cxcalc calculations
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.
| -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) |
cxcalc atomcount -z 7 test.mol
Elemental composition calculation (w/w%).
| -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) |
cxcalc composition -s true test.mol
Dot-disconnected molecular formula calculation.
cxcalc dotdisconnectedformula test.mol
Dot-disconnected molecular formula calculation, isotopes included.
| -D, --symbolD | [true|false] use D / T symbols for Deuterium / Tritium (default: true) |
|---|
cxcalc dotdisconnectedisotopeformula test.mol
Molecule data calculation: formula, isotopeformula, dotdisconnectedformula, dotdisconnectedisotopeformula, mass, exactmass, composition, isotopecomposition, atomcount.
| -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) |
cxcalc elemanal -t "mass,composition,formula" test.mol
Molecule data calculation: formula, isotopeformula, dotdisconnectedformula, dotdisconnectedisotopeformula, mass, exactmass, composition, isotopecomposition, atomcount.
| -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) |
cxcalc elementalanalysistable -t "mass,composition,formula" test.mol
Exact molecule mass calculation based on the most frequent natural isotopes of the elements.
| -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) |
cxcalc exactmass test.mol
Molecular formula calculation.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc formula -s true test.mol
Elemental composition calculation, isotopes included (w/w%).
| -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) |
cxcalc icomposition -s true test.mol
Molecular formula calculation, isotopes included.
| -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) |
cxcalc iformula -s true test.mol
Elemental composition calculation, isotopes included (w/w%).
| -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) |
cxcalc isotopecomposition -s true test.mol
Molecular formula calculation, isotopes included.
| -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) |
cxcalc isotopeformula -s true test.mol
Molecule mass calculation.
| -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) |
cxcalc mass test.mol
Atomic polarizability calculation.
| -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) |
cxcalc atomicpolarizability test.mol
Atomic polarizability calculation.
| -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) |
cxcalc atompol test.mol
Average molecular polarizability calculation.
| -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) |
cxcalc averagemolecularpolarizability test.mol
Average molecular polarizability calculation.
| -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) |
cxcalc averagepol test.mol
Average molecular polarizability calculation.
| -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) |
cxcalc avgpol test.mol
Calculation of principal component of polarizability tensor axx.
| -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) |
cxcalc axxpol test.mol
Calculation of principal component of polarizability tensor ayy.
| -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) |
cxcalc ayypol test.mol
Calculation of principal component of polarizability tensor azz.
| -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) |
cxcalc azzpol test.mol
Partial charge calculation. Types aromaticsystem / aromaticring calculate the sum of charges in the aromatic system / aromatic ring containing the atom.
| -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) |
cxcalc -S -o result.sdf -t myCHARGE charge -t "pi,total" -p 3 test.mol
Formal charge calculation.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc formalcharge test.mol
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.
| -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) |
cxcalc ioncharge -n 6 -H 8 -m 1 -t accumulated test.mol
Molecular polarizability calculation.
| -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) |
cxcalc molecularpolarizability test.mol
Molecular polarizability calculation.
| -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) |
cxcalc molpol test.mol
Orbital electronegativity calculation.
| -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) |
cxcalc oen -t sigma test.mol
Orbital electronegativity calculation.
| -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) |
cxcalc orbitalelectronegativity -p 3 test.mol
Atomic and molecular polarizability calculation.
| -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) |
cxcalc pol -p 3 test.mol
Atomic and molecular polarizability calculation.
| -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) |
cxcalc polarizability -p 3 test.mol
Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
| -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) |
cxcalc tholepolarizability test.mol
Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
| -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) |
cxcalc tpol test.mol
Calculation of average molecular polarizability and principal components of polarizability tensor (axx, ayy, azz).
| -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) |
cxcalc tpolarizability test.mol
Calculates the conformers of the molecule.
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -m, --maxconformers | <maximum number of conformers to be generated> (default: 100) |
| -d, --diversity | <diversity limit> (default: 0.1) |
| -s, --saveconfdesc | [true|false] if true a single conformer is saved with a property containing conformer information (default: false) |
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
cxcalc conformers -m 250 -s true test.sdf
Calculates if the molecule has a conformer.
cxcalc hasvalidconformer test.sdf
Calculates the lowest energy conformer of the molecule.
