BondList

BondList[mol]

gives the list of bonds in the molecule mol.

BondList[mol,patt]

gives the list of bonds in the molecule mol matching the atom pattern patt.

BondList[mol,patt,"prop"]

gives the value for the specified property of the bonds matching patt.

Details and Options

  • Possible forms for patt include:
  • "type"a bond with a specified bond type
    Bond[{a1,a2},"type"]a bond with atoms defined by ai
    MoleculePattern[…]a molecule pattern with one bond
  • The ai may be an atom index or a pattern representing an atom.
  • Possible values for "prop" include:
  • "BondIndex"bond index
    "BondLength"Euclidean distance between the given atoms
    "BondType"bond type
    "ConjugatedBondQ"conjugated bond
  • With the default option setting IncludeHydrogensAll, all bonds will be returned by BondList. Use the option value "ExplicitOnly" to exclude bonds to implicit hydrogen atoms.

Examples

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Basic Examples  (3)

Get all the bonds from a molecule:

Get only the carbon-carbon bonds:

Get only the double bonds:

Get only the carbon-carbon double bonds:

Use a pattern to find all exocyclic bonds:

Give the results to MoleculePlot to visualize the bonds in place:

Compare bond lengths for different types of carbon bonds:

Options  (1)

IncludeHydrogens  (1)

BondList will include all atoms by default:

Use IncludeHydrogensNone to exclude the hydrogens, which make up the majority of atoms:

This is equivalent to using a pattern excluding hydrogen atoms:

Possible Issues  (2)

Aromatic bonds are displayed visually as single or double bonds:

Asking for the number of "Double" bonds does not include aromatic bonds:

Convert the aromatic bonds to single/double using MoleculeModify before taking the count:

Because Molecule will try to fill valences with hydrogen atoms, hydrogen atoms will be included in the count even if they were not in the original molecule expression:

To exclude implicit hydrogen atoms, use IncludeHydrogens"ExplicitOnly":

Alternatively, to stop hydrogen atoms from appearing, use the Molecule option ValenceFillingNone:

The resulting molecule contains a single atom with no bonds:

Neat Examples  (1)

Create a molecule using data retrieved from "PubChem" using an ExternalIdentifier:

Create a Dataset showing the bond types present and their average bond lengths:

Wolfram Research (2019), BondList, Wolfram Language function, https://reference.wolfram.com/language/ref/BondList.html (updated 2020).

Text

Wolfram Research (2019), BondList, Wolfram Language function, https://reference.wolfram.com/language/ref/BondList.html (updated 2020).

CMS

Wolfram Language. 2019. "BondList." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2020. https://reference.wolfram.com/language/ref/BondList.html.

APA

Wolfram Language. (2019). BondList. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BondList.html

BibTeX

@misc{reference.wolfram_2024_bondlist, author="Wolfram Research", title="{BondList}", year="2020", howpublished="\url{https://reference.wolfram.com/language/ref/BondList.html}", note=[Accessed: 21-November-2024 ]}

BibLaTeX

@online{reference.wolfram_2024_bondlist, organization={Wolfram Research}, title={BondList}, year={2020}, url={https://reference.wolfram.com/language/ref/BondList.html}, note=[Accessed: 21-November-2024 ]}