cxcalc calculator functions

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

• cxcalc calculations

  • Elemental Analysis

    • atomcount
    • composition
    • dotdisconnectedformula
    • dotdisconnectedisotopeformula
    • elemanal
    • elementalanalysistable
    • exactmass
    • formula
    • icomposition
    • iformula
    • isotopecomposition
    • isotopeformula
    • mass
    • massspectrum
    • sortableformula

  • Charge

    • atomicpolarizability
    • atompol
    • averagemolecularpolarizability
    • averagepol
    • avgpol
    • axxpol
    • ayypol
    • azzpol
    • charge
    • dipole
    • formalcharge
    • ioncharge
    • molecularpolarizability
    • molpol
    • oen
    • orbitalelectronegativity
    • pol
    • polarizability
    • tholepolarizability
    • tpol
    • tpolarizability

  • Conformation

    • conformers
    • hasvalidconformer
    • leconformer
    • lowestenergyconformer
    • moldyn
    • moleculardynamics

  • Geometry

    • aliphaticatom
    • aliphaticatomcount
    • aliphaticbondcount
    • aliphaticringcount
    • aliphaticringcountofsize
    • angle
    • aromaticatom
    • aromaticatomcount
    • aromaticbondcount
    • aromaticringcount
    • aromaticringcountofsize
    • asa
    • asymmetricatom
    • asymmetricatomcount
    • asymmetricatoms
    • balabanindex
    • bondcount
    • bondtype
    • carboaliphaticringcount
    • carboaromaticringcount
    • carboringcount
    • chainatom
    • chainatomcount
    • chainbond
    • chainbondcount
    • chiralcenter
    • chiralcentercount
    • chiralcenters
    • connected
    • connectedgraph
    • cyclomaticnumber
    • dihedral
    • distance
    • distancedegree
    • dreidingenergy
    • eccentricity
    • fragmentcount
    • fsp3
    • fusedaliphaticringcount
    • fusedaromaticringcount
    • fusedringcount
    • hararyindex
    • heteroaliphaticringcount
    • heteroaromaticringcount
    • heteroringcount
    • hindrance
    • hyperwienerindex
    • largestatomringsize
    • largestringsize
    • largestringsystemsize
    • maximalprojectionarea
    • maximalprojectionradius
    • maximalprojectionsize
    • minimalprojectionarea
    • minimalprojectionradius
    • minimalprojectionsize
    • mmff94energy
    • molecularsurfacearea
    • msa
    • plattindex
    • polarsurfacearea
    • psa
    • randicindex
    • ringatom
    • ringatomcount
    • ringbond
    • ringbondcount
    • ringcount
    • ringcountofatom
    • ringcountofsize
    • ringsystemcount
    • ringsystemcountofsize
    • rotatablebond
    • rotatablebondcount
    • shortestpath
    • smallestatomringsize
    • smallestringsize
    • smallestringsystemsize
    • stereodoublebondcount
    • stericeffectindex
    • sterichindrance
    • szegedindex
    • topanal
    • topologyanalysistable
    • vdwsa
    • volume
    • wateraccessiblesurfacearea
    • wienerindex
    • wienerpolarity

  • Isomers

    • canonicaltautomer
    • dominanttautomerdistribution
    • doublebondstereoisomercount
    • doublebondstereoisomers
    • generictautomer
    • majortautomer
    • moststabletautomer
    • stereoisomercount
    • stereoisomers
    • stereoanalysis
    • tautomercount
    • tautomers
    • tetrahedralstereoisomercount
    • tetrahedralstereoisomers

  • Markush enumeration

    • enumerationcount
    • enumerations
    • markushenumerationcount
    • markushenumerations
    • randommarkushenumerations

  • Naming

    • name

  • Partitioning

    • logd
    • logp

  • Protonation

    • averagemicrospeciescharge
    • chargedistribution
    • isoelectricpoint
    • majormicrospecies
    • majorms
    • microspeciesdistribution
    • msdistr
    • pi
    • pka

  • Other calculator functions

    • acc
    • acceptor
    • acceptorcount
    • acceptormultiplicity
    • acceptorsitecount
    • acceptortable
    • accsitecount
    • aromaticelectrophilicityorder
    • aromaticnucleophilicityorder
    • canonicalresonant
    • chargedensity
    • don
    • donor
    • donorcount
    • donormultiplicity
    • donorsitecount
    • donortable
    • donsitecount
    • electrondensity
    • electrophilicityorder
    • electrophiliclocalizationenergy
    • frameworks
    • hbda
    • hbonddonoracceptor
    • hmochargedensity
    • hmoelectrondensity
    • hmoelectrophilicityorder
    • hmoelectrophiliclocalizationenergy
    • hmohuckel
    • hmohuckeleigenvalue
    • hmohuckeleigenvector
    • hmohuckelorbitals
    • hmohuckeltable
    • hmolocalizationenergy
    • hmonucleophilicityorder
    • hmonucleophiliclocalizationenergy
    • hmopienergy
    • huckel
    • huckeleigenvalue
    • huckeleigenvector
    • huckelorbitals
    • huckeltable
    • localizationenergy
    • msacc
    • msdon
    • nucleophilicityorder
    • nucleophiliclocalizationenergy
    • pichargedensity
    • pienergy
    • refractivity
    • resonantcount
    • resonants
    • solubility
    • totalchargedensity
      

cxcalc calculations

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

Elemental Analysis

The following features and properties can be calculated:

atomcount

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

Options :

-z, --atno
-m, --massno
-s, --single	[true

Example:

cxcalc atomcount -z 7 test.mol

composition

Elemental composition calculation (w/w%).

