This page contains a full list of calculator functions implemented in cxcalc:
The calculator functions are grouped based on the plugin they belong to.
The following features and properties can be calculated:
Number of atoms in the molecule: no atno: counts all atoms in the molecule; atno, but no massno: counts atoms of the given type in the molecule; atno, massno: counts atoms of the given isotope type in the molecule; atno, massno=0: counts atoms of the given type in the molecule, but excludes its isotopes.
Options :
-z, --atno | <atomic number> | |
---|---|---|
-m, --massno | <mass number> | |
-s, --single | [true | false] in case of multi-fragment molecules: takes largest fragment if true, takes whole molecule if false (default: false) |
Example:
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:
Dot-disconnected molecular formula calculation.
Options:
No options
Example:
Dot-disconnected molecular formula calculation, isotopes included.
Options:
-D, --symbolD | [true | false] use D / T symbols for Deuterium / Tritium (default: true) |
---|
Example:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
The following features and properties can be calculated:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
Formal charge calculation.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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:
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:
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:
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:
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:
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:
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 :
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:
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:
The following features and properties can be calculated:
Calculates the conformers of the molecule.
Options:
-f, --format | ||||
---|---|---|---|---|
-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:
Calculates if the molecule has a conformer.
Options:
No options
Example:
Calculates the lowest energy conformer of the molecule.
Options:
-f, --format | ||||
---|---|---|---|---|
-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:
Calculates the lowest energy conformer of the molecule.
Options:
-f, --format | ||||
---|---|---|---|---|
-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:
Runs a molecular dynamics simulation for the molecule.
Options:
-f, --format | |||
---|---|---|---|
-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 | |||
-T, --temperature | <temperature in Kelvin> (default: 300 K) | ||
-s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
Example:
Runs a molecular dynamics simulation for the molecule.
Options:
-f, --format | |||
---|---|---|---|
-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 | |||
-T, --temperature | <temperature in Kelvin> (default: 300 K) | ||
-s, --samplinginterval | <sampling interval in femtoseconds> (default: 10) |
Example:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
Checks if the bond is a chain bond.
Options:
-a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
---|
Example:
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:
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:
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:
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:
Checks if two atoms are in the same connected component.
Options:
-a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the atom pair |
---|
Example:
Checks if the molecule graph is connected.
Options: No options
Example:
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:
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:
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:
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:
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:
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:
Fragment count.
Options:
No options
Example:
Fsp3 value of the molecule.
Options:
No options
Example:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
Checks if the bond is a ring bond.
Options:
-a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
---|
Example:
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:
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:
Ring counts of atoms.
Options:
No options
Example:
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:
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:
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:
Checks if the bond is a rotatable bond.
Options:
-a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the bond atoms |
---|
Example:
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:
Length of shortest path between two atoms.
Options:
-a, --atoms | [<atom1>-<atom2>] (1-based) atom indexes of the atom pair |
---|
Example:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
Canonical tautomer.
Options:
-f, --format | ||
---|---|---|
-n, --normal | [true | false] true: generates only normal tautomers (default: false) |
-a, --protectaromaticity | [true | false] true: protect aromaticity (default: true) |
-C, --protectcharge | [true | false] true: protect charge (default: true) |
-e, --excludeantiaroma | [true | false] true: exclude antiaromatic compounds (default: true) |
-P, --protectdoublebondstereo | [true | false] true: protect double bond stereo (default: false) |
-T, --protectalltetrahedralcenters | [true | false] true: protect all tetrahedral stereo centers (default: false) |
-L, --protectlabeledtetrahedralcenters | [true | false] true: protect labeled tetrahedral stereo centers (default: false) |
-E, --protectestergroups | [true | false] true: protect ester groups (default: true) |
Example:
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 | ||
-t, --tag | <SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION) |
Example:
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:
Generates double-bond stereoisomers of the molecule.
Options:
-f, --format | ||
---|---|---|
-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:
Generic tautomer.
Options:
-f, --format | ||
---|---|---|
-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:
Major tautomer.
Options:
-f, --format | ||
---|---|---|
-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:
Most stable tautomer. Depreacated, use "majortautomer" instead.
Options:
-f, --format | ||
---|---|---|
-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:
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:
Generates stereoisomers of the molecule.
Options:
-f, --format | ||
---|---|---|
-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:
Calculate stereo descriptors.
Options:
-T --type | stereo descriptor type [tetrahedral | cistrans | axial | atrop] (default: not set) |
---|
Example:
The number of tautomers.
Options:
-d, --dominants | [true | false] true: take dominant tautomers (default: true) |
---|---|---|
-n, --normal | [true | false] true: takes only normal tautomers (default: false) |
-m, --max | <count> max. number of structures to be generated (default: 200) | |
-l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds | |
-H, --pH | <pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect) | |
-a, --protectaromaticity | [true | false] true: protect aromaticity (default: true) |
-C, --protectcharge | [true | false] true: protect charge (default: true) |
-e, --excludeantiaroma | [true | false] true: exclude antiaromatic compounds (default: true) |
-s, --symfilter | [true | false] true: filter out symmetrical structures false: allow duplicates (default: true) |
-P, --protectdoublebondstereo | [true | false] true: protect double bond stereo (default: false) |
-T, --protectalltetrahedralcenters | [true | false] true: protect all tetrahedral stereo centers (default: false) |
-L, --protectlabeledtetrahedralcenters | [true | false] true: protect labeled tetrahedral stereo centers (default: false) |
-E, --protectestergroups | [true | false] true: protect ester groups (default: true) |
Example:
Tautomers.