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
cxcalc leconformer -f mrv test.sdf
Calculates the lowest energy conformer of the molecule.
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -e, --hyperfine | [true|false] if true hyperfine option is set (default: false) |
| -y, --prehydrogenize | [true|false] if true prehydrogenize is done before calculation, if false calculation is done without hydrogens (default: true) |
| -l, --timelimit | <timelimit for calculation in sec> (default: 900) |
| -O, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
cxcalc lowestenergyconformer -f mrv test.sdf
Molecular Dynamics.
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding] forcefield used for calculation (default: dreiding) |
| -i, --integrator | [positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet) |
| -n, --stepno | <number of simulation steps> (default: 1000) |
| -m, --steptime | <time between steps in femtoseconds> (default: 0.1) |
| -T, --temperature | <temperature in Kelvin> (default: 300 K) |
| -s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
cxcalc moldyn test.mol
Molecular Dynamics.
| -f, --format | <output format> should be a 3D format (default: sdf) |
|---|---|
| -x, --forcefield | [dreiding] forcefield used for calculation (default: dreiding) |
| -i, --integrator | [positionverlet|velocityverlet|leapfrog] integrator type used for calculation (default: velocityverlet) |
| -n, --stepno | <number of simulation steps> (default: 1000) |
| -m, --steptime | <time between steps in femtoseconds> (default: 0.1) |
| -T, --temperature | <temperature in Kelvin> (default: 300 K) |
| -s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
cxcalc moleculardynamics test.mol
Checks if a specified atom is aliphatic.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aliphaticatom test.mol
Aliphatic atom count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aliphaticatomcount test.mol
Aliphatic bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aliphaticbondcount test.mol
Aliphatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aliphaticringcount test.mol
Aliphatic ring count of size.
| -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 |
cxcalc aliphaticringcountofsize -z 5 test.mol
Angle of three atoms.
| -a, --atoms | [<atom1>-<atom2>-<atom3>] (1-based) atom indexes of the atom pair |
|---|---|
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc angle -a 2-4-6 test.mol
Checks if a specified atom is aromatic.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aromaticatom test.mol
Aromatic atom count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aromaticatomcount test.mol
Aromatic bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aromaticbondcount test.mol
Aromatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc aromaticringcount test.mol
Aromatic ring count of size.
| -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 |
cxcalc aromaticringcountofsize -z 6 test.mol
Water Accessible Surface Area calculation.
| -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) |
cxcalc asa test.mol
Checks if a specified atom is an asymmetric atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc asymmetricatom test.mol
The number of asymmetric atoms.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc asymmetricatomcount test.mol
The asymmetric atoms.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc asymmetricatoms test.mol
The Balaban index.
| -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) |
cxcalc balabanindex test.mol
Bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc bondcount test.mol
The bond type between two atoms.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
|---|
cxcalc bondtype -a 2-3 test.mol
Carboaliphatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc carboaliphaticringcount test.mol
Carboaromatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc carboaromaticringcount test.mol
Carbo ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc carboringcount test.mol
Checks if a specified atom is a chain atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chainatom test.mol
Chain atom count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chainatomcount test.mol
Checks if the bond is a chain bond.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
|---|
cxcalc chainbond -a 2-3 test.mol
Chain bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chainbondcount test.mol
Checks if a specified atom is a tetrahedral stereogenic center.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chiralcenter test.mol
The number of tetrahedral stereogenic center atoms.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chiralcentercount test.mol
The the chiral center atoms.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc chiralcenters test.mol
Checks if two atoms are in the same connected component.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the atom pair |
|---|
cxcalc connected -a 2-3 test.mol
Checks if the molecule graph is connected.
cxcalc connectedgraph test.mol
The cyclomatic number.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc cyclomaticnumber test.mol
Dihedral of four atoms.
| -a, --atoms | [<atom1>-<atom2>-<atom3>-<atom4>] (1-based) atom indexes of the atom pair |
|---|---|
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc dihedral -a 1-2-4-6 test.mol
Distance between two atoms.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the atom pair |
|---|---|
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc distance -a 2-4 test.mol
Distance degree of atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc distancedegree test.mol
Calculates the dreiding energy of a conformer of the molecule in kcal/mol.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc dreidingenergy -p 1 -l always test.sdf
Eccentricity of atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc eccentricity test.mol
Fragment count.
cxcalc fragmentcount test.mol
The number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings).
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc fusedaliphaticringcount test.mol
The number of fused aromatic rings (SSSR smallest set of smallest aromatic rings).
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc fusedaromaticringcount test.mol
The number of fused rings (SSSR smallest set of smallest rings).
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc fusedringcount test.mol
Harary index.
| -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) |
cxcalc hararyindex test.mol
Heteroaliphatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc heteroaliphaticringcount test.mol
Heteroaromatic ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc heteroaromaticringcount test.mol
Hetero ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc heteroringcount test.mol
Steric hindrance.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc hindrance test.mol
Hyper Wiener index.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc hyperwienerindex test.mol
Size of largest ring containing a specified atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc largestatomringsize test.mol
Largest ring size.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc largestringsize test.mol
Largest ring system size.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc largestringsystemsize test.mol
Calculates the maximal projection area.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc maximalprojectionarea test.sdf
Calculates the maximal projection radius.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc maximalprojectionradius test.sdf
Calculates the size of the molecule perpendicular to the maximal projection area surface.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc maximalprojectionsize test.sdf
Calculates the minimal projection area.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc minimalprojectionarea test.sdf
Calculates the minimal projection radius.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc minimalprojectionradius test.sdf
Calculates the size of the molecule perpendicular to the minimal projection area surface.
| -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, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc minimalprojectionsize test.sdf
Molecular Surface Area calculation (3D).
| -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) |
cxcalc molecularsurfacearea -t ASA+ -i true -H 7.4 test.mol
Molecular Surface Area calculation (3D).
| -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) |
cxcalc msa -t ASA+ -i true -H 7.4 test.mol
The Platt index.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc plattindex test.mol
Topological Polar Surface Area calculation (2D).
| -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) |
cxcalc -S -t myPSA polarsurfacearea test.mol
Topological Polar Surface Area calculation (2D).
| -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) |
cxcalc -S -t myPSA psa test.mol
The Randic index.
| -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) |
cxcalc randicindex test.mol
Checks if a specified atom is a ring atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc ringatom test.mol
Ring atom count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc ringatomcount test.mol
Checks if the bond is a ring bond.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
|---|
cxcalc ringbond -a 2-3 test.mol
Ring bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc ringbondcount test.mol
Ring count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc ringcount test.mol
Ring counts of atoms.
cxcalc ringcountofatoms -a 2-3 test.mol
Ring count of size.
| -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 |
cxcalc ringcountofsize -z 5 test.mol
The number of ring systems.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc ringsystemcount test.mol
Ring system count of size.
| -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 |
cxcalc ringsystemcountofsize -z 3 test.mol
Checks if the bond is a rotatable bond.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
|---|
cxcalc rotatablebond -a 2-3 test.mol
Rotatable bond count.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc rotatablebondcount test.mol
Length of shortest path between two atoms.
| -a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the atom pair |
|---|
cxcalc shortestpath -a 2-3 test.mol
Size of smallest ring containing a specified atom.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc smallestatomringsize test.mol
Smallest ring size.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc smallestringsize test.mol
Smallest ring system size.
| -s, --single | [true|false] in case of multi-fragment molecules: takes smallest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc smallestringsystemsize test.mol
The number of stereo double bonds.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc stereodoublebondcount test.mol
Steric effect index.
| -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) |
cxcalc stericeffectindex test.mol
Steric hindrance.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc sterichindrance test.mol
Szeged index.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc szegedindex test.mol
Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize.
| -t, --type | [atomcount|aliphaticatomcount|aromaticatomcount| bondcount|aliphaticbondcount|aromaticbondcount| rotatablebondcount|ringcount|aliphaticringcount| aromaticringcount|heteroringcount|heteroaliphaticringcount| heteroaromaticringcount|ringatomcount|ringbondcount| chainatomcount|chainbondcount| smallestringsize|largestringsize] (default: all) |
|---|---|
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
cxcalc topanal test.mol
Molecule topology data calculation: atomcount,aliphaticatomcount, aromaticatomcount,bondcount,aliphaticbondcount,aromaticbondcount, rotatablebondcount,ringcount,aliphaticringcount,aromaticringcount, heteroringcount,heteroaliphaticringcount,heteroaromaticringcount, ringatomcount,ringbondcount,chainatomcount,chainbondcount, smallestringsize,largestringsize.
