Thanks to all of you. That was very helpful,
Gaetano
On 11/20/2015 12:38 AM, Stiefl, Nikolaus wrote:
> 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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>
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