GlobalChem Molecule

We can use the example located in the forcefield demo:

Google Colaboratory

Load the Package

from global_chem_extensions import GlobalChemExtensions
ff = GlobalChemExtensions().forcefields()

Load the Molecule

We can use the perflurobutanoic acid located in the repository as an example where we load the SMILES and the stream file where the rank ordering is preserved.

# Load the Molecule

global_chem_molecule = ff.initialize_globalchem_molecule(
    'FC(F)(C(F)(C(O)=O)F)C(F)(F)F',
    stream_file='global-chem/example_data/forcefield_parameterization/perfluorobutanoic_acid.str',
    # frcmod_file='gaff2.frcmod',
)

Determine the Name

Determine the name of the compound based on the dictionary.

Code

global_chem_molecule.determine_name()
name = global_chem_molecule.name
print (name)

Output

perfluorobutanoic acid

Determine the Attributes of a Molecule

Code

attributes = global_chem_molecule.get_attributes()
for k, v in attributes.items():
  print (f'{k}: {v}')

Output

Attributes: {
'name': 'cyclopentane', 'smiles': 'C1CCCC1',
'molecular_weight': 70.07825032, 
'logp': 1.9505000000000001,
'h_bond_donor': 0,
'h_bond_acceptors': 0,
'rotatable_bonds': 0, 
'number_of_atoms': 5,
'molar_refractivity': 23.084999999999994,
'topological_surface_area_mapping': 0.0,
'formal_charge': 0,
'heavy_atoms': 5,
'num_of_rings': 1
}

Convert to Different Interoperable mol or SMILES objects

To allow for any interoperability with different software we can provide a conversion into their respective objects.

Code

pysmiles_mol = global_chem_molecule.get_pysmiles()
rdkit_mol = global_chem_molecule.get_rdkit_molecule()
partial_smiles_mol = global_chem_molecule.get_partial_smiles()
deep_smiles_mol = global_chem_molecule.encode_deep_smiles()
selfies_mol = global_chem_molecule.encode_selfies()
validate_smiles = global_chem_molecule.validate_molvs()

print ("RDKit Mol: %s" % rdkit_mol)
print ("PySMILES: %s" % pysmiles_mol)
print ("Partial SMILES: %s" % partial_smiles_mol)
print ("DeepSMILES: %s" % deep_smiles_mol)
print ("Selfies Mol: %s" % selfies_mol)
print ("Validation: %s" % validate_smiles)

Output

RDKit Mol: <rdkit.Chem.rdchem.Mol object at 0x7f7259a7cb20>
PySMILES: Graph with 5 nodes and 5 edges
Partial SMILES: Molecule(atoms=['Atom(elem=6,chg=0,idx=0)', 'Atom(elem=6,chg=0,idx=1)', 'Atom(elem=6,chg=0,idx=2)', 'Atom(elem=6,chg=0,idx=3)', 'Atom(elem=6,chg=0,idx=4)'])
DeepSMILES: CCCCC5
Selfies Mol: [C][C][C][C][C][Ring1][Branch1]
Validation: ['INFO: [FragmentValidation] pentane is present']

If a failure at the conversion happens, it must be because perhaps the SMILES is invalid. Please check with the validation module.

Draw CGenFF Molecule

Code

global_chem_molecule.draw_cgenff_molecule(
    height=1000, 
    width=1000
 )

Output

Create a Curly SMILES representation of SMILES and Atom Types

CurlySMILES contain their features inside of curly braces and is stable SMILES to pass through RDKit.

Code

curly_smiles = global_chem_molecule.get_curly_smiles()

Output

F{FGA2}C{CG312}(F{FGA2})(C{CG312}(F{FGA2})(C{CG2O2}(O{OG311})=O{OG2D1})F{FGA2})C{CG302}(F{FGA3})(F{FGA3})F{FGA3}

Get CGenFF CXSMILES

CXSMILES is a atoms in the SMILES string followed by a | and then a set of features, or metadata, to accommodate each atom. This allows the user to embed whatever information they wish into the molecule.

We decided to embed atom-type information since the atom-type ordering is preserved.

Code

print (global_chem_molecule.get_cgenff_cxsmiles())

Output

O=C(O)C(F)(F)C(F)(F)C(F)(F)F |atomProp:0.atom_type.OG2D1:0.atom_idx.7:1.atom_type.CG2O2:1.atom_idx.5:2.atom_type.OG311:2.atom_idx.6:3.atom_type.CG312:3.atom_idx.3:4.atom_type.FGA2:4.atom_idx.4:5.atom_type.FGA2:5.atom_idx.8:6.atom_type.CG312:6.atom_idx.1:7.atom_type.FGA2:7.atom_idx.0:8.atom_type.FGA2:8.atom_idx.2:9.atom_type.CG302:9.atom_idx.9:10.atom_type.FGA3:10.atom_idx.10:11.atom_type.FGA3:11.atom_idx.11:12.atom_type.FGA3:12.atom_idx.12|

Get CGenFF CXSMARTS

CXSMARTS is a atoms in the SMARTS string followed by a | and then a set of features, or metadata, to accommodate each atom. This allows the user to embed whatever information they wish into the molecule.

Code

cx_smarts = global_chem_molecule.get_cgenff_cxsmarts()

Output

[#9]-[#6](-[#9])(-[#6](-[#9])(-[#6](-[#8])=[#8])-[#9])-[#6](-[#9])(-[#9])-[#9] |atomProp:0.atom_type.FGA2:0.atom_idx.0:1.atom_type.CG312:1.atom_idx.1:2.atom_type.FGA2:2.atom_idx.2:3.atom_type.CG312:3.atom_idx.3:4.atom_type.FGA2:4.atom_idx.4:5.atom_type.CG2O2:5.atom_idx.5:6.atom_type.OG311:6.atom_idx.6:7.atom_type.OG2D1:7.atom_idx.7:8.atom_type.FGA2:8.atom_idx.8:9.atom_type.CG302:9.atom_idx.9:10.atom_type.FGA3:10.atom_idx.10:11.atom_type.FGA3:11.atom_idx.11:12.atom_type.FGA3:12.atom_idx.12|