Hi Gaetano
The properties of the mol2 file are stored as atom properties. Here is an
example (sorry - the only thing I have at hand right now is a benzene mol2
file created with moe - note the mol2 file parser was tested on corina
mol2 files)
Here is the file
stiefni2@nrchbs-ldl30105:rdkitMol2>cat benzenePC.mol2
@<TRIPOS>MOLECULE
NoName
12 12 1 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 -0.0278 1.3844 0.0097 C.ar 1 <1> -0.0618
2 H1 -0.9760 1.9148 0.0213 H 1 <1> 0.0618
3 C2 1.1708 2.0983 0.0020 C.ar 1 <1> -0.0618
4 H2 1.1561 3.1847 0.0074 H 1 <1> 0.0618
5 C3 2.3883 1.4173 -0.0129 C.ar 1 <1> -0.0618
6 H3 3.3217 1.9733 -0.0188 H 1 <1> 0.0618
7 C4 2.4072 0.0223 -0.0200 C.ar 1 <1> -0.0618
8 H4 3.3554 -0.5081 -0.0316 H 1 <1> 0.0618
9 C5 1.2087 -0.6916 -0.0123 C.ar 1 <1> -0.0618
10 H5 1.2235 -1.7781 -0.0179 H 1 <1> 0.0618
11 C6 -0.0088 -0.0106 0.0026 C.ar 1 <1> -0.0618
12 H6 -0.9423 -0.5667 0.0087 H 1 <1> 0.0618
@<TRIPOS>BOND
1 1 2 1
2 1 3 ar
3 1 11 ar
4 3 4 1
5 3 5 ar
6 5 6 1
7 5 7 ar
8 7 8 1
9 7 9 ar
10 9 10 1
11 9 11 ar
12 11 12 1
@<TRIPOS>SUBSTRUCTURE
1 **** 5 GROUP 4 **** **** 0
# MOE 2014.09 (io_trps.svl 2012.10)
And this is the file parsed
In [21]: from __future__ import print_function
In [22]: mol2 = Chem.MolFromMol2File('benzenePC.mol2¹)
In [23]: atoms = mol2.GetAtoms()
In [24]: list(atoms[0].GetPropNames())
Out[24]: ['_TriposAtomName', '_TriposAtomType', '_TriposPartialCharge']
In [25]: for a in atoms:
print(" ".join([a.GetProp(x) for x in a.GetPropNames()]))
....:
C1 C.ar -0.0618
C2 C.ar -0.0618
C3 C.ar -0.0618
C4 C.ar -0.0618
C5 C.ar -0.0618
C6 C.ar -0.0618
Hope this helps
Nik
On 20/11/15 00:28, "Gaetano Calabro" <[email protected]> wrote:
>Hi there,
>
>I would like to load a mol2 file with partial charge information in
>RDkit. How can I retrieve the atomic partial charge in RDkit? I haven't
>seen any function related to it.
>
>Cheers,
>
>Gaetano
>
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