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with atoms having unique names. However after processing this RDKit molecule to get the corresponding .pdbqt file:
preparator = MoleculePreparation()
preparator.prepare(m3d)
pdbqt_string = preparator.write_pdbqt_string()
pdbqt_string_ready = pdbqt_string.replace('UNL','MOL')
ligand_file = '/home/fredy/Desktop/test.pdbqt'
with open(ligand_file,'w') as pdbqt_file:
pdbqt_file.write(pdbqt_string_ready)
I get:
REMARK SMILES CCCCO
REMARK SMILES IDX 3 1 2 2 1 3 4 4 5 5
REMARK H PARENT 5 6
REMARK Flexibility Score: inf
ROOT
ATOM 1 C MOL 1 0.290 -0.899 -0.311 1.00 0.00 0.028 C
ENDROOT
BRANCH 1 2
ATOM 2 C MOL 1 -0.734 -0.344 0.622 1.00 0.00 -0.001 C
ATOM 3 C MOL 1 -1.515 0.808 0.093 1.00 0.00 0.004 C
ENDBRANCH 1 2
BRANCH 1 4
ATOM 4 C MOL 1 1.341 0.103 -0.717 1.00 0.00 0.156 C
BRANCH 4 5
ATOM 5 O MOL 1 2.046 0.592 0.381 1.00 0.00 -0.396 OA
ATOM 6 H MOL 1 1.801 0.136 1.204 1.00 0.00 0.210 HD
ENDBRANCH 4 5
ENDBRANCH 1 4
TORSDOF 3
I revised preparator options looking for some keyword to retain unique atom names, however I was not able to find this feature. Is it possible to retain unique atom names in the .pdbqt file?
Thanks in advance for the support,
best
The text was updated successfully, but these errors were encountered:
hello,
when preparing a .pdbqt file I noticed that the unique atom name generated by RDKit are removed. An example below:
from rdkit import Chem
from rdkit.Chem import AllChem
smiles = "CCCCO"
m = Chem.MolFromSmiles(smiles)
m3d = Chem.AddHs(m)
AllChem.EmbedMolecule(m3d)
pdb_file = Chem.MolToPDBBlock(m3d)
in this case pdb_file contains:
HETATM 1 C1 UNL 1 -1.515 0.808 0.093 1.00 0.00 C
HETATM 2 C2 UNL 1 -0.734 -0.344 0.622 1.00 0.00 C
HETATM 3 C3 UNL 1 0.290 -0.899 -0.311 1.00 0.00 C
HETATM 4 C4 UNL 1 1.341 0.103 -0.717 1.00 0.00 C
HETATM 5 O1 UNL 1 2.046 0.592 0.381 1.00 0.00 O
HETATM 6 H1 UNL 1 -2.495 0.475 -0.327 1.00 0.00 H
HETATM 7 H2 UNL 1 -1.772 1.505 0.929 1.00 0.00 H
HETATM 8 H3 UNL 1 -1.014 1.393 -0.690 1.00 0.00 H
HETATM 9 H4 UNL 1 -1.445 -1.161 0.864 1.00 0.00 H
HETATM 10 H5 UNL 1 -0.203 -0.023 1.548 1.00 0.00 H
HETATM 11 H6 UNL 1 0.838 -1.695 0.263 1.00 0.00 H
HETATM 12 H7 UNL 1 -0.134 -1.413 -1.197 1.00 0.00 H
HETATM 13 H8 UNL 1 2.046 -0.435 -1.397 1.00 0.00 H
HETATM 14 H9 UNL 1 0.948 0.957 -1.266 1.00 0.00 H
HETATM 15 H10 UNL 1 1.801 0.136 1.204 1.00 0.00 H
with atoms having unique names. However after processing this RDKit molecule to get the corresponding .pdbqt file:
preparator = MoleculePreparation()
preparator.prepare(m3d)
pdbqt_string = preparator.write_pdbqt_string()
pdbqt_string_ready = pdbqt_string.replace('UNL','MOL')
ligand_file = '/home/fredy/Desktop/test.pdbqt'
with open(ligand_file,'w') as pdbqt_file:
pdbqt_file.write(pdbqt_string_ready)
I get:
REMARK SMILES CCCCO
REMARK SMILES IDX 3 1 2 2 1 3 4 4 5 5
REMARK H PARENT 5 6
REMARK Flexibility Score: inf
ROOT
ATOM 1 C MOL 1 0.290 -0.899 -0.311 1.00 0.00 0.028 C
ENDROOT
BRANCH 1 2
ATOM 2 C MOL 1 -0.734 -0.344 0.622 1.00 0.00 -0.001 C
ATOM 3 C MOL 1 -1.515 0.808 0.093 1.00 0.00 0.004 C
ENDBRANCH 1 2
BRANCH 1 4
ATOM 4 C MOL 1 1.341 0.103 -0.717 1.00 0.00 0.156 C
BRANCH 4 5
ATOM 5 O MOL 1 2.046 0.592 0.381 1.00 0.00 -0.396 OA
ATOM 6 H MOL 1 1.801 0.136 1.204 1.00 0.00 0.210 HD
ENDBRANCH 4 5
ENDBRANCH 1 4
TORSDOF 3
I revised preparator options looking for some keyword to retain unique atom names, however I was not able to find this feature. Is it possible to retain unique atom names in the .pdbqt file?
Thanks in advance for the support,
best
The text was updated successfully, but these errors were encountered: