type_command.csv

short_name,calc_definition,human readable description,input,alternative_input,actor_org,actor_systemtool_name,actor_systemtool_version,notes
heteroaromaticringcount_std,heteroaromaticringcount,heteroaromatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
aliphaticatomcount_std,aliphaticatomcount,aliphatic atom count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asa+_std,molecularsurfacearea -t asa+ -H 3.0,Molecular Surface Area calculation (3D). asa+ (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asap_std,molecularsurfacearea -t asa_p -H 3.0,Molecular Surface Area calculation (3D). asa_p (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asah_std,molecularsurfacearea -t asa_h -H 3.0,Molecular Surface Area calculation (3D). asa_h (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asa-_std,molecularsurfacearea -t asa- -H 3.0,Molecular Surface Area calculation (3D). asa-(std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asa_std,molecularsurfacearea -t ASA -H 3.0,Molecular Surface Area calculation (3D). asa(std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
asavdwp_std,molecularsurfacearea -t vanderwaals -H 3.0,Molecular Surface Area calculation (3D). Vanderwaals(std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
hdonorcount_std,donorcount -H 3.0,hydrogen bond donor atom count in molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
hacceptorcount_std,acceptorcount -H 3.0,hydrogen bond acceptor atom count in molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
protpsa_std,psa -H 3.0,topological polar surface area calculation (2d) (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
minimalprojectionsize_std,minimalprojectionsize,calculates the size of the molecule perpendicular to the minimal projection area surface (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
maximalprojectionsize_std,maximalprojectionsize,calculates the size of the molecule perpendicular to the maximal projection area surface (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
donsitecount_std,donorsitecount -H 3.0,hydrogen bond donor multiplicity in molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
accsitecount_std,acceptorsitecount -H 3.0,hydrogen bond acceptor multiplicity in molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
vanderwaalsvolume_std,volume ,calculates the van der waals volume of the molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
maximalprojectionradius_std,maximalprojectionradius ,calculates the maximal projection radius (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
minimalprojectionradius_std,minimalprojectionradius ,calculates the minimal projection radius (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
maximalprojectionarea_std,maximalprojectionarea ,calculates the maximal projection area (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
minimalprojectionarea_std,minimalprojectionarea ,calculates the minimal projection area (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
wienerpolarity_std,wienerpolarity ,wiener polarity (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
wienerindex_std,wienerindex,wiener index (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
hyperwienerindex_std,hyperwienerindex,hyper wiener index (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
cyclomaticnumber_std,cyclomaticnumber,the cyclomatic number (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
balabanindex_std,balabanindex,the balaban index (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
rotatablebondcount_std,rotatablebondcount,rotatable bond count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
heteroaliphaticringcount_std,heteroaliphaticringcount,heteroaliphatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
largestringsize_std,largestringsize,largest ring size (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
smallestringsize_std,smallestringsize,smallest ring size (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
ringatomcount_std,ringatomcount,ring atom count(std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
chiralcentercount_std,chiralcentercount,the number of tetrahedral stereogenic center atoms (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
chainatomcount_std,chainatomcount,chain atom count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
carboringcount_std,carboringcount,carbo ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
carboaromaticringcount_std,carboaromaticringcount,carboaromatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
carboaliphaticringcount_std,carboaliphaticringcount,carboaliphatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
bondcount_std,bondcount,bond count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
aromaticatomcount_std,aromaticatomcount,aromatic atom count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
aromaticringcount_std,aromaticringcount ,aromatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
aliphaticringcount_std,aliphaticringcount ,aliphatic ring count (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
