[gmx-users] Insane.py problem

Wed May 13 17:29:39 CEST 2015

I know it's a non issue now, but I was on my way home when I realized why
it doesn't work with spaces.
Since your values are being passed without quotes, the program interprets
them as separate arguments due to the spaces. When splitting each one by
the comma you get lists of two strings, one number string and one empty
string. The empty string cannot be 'floated' and thus the error.
On May 13, 2015 3:53 PM, "João Henriques" <joao.henriques.32353 at gmail.com>
wrote:

> If it works, it works, but for example:
>
> >>>a = '1,       1   ,      2   '
> >>>[float(i) for i in a.split(',')]
> [1.0, 1.0, 2.0]
>
> Best regards,
> João
>
> On Wed, May 13, 2015 at 3:49 PM, Carlos Navarro Retamal <
> cnavarro at utalca.cl> wrote:
>
>> I have no idea either.
>> with:
>> ./insane.py -f PSII-CG.pdb -pbc square -box 25,20,15 -l CPG:0.5557 -l
>> PPG:0.0543 -l CDGDG:2.56 -l CMGDG:4.35 -l CSQDB:2.4774 -l CSQDG:0.0026 -sol
>> W -o system.gro
>> works perfectly.
>> Best,
>> carlos
>>
>> --
>> Carlos Navarro Retamal
>> Bioinformatics Engineering
>> Ph. D (c) Applied Sciences.
>> Center of Bioinformatics and Molecular Simulations. CBSM
>> University of Talca
>> Av. Lircay S/N, Talca, Chile
>> T: (+56) 712201 798
>> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>>
>>
>>
>> On May 13, 2015 at 3:45:24 PM, João Henriques (
>> joao.henriques.32353 at gmail.com<mailto:joao.henriques.32353 at gmail.com>)
>> wrote:
>>
>> That's strange. x = [ float(i) for i in a.split(",") ] + 6*[0] creates a
>> list x that is [20.0, 20.0, 10.0, 0, 0, 0, 0, 0, 0]. There should be no
>> error for having an empty space in between comma separated values...
>>
>> But then again, I'm not looking at the full code...
>>
>> /J
>>
>> On Wed, May 13, 2015 at 3:35 PM, Carlos Navarro Retamal <
>> cnavarro at utalca.cl>
>> wrote:
>>
>> > Hi Tsjerk
>> > Thanks for your reply.
>> > I found that the problem was the empty space between the number and the
>> > comma. How silly of me.
>> > Thanks in any case :)
>> > Carlos
>> > --
>> > Carlos Navarro Retamal
>> > Bioinformatics Engineering
>> > Ph. D (c) Applied Sciences.
>> > Center of Bioinformatics and Molecular Simulations. CBSM
>> > University of Talca
>> > Av. Lircay S/N, Talca, Chile
>> > T: (+56) 712201 798
>> > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>> >
>> >
>> >
>> > On May 13, 2015 at 3:28:52 PM, Tsjerk Wassenaar (tsjerkw at gmail.com
>> <mailto:
>> > tsjerkw at gmail.com>) wrote:
>> >
>> > Hi Carlos,
>> >
>> > Use -box 20 20 10, without commas.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> > On May 13, 2015 2:25 PM, "João Henriques" <
>> joao.henriques.32353 at gmail.com>
>> > wrote:
>> >
>> > > Dear Carlos,
>> > >
>> > > It's actually the other way around, it's trying to convert a string
>> into
>> > a
>> > > float. I am absolutely not familiar with the code or the procedure,
>> but
>> > > form a programming perspective, this is likely due to some input
>> you're
>> > > providing that is not convertible to a float. For example, if you
>> > provide:
>> > > 'ABC123' as an argument to be internally converted to a float, it will
>> > fail
>> > > and raise an error such as yours.
>> > >
>> > > Maybe one of your inputs is required to be a 'number' and it's not.
>> > >
>> > > This as how far as I can go, being unfamiliar with Insane.py.
>> > >
>> > > Best regards,
>> > > João
>> > >
>> > > On Wed, May 13, 2015 at 12:03 PM, Carlos Navarro Retamal <
>> > > cnavarro at utalca.cl
>> > > > wrote:
>> > >
>> > > > Dear gmx users,
>> > > > I’m trying to create a thylakoid membrane (from cyanobacteria) with
>> the
>> > > > following lipid composition:
>> > > > 18:1-16:0 PG 5.557%
>> > > > 16:1-16:0 PG 0.543%
>> > > > 18:1-16:0 DGDG 25.600%
>> > > > 18:1-16:0 MGDG 43.500%
>> > > > 18:1-16:0 SQDG 24.774%
>> > > > 16:0-16:0 SQDG 0.026%
>> > > > To do that, i’m using insane.py, by the following command line:
>> > > >
>> > > > ./insane.py -f PSII-CG.pdb -pbc square -box 20, 20, 10 -l
>> CPG:0.5557 -l
>> > > > PPG:0.0543 -l CDGDG:2.56 -l CMGDG:4.35 -l CSQDB:2.4774 -l
>> CSQDG:0.0026
>> > > -sol
>> > > > W -o system.gro
>> > > > But i’m getting the next error message:
>> > > > Traceback (most recent call last):
>> > > > File "./insane.py", line 559, in <module>
>> > > > options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
>> > > > File "./insane.py", line 441, in setvalue
>> > > > self.value = self.func(v[0])
>> > > > File "./insane.py", line 302, in readBox
>> > > > x = [ float(i) for i in a.split(",") ] + 6*[0]
>> > > > ValueError: could not convert string to float:
>> > > >
>> > > > Is this because i’m using float numbers to describe the specific
>> amount
>> > > of
>> > > > lipids?
>> > > >
>> > > > If this is the case, can someone suggest me an approach to overcome
>> > this
>> > > > issue?
>> > > >
>> > > > Thanks in advance,
>> > > >
>> > > > Carlos
>> > > >
>> > > > --
>> > > > Carlos Navarro Retamal
>> > > > Bioinformatics Engineering
>> > > > Ph. D (c) Applied Sciences.
>> > > > Center of Bioinformatics and Molecular Simulations. CBSM
>> > > > University of Talca
>> > > > Av. Lircay S/N, Talca, Chile
>> > > > T: (+56) 712201 798
>> > > > E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>> > > >
>> > > > --
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>
>