Options:
-p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 0) | |
---|---|---|
-c, --canonical | [true | false] true: take canonical tautomer (default: false) |
-n, --normal | [true | false] true: generates only normal tautomers (default: false) |
-g, --generic | [true | false] true: take generic tautomer (default: false) |
-M, --major | [true | false] true: take major tautomer (default: false) |
-d, --dominants | [true | false] true: take dominant tautomers (default: true) |
-D, --distribution | [true | false] true: calculate dominant tautomer distribution (default: false) |
-m, --max | <count> maximum number of structures to be generated (default: 200) | |
-l, --pathlength | <length> maximum allowed length of the tautomerization path in chemical bonds (default: 4) | |
-H, --pH | <pH value> considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect) | |
-a, --protectaromaticity | [true | false] true: protect aromaticity (default: true) |
-C, --protectcharge | [true | false] true: protect charge (default: true) |
-e, --excludeantiaroma | [true | false] true: exclude antiaromatic compounds (default: true) |
-P, --protectdoublebondstereo | [true | false] true: protect double bond stereo (default: false) |
-T, --protectalltetrahedralcenters | [true | false] true: protect all tetrahedral stereo centers (default: false) |
-L, --protectlabeledtetrahedralcenters | [true | false] true: protect labeled tetrahedral stereo centers (default: false) |
-E, --protectestergroups | [true | false] true: protect ester groups (default: true) |
-s, --symfilter | [true | false] true: filter out symmetrical structures false: allow duplicates (default: true) |
-f, --format | ||
-t, --tag | <SDF/MRV tag to store the distribution value> (default: TAUTOMER_DISTRIBUTION) | |
-r, --ring | [true | false] Enable/disable ring tautomers. Default false. |
Example:
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:
Generates tetrahedral stereoisomers of the molecule.
Options:
-f, --format | ||
---|---|---|
-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:
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:
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 | ||||
-C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
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:
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 | ||||
-C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
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 | ||||
-C, --clean | <dim[:opts]> clean dimension with options (default: no clean) |
Example:
Generates the IUPAC name for the molecule.
Options:
-t, --type | [preferred | traditional] (default: preferred) preferred: Preferred IUPAC Name traditional: traditional name |
---|
Example:
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:
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:
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:
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:
Isoelectric point calculation.
Options:
-p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
---|
Example:
Major microspecies at given pH.
Options:
-H, --pH | <pH value> gets major microspecies at this pH (default: no pH, all microspecies) | |
---|---|---|
-f, --format | ||
-M, --majortautomer | [true | false] take major tautomeric form (default: false) |
-K, --keephydrogens | [true | false] keep explicit hydrogen on result molecule (default: false) |
Example:
Major microspecies at given pH.
Options:
-H, --pH | <pH value> gets major microspecies at this pH (default: no pH, all microspecies) | |
---|---|---|
-f, --format | ||
-M, --majortautomer | [true | false] take major tautomeric form (default: false) |
-K, --keephydrogens | [true | false] keep explicit hydrogen on result molecule (default: false) |
Example:
Microspecies list with distributions at given pH.
Options:
-H, --pH | <pH value> gets major microspecies at this pH (default: 7.4) | |
---|---|---|
-f, --format | ||
-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:
Microspecies list with distributions at given pH.
Options:
-H, --pH | <pH value> gets major microspecies at this pH (default: 7.4) | |
---|---|---|
-f, --format | ||
-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:
Isoelectric point calculation.
Options:
-p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) |
---|
Example:
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:
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:
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:
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:
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:
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:
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:
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:
Order in E(+) attack. Deprecated.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
Order in Nu(-) attack. Deprecated.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
Canonical resonant structure.
Options:
-f, --format |
---|
Example:
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:
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:
Hydrogen bond donor calculation.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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:
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:
Hydrogen bond donor calculation.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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:
Order in E(+) attack. Deprecated.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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 |
Example:
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:
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:
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:
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:
Order in E(+) attack (HMO).
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
HMO Huckel analysis parameters.
Options:
-p, --precision | <floating point precision as number of fractional digits: 0-8 or inf> (default: 2) | ||||||||
---|---|---|---|---|---|---|---|---|---|
-t, --type | [order | order:e | order:n | localizationenergy | localizationenergy:e | localizationenergy:n | pienergy | electrondensity | chargedensity] (default: order,localizationenergy, pienergy,electrondensity,chargedensity) |
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
Example:
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:
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:
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:
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:
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:
Order in Nu(-) attack (HMO).
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
Order in Nu(-) attack. Deprecated.
Options:
-H, --pH | <pH value> takes major microspecies at this pH (default: no pH, takes the input molecule) |
---|
Example:
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:
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:
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:
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:
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:
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 | ||
-s, --symfilter | [true | false] true: filter out symmetrical structures false: allow duplicates (default: true) |
Example:
Calculates aqueous solubility.
Options :
U, --unit | measurement unit [mg/ml | mol/l | logS] (default: logS) |
---|---|---|---|
-i, --intrinsic | intrinsic solubility (default: false) | ||
-c, --category | solubility category (default: false) | ||
-H, --pH | <pH value> solubility at this pH (default: not set) | ||
-l, --lower | <pH lower limit> (default: 0) | ||
-u, --upper | <pH upper limit> (default: 14) | ||
-s, --step | <pH step size> (default: 1) |
Example :
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: