mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
d41752d558
* run clang-tidy with readability-braces-around-statements clang-format the results clean up all the parts that clang-tidy-8 broke * fix problem on windows
646 lines
18 KiB
C
646 lines
18 KiB
C
// $Id$
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//
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// Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written
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// permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <postgres.h>
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#include <fmgr.h>
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#include <utils/bytea.h>
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#include <utils/builtins.h>
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#include "rdkit.h"
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#include "cache.h"
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PG_MODULE_MAGIC;
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PGDLLEXPORT Datum mol_in(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_in);
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Datum
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mol_in(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CROMol mol;
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Mol *res;
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mol = parseMolText(data,false,false,false);
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if(!mol){
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ereport(ERROR,
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(errcode(ERRCODE_DATA_EXCEPTION),
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errmsg("could not construct molecule")));
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_recv(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_recv);
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Datum
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mol_recv(PG_FUNCTION_ARGS) {
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bytea *data = PG_GETARG_BYTEA_P(0);
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int len=VARSIZE(data)-VARHDRSZ;
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CROMol mol;
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Mol *res;
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mol = parseMolBlob(VARDATA(data),len);
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_FREE_IF_COPY(data, 0);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_out(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_out);
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Datum
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mol_out(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolText(mol, &len,false,true);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum mol_send(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_send);
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Datum
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mol_send(PG_FUNCTION_ARGS) {
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CROMol mol;
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bytea *res;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolBlob(mol, &len);
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res=(bytea *)palloc(len+VARHDRSZ);
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SET_VARSIZE(res,len+VARHDRSZ);
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memcpy(VARDATA(res),str,len);
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PG_RETURN_BYTEA_P( res );
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}
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PGDLLEXPORT Datum mol_from_ctab(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_from_ctab);
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Datum
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mol_from_ctab(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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bool keepConformer = PG_GETARG_BOOL(1);
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CROMol mol;
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Mol *res;
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mol = parseMolCTAB(data,keepConformer,true,false);
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if (!mol) {
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PG_RETURN_NULL();
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum qmol_from_ctab(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(qmol_from_ctab);
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Datum
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qmol_from_ctab(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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bool keepConformer = PG_GETARG_BOOL(1);
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CROMol mol;
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Mol *res;
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mol = parseMolCTAB(data,keepConformer,true,true);
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if (!mol) {
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PG_RETURN_NULL();
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_from_smarts(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_from_smarts);
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Datum
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mol_from_smarts(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CROMol mol;
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Mol *res;
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mol = parseMolText(data,true,true,false);
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if (!mol) {
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PG_RETURN_NULL();
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_from_smiles(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_from_smiles);
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Datum
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mol_from_smiles(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CROMol mol;
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Mol *res;
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mol = parseMolText(data,false,true,false);
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if (!mol) {
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PG_RETURN_NULL();
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum qmol_from_smiles(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(qmol_from_smiles);
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Datum
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qmol_from_smiles(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CROMol mol;
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Mol *res;
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mol = parseMolText(data,false,true,true);
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if (!mol) {
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PG_RETURN_NULL();
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_to_ctab(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_to_ctab);
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Datum
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mol_to_ctab(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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bool createDepictionIfMissing = PG_GETARG_BOOL(1);
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeCtabText(mol, &len, createDepictionIfMissing);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum mol_to_smiles(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_to_smiles);
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Datum
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mol_to_smiles(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolText(mol, &len,false,false);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum mol_to_cxsmiles(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_to_cxsmiles);
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Datum
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mol_to_cxsmiles(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolText(mol, &len,false,true);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum mol_to_smarts(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_to_smarts);
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Datum
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mol_to_smarts(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolText(mol, &len,true,false);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum mol_from_pkl(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_from_pkl);
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Datum
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mol_from_pkl(PG_FUNCTION_ARGS) {
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bytea *data = PG_GETARG_BYTEA_P(0);
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int len=VARSIZE(data)-VARHDRSZ;
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CROMol mol;
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Mol *res;
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mol = parseMolBlob(VARDATA(data),len);
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_FREE_IF_COPY(data, 0);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum mol_to_pkl(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(mol_to_pkl);
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Datum
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mol_to_pkl(PG_FUNCTION_ARGS) {
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CROMol mol;
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bytea *res;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolBlob(mol, &len);
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res=(bytea *)palloc(len+VARHDRSZ);
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SET_VARSIZE(res,len+VARHDRSZ);
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memcpy(VARDATA(res),str,len);
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PG_RETURN_BYTEA_P( res );
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}
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PGDLLEXPORT Datum qmol_in(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(qmol_in);
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Datum
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qmol_in(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CROMol mol;
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Mol *res;
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mol = parseMolText(data,true,false,false);
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if(!mol){
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ereport(ERROR,
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(errcode(ERRCODE_DATA_EXCEPTION),
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errmsg("could not construct molecule")));
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}
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res = deconstructROMol(mol);
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freeCROMol(mol);
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PG_RETURN_MOL_P(res);
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}
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PGDLLEXPORT Datum qmol_out(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(qmol_out);
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Datum
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qmol_out(PG_FUNCTION_ARGS) {
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CROMol mol;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchMolCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &mol, NULL);
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str = makeMolText(mol, &len,true,false);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum bfp_in(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(bfp_in);
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Datum
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bfp_in(PG_FUNCTION_ARGS) {
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CBfp fp;
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Bfp *b = DatumGetBfpP( DirectFunctionCall1( byteain, PG_GETARG_DATUM(0) ) );
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/* check correctness */
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fp = constructCBfp(b);
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freeCBfp(fp);
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PG_RETURN_BFP_P(b);
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}
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PGDLLEXPORT Datum bfp_out(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(bfp_out);
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Datum
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bfp_out(PG_FUNCTION_ARGS) {
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PG_RETURN_DATUM( DirectFunctionCall1( byteaout, PG_GETARG_DATUM(0) ) );
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}
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PGDLLEXPORT Datum bfp_from_binary_text(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(bfp_from_binary_text);
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Datum
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bfp_from_binary_text(PG_FUNCTION_ARGS) {
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CBfp fp;
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Bfp *b =PG_GETARG_BYTEA_P(0);
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fp = constructCBfp(b);
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freeCBfp(fp);
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PG_RETURN_BFP_P(b);
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}
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PGDLLEXPORT Datum bfp_to_binary_text(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(bfp_to_binary_text);
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Datum
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bfp_to_binary_text(PG_FUNCTION_ARGS) {
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CBfp abfp;
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fcinfo->flinfo->fn_extra = searchBfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &abfp, NULL);
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PG_RETURN_BYTEA_P( deconstructCBfp(abfp) );
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}
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PGDLLEXPORT Datum sfp_in(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_in);
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Datum
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sfp_in(PG_FUNCTION_ARGS) {
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CSfp fp;
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Sfp *b = DatumGetSfpP(DirectFunctionCall1( byteain, PG_GETARG_DATUM(0) ));
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/* check correctness */
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fp = constructCSfp(b);
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freeCSfp(fp);
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PG_RETURN_SