[gmx-developers] Coordinate scaling in pdbio.c

[Erik Marklund]

11 apr 2012 kl. 13.40 skrev Mark Abraham:

>  
>  
> On 11/04/12, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>> 
>> 
>> 11 apr 2012 kl. 01.38 skrev Mark Abraham:
>> 
>>> On 11/04/2012 5:21 AM, David van der Spoel wrote:
>>>> On 2012-04-10 21:10, Anton Feenstra wrote:
>>>>> On 09/04/12 21:47, Justin A. Lemkul wrote:
>>>>>> 
>>>>>> 
>>>>>> Radhakrishna Bettadapura wrote:
>>>>>>> All,
>>>>>>> 
>>>>>>> I'm trying to figure out why a pdb input to pdb2gmx results in
>>>>>>> coordinates that are scaled by a factor of 0.1. That is, if a line in
>>>>>>> the PDB file reads
>>>>>>> 
>>>>>>> 
>>>>>>> ATOM 1 N ALA B 3 -1.221 20.481 12.450 1.00 34.64 N
>>>>>>> 
>>>>>>> then the corresponding line in the .gro file reads
>>>>>>> 
>>>>>>> 3ALA N 1 -0.122 2.048 1.245
>>>>>>> 
>>>>>>> The culprit seems to be the following lines in pdbio.c:
>>>>>>> 
>>>>>>> static int read_atom(t_symtab *symtab,
>>>>>>> char line[],int type,int natom,
>>>>>>> t_atoms *atoms,rvec x[],int chainnum,gmx_bool bChange)
>>>>>>> {
>>>>>>> 
>>>>>>> // do stuff
>>>>>>> 
>>>>>>> x[natom][XX]=strtod(xc,NULL)*0.1; /*all coordinates scaled by 0.1...
>>>>>>> why?*/
>>>>>>> x[natom][YY]=strtod(yc,NULL)*0.1;
>>>>>>> x[natom][ZZ]=strtod(zc,NULL)*0.1;
>>>>>>> 
>>>>>>> //do more stuff
>>>>>>> 
>>>>>>> }
>>>>>>> 
>>>>>>> 
>>>>>>> There's also a line in the output function that multiplies all
>>>>>>> incoming coordinates by 10 before writing it to output:
>>>>>>> 
>>>>>>> void write_pdbfile_indexed(FILE *out,const char *title,
>>>>>>> t_atoms *atoms,rvec x[],
>>>>>>> int ePBC,matrix box,char chainid,
>>>>>>> int model_nr, atom_id nindex, atom_id index[],
>>>>>>> gmx_conect conect, gmx_bool bTerSepChains)
>>>>>>> {
>>>>>>> 
>>>>>>> 
>>>>>>> //do stuff...
>>>>>>> 
>>>>>>> 
>>>>>>> fprintf(out,pdbform,pdbtp[type],(i+1)%100000,nm,resnm,ch,resnr,
>>>>>>> (resic == '\0') ? ' ' : resic,
>>>>>>> 10*x[i][XX],10*x[i][YY],10*x[i][ZZ],occup,bfac,atoms->atom[i].elem);
>>>>>>> // do more stuff...
>>>>>>> 
>>>>>>> }
>>>>>>> 
>>>>>>> 
>>>>>>> Can someone tell me why this coordinate scaling occurs? And why the
>>>>>>> scale factor is a single hard-coded number than, say, something that
>>>>>>> depends on the input?
>>>>>>> 
>>>>>> 
>>>>>> PDB coordinates are in Angstrom, while .gro coordinates are in nm. Hence
>>>>>> the conversion factor of 0.1.
>>>>> 
>>>>> What happened to A2NM and NM2A?
>>>>> In my (4.0.5, yes that is very old) includes/physics.h I still see:
>>>>> 
>>>>> #define A2NM (ANGSTROM/NANO) /* NANO */
>>>>> #define NM2A (NANO/ANGSTROM) /* 10.0 */
>>>>> 
>>>>> Why aren't these still used for that?
>>>>> 
>>>>> 
>>>> At some stage macros were removed from the code, even though these seem rather harmless. I agree that it is confusing to hard code these numbers. If we cannot use macro's like this we should probably replace them by
>>>> static const real ANGSTROM=1e-10;
>>>> static const real NANO=1e-9;
>>>> 
>>>> etc.
>>>> 
>>>> Comments?
>>> 
>>> include/physics.h still has these macros. IMO, hard-coded constants are a greater evil than macros to prevent that, though I expect we will transition to const values at some stage soon.
>> 
>> But are these the kind of macros we want to avoid? Aren't function-like macros the ones to kill in the first place?
>  They're taking no parameters, so they're hardly function-like. The code fragments above are compiled into constants by the pre-processor. A macro that is used as
>  
> dist_in_nm = dist_in_angstrom * A2NM;
>  
> is much less evil than a macro 
>  
> dist_in_nm = A2NM(dist_in_angstrom);

My point exactly. I'm just not seeing the harm in using macros in cases like these.

Erik

>  
> and physics.h has only the first type. Inlined functions of the second type would be best of all, of course. 
>  
> Mark 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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