In case anybody is willing I have attached a patch. This introduces a
new option 'r' which, when set, switches off residue number appending
unless 'l' is also set and residue name is simply '<1>'. The defaults
are as they used to be.
On Mon, 14 Jul 2014 12:03:45 +0100
Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote:
> Hi,
>
> here is something that has bugged me for some time now and is quite an
> annoying misfeature of MOL2Format::WriteMolecule(). In line 591 of
> src/formats/mol2format.cpp (checked out just a minute ago) the residue
> name is appended with its number (res->GetNum()).
>
> The practical problem is that whenever I change the residue name to a
> desired string in my Python script I get a modified residue on
> output. This is obviously exacerbated by multiple read/writes.
>
> If this is really a vital option to some I think it should be possible
> to switch this off with a write option.
>
> Cheers,
> Hannes.
--
Scanned by iCritical.
--- mol2format.cpp.orig 2014-07-23 13:37:43.000000000 +0100
+++ mol2format.cpp 2014-07-23 13:44:59.000000000 +0100
@@ -34,6 +34,7 @@
OBConversion::RegisterFormat("ml2",this);
OBConversion::RegisterFormat("sy2",this);
OBConversion::RegisterOptionParam("l", NULL, 0, OBConversion::OUTOPTIONS);
+ OBConversion::RegisterOptionParam("r", NULL, 0, OBConversion::OUTOPTIONS);
}
virtual const char* Description() //required
@@ -42,6 +43,7 @@
"Sybyl Mol2 format\n"
"Write Options e.g. -xl\n"
" l Output ignores residue information (only ligands)\n\n";
+ " r Output does not append residue number to residue name\n\n";
};
virtual const char* SpecificationURL()
@@ -503,6 +505,7 @@
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
bool ligandsOnly = pConv->IsOption("l", OBConversion::OUTOPTIONS)!=NULL;
+ bool resNum = pConv->IsOption("r", OBConversion::OUTOPTIONS)!=NULL;
//The old code follows....
string str,str1;
@@ -588,7 +591,11 @@
// use original atom names defined by residue
snprintf(label,BUFF_SIZE,"%s",(char*)res->GetAtomID(atom).c_str());
// make sure that residue name includes its number
- snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
+ if (resNum) {
+ snprintf(rlabel,BUFF_SIZE,"%s",res->GetName().c_str());
+ } else {
+ snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
+ }
snprintf(rnum,BUFF_SIZE,"%d",res->GetNum());
}
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