Options:

-p, --precision	(default: 2)
-s, --single	[true

Example:

cxcalc composition -s true test.mol

dotdisconnectedformula

Dot-disconnected molecular formula calculation.

Options:

No options

Example:

cxcalc dotdisconnectedformula test.mol

dotdisconnectedisotopeformula

Dot-disconnected molecular formula calculation, isotopes included.

Options:

-D, --symbolD	[true

Example:

cxcalc dotdisconnectedisotopeformula test.mol

elemanal

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

Options:

-t, --type	[formula
-s, --single	[true

Example:

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

elementalanalysistable

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

Options:

-t, --type	[formula
-s, --single	[true

Example:

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

exactmass

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

Options:

-p, --precision	(default: precision of the least precise atomic mass)
-s, --single	[true

Example:

cxcalc exactmass test.mol

formula

Molecular formula calculation.

Options:

-s, --single	[true

Example:

cxcalc formula -s true test.mol

icomposition

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

Options:

-p, --precision	(default: 2)
-D, --symbolD	[true
-s, --single	[true

Example:

cxcalc icomposition -s true test.mol

iformula

Molecular formula calculation, isotopes included.

Options:

-D, --symbolD	[true
-s, --single	[true

Example:

cxcalc iformula -s true test.mol

isotopecomposition

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

Options:

-p, --precision	(default: 2)
-D, --symbolD	[true
-s, --single	[true

Example:

cxcalc isotopecomposition -s true test.mol

isotopeformula

Molecular formula calculation, isotopes included.

Options:

-D, --symbolD	[true
-s, --single	[true

Example:

cxcalc isotopeformula -s true test.mol

mass

Molecule mass calculation.

Options:

-p, --precision	(default: precision of the least precise atomic mass)
-s, --single	[true

Example:

cxcalc mass test.mol

massspectrum

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

Options:

-p, --precision	(default: precision of the least precise atomic mass)
-s, --single	[true

Example:

cxcalc massspectrum -p 4 sildenafil

sortableformula

Calculates a fixed digit sortable molecular formula.

Options:

-d, --digits	(default: 5)
-s, --single	[true

Example:

cxcalc sortableformula -d 4 test.mol

Charge

The following features and properties can be calculated:

atomicpolarizability

Atomic polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc atomicpolarizability test.mol

atompol

Atomic polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc atompol test.mol

averagemolecularpolarizability

Average molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc averagemolecularpolarizability test.mol

averagepol

Average molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc averagepol test.mol

avgpol

Average molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc avgpol test.mol

axxpol

Calculation of principal component of polarizability tensor axx.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc axxpol test.mol

ayypol

Calculation of principal component of polarizability tensor ayy.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc ayypol test.mol

azzpol

Calculation of principal component of polarizability tensor azz.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc azzpol test.mol

charge

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

Options:

-p, --precision	(default: 2)
-t, --type	[sigma
-i, --implh	[true
-r, --resonance	[true
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

dipole

Calculates the absolute value of the dipole moment vector.

Options :

f, --format	(default: length)

Example:

cxcalc dipole -f sdf test.mol

formalcharge

Formal charge calculation.

Options:

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

Example:

cxcalc formalcharge test.mol

ioncharge

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

Options:

-p, --precision	(default: 2)
-H, --pH	(default: 7)
-n, --max-ions	max number of ionizable atoms to be considered (default: 9)
-m, --min-percent	(optional, if omitted then only the ionic form with max percentage is considered)
-t, --charge-type	[single

Example:

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

molecularpolarizability

Molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc molecularpolarizability test.mol

molpol

Molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc molpol test.mol

oen

Orbital electronegativity calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[sigma
-r, --resonance	[true
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc oen -t sigma test.mol

orbitalelectronegativity

Orbital electronegativity calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[sigma
-r, --resonance	[true
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc orbitalelectronegativity -p 3 test.mol

pol

Atomic and molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[molecular
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pol -p 3 test.mol

polarizability

Atomic and molecular polarizability calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[molecular
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc polarizability -p 3 test.mol

tholepolarizability

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

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example :

cxcalc tholepolarizability test.mol

tpol

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

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc tpol test.mol

tpolarizability

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

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc tpolarizability test.mol

Conformation

The following features and properties can be calculated:

conformers

Calculates the conformers of the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding
-m, --maxconformers	(default: 100)
-d, --diversity	(default: 0.1)
-s, --saveconfdesc	[true
-e, --hyperfine	[true
-y, --prehydrogenize	[true
-l, --timelimit	(default: 900)
-O, --optimization	[0

Example:

cxcalc conformers -m 250 -s true test.sdf

hasvalidconformer

Calculates if the molecule has a conformer.

Options:

No options

Example:

cxcalc hasvalidconformer test.sdf

leconformer

Calculates the lowest energy conformer of the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding
-e, --hyperfine	[true
-y, --prehydrogenize	[true
-l, --timelimit	(default: 900)
-O, --optimization	[0
-m, --multifrag	[true

Example:

cxcalc leconformer -f mrv test.sdf

lowestenergyconformer

Calculates the lowest energy conformer of the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding
-e, --hyperfine	[true
-y, --prehydrogenize	[true
-l, --timelimit	(default: 900)
-O, --optimization	[0
-m, --multifrag	[true

Example:

cxcalc lowestenergyconformer -f mrv test.sdf

moldyn

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding
-i, --integrator	[positionverlet
-n, --stepno	(default: 1000)
-m, --steptime	(default: 0.1)
-T, --temperature	(default: 300 K)
-s, --samplinginterval	(default: 10)

Example:

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

moleculardynamics

Runs a molecular dynamics simulation for the molecule.

Options:

-f, --format	should be a 3D format (default: sdf)
-x, --forcefield	[dreiding
-i, --integrator	[positionverlet
-n, --stepno	(default: 1000)
-m, --steptime	(default: 0.1)
-T, --temperature	(default: 300 K)
-s, --samplinginterval	(default: 10)

Example:

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

Geometry

aliphaticatom

Checks if a specified atom is aliphatic.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aliphaticatom test.mol

aliphaticatomcount

Counts the number of aliphatic atoms in the molecule.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aliphaticatomcount test.mol

aliphaticbondcount

Aliphatic bond count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aliphaticbondcount test.mol

aliphaticringcount

Aliphatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aliphaticringcount test.mol

aliphaticringcountofsize

Aliphatic ring count of size.

Options:

-a --arom	[general
-s, --single	[true
-z, --size	size of rings to count

Example:

cxcalc aliphaticringcountofsize -z 5 test.mol

angle

Angle of three atoms.

Options:

-a, --atoms	[--] (1-based) atom indexes of the atom pair
-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

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

aromaticatom

Checks if a specified atom is aromatic.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aromaticatom test.mol

aromaticatomcount

Aromatic atom count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aromaticatomcount test.mol

aromaticbondcount

Aromatic bond count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aromaticbondcount test.mol

aromaticringcount

Aromatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc aromaticringcount test.mol

aromaticringcountofsize

Aromatic ring count of size.

Options:

-a --arom	[general
-s, --single	[true
-z, --size	size of rings to count

Example:

cxcalc aromaticringcountofsize -z 6 test.mol

asa

Water Accessible Surface Area calculation.

Options:

-p, --precision	(default: 2)
-r, --solventradius	(default: 1.4)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true

Example:

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

asymmetricatom

Checks if a specified atom is an asymmetric atom.

Options:

-s, --single	[true

Example:

cxcalc asymmetricatom test.mol

asymmetricatomcount

The number of asymmetric atoms.

Options:

-s, --single	[true

Example:

cxcalc asymmetricatomcount test.mol

asymmetricatoms

The asymmetric atoms.

Options:

-s, --single	[true

Example:

cxcalc asymmetricatoms test.mol

balabanindex

The Balaban index.

Options:

-p, --precision	(default: 2)
-s, --single	[true

Example:

cxcalc balabanindex test.mol

bondcount

Bond count.

Options:

-s, --single	[true

Example:

cxcalc bondcount test.mol

bondtype

The bond type between two atoms.

Options:

-a --arom	[general
-a, --atoms	[-] (1-based) atom indexes of the bond atoms

Example:

cxcalc bondtype -a 2-3 test.mol

carboaliphaticringcount

Carboaliphatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc carboaliphaticringcount test.mol

carboaromaticringcount

Carboaromatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc carboaromaticringcount test.mol

carboringcount

Carbo ring count.

Options:

-s, --single	[true

Example:

cxcalc carboringcount test.mol

chainatom

Checks if a specified atom is a chain atom.

Options:

-s, --single	[true

Example:

cxcalc chainatom test.mol

chainatomcount

Chain atom count.

Options:

-s, --single	[true

Example:

cxcalc chainatomcount test.mol

chainbond

Checks if the bond is a chain bond.

Options:

-a, --atoms	[-] (1-based) atom indexes of the bond atoms

Example:

cxcalc chainbond -a 2-3 test.mol

chainbondcount

Chain bond count.

Options:

-s, --single	[true

Example:

cxcalc chainbondcount test.mol

chiralcenter

Checks if a specified atom is a tetrahedral stereogenic center.

Options:

-s, --single	[true

Example:

cxcalc chiralcenter test.mol

chiralcentercount

The number of tetrahedral stereogenic center atoms.

Options:

-s, --single	[true

Example:

cxcalc chiralcentercount test.mol

chiralcenters

The the chiral center atoms.

Options:

-s, --single	[true

Example:

cxcalc chiralcenters test.mol

connected

Checks if two atoms are in the same connected component.

Options:

-a, --atoms	[-] (1-based) atom indexes of the atom pair

Example:

cxcalc connected -a 2-3 test.mol

connectedgraph

Checks if the molecule graph is connected.

Options: No options

Example:

cxcalc connectedgraph test.mol

cyclomaticnumber

The cyclomatic number.

Options:

-s, --single	[true

Example:

cxcalc cyclomaticnumber test.mol

dihedral

Calculates the dihedral angle between four atoms.

Options:

-a, --atoms	[---] (1-based) atom indexes of the atom pair
-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

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

distance

Distance between two atoms.

Options:

-a, --atoms	[-] (1-based) atom indexes of the atom pair
-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

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

distancedegree

Distance degree of atom.

Options:

-s, --single	[true

Example:

cxcalc distancedegree test.mol

dreidingenergy

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

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

cxcalc dreidingenergy -p 1 -l always test.sdf

eccentricity

Eccentricity of atom.

Options:

-s, --single	[true

Example:

cxcalc eccentricity test.mol

fragmentcount

Fragment count.

Options:

No options

Example:

cxcalc fragmentcount test.mol

fsp3

Fsp3 value of the molecule.

Options:

No options

Example:

cxcalc fsp3 test.mol

fusedaliphaticringcount

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

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc fusedaliphaticringcount test.mol

fusedaromaticringcount

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

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc fusedaromaticringcount test.mol

fusedringcount

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

Options:

-s, --single	[true

Example:

cxcalc fusedringcount test.mol

hararyindex

Harary index.

Options:

-p, --precision	(default: 2)
-s, --single	[true

Example:

cxcalc hararyindex test.mol

heteroaliphaticringcount

Heteroaliphatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc heteroaliphaticringcount test.mol

heteroaromaticringcount

Heteroaromatic ring count.

Options:

-a --arom	[general
-s, --single	[true

Example:

cxcalc heteroaromaticringcount test.mol

heteroringcount

Hetero ring count.

Options:

-s, --single	[true

Example:

cxcalc heteroringcount test.mol

hindrance

Steric hindrance.

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

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

hyperwienerindex

Hyper Wiener index.

Options:

-s, --single	[true

Example:

cxcalc hyperwienerindex test.mol

largestatomringsize

Size of largest ring containing a specified atom.

Options:

-s, --single	[true

Example:

cxcalc largestatomringsize -s true test.mol

largestringsize

Largest ring size.

Options:

-s, --single	[true

Example:

cxcalc largestringsize test.mol

largestringsystemsize

Largest ring system size.

Options:

-s, --single	[true

Example:

cxcalc largestringsystemsize test.mol

maximalprojectionarea

Calculates the maximal projection area.

Options:

-p, --precision	(default: 2)
-s, --scalefactor
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

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

maximalprojectionradius

Calculates the maximal projection radius.

Options:

-p, --precision	(default: 2)
-s, --scalefactor
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

cxcalc maximalprojectionradius -s 1.2 -o 3 test.sdf

maximalprojectionsize

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

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

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

minimalprojectionarea

Calculates the minimal projection area.

Options:

-p, --precision	(default: 2)
-s, --scalefactor
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

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

minimalprojectionradius

Calculates the minimal projection radius.

Options:

-p, --precision	(default: 2)
-s, --scalefactor
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

cxcalc minimalprojectionradius -s 1.3 -o true test.sdf

minimalprojectionsize

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

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-O, --optimizeprojection	[true
-l, --calcforleconformer	[if2D

Example:

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

mmff94energy

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

Options:

-p, --precision	(default: 2)
-l, --calcforleconformer	[if2D
--mmff94optimization	[true

Example:

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

molecularsurfacearea

Molecular Surface Area calculation (3D).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-t, --type	[vanderwaals
-i, --increments	[true

Example:

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

msa

Molecular Surface Area calculation (3D).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-t, --type	[vanderwaals
-i, --increments	[true

Example:

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

plattindex

The Platt index.

Options:

-s, --single	[true

Example:

cxcalc plattindex test.mol

polarsurfacearea

Topological Polar Surface Area calculation (2D).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-S, --excludesulfur	[true
-P, --excludephosphorus	[true

Example:

cxcalc -S -t myPSA polarsurfacearea test.mol

psa

Topological Polar Surface Area calculation (2D).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-S, --excludesulfur	[true
-P, --excludephosphorus	[true

Example:

cxcalc -S false -p 3 psa test.mol

randicindex

The Randic index.

Options:

-p, --precision	(default: 2)
-s, --single	[true

Example:

cxcalc randicindex test.mol

ringatom

Checks if a specified atom is a ring atom.

Options:

-s, --single	[true

Example:

cxcalc ringatom test.mol

ringatomcount

Ring atom count.

Options:

-s, --single	[true

Example:

cxcalc ringatomcount test.mol

ringbond

Checks if the bond is a ring bond.

Options:

-a, --atoms	[-] (1-based) atom indexes of the bond atoms

Example:

cxcalc ringbond -a 2-3 test.mol

ringbondcount

Ring bond count.

