Creating and Adding Groups¶

import cctk is assumed.

Using a Preloaded Group¶

cctk comes with several groups defined by default (listed below).
To add a group, use the add_group_to_molecule function to generate a new molecule.
The atom the group is added to must only be making one bond; usually a hydrogen is a good choice.

Preloaded Groups

Name	Synonyms
`methyl`	`Me` `CH3`
`ethyl`	`Et`, `C2H5`
`isopropyl`	`iPr`, `iC3H7`
`tert-butyl`	`tBu`, `tC4H9`
`hydroxy`	`OH`
`methoxy`	`MeO`, `OMe`, `CH3O`
`acetamido`	`NHAc`
`amino`	`NH2`
`dimethylamino`	`Me2N`, `NMe2`
`trifluoromethyl`	`CF3`
`cyano`	`CN`
`nitro`	`NO2`
`carboxylmethyl`	`MeO2C`, `CO2Me`
`fluoro`	`F`
`chloro`	`Cl`
`bromo`	`Br`
`iodo`	`I`
`pentafluorosulfanyl`	`SF5`
`sulfonyl`	`SO3H`
`acetyl`	`Ac`, `COMe`
`formyl`	`CHO`

from cctk.load_groups import load_group

# load our starting molecule
formic_acid = cctk.GaussianFile.read_file("formic_acid.out").get_molecule()

# to load a predefined group, use the group's name
trifluoromethyl = load_group("trifluoromethyl")
assert isinstance(trifluoromethyl, cctk.Group)

# now we can create a new molecule by adding our group to an existing molecule
# here we specify to add the group to atom 4, the formyl proton, to give us TFA
trifluoroacetic_acid = cctk.Group.add_group_to_molecule(formic_acid, trifluoromethyl, 4)
assert isinstance(trifluoroacetic_acid, cctk.Molecule)

# if we want to track old atom numbers in the new molecule, we can return a dictionary converting between old and new numberings
trifluoroacetic_acid, m_map, g_map = cctk.Group.add_group_to_molecule(formic_acid, trifluoromethyl, 4, return_mapping=True)
# now mmap[1] tells us the new number of atom #1 in formic acid and gmap[1] tells us the new number of atom #1 in the trifluoromethyl group

Creating a New Group¶

We can create a new Group object from any molecule by specifying which atom to make the attachment point from.
As before, the attach_to atom must only be making one bond; usually a hydrogen is a good choice.

# define a new group, where the attachment point is atom 6 (a methyl-group hydrogen)
file = cctk.GaussianFile.read_file("acetaldehyde.out")
acetaldehyde = file.get_molecule()
group = cctk.Group.new_from_molecule(attach_to=6, molecule=acetaldehyde)

# now create a new molecule by adding the new group to atom 5 (another hydrogen on acetaldehyde)
new_mol = cctk.Group.add_group_to_molecule(acetaldehyde, group, 5)
file.write_file("1,4-butanedione.gjf", molecule=new_mol)

# we can also define a group by using the remove_group_from_molecule function
# this code will split the molecule along the C1–C7 bond -- the C1 fragment will become a molecule and the C7 fragment will become a group
alanine = cctk.GaussianFile.read_file("alanine.gjf").get_molecule().assign_connectivity()
molecule, carboxyl_group = cctk.Group.remove_group_from_molecule(alanine, 1, 7)

Epimerization¶

cctk can automatically combine group addition/removal to epimerize stereogenic centers.

# exchanges substituent atoms sub1 and sub2 (and attached groups) around atom center
enantiomer = molecule.epimerize(center, sub1, sub2)

Detecting Groups¶

cctk can search within existing molecules for groups and return the relevant atom numbers.

import cctk.topology as top
from cctk.load_groups import load_group

methyl = cctk.load_group("methyl")
camphor = cctk.Molecule.new_from_name("camphor").assign_connectivity()

top.find_group(camphor, methyl)
# returns a list of dictionaries
# each element is a mapping from atomic numbers of camphor (keys) to atomic numbers of the group (values)
# in this case, camphor contains 3 methyl groups, so there are 3 matches
# [{1: 1, 12: 3, 13: 4, 14: 5}, {3: 1, 16: 3, 17: 4, 15: 5}, {8: 1, 24: 3, 25: 4, 23: 5}]