refractivity_std,refractivity ,refractivity calculation (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
molpol_std,molpol ,molecular polarizability calculation (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
avgpol_std,avgpol -H 3.0,average molecular polarizability calculation (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
atomcount_n_std,atomcount -z 7 ,number of nitrogen atoms in the molecule (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
atomcount_c_std,atomcount -z 6,number of carbon atoms in the molecule  (std: considering the largest fragment component - if applicable),organic,,ChemAxon,cxcalc_std,19.27.0,
organoammoniummolecularweight_std,mass,molecular weight of the standardized smiles string after retaining the largest frament - this is typically the organic species only in an organoammonium salt,organic,,ChemAxon,cxcalc_std,19.27.0,
saltmolecularweight,mass,molecular weight of the entire organoammonium salt,organic,,ChemAxon,cxcalc,19.27.0,
minimalprojectionsize,minimalprojectionsize,calculates the size of the molecule perpendicular to the minimal projection area surface,solvent,,ChemAxon,cxcalc,19.27.0,
maximalprojectionsize,maximalprojectionsize,calculates the size of the molecule perpendicular to the maximal projection area surface,solvent,,ChemAxon,cxcalc,19.27.0,
hdonorcount,donorcount -H 3.0,hydrogen bond donor atom count in molecule,solvent,,ChemAxon,cxcalc,19.27.0,
solventmolecularweight,mass,molecular weight of the solvent,solvent,,ChemAxon,cxcalc,19.27.0,
hacceptorcount,acceptorcount -H 3.0,hydrogen bond acceptor atom count in molecule,solvent,,ChemAxon,cxcalc,19.27.0,
asavdwp,molecularsurfacearea -t vanderwaals -H 3.0,Molecular Surface Area calculation (3D). Vanderwaals,solvent,,ChemAxon,cxcalc,19.27.0,
vanderwaalsvolume,volume ,calculates the van der waals volume of the molecule,solvent,,ChemAxon,cxcalc,19.27.0,
refractivity,refractivity ,refractivity calculation,solvent,,ChemAxon,cxcalc,19.27.0,
avgpol,avgpol -H 3.0,average molecular polarizability calculation,solvent,,ChemAxon,cxcalc,19.27.0,
inorganicmolecularweight,mass,molecular weight of the inorganic,inorganic,,ChemAxon,cxcalc,19.27.0,
fr_halogen,fr_halogen,number of halogens,inorganic,,RDKit open source software,RDKit,19.03.4,
fr_imine,fr_Imine,number of imines,organic,,RDKit open source software,RDKit,19.03.4,
fr_ar_nh,fr_Ar_NH,number of aromatic amines,organic,,RDKit open source software,RDKit,19.03.4,
fr_arn,fr_ArN,number of aromatic nitrogens,organic,,RDKit open source software,RDKit,19.03.4,
fr_quatn,fr_quatN,number of quarternary nitrogens,organic,,RDKit open source software,RDKit,19.03.4,
fr_nh0,fr_NH0,number of tertiary amines,organic,,RDKit open source software,RDKit,19.03.4,
fr_nh1,fr_NH1,number of primary amines,organic,,RDKit open source software,RDKit,19.03.4,
fr_nh2,fr_NH2,number of secondary amines,organic,,RDKit open source software,RDKit,19.03.4,
fr_pyridine,fr_pyridine,number of pyridine rings,organic,,RDKit open source software,RDKit,19.03.4,
fr_piperzine,fr_piperzine,number of piperzine rings,organic,,RDKit open source software,RDKit,19.03.4,
fr_piperdine,fr_piperdine,number of piperdine rings,organic,,RDKit open source software,RDKit,19.03.4,
fr_guanido,fr_guanido,number of guanidine groups,organic,,RDKit open source software,RDKit,19.03.4,
fr_dihydropyridine,fr_dihydropyridine,number of dihydropyridines,organic,,RDKit open source software,RDKit,19.03.4,
fr_amidine,fr_amidine,number of amidine groups,organic,,RDKit open source software,RDKit,19.03.4,
fr_halogen,fr_halogen,number of halogens,organic,,RDKit open source software,RDKit,19.03.4,
atomic_electronegativity,Electronegativity,creates a column containing electronegativity for each unique atom in molecule,inorganic,,escalate,EscalateFeats,1,
hansentriple,hansentriple,"returns three columns (deltad, deltap, deltah) for each species if present in JS_HansenSolubility external repository",solvent,,escalate,EscalateFeats,1,
molarityratio,molarity_ratio,calculates the molarity ratio between the sum of all chemicals of the primary chemical types (first type reference in inventory) named:  `_calc_ratio_<type>_<type>_molarity` -- column name structure is fixed and cannot be changed (alternative_input dictates the value used to fill blanks and infinities after calculating numericals),all,0,escalate,EscalateCalcs,1,exists in this table so that it can be toggled without changing pipeline code -- removing will disable
molarityratio_bytype,type_molarity_ratio,calculates the molarity ratio between all unique members which have a given chemical type in the chemical inventory -- column name: ## and %% are instances of a pariticular type -- e.g. `_calc_ratiobytype_organic_0_molarity...` would refer to identity in the  _raw_organic_0_inchikey -- column name structure is fixed and cannot be changed (alternative_input dictates the value used to fill blanks and infinities after calculating numericals),all,0,escalate,EscalateCalcs,1,exists in this table so that it can be toggled without changing pipeline code -- removing will disable