Options:

-s, --single	[true

Example:

cxcalc ringbondcount test.mol

ringcount

Ring count.

Options:

-s, --single	[true

Example:

cxcalc ringcount test.mol

ringcountofatom

Ring counts of atoms.

Options:

No options

Example:

cxcalc ringcountofatom test.mol

ringcountofsize

Ring count of size.

Options:

-a --arom	[general
-s, --single	[true
-z, --size	size of rings to count

Example:

cxcalc ringcountofsize -z 5 test.mol

ringsystemcount

The number of ring systems.

Options:

-s, --single	[true

Example:

cxcalc ringsystemcount test.mol

ringsystemcountofsize

Ring system count of size.

Options:

-s, --single	[true
-z, --size	size of ring systems to count

Example:

cxcalc ringsystemcountofsize -z 3 test.mol

rotatablebond

Checks if the bond is a rotatable bond.

Options:

-a, --atoms	[-] (1-based) atom indexes of the bond atoms

Example:

cxcalc rotatablebond -a 2-3 test.mol

rotatablebondcount

Rotatable bond count.

Options:

-s, --single	[true

Example:

cxcalc rotatablebondcount test.mol

shortestpath

Length of shortest path between two atoms.

Options:

-a, --atoms	[-] (1-based) atom indexes of the atom pair

Example:

cxcalc shortestpath -a 2-3 test.mol

smallestatomringsize

Size of smallest ring containing a specified atom.

Options:

-s, --single	[true

Example:

cxcalc smallestatomringsize test.mol

smallestringsize

Smallest ring size.

Options:

-s, --single	[true

Example:

cxcalc smallestringsize test.mol

smallestringsystemsize

Smallest ring system size.

Options:

-s, --single	[true

Example:

cxcalc smallestringsystemsize -s true test.mol

stereodoublebondcount

The number of stereo double bonds.

Options:

-s, --single	[true

Example:

cxcalc stereodoublebondcount -s true test.mol

stericeffectindex

Steric effect index.

Options:

-p, --precision	(default: 2)
-s, --single	[true

Example:

cxcalc stericeffectindex -p 3 -s true test.mol

sterichindrance

Steric hindrance.

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

cxcalc sterichindrance test.mol

szegedindex

Szeged index.

Options:

-s, --single	[true

Example:

cxcalc szegedindex test.mol

topanal

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

Options:

-a --arom	[general
-t, --type	[atomcount
-s, --single	[true

Example:

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

topologyanalysistable

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

Options:

-a --arom	[general
-t, --type	[atomcount
-s, --single	[true

Example:

cxcalc topologyanalysistable -a basic -s true test.mol

vdwsa

Van der Waals Surface Area calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true

Example:

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

volume

Calculates the van der Waals volume of the molecule.

Options:

-p, --precision	(default: 2)
-o, --optimization	[0
-l, --calcforleconformer	[if2D

Example:

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

wateraccessiblesurfacearea

Water Accessible Surface Area calculation.

Options:

-p, --precision	(default: 2)
-r, --solventradius	(default: 1.4)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-i, --increments	[true

Example:

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

wienerindex

Wiener index.

Options:

-s, --single	[true

Example:

cxcalc wienerindex test.mol

wienerpolarity

Wiener polarity.

Options:

-s, --single	[true

Example:

cxcalc wienerpolarity test.mol

Isomers

canonicaltautomer

Canonical tautomer.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-n, --normal	[true
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true

Example:

cxcalc canonicaltautomer -f sdf -a false -C false test.mol

dominanttautomerdistribution

Dominant tautomer distribution.

Options:

-p, --precision	(default: 0)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true
-f, --format	(default: sdf:-a)
-t, --tag	(default: TAUTOMER_DISTRIBUTION)

Example:

cxcalc dominanttautomerdistribution test.mol

doublebondstereoisomercount

The number of double-bond stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	(default: 1000)
-D, --protectdoublebondstereo	[true

Example:

cxcalc doublebondstereoisomercount test.sdf

doublebondstereoisomers

Generates double-bond stereoisomers of the molecule.

Options:

-f, --format	(default: sdf)
-m, --maxstereoisomers	(default: 1000)
-D, --protectdoublebondstereo	[true
-v, --verify3d	[true
-3, --in3d	[true

Example:

cxcalc doublebondstereoisomers -f mrv test.sdf

generictautomer

Generic tautomer.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true

Example:

cxcalc generictautomer -f sdf test.mol

majortautomer

Major tautomer.

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	considers pH effect at this pH. (default: do not consider pH effect)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true

Example:

cxcalc majortautomer -H 7.4 -f sdf test.mol

moststabletautomer

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

Options:

-f, --format	(default: smiles table, multiple molecule output if specified)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true

Example:

cxcalc moststabletautomer -f sdf test.mol

stereoisomercount

The number of stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	(default: 1000)
-D, --protectdoublebondstereo	[true
-T, --protecttetrahedralstereo	[true

Example:

cxcalc stereoisomercount -m 100 test.sdf

stereoisomers

Generates stereoisomers of the molecule.

