On Oct 24, 2014, at 3:15 AM, ftorazyne wrote:
> Your code returns
...
> Trying words of length 4
> Trying words of length 5
> Trying words of length 6
I don't know the registration system well enough to figure out how it can be
that the formats are registered, but not available in any form.
> and uses FindFormat() function. I searched its definition with grep and
> didn't find it.
It starts as you said in obconversion.cpp:
bool OBConversion::SetInFormat(const char* inID)
{
if(inID)
pInFormat = FindFormat(inID);
return pInFormat && !(pInFormat->Flags() & NOTREADABLE);
}
which calls another function further on down in that file:
OBFormat* OBConversion::FindFormat(const char* ID)
{
return OBFormat::FindType(ID);
}
Here's the complicated part. FindType is defined in
the MAKE_PLUGIN(BaseClass) macro in include/openbabel/plugin.h
static BaseClass* FindType(const char* ID) {\
if (!ID || *ID==0 || *ID==' ') {\
return Default();\
}\
return static_cast<BaseClass*>(BaseFindType(Map(),ID));\
}
This is use for fingerprint, forcefield, descriptor, format
and charge model registration. See include/fingerprint.h where
it has "MAKE_PLUGIN(OBFingerprint)" to see it in use.
The BaseFindType is in src/plugin.cpp and is a simple function:
OBPlugin* OBPlugin::BaseFindType(PluginMapType& Map, const char* ID)
{
// Make sure the plugins are loaded
if (AllPluginsLoaded == 0) {
OBPlugin::LoadAllPlugins();
}
if(!ID || !*ID)
return NULL;
PluginMapType::iterator itr = Map.find(ID);
if(itr==Map.end())
return NULL;
else
return itr->second;
}
although LoadAllPlugins() is more complicated.
For what it's worth, my local copy of OpenBabel hasn't
been updated for a year or so. I don't see any relevant
changes in version control though.
I traced obconversion.GetSupportedInputFormat() as well,
and it's quite simple. Starting from obconversion.cpp:
std::vector<std::string> OBConversion::GetSupportedInputFormat()
{
vector<string> vlist;
OBPlugin::ListAsVector("formats", "in", vlist);
return vlist;
}
it goes directly to plugin.cpp, and the core loop is:
for(itr=Map.begin(); itr!=Map.end(); ++itr)
{
if(*(itr->first)=='_')//no listing when ID starts with '_'
continue;
if(onlyIDs)
vlist.push_back(itr->first);
else
{
string txt;
if((itr->second)->Display(txt, param, itr->first))
vlist.push_back(txt);
}
}
Basically, if it can do the following:
import openbabel as ob
print "plugins", repr(ob.OBPlugin_ListAsString("plugins", None))
print "formats", repr(ob.OBPlugin_ListAsString("formats", "ids"))
then I can't see why it can't recognize the "smi" format.
FWIW, I get:
>>> import openbabel as ob
>>> ob.OBPlugin_ListAsString("plugins", None)
'charges\ndescriptors\nfingerprints\nforcefields\nformats\nloaders\nops\n'
>>> ob.OBPlugin_ListAsString("formats", "ids")
'abinit\nacesin\nacesout\nacr\nadf\nadfout\nalc\narc\nascii\naxsf\nbgf\nbox\nbs\nc09out\nc3d1\nc3d2\ncac\ncaccrt\ncache\ncacint\ncan\ncar\ncastep\nccc\ncdx\ncdxml\ncht\ncif\nck\ncml\ncmlr\ncom\nCONFIG\nCONTCAR\ncopy\ncrk2d\ncrk3d\ncsr\ncssr\nct\ncub\ncube\ndat\ndmol\ndx\nent\nfa\nfasta\nfch\nfchk\nfck\nfeat\nfh\nfhiaims\nfix\nfps\nfpt\nfract\nfs\nfsa\ng03\ng09\ng92\ng94\ng98\ngal\ngam\ngamess\ngamin\ngamout\ngau\ngjc\ngjf\ngot\ngpr\ngr96\ngro\ngukin\ngukout\ngzmat\nhin\nHISTORY\ninchi\ninchikey\ninp\nins\njin\njout\nk\nlmpdat\nlog\nmcdl\nmcif\nmdl\nml2\nmmcif\nmmd\nmmod\nmna\nmol\nmol2\nmold\nmolden\nmolf\nmolreport\nmoo\nmop\nmopcrt\nmopin\nmopout\nmp\nmpc\nmpd\nmpo\nmpqc\nmpqcin\nmrv\nmsi\nmsms\nnul\nnw\nnwo\nobapi\nout\noutmol\noutput\npaint\npc\npcm\npdb\npdbqt\npng\npos\nPOSCAR\npov\npqr\npqs\nprep\npwscf\nqcin\nqcout\nreport\nres\nrsmi\nrxn\nsd\nsdf\nsmi\nsmiles\nsvg\nsy2\nt41\ntdd\ntext\ntherm\ntmol\ntxt\ntxyz\nunixyz\nVASP\nvmol\nxed\nxml\nxsf\nxyz\nyob\nzin\n'
Andrew
da...@dalkescientific.com
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