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da579451eeb66b02fcafc41c928cec5de47977a7
rdkit/Code/PgSQL/rdkit/rdkit_io.c
Paolo Tosco cf8180e435 - added PGDLLEXPORT to allow exporting the relevant symbols in the Windows 
rdkit.dll PostgreSQL cartridge DLL
2016-02-21 21:38:13 +00:00

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// $Id$
//
// Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include "rdkit.h"
#include "fmgr.h"
#if PG_VERSION_NUM>=90000
#include "utils/bytea.h"
#endif
#include "utils/builtins.h"
PG_MODULE_MAGIC;
PGDLLEXPORT Datum mol_in(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_in);
Datum
mol_in(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CROMol mol;
Mol *res;
mol = parseMolText(data,false,false,false);
if(!mol){
ereport(ERROR,
(errcode(ERRCODE_DATA_EXCEPTION),
errmsg("could not construct molecule")));
}
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_recv(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_recv);
Datum
mol_recv(PG_FUNCTION_ARGS) {
bytea *data = PG_GETARG_BYTEA_P(0);
int len=VARSIZE(data)-VARHDRSZ;
CROMol mol;
Mol *res;
mol = parseMolBlob(VARDATA(data),len);
res = deconstructROMol(mol);
freeCROMol(mol);
PG_FREE_IF_COPY(data, 0);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_out(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_out);
Datum
mol_out(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);
str = makeMolText(mol, &len,false);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum mol_send(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_send);
Datum
mol_send(PG_FUNCTION_ARGS) {
CROMol mol;
bytea *res;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchMolCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &mol, NULL);
str = makeMolBlob(mol, &len);
res=(bytea *)palloc(len+VARHDRSZ);
SET_VARSIZE(res,len+VARHDRSZ);
memcpy(VARDATA(res),str,len);
PG_RETURN_BYTEA_P( res );
}
PGDLLEXPORT Datum mol_from_ctab(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_from_ctab);
Datum
mol_from_ctab(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
bool keepConformer = PG_GETARG_BOOL(1);
CROMol mol;
Mol *res;
mol = parseMolCTAB(data,keepConformer,true,false);
if(!mol) PG_RETURN_NULL();
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum qmol_from_ctab(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(qmol_from_ctab);
Datum
qmol_from_ctab(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
bool keepConformer = PG_GETARG_BOOL(1);
CROMol mol;
Mol *res;
mol = parseMolCTAB(data,keepConformer,true,true);
if(!mol) PG_RETURN_NULL();
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_from_smarts(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_from_smarts);
Datum
mol_from_smarts(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CROMol mol;
Mol *res;
mol = parseMolText(data,true,true,false);
if(!mol) PG_RETURN_NULL();
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_from_smiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_from_smiles);
Datum
mol_from_smiles(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CROMol mol;
Mol *res;
mol = parseMolText(data,false,true,false);
if(!mol) PG_RETURN_NULL();
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum qmol_from_smiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(qmol_from_smiles);
Datum
qmol_from_smiles(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CROMol mol;
Mol *res;
mol = parseMolText(data,false,true,true);
if(!mol) PG_RETURN_NULL();
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_to_ctab(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_to_ctab);
Datum
mol_to_ctab(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);
bool createDepictionIfMissing = PG_GETARG_BOOL(1);
str = makeCtabText(mol, &len, createDepictionIfMissing);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum mol_to_smiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_to_smiles);
Datum
mol_to_smiles(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);