Options:

-f, --format	(default: sdf)
-m, --maxstereoisomers	(default: 1000)
-D, --protectdoublebondstereo	[true
-T, --protecttetrahedralstereo	[true
-v, --verify3d	[true
-3, --in3d	[true

Example:

cxcalc stereoisomers -v true test.sdf

stereoanalysis

Calculate stereo descriptors.

Options:

-T --type	stereo descriptor type [tetrahedral

Example:

cxcalc stereoanalysis test.mol

tautomercount

The number of tautomers.

Options:

-d, --dominants	[true
-n, --normal	[true
-m, --max	max. number of structures to be generated (default: 200)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds
-H, --pH	considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-s, --symfilter	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true

Example:

cxcalc tautomerCount -s false test.mol

tautomers

Tautomers.

Options:

-p, --precision	(default: 0)
-c, --canonical	[true
-n, --normal	[true
-g, --generic	[true
-M, --major	[true
-d, --dominants	[true
-D, --distribution	[true
-m, --max	maximum number of structures to be generated (default: 200)
-l, --pathlength	maximum allowed length of the tautomerization path in chemical bonds (default: 4)
-H, --pH	considers pH effect at this pH. Only has effect when dominant tautomers are generated. (default: do not consider pH effect)
-a, --protectaromaticity	[true
-C, --protectcharge	[true
-e, --excludeantiaroma	[true
-P, --protectdoublebondstereo	[true
-T, --protectalltetrahedralcenters	[true
-L, --protectlabeledtetrahedralcenters	[true
-E, --protectestergroups	[true
-s, --symfilter	[true
-f, --format	(default: fused smiles, multiple molecule output if specified)
-t, --tag	(default: TAUTOMER_DISTRIBUTION)
-r, --ring	[true

Example:

cxcalc tautomers -f sdf test.mol
cxcalc tautomers --dominants false --normal true test.mol --format smiles

tetrahedralstereoisomercount

The number of tetrahedral stereoisomers of the molecule.

Options:

-m, --maxstereoisomers	(default: 1000)
-T, --protecttetrahedralstereo	[true

Example:

cxcalc tetrahedralstereoisomercount test.sdf

tetrahedralstereoisomers

Generates tetrahedral stereoisomers of the molecule.

Options:

-f, --format	(default: sdf)
-m, --maxstereoisomers	(default: 1000)
-T, --protecttetrahedralstereo	[true
-v, --verify3d	[true
-3, --in3d	[true

Example:

cxcalc tetrahedralstereoisomers -3 true test.sdf

Markush enumeration

enumerationcount

Number of Markush enumerated structures.

Options:

-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-m, --magnitude	[true
-g, --enumhomology	[true

Example:

cxcalc enumerationcount -m true test.mol

enumerations

Generates Markush enumerated structures.

Options:

-m, --max	max. number of structures to be generated (default: all)
-v, --valencecheck	[true
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true
-c, --coloring	[none
-r, --random	[true
-g, --enumhomology	[true
-o, --code	[true
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	clean dimension with options (default: no clean)

Example:

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

markushenumerationcount

Number of Markush enumerated structures.

Options:

-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-m, --magnitude	[true
-g, --enumhomology	[true

Example:

cxcalc markushenumerationcount -m true test.mol

markushenumerations

Markush enumerated structures.

Options:

-m, --max	max. number of structures to be generated (default: all)
-v, --valencecheck	[true
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true
-c, --coloring	[none
-r, --random	[true
-g, --enumhomology	[true
-o, --code	[true
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	clean dimension with options (default: no clean)

Example:

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

randommarkushenumerations

Randomly constructed Markush enumerated structures.

Options:

-m, --max	max. number of structures to be generated (default: all)
-v, --valencecheck	[true
-a, --atoms	[atom1,atom2,atom3,...] (1-based) atom indexes of the atoms to be enumerated (default: all)
-s, --alignscaffold	[true
-c, --coloring	[none
-g, --enumhomology	[true
-o, --code	[true
-i, --structureid	[id or tag name] structure ID or SDF/MRV tag name storing the ID (default: no structure ID)
-f, --format	(default: concatenated smiles)
-C, --clean	clean dimension with options (default: no clean)

Example:

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

Naming

name

Generates the IUPAC name for the molecule.

Options:

-t, --type	[preferred

Example:

cxcalc name test.sdf

Partitioning

logd

logD calculation.

Options:

-p, --precision	(default: 2)
-m, --method	[vg
--logptrainingid
-w, --weights	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	(default: 0.1, range: [0.0, 0.25])
-k, --kation	(default: 0.1, range: [0.0, 0.25])
-H, --pH	takes logD at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)
-1, --ref1	(default: none)
-2, --ref2	(default: none)
-3, --ref3	(default: none)
-4, --ref4	(default: none)
--considertautomerization	[true
--pkacorrectionlibrary

Example:

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

logp

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

Options:

-p, --precision	(default: 2)
-m, --method	[vg
--trainingid
-w, --weights	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	(default: 0.1, range: [0.0, 0.25])
-k, --kation	(default: 0.1, range: [0.0, 0.25])
-t, --type	[increments
-i, --increments	[true
--considertautomerization	[true
-H, --pH	gets logp of the major microspecies at this pH (default: no pH, use given protonation state)

Example:

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

Protonation

averagemicrospeciescharge

Average microspecies charge calculation.

