Standardize options

Stereo

standardize-stereo

type:boolean
default:false
description:Sets or repairs the stereo on a molecule.

standardize-clear-stereo

type:boolean
default:false
description:Sets all atoms and bonds to NoStereo.

standardize-clear-enhanced-stereo

type:boolean
default:false
description:Removes all relative stereo groupings.

standardize-clear-unknown-stereo

type:boolean
default:false
description:Sets all atoms and bonds marked UnknownStereo to NoStereo.

standardize-clear-unknown-atom-stereo

type:boolean
default:false
description:Sets all atoms marked UnknownStereo to NoStereo.

standardize-clear-unknown-bond-stereo

type:boolean
default:false
description:Sets all bonds marked UnknownStereo to NoStereo.

standardize-clear-cis-trans

type:boolean
default:false
description:Sets all bonds marked CisStereo or TransStereo to UnknownStereo.

standardize-stereo-from-coordinates

type:boolean
default:false
description:Uses 2D coordinates and up/down bond markings (or 3D coordinates) to assign the stereochemistry of the atoms or bonds.

standardize-reposition-stereo-bonds

type:boolean
default:false
description:Repositions the stereo bond markings in an attempt to find the best bond to mark as a wedge bond for each stereo atom.

standardize-reposition-axial-stereo-bonds

type:boolean
default:false
description:Repositions the stereo bond markings for axial stereo centers (allenes and atropisomers) in an attempt to find the best bond to mark as a wedge bond for each center.

standardize-fix-direction-wedge-bonds

type:boolean
default:false
description:Checks the wedge bonds in the molecule to ensure that the wedge is drawn with the stereo atom at the narrow end of the wedge.

Charges

standardize-charges

type:boolean
default:false
description:Sets the charges on a molecule to a standard form.

standardize-clear-charges

type:boolean
default:false
description:Sets all formal charges to zero.

standardize-neutralize-zwitterions

type:boolean
default:false
description:Converts directly bonded zwitterions (positively charged atom bonded to negatively charged atom, A+B-) to the neutral representation (A=B).

Geometry

standardize-center-molecule

type:boolean
default:false
description:Translates a molecule so its geometric center lies at the origin.

standardize-remove-single-atoms

type:boolean
default:false
description:Removes fragments that consist of only a single heavy atom.

standardize-keep-smallest

type:boolean
default:false
description:Keeps only the smallest fragment in the molecule.

standardize-keep-largest

type:boolean
default:false
description:Keeps only the largest fragment in the molecule.

standardize-remove-largest

type:boolean
default:false
description:Removes the largest fragment in the molecule.

standardize-clear-coordinates

type:boolean
default:false
description:Sets all x, y, z coordinates to zero.

standardize-straighten-triple-bonds

type:boolean
default:false
description:Finds atoms with triple bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees.

standardize-straighten-allens

type:boolean
default:false
description:Finds atoms with two double-bonds and non-linear geometry and fixes them so that the bond angles are 180 degrees.

standardize-clear-molecule

type:boolean
default:false
description:Deletes all atoms and bonds in the molecule, keeping the molecule object in the data record.

Query

standardize-make-non-h-to-c-atoms

type:boolean
default:false
description:Converts all non-Hydrogen atoms atoms in the molecule to carbon.

standardize-make-non-h-to-a-atoms

type:boolean
default:false
description:Converts all non-Hydrogen atoms in the molecule to the A query atom type.

standardize-make-non-h-c-to-q-atoms

type:boolean
default:false
description:Converts all non-Carbon, non-Hydrogen atoms in the molecule to the Q query atom type.

Misc

standardize-make-all-bonds-single

type:boolean
default:false
description:Converts all bonds in the molecule to single bonds.

standardize-highlight-colors

type:boolean
default:false
description:Clears any highlight colors from atoms and bonds.

standardize-clear-unusual-valences

type:boolean
default:false
description:Clears any atom valence query features and resets all implicit hydrogen counts to their standard values.

standardize-clear-isotopes

type:boolean
default:false
description:Clears all isotope markings from atoms.

standardize-clear-dative-bonds

type:boolean
default:false
description:Clears all explicit zero-order coordination bonds of dative type (V3000 type-9 bonds).

standardize-clear-hydrogen-bonds

type:boolean
default:false
description:Clears all explicit zero-order hydrogen bonds (V3000 type-10 bonds).

standardize-create-dative-bonds

type:boolean
default:false
description:Create coordination bond (zero-order bond) instead of wrong co-valent bond.

standardize-create-hydrogen-bonds

type:boolean
default:false
description:Create hydrogen bond (zero-order bond) instead of wrong co-valent bond.