str = makeMolText(mol, &len,false);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum mol_to_smarts(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_to_smarts);
Datum
mol_to_smarts(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);
str = makeMolText(mol, &len,true);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum mol_from_pkl(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_from_pkl);
Datum
mol_from_pkl(PG_FUNCTION_ARGS) {
bytea *data = PG_GETARG_BYTEA_P(0);
int len=VARSIZE(data)-VARHDRSZ;
CROMol mol;
Mol *res;
mol = parseMolBlob(VARDATA(data),len);
res = deconstructROMol(mol);
freeCROMol(mol);
PG_FREE_IF_COPY(data, 0);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum mol_to_pkl(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(mol_to_pkl);
Datum
mol_to_pkl(PG_FUNCTION_ARGS) {
CROMol mol;
bytea *res;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchMolCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &mol, NULL);
str = makeMolBlob(mol, &len);
res=(bytea *)palloc(len+VARHDRSZ);
SET_VARSIZE(res,len+VARHDRSZ);
memcpy(VARDATA(res),str,len);
PG_RETURN_BYTEA_P( res );
}
PGDLLEXPORT Datum qmol_in(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(qmol_in);
Datum
qmol_in(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CROMol mol;
Mol *res;
mol = parseMolText(data,true,false,false);
if(!mol){
ereport(ERROR,
(errcode(ERRCODE_DATA_EXCEPTION),
errmsg("could not construct molecule")));
}
res = deconstructROMol(mol);
freeCROMol(mol);
PG_RETURN_MOL_P(res);
}
PGDLLEXPORT Datum qmol_out(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(qmol_out);
Datum
qmol_out(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);
str = makeMolText(mol, &len,true);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum bfp_in(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(bfp_in);
Datum
bfp_in(PG_FUNCTION_ARGS) {
MolBitmapFingerPrint fp;
BitmapFingerPrint *b = DatumGetBitmapFingerPrintP(DirectFunctionCall1(
byteain,
PG_GETARG_DATUM(0)
));
/* check correctness */
fp = constructMolBitmapFingerPrint(b);
freeMolBitmapFingerPrint(fp);
PG_RETURN_BITMAPFINGERPRINT_P(b);
}
PGDLLEXPORT Datum bfp_out(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(bfp_out);
Datum
bfp_out(PG_FUNCTION_ARGS) {
PG_RETURN_DATUM( DirectFunctionCall1( byteaout, PG_GETARG_DATUM(0) ) );
}
PGDLLEXPORT Datum bfp_from_binary_text(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(bfp_from_binary_text);
Datum
bfp_from_binary_text(PG_FUNCTION_ARGS) {
MolBitmapFingerPrint fp;
BitmapFingerPrint *b =PG_GETARG_BYTEA_P(0);
fp = constructMolBitmapFingerPrint(b);
freeMolBitmapFingerPrint(fp);
PG_RETURN_BITMAPFINGERPRINT_P(b);
}
PGDLLEXPORT Datum bfp_to_binary_text(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(bfp_to_binary_text);
Datum
bfp_to_binary_text(PG_FUNCTION_ARGS) {
MolBitmapFingerPrint abfp;
fcinfo->flinfo->fn_extra = SearchBitmapFPCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &abfp, NULL);
BitmapFingerPrint *b=deconstructMolBitmapFingerPrint(abfp);
PG_RETURN_BYTEA_P( b );
}
PGDLLEXPORT Datum sfp_in(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(sfp_in);
Datum
sfp_in(PG_FUNCTION_ARGS) {
MolSparseFingerPrint fp;
SparseFingerPrint *b = DatumGetSparseFingerPrintP(DirectFunctionCall1(
byteain,
PG_GETARG_DATUM(0)
));
/* check correctness */
fp = constructMolSparseFingerPrint(b);
freeMolSparseFingerPrint(fp);
PG_RETURN_SPARSEFINGERPRINT_P(b);
}
PGDLLEXPORT Datum sfp_out(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(sfp_out);
Datum
sfp_out(PG_FUNCTION_ARGS) {
PG_RETURN_DATUM( DirectFunctionCall1( byteaout, PG_GETARG_DATUM(0) ) );
}
PGDLLEXPORT Datum rdkit_version(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rdkit_version);
Datum
rdkit_version(PG_FUNCTION_ARGS) {
char *ver = "" RDKITVER;
char buf[1024];
Assert(strlen(ver) == 6);
snprintf(buf, sizeof(buf), "%d.%d.%d",
atoi( pnstrdup(ver, 2) ),
atoi( pnstrdup(ver + 2 , 2) ),
atoi( pnstrdup(ver + 4, 2) ));
PG_RETURN_TEXT_P(cstring_to_text(buf));
}
/* chemical reactions */
PGDLLEXPORT Datum reaction_in(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_in);