Options:

-p, --precision	(default: 2)
-H, --pH	calculates average charge at this pH (default: 7.4)

Example:

cxcalc averagemicrospeciescharge test.mol

chargedistribution

Charge distribution calculation.

*Options: *

-p, --precision	(default: 2)
-H, --pH	calculates average charge at this pH (default: no single pH, takes pH values in interval [lower, upper] by given step size)
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)

Example:

cxcalc chargedistribution test.mol

isoelectricpoint

Isoelectric point calculation.

Options:

-p, --precision	(default: 2)

Example:

cxcalc isoelectricpoint test.mol

majormicrospecies

Major microspecies at given pH.

*Options: *

-H, --pH	gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	(default: smiles)
-M, --majortautomer	[true
-K, --keephydrogens	[true

Example:

cxcalc majormicrospecies -H 3.5 -f mol test.mol

majorms

Major microspecies at given pH.

Options:

-H, --pH	gets major microspecies at this pH (default: no pH, all microspecies)
-f, --format	(default: smiles)
-M, --majortautomer	[true
-K, --keephydrogens	[true

Example:

cxcalc majorms -H 3.5 -f mol test.mol

microspeciesdistribution

Microspecies list with distributions at given pH.

Options:

-H, --pH	gets major microspecies at this pH (default: 7.4)
-f, --format	(default: sdf:-a)
-t, --tag	(default: MSDISTR[pH=...])
-M, --majortautomer	[true
-K, --keephydrogens	[true

Example:

cxcalc microspeciesdistribution -H 3.5 test.mol

msdistr

Microspecies list with distributions at given pH.

Options:

-H, --pH	gets major microspecies at this pH (default: 7.4)
-f, --format	(default: sdf:-a)
-t, --tag	(default: MSDISTR[pH=...])
-M, --majortautomer	[true
-K, --keephydrogens	[true

Example:

cxcalc msdistr -H 3.5 test.mol

pi

Isoelectric point calculation.

Options:

-p, --precision	(default: 2)

Example:

cxcalc pI test.mol

pka

pKa calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[pKa
-m, --mode	[macro
-P, --prefix	[static
-d, --model	[small
-i, --min	(default: -10)
-x, --max	(default: 20)
-T, --temperature	(default: 298 K)
-a, --na	(default: 2)
-b, --nb	(default: 2)
--considertautomerization	[true
-L, --correctionlibrary
-P, --correctionlibrarypath	use this parameter when the correction library not stored on the default location

Example:

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

Other calculator functions

acc

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acc test.sdf

acceptor

Hydrogen bond acceptor calculation.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acceptor test.sdf

acceptorcount

Hydrogen bond acceptor atom count in molecule.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acceptorcount -H 7.4 test.sdf

acceptormultiplicity

Hydrogen bond acceptor multiplicity calculation on atoms.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acceptormultiplicity test.sdf

acceptorsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acceptorsitecount test.sdf

acceptortable

Hydrogen bond acceptor calculation.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc acceptortable test.sdf

accsitecount

Hydrogen bond acceptor multiplicity in molecule.

Options:

-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc accsitecount test.sdf

aromaticelectrophilicityorder

Order in E(+) attack. Deprecated.

Options:

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

Example:

cxcalc aromaticelectrophilicityorder -H 7.4 test.mol

aromaticnucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

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

Example:

cxcalc aromaticnucleophilicityorder -H 7.4 test.mol

canonicalresonant

Canonical resonant structure.

Options:

-f, --format	(default: smiles)

Example:

cxcalc canonicalResonant -f sdf test.mol

chargedensity

Charge density.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc chargedensity -p 4 -H 6.5 test.mol

don

Hydrogen bond donor multiplicity calculation on atoms.

Options:

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

Example:

cxcalc don test.sdf

donor

Hydrogen bond donor calculation.

Options:

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

Example:

cxcalc donor test.sdf

donorcount

Hydrogen bond donor atom count in molecule.

Options:

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

Example:

cxcalc donorcount -H 7.4 test.sdf

donormultiplicity

Hydrogen bond donor multiplicity calculation on atoms.

Options:

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

Example:

cxcalc don test.sdf

donorsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

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

Example:

cxcalc donorsitecount test.sdf

donortable

Hydrogen bond donor calculation.

Options:

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

Example:

cxcalc donortable test.sdf

donsitecount

Hydrogen bond donor multiplicity in molecule.

Options:

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

Example:

cxcalc donsitecount test.sdf

electrondensity

Electron density.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc electrondensity -p 4 -H 6.5 test.mol

electrophilicityorder

Order in E(+) attack. Deprecated.