| -t, --type | [atomcount|aliphaticatomcount|aromaticatomcount| bondcount|aliphaticbondcount|aromaticbondcount| rotatablebondcount|ringcount|aliphaticringcount| aromaticringcount|heteroringcount|heteroaliphaticringcount| heteroaromaticringcount|ringatomcount|ringbondcount| chainatomcount|chainbondcount| smallestringsize|largestringsize] (default: all) |
|---|---|
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
cxcalc topologyanalysistable test.mol
Van der Waals Surface Area calculation.
| -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) |
cxcalc vdwsa -H 7.4 test.mol
Calculates the van der Waals volume of the molecule.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -o, --optimization | [0|1|2|3] conformer generation optimiztaion limit for different enviroments {0}: very loose (limit=0.01) {1}: normal (limit=0.0010) {2}: strict (limit=1.0E-4) {3}: very strict (limit=1.0E-5) (default: 1) |
| -l, --leconformer | [if2D|never|always] (default: if2D) |
cxcalc volume test.sdf
Water Accessible Surface Area calculation.
| -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) |
cxcalc wateraccessiblesurfacearea test.mol
Wiener index.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc wienerindex test.mol
Wiener polarity.
| -s, --single | [true|false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
|---|
cxcalc wienerpolarity test.mol
Canonical tautomer.
| -f, --format | <output format> (default: smiles table, multiple molecule output if specified) |
|---|---|
| -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) |
cxcalc canonicaltautomer -f sdf test.mol
Dominant tautomer distribution.
| -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) |
cxcalc dominanttautomerdistribution test.mol
The number of double-bond stereoisomers of the molecule.
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
|---|---|
| -D, --protectdoublebondstereo | [true|false] true: protect double bond stereo (default: false) |
cxcalc doublebondstereoisomercount test.sdf
Generates double-bond stereoisomers of the molecule.
| -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) |
cxcalc doublebondstereoisomers -f mrv test.sdf
Generic tautomer.
| -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) |
cxcalc generictautomer -f sdf test.mol
Major tautomer.
| -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) |
cxcalc majortautomer -H 7.4 -f sdf test.mol
Most stable tautomer. Depreacated, use "majortautomer" instead.
| -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) |
cxcalc moststabletautomer -f sdf test.mol
The number of stereoisomers of the molecule.
| -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) |
cxcalc stereoisomercount test.sdf
Generates stereoisomers of the molecule.
| -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) |
cxcalc stereoisomers -v true test.sdf
The number of tautomers.
| -d, --dominants | [true|false] true: take dominant tautomers (default: true) |
|---|---|
| -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) |
cxcalc tautomerCount -s false test.mol
Tautomers.
| -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) |
| -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) |
cxcalc tautomers -f sdf test.mol
The number of tetrahedral stereoisomers of the molecule.
| -m, --maxstereoisomers | <maximum number of double bond stereoisomers to be generated> (default: 1000) |
|---|---|
| -T, --protecttetrahedralstereo | [true|false] true: protect tetrahedral stereo centers (default: false) |
cxcalc tetrahedralstereoisomercount test.sdf
Generates tetrahedral stereoisomers of the molecule.
| -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) |
cxcalc tetrahedralstereoisomers -3 true test.sdf
Number of Markush enumerated structures.
| -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) |
cxcalc enumerationcount -m true test.mol
Markush enumerated structures.
| -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) |
cxcalc enumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol
Number of Markush enumerated structures.
| -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) |
cxcalc markushenumerationcount -m true test.mol
Markush enumerated structures.
| -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) |
cxcalc markushenumerations -f sdf -C 2:t3000 -a 2,3,5 test.mol
Randomly constructed Markush enumerated structures.
