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.