Options:

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

Example:

cxcalc electrophilicityorder -H 7.4 test.mol

electrophiliclocalizationenergy

Electrophilic localization energy L(+).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc electrophiliclocalizationenergy test.mol

frameworks

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

Options:

-t, --type	[bmf
-i, --lfin	[true
-p, --prunein	[true
-h, --hydrogenize	[true
-d, --dehydrogenize	[true
-r, --pruneout	[true
-o, --lfout	[true
-q, --oeqcheck	[true
-s, --keepsingleatom	[true
-f, --format	(default: sdf)

Example:

cxcalc frameworks -t bmf -s true test.mol

hbda

Hydrogen bond acceptor-donor calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[acc
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

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

hbonddonoracceptor

Hydrogen bond acceptor-donor calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[acc
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule))
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

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

hmochargedensity

HMO Charge density.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmochargedensity -p 4 -H 6.5 test.mol

hmoelectrondensity

HMO Electron density.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmoelectrondensity -p 4 -H 6.5 test.mol

hmoelectrophilicityorder

Order in E(+) attack (HMO).

Options:

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

Example:

cxcalc hmoelectrophilicityorder -H 7.4 test.mol

hmoelectrophiliclocalizationenergy

HMO Electrophilic localization energy L(+).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmoelectrophiliclocalizationenergy test.mol

hmohuckel

HMO Huckel analysis parameters.

Options:

-p, --precision	(default: 2)
-t, --type	[order
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

hmohuckeleigenvalue

HMO Huckel eigenvalue.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckeleigenvalue test.mol

hmohuckeleigenvector

HMO Huckel eigenvector.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckeleigenvector test.mol

hmohuckelorbitals

HMO Huckel orbital coefficients.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmohuckelorbitals test.mol

hmohuckeltable

HMO Huckel analysis parameters.

Options:

-p, --precision	(default: 2)
-t, --type	[hmoorder
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

hmolocalizationenergy

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

Options:

-p, --precision	(default: 2)
-s, --subtype	[e
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmolocalizationenergy test.mol

hmonucleophilicityorder

Order in Nu(-) attack (HMO).

Options:

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

Example:

cxcalc hmonucleophilicityorder -H 7.4 test.mol

hmonucleophiliclocalizationenergy

HMO Nucleophilic localization energy L(-).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmonucleophiliclocalizationenergy test.mol

hmopienergy

HMO Pi energy.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc hmopienergy test.mol

huckel

Huckel analysis parameters.

Options:

-p, --precision	(default: 2)
-t, --type	[order
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

huckeleigenvalue

Huckel eigenvalue. Deprecated.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckeleigenvalue test.mol

huckeleigenvector

Huckel eigenvector. Deprecated.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckeleigenvector test.mol

huckelorbitals

Huckel orbital coefficients. Deprecated.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc huckelorbitals test.mol

huckeltable

Huckel analysis parameters.

Options:

-p, --precision	(default: 2)
-t, --type	[order
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

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

localizationenergy

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

Options:

-p, --precision	(default: 2)
-s, --subtype	[e
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc localizationenergy test.mol

msacc

Hydrogen bond acceptor average multiplicity over microspecies by pH.

Options:

-p, --precision	(default: 2)
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)
-e, --excludesulfur	[true
-x, --excludehalogens	[true

Example:

cxcalc msacc -l 2.0 -u 12.0 test.sdf

msdon

Hydrogen bond donor average multiplicity over microspecies by pH.

Options:

-p, --precision	(default: 2)
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)

Example:

cxcalc msdon -l 2.0 -u 12.0 test.sdf

nucleophilicityorder

Order in Nu(-) attack. Deprecated.

Options:

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

Example:

cxcalc nucleophilicityorder -H 7.4 test.mol

nucleophiliclocalizationenergy

Nucleophilic localization energy L(-).

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc nucleophiliclocalizationenergy test.mol

pichargedensity

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

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pichargedensity -p 4 -H 6.5 test.mol

pienergy

Pi energy. Deprecated.

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc pienergy test.mol

refractivity

Refractivity calculation.

Options:

-p, --precision	(default: 2)
-t, --type	[increments
-i, --inch	[true

Example:

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

resonantcount

The number of resonant structures.

Options:

-r, --mcontrib	[true
-m, --max	max. number of structures to be generated (default: 200)
-s, --symfilter	[true

Example:

cxcalc resonantCount test.mol

resonants

Resonant structures.

Options:

-c, --canonical	[true
-r, --mcontrib	[true
-m, --max	max. number of structures to be generated (default: 200)
-f, --format	(default: fused smiles, multiple molecule output if specified)
-s, --symfilter	[true

Example:

cxcalc resonants -f sdf test.mol

solubility

Calculates aqueous solubility.

Options :

U, --unit	measurement unit [mg/ml
-i, --intrinsic	intrinsic solubility (default: false)
-c, --category	solubility category (default: false)
-H, --pH	solubility at this pH (default: not set)
-l, --lower	(default: 0)
-u, --upper	(default: 14)
-s, --step	(default: 1)

Example :

 cxcalc logs -i true -H 7.4 test.mol

totalchargedensity

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

Options:

-p, --precision	(default: 2)
-H, --pH	takes major microspecies at this pH (default: no pH, takes the input molecule)

Example:

cxcalc totalchargedensity -p 4 -H 6.5 test.mol