| -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) |
cxcalc randommarkushenumerations -f sdf -C 2:t5000 test.mol
Generates the IUPAC name of the molecule.
| -t, --type | [preferred|traditional] (default: preferred) preferred: Preferred IUPAC Name traditional: traditional name |
|---|
cxcalc name test.sdf
logD calculation.
| -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) |
| -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) |
| -c, --considertautomerization | [true|false] consider tautomerization (default: false) |
cxcalc -i ID logd -l 2 -u 3 -s 0.5 test.sdf
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.
| -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) |
| -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|inch|logPMicro|logPTrue] (default: logPTrue) |
| -i, --inch | [true|false] incremental logP on H atoms shown in brackets (for incremental logP only) (default: false) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
cxcalc -S -t myLOGP logp -a 0.15 -k 0.05 test.mol
Average microspecies charge calculation.
| -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) |
cxcalc averagemicrospeciescharge test.mol
Charge distribution calculation.
| -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) |
cxcalc chargedistribution test.mol
Isoelectric point calculation.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|
cxcalc isoelectricpoint test.mol
Major microspecies at given pH.
| -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) |
cxcalc majormicrospecies -H 3.5 -f mol test.mol
Major microspecies at given pH.
| -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) |
cxcalc majorms -H 3.5 -f mol test.mol
Microspecies list with distributions at given pH.
| -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) |
cxcalc microspeciesdistribution -H 3.5 test.mol
Microspecies list with distributions at given pH.
| -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) |
cxcalc msdistr -H 3.5 test.mol
Isoelectric point calculation.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|
cxcalc pI test.mol
pKa calculation.
| -p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
|---|---|
| -t, --type | [pKa|acidic|basic] (default: pKa) |
| -m, --mode | [macro|micro] (default: macro) |
| -P, --prefix | [static|dynamic] (default: static) |
| -d, --model | [small|large] calculation model small: optimized for at most 8 ionizable atoms large: optimized for a large number of ionizable atoms (default: small) |
| -i, --min | <min basic pKa> (default: -10) |
| -x, --max | <max acidic pKa> (default: 20) |
| -T, --temperature | <temperature in Kelvin> (default: 298 K) |
| -a, --na | <number of acidic pKa values displayed> (default: 2) |
| -b, --nb | <number of basic pKa values displayed> (default: 2) |
| -M, --majortautomer | [true|false] take major tautomeric form (default: false) |
| -c, --usecorrectionlibrary | [true|false] use correction library (default: false) |
cxcalc pka -i -15 -x 25 -a 3 -b 3 -d large test.mol
Hydrogen bond acceptor multiplicity calculation on atoms.
| -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)) |
cxcalc acc test.sdf
Hydrogen bond acceptor calculation.
| -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) |
cxcalc acceptor test.sdf
Hydrogen bond acceptor atom count in molecule.
| -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) |
cxcalc acceptorcount -H 7.4 test.sdf
Hydrogen bond acceptor multiplicity calculation on atoms.
| -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) |
cxcalc acceptormultiplicity test.sdf
Hydrogen bond acceptor multiplicity in molecule.
| -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) |
cxcalc acceptorsitecount test.sdf
Hydrogen bond acceptor calculation.
| -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) |
cxcalc acceptortable test.sdf
Hydrogen bond acceptor multiplicity in molecule.
| -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) |
cxcalc accsitecount test.sdf
Order in E(+) attack. Deprecated.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc aromaticelectrophilicityorder -H 7.4 test.mol
Order in Nu(-) attack. Deprecated.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc aromaticnucleophilicityorder -H 7.4 test.mol
Canonical resonant structure.
| -f, --format | <output format> (default: smiles) |
|---|
cxcalc canonicalResonant -f sdf test.mol
Charge density.
| -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) |
cxcalc chargedensity -p 4 -H 6.5 test.mol
Hydrogen bond donor multiplicity calculation on atoms.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc don test.sdf
Hydrogen bond donor calculation.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc donor test.sdf
Hydrogen bond donor atom count in molecule.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc donorcount -H 7.4 test.sdf
Hydrogen bond donor multiplicity calculation on atoms.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc don test.sdf
Hydrogen bond donor multiplicity in molecule.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc donorsitecount test.sdf
Hydrogen bond donor calculation.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc donortable test.sdf
Hydrogen bond donor multiplicity in molecule.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc donsitecount test.sdf
Electron density.
| -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) |
cxcalc electrondensity -p 4 -H 6.5 test.mol
Order in E(+) attack. Deprecated.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc electrophilicityorder -H 7.4 test.mol
Electrophilic localization energy L(+).
| -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) |
cxcalc electrophiliclocalizationenergy test.mol
Calculates different structural frameworks (Bemis-Murcko, MCS, etc) of the molecule
| -t, --type | [bmf|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) |
cxcalc frameworks -t bmf -s true test.mol
Hydrogen bond acceptor-donor calculation.
| -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) |
cxcalc hbda -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf
Hydrogen bond acceptor-donor calculation.
| -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) |
cxcalc hbonddonoracceptor -t "msacc,msdon" -l 2 -u 12 -s 0.5 test.sdf
HMO Charge density.
| -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) |
cxcalc hmochargedensity -p 4 -H 6.5 test.mol
HMO Electron density.
| -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) |
cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol
Order in E(+) attack (HMO).
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc hmoelectrophilicityorder -H 7.4 test.mol
HMO Electrophilic localization energy L(+).
| -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) |
cxcalc hmoelectrophiliclocalizationenergy test.mol
HMO Huckel analysis parameters.
| -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) |
cxcalc -S -o result.sdf hmohuckel -H 7.4 -p 3 test.mol
HMO Huckel eigenvalue.
| -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) |
cxcalc hmohuckeleigenvalue test.mol
HMO Huckel eigenvector.
| -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) |
cxcalc hmohuckeleigenvector test.mol
HMO Huckel orbital coefficients.
| -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) |
cxcalc hmohuckelorbitals test.mol
HMO Huckel analysis parameters.
| -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) |
cxcalc -S -o result.sdf hmohuckeltable -H 7.4 -p 3 test.mol
HMO Localization energy L(+)/L(-).
| -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) |
cxcalc hmolocalizationenergy test.mol
Order in Nu(-) attack (HMO).
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc hmonucleophilicityorder -H 7.4 test.mol
HMO Nucleophilic localization energy L(-).
| -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) |
cxcalc hmonucleophiliclocalizationenergy test.mol
HMO Pi energy.
| -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) |
cxcalc hmopienergy test.mol
Huckel analysis parameters.
| -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) |
cxcalc -S -o result.sdf huckel -H 7.4 -p 3 test.mol
Huckel eigenvalue. Deprecated.
| -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) |
cxcalc huckeleigenvalue test.mol
Huckel eigenvector. Deprecated.
| -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) |
cxcalc huckeleigenvector test.mol
Huckel orbital coefficients. Deprecated.
| -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) |
cxcalc huckelorbitals test.mol
Huckel analysis parameters.
| -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) |
cxcalc -S -o result.sdf huckeltable -H 7.4 -p 3 test.mol
Localization energy L(+)/L(-).
| -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) |
cxcalc localizationenergy test.mol
Hydrogen bond acceptor average multiplicity over microspecies by pH.
| -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) |
cxcalc msacc test.sdf
Hydrogen bond donor average multiplicity over microspecies by pH.
| -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) |
cxcalc msdon test.sdf
Order in Nu(-) attack. Deprecated.
| -H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
|---|
cxcalc nucleophilicityorder -H 7.4 test.mol
Nucleophilic localization energy L(-).
| -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) |
cxcalc nucleophiliclocalizationenergy test.mol
Pi charge density. Deprecated, use "electrondensity" calculation.
| -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) |
cxcalc pichargedensity -p 4 -H 6.5 test.mol
Pi energy. Deprecated.
| -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) |
cxcalc pienergy test.mol
Refractivity calculation.
| -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) |
cxcalc refractivity -p 3 -t refractivity,increments test.mol
The number of resonant structures.
| -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) |
cxcalc resonantCount test.mol
Resonant structures.
| -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) |
cxcalc resonants -f sdf test.mol
Total charge density. Deprecated, use "chargedensity" calculation.
| -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) |
cxcalc totalchargedensity -p 4 -H 6.5 test.mol