Datum
reaction_in(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CChemicalReaction rxn;
ChemReactionBA *rxnBA;
rxn = parseChemReactText(data,false,false);
if(!rxn){
ereport(ERROR,
(errcode(ERRCODE_DATA_EXCEPTION),
errmsg("could not construct chemical reaction")));
}
rxnBA = deconstructChemReact(rxn);
freeChemReaction(rxn);
PG_RETURN_CHEMREACTION_P(rxnBA);
}
PGDLLEXPORT Datum reaction_recv(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_recv);
Datum
reaction_recv(PG_FUNCTION_ARGS) {
bytea *data = PG_GETARG_BYTEA_P(0);
int len=VARSIZE(data)-VARHDRSZ;
CChemicalReaction rxn;
ChemReactionBA *rxnBA;
rxn = parseChemReactBlob(VARDATA(data),len);
rxnBA = deconstructChemReact(rxn);
freeChemReaction(rxn);
PG_FREE_IF_COPY(data, 0);
PG_RETURN_CHEMREACTION_P(rxnBA);
}
PGDLLEXPORT Datum reaction_out(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_out);
Datum
reaction_out(PG_FUNCTION_ARGS) {
CChemicalReaction rxn;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchChemReactionCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &rxn, NULL);
str = makeChemReactText(rxn, &len,false);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum reaction_send(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_send);
Datum
reaction_send(PG_FUNCTION_ARGS) {
CChemicalReaction rxn;
bytea *res;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchChemReactionCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &rxn, NULL);
str = makeChemReactBlob(rxn, &len);
res=(bytea *)palloc(len+VARHDRSZ);
SET_VARSIZE(res,len+VARHDRSZ);
memcpy(VARDATA(res),str,len);
PG_RETURN_BYTEA_P( res );
}
PGDLLEXPORT Datum reaction_from_ctab(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_from_ctab);
Datum
reaction_from_ctab(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CChemicalReaction rxn;
ChemReactionBA *rxnBA;
rxn = parseChemReactCTAB(data,true);
if(!rxn) PG_RETURN_NULL();
rxnBA = deconstructChemReact(rxn);
freeChemReaction(rxn);
PG_RETURN_CHEMREACTION_P(rxnBA);
}
PGDLLEXPORT Datum reaction_from_smarts(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_from_smarts);
Datum
reaction_from_smarts(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CChemicalReaction rxn;
ChemReactionBA *rxnBA;
rxn = parseChemReactText(data,true,true);
if(!rxn) PG_RETURN_NULL();
rxnBA = deconstructChemReact(rxn);
freeChemReaction(rxn);
PG_RETURN_CHEMREACTION_P(rxnBA);
}
PGDLLEXPORT Datum reaction_from_smiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_from_smiles);
Datum
reaction_from_smiles(PG_FUNCTION_ARGS) {
char *data = PG_GETARG_CSTRING(0);
CChemicalReaction rxn;
ChemReactionBA *rxnBA;
rxn = parseChemReactText(data,false,true);
if(!rxn) PG_RETURN_NULL();
rxnBA = deconstructChemReact(rxn);
freeChemReaction(rxn);
PG_RETURN_CHEMREACTION_P(rxnBA);
}
PGDLLEXPORT Datum reaction_to_ctab(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_to_ctab);
Datum
reaction_to_ctab(PG_FUNCTION_ARGS) {
CChemicalReaction rxn;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchChemReactionCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &rxn, NULL);
str = makeCTABChemReact(rxn, &len);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum reaction_to_smiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_to_smiles);
Datum
reaction_to_smiles(PG_FUNCTION_ARGS) {
CChemicalReaction rxn;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchChemReactionCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &rxn, NULL);
str = makeChemReactText(rxn, &len,false);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
PGDLLEXPORT Datum reaction_to_smarts(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(reaction_to_smarts);
Datum
reaction_to_smarts(PG_FUNCTION_ARGS) {
CChemicalReaction rxn;
char *str;
int len;
fcinfo->flinfo->fn_extra = SearchChemReactionCache(
fcinfo->flinfo->fn_extra,
fcinfo->flinfo->fn_mcxt,
PG_GETARG_DATUM(0),
NULL, &rxn, NULL);
str = makeChemReactText(rxn, &len,true);
PG_RETURN_CSTRING( pnstrdup(str, len) );
}
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