---|---|
| -f, --format | <output format> (default: sdf:-a) |
| -t, --tag | <SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...]) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
| -K, --keephydrogens | [true|false] keep explicit hydrogen on result molecule (default: false) |
Example:
cxcalc microspeciesdistribution -H 3.5 test.mol
msdistr
Microspecies list with distributions at given pH.
Options:
| -H, --pH | <pH value> gets major microspecies at this pH (default: 7.4) |
|---|---|
| -f, --format | <output format> (default: sdf:-a) |
| -t, --tag | <SDF/MRV tag to store the distribution value> (default: MSDISTR[pH=...]) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
| -K, --keephydrogens | [true|false] keep explicit hydrogen on result molecule (default: false) |
Example:
cxcalc msdistr -H 3.5 test.mol
pi
Isoelectric point calculation.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|
Example:
cxcalc pI test.mol
pka
pKa calculation.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -t, --type | [pKa|acidic|basic] (default: pKa) |
| -m, --mode | [macro|micro] (default: macro) |
| -P, --prefix | [static|dynamic] (default: static) |
| -d, --model | [small|large] calculation model small: optimized for at most 8 ionizable atoms large: optimized for a large number of ionizable atoms (default: small) |
| -i, --min | <min basic pKa> (default: -10) |
| -x, --max | <max acidic pKa> (default: 20) |
| -T, --temperature | <temperature in Kelvin> (default: 298 K) |
| -a, --na | <number of acidic pKa values displayed> (default: 2) |
| -b, --nb | <number of basic pKa values displayed> (default: 2) |
| --considertautomerization | [true|false] consider tautomerization and resonance (default: false) |
| -L, --correctionlibrary | <correction library ID> |
| -P, --correctionlibrarypath | <path of the correction library> use this parameter when the correction library not stored on the default location |
Example:
cxcalc pka -i -15 -x 25 -a 3 -b 3 -d large test.mol
Other 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 | <output format> (default: smiles) |
|---|
Example:
cxcalc canonicalResonant -f sdf test.mol
chargedensity
Charge density.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc chargedensity -p 4 -H 6.5 test.mol
don
Hydrogen bond donor multiplicity calculation on atoms.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc don test.sdf
donor
Hydrogen bond donor calculation.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc donor test.sdf
donorcount
Hydrogen bond donor atom count in molecule.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc donorcount -H 7.4 test.sdf
donormultiplicity
Hydrogen bond donor multiplicity calculation on atoms.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc don test.sdf
donorsitecount
Hydrogen bond donor multiplicity in molecule.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc donorsitecount test.sdf
donortable
Hydrogen bond donor calculation.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc donortable test.sdf
donsitecount
Hydrogen bond donor multiplicity in molecule.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc donsitecount test.sdf
electrondensity
Electron density.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc electrondensity -p 4 -H 6.5 test.mol
electrophilicityorder
Order in E(+) attack. Deprecated.
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc electrophilicityorder -H 7.4 test.mol
electrophiliclocalizationenergy
Electrophilic localization energy L(+).
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc electrophiliclocalizationenergy test.mol
frameworks
Calculates different structural frameworks (Bemis-Murcko, MCS, etc) of the molecule
Options:
| -t, --type | [bmf|bmfl|mcs|largestring|allringsystems| largestringsystem|sssr|cssr|keep] Framework type to calculate |
|---|---|
| -i, --lfin | [true|false] Process only the largest fragment of input structure (default: false) |
| -p, --prunein | [true|false] Prune input: generalize input atom and bond types (default: false) |
| -h, --hydrogenize | [true|fase] Add explicit hydrogens to the input structure (default: false) |
| -d, --dehydrogenize | [true|false] Remove explicit hydrogens from the input structure (default: false) |
| -r, --pruneout | [true|false] Prune results: generalize result atom and bond types (default: false) |
| -o, --lfout | [true|false] Return only the largest fragment of the result (default: false) |
| -q, --oeqcheck | [true|false] Remove topologically equivalent output fragments (default: false) |
| -s, --keepsingleatom | [true|false] Return a single atom for non-empty acyclic input structures (default: true) |
| -f, --format | <output format> (default: sdf) |
Example:
cxcalc frameworks -t bmf -s true test.mol
hbda
Hydrogen bond acceptor-donor calculation.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -t, --type | [acc|don|accsitecount|donsitecount| acceptorcount|donorcount|msacc|msdon] (default: acceptorcount,donorcount,accsitecount, donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH |
| -l, --lower | <pH lower limit> (default: 0) |
| -u, --upper | <pH upper limit> (default: 14) |
| -s, --step | <pH step size> (default: 1) |
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)) |
| -e, --excludesulfur | [true|false] exclude sulfur atom from acceptors (default: true) |
| -x, --excludehalogens | [true|false] exclude halogens from acceptors (default: true) |
Example:
cxcalc hbda -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf
hbonddonoracceptor
Hydrogen bond acceptor-donor calculation.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -t, --type | [acc|don|accsitecount|donsitecount| acceptorcount|donorcount|msacc|msdon] (default: acceptorcount,donorcount,accsitecount, donsitecount) acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in molecule donsitecount: donor multiplicity in molecule acceptorcount: number of acceptor atoms in molecule donorcount: number of donor atoms in molecule msacc: average acceptor multiplicity over microspecies by pH msdon: average donor multiplicity over microspecies by pH |
| -l, --lower | <pH lower limit> (default: 0) |
| -u, --upper | <pH upper limit> (default: 14) |
| -s, --step | <pH step size> (default: 1) |
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule)) |
| -e, --excludesulfur | [true|false] exclude sulfur atom from acceptors (default: true) |
| -x, --excludehalogens | [true|false] exclude halogens from acceptors (default: true) |
Example:
cxcalc hbonddonoracceptor -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf
hmochargedensity
HMO Charge density.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc hmochargedensity -p 4 -H 6.5 test.mol
hmoelectrondensity
HMO Electron density.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol
hmoelectrophilicityorder
Order in E(+) attack (HMO).
Options:
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
Example:
cxcalc hmoelectrophilicityorder -H 7.4 test.mol
hmoelectrophiliclocalizationenergy
HMO Electrophilic localization energy L(+).
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
cxcalc hmoelectrophiliclocalizationenergy test.mol
hmohuckel
HMO Huckel analysis parameters.
Options:
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -t, --type | [order|order:e|order:n| |
| -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 | <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
solubility
Calculates aqueous solubility.
Options:
| U, --unit | measurement unit [mg/ml | mol/l | logS] (default: |
|---|---|
| -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
Overview
Content Tools