Datum mol_rsubstruct(PG_FUNCTION_ARGS) {
CROMol i, a;
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &i, NULL);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(1), NULL, &a, NULL);
PG_RETURN_BOOL(MolSubstruct(a, i));
}
Datum mol_substruct_count(PG_FUNCTION_ARGS) {
CROMol i, a;
bool uniquify = PG_GETARG_BOOL(2);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &i, NULL);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(1), NULL, &a, NULL);
PG_RETURN_INT32(MolSubstructCount(i, a, uniquify));
}
Datum mol_hash(PG_FUNCTION_ARGS) {
CROMol mol;
char *str;
int len;
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &mol, NULL);
Assert(mol != 0);
str = computeMolHash(mol, &len);
Assert(str != 0 && strlen(str) != 0);
PG_RETURN_CSTRING(pnstrdup(str, len));
}
Datum mol_murckoscaffold(PG_FUNCTION_ARGS) {
CROMol mol;
Mol *res;
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &mol, NULL);
CROMol scaffold = MolMurckoScaffold(mol);
if (!scaffold) PG_RETURN_NULL();
res = deconstructROMol(scaffold);
freeCROMol(scaffold);
PG_RETURN_MOL_P(res);
}
Datum mol_inchikey(PG_FUNCTION_ARGS) {
CROMol mol;
const char *str;
char *res, *opts = PG_GETARG_CSTRING(1);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &mol, NULL);
str = MolInchiKey(mol, opts);
res = pnstrdup(str, strlen(str));
free((void *)str);
PG_RETURN_CSTRING(res);
}
Datum mol_adjust_query_properties(PG_FUNCTION_ARGS) {
CROMol mol;
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &mol, NULL);
Assert(mol != 0);
char *data = PG_GETARG_CSTRING(1);
CROMol adj = MolAdjustQueryProperties(mol, data);
if (!adj) PG_RETURN_NULL();
Mol *res = deconstructROMol(adj);
freeCROMol(adj);
PG_RETURN_MOL_P(res);
}
Datum mol_formula(PG_FUNCTION_ARGS) {
CROMol mol;
char *str;
int len;
bool separateIsotopes = PG_GETARG_BOOL(1);
bool abbreviateHIsotopes = PG_GETARG_BOOL(2);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0), NULL, &mol, NULL);
str = makeMolFormulaText(mol, &len, separateIsotopes, abbreviateHIsotopes);
PG_RETURN_CSTRING(pnstrdup(str, len));
}
Datum
gmol_consistent(PG_FUNCTION_ARGS)
{
GISTENTRY *entry = (GISTENTRY *) PG_GETARG_POINTER(0);
StrategyNumber strategy = (StrategyNumber) PG_GETARG_UINT16(2);
bool *recheck = (bool *) PG_GETARG_POINTER(4);
bytea *key = (bytea*)DatumGetPointer(entry->key);
bytea *query;
bool res = true;
int siglen = SIGLEN(key);
fcinfo->flinfo->fn_extra = searchMolCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(1),
NULL, NULL,&query);
/*
** recheck is required for all strategies
*/
*recheck = true;
switch (strategy) {
case RDKitContains:
if (!ISALLTRUE(key)) {
if (siglen != SIGLEN(query)) {
elog(ERROR, "All fingerprints should be the same length");
}
uint8 *k = (uint8 *)VARDATA(key);
uint8 *q = (uint8 *)VARDATA(query);
res = bitstringContains(siglen, k, q);
}
break;
case RDKitContained:
if (!ISALLTRUE(key)) {
if (siglen != SIGLEN(query)) {
elog(ERROR, "All fingerprints should be the same length");
}
uint8 *k = (uint8 *)VARDATA(key);
uint8 *q = (uint8 *)VARDATA(query);
if (GIST_LEAF(entry)) {
res = bitstringContains(siglen, q, k);
}
else {
/*
* Due to superimposed key on inner page we could only check
* overlapping
*/
res = bitstringIntersects(siglen, q, k);
}
}
else if (GIST_LEAF(entry)) {
/*
* key is all true, it may be contained in query, iff query is also
* all true
*/
res = bitstringAllTrue(siglen, (uint8 *)VARDATA(query));
}
break;
case RDKitEquals:
if (!ISALLTRUE(key)) {
/*
** verify the necessary condition that key should contain the query
** (on leaf nodes, couldn't it also verify that query contains key?)
*/
if (siglen != SIGLEN(query)) {
elog(ERROR, "All fingerprints should be the same length");
}
uint8 *k = (uint8 *)VARDATA(key);
uint8 *q = (uint8 *)VARDATA(query);
res = bitstringContains(siglen, k, q);
}
break;
default:
elog(ERROR,"Unknown strategy: %d", strategy);
}
PG_RETURN_BOOL(res);
}
Datum fmcs_mol2s_transition(PG_FUNCTION_ARGS) {
// elog(WARNING, (PG_ARGISNULL(0)) ? "arg 0 is NULL" : "arg 0 is NOT NULL");
// elog(WARNING, (PG_ARGISNULL(1)) ? "arg 1 is NULL" : "arg 1 is NOT NULL");
if (!AggCheckCallContext(fcinfo, NULL)) {
// elog(WARNING, "fmcs_mol2s_transition() called in out of aggregate
// context");
ereport(
ERROR,
(errmsg("fmcs_mol2s_transition() called in out of aggregate context")));
}
if (PG_ARGISNULL(0) && !PG_ARGISNULL(1)) { // first call
/// elog(WARNING, "fmcs_mol2s_transition() called first time");
CROMol mol = PG_GETARG_DATUM(1);
int len, ts_size;
char *smiles;
elog(WARNING, "mol=%p, fcinfo: %p, %p", mol, fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(1), NULL, &mol, NULL);
smiles = makeMolText(mol, &len, false);
// char *smiles= Mol2Smiles(mol);
// int len = strlen(smiles);
/// elog(WARNING, smiles);
ts_size = len + VARHDRSZ;
text *ts = (text *)palloc(ts_size); // new return value
SET_VARSIZE(ts, ts_size);
memcpy(VARDATA(ts), smiles, len);
PG_RETURN_TEXT_P(ts);
} else if (!PG_ARGISNULL(0) &&
!PG_ARGISNULL(1)) { // Called in aggregate context...
text *t0 = PG_GETARG_TEXT_P(0);
/// elog(WARNING, "fmcs_mol2s_transition(): next iteration in the same
/// run");
// elog(WARNING, VARDATA(t0));
// mol_to_smiles():
CROMol mol = PG_GETARG_DATUM(1);
int len;
elog(WARNING, "mol=%p, fcinfo: %p, %p", mol, fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt);
fcinfo->flinfo->fn_extra =
searchMolCache(fcinfo->flinfo->fn_extra, fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(1), NULL, &mol, NULL);
char *smiles = makeMolText(mol, &len, false);
// char *smiles= Mol2Smiles(mol);
// int len = strlen(smiles);
/// elog(WARNING, smiles);
int32 ts_size = VARSIZE(t0) + 1 + len;
text *ts = (text *)palloc(ts_size); // new return value
SET_VARSIZE(ts, ts_size);
memcpy(VARDATA(ts), VARDATA(t0), VARSIZE(t0) - VARHDRSZ);
*(char *)(VARDATA(ts) + VARSIZE(t0) - VARHDRSZ) = ' ';
memcpy(VARDATA(ts) + VARSIZE(t0) - VARHDRSZ + 1, smiles, len);
// elog(WARNING, VARDATA(ts));
PG_RETURN_TEXT_P(ts);
}
//------
/// elog(WARNING, "fmcs_mol2s_transition(): return empty text block");
{
int32 ts_size = VARHDRSZ;
text *ts = (text *)palloc(ts_size); // return empty text block
SET_VARSIZE(ts, ts_size);
PG_RETURN_TEXT_P(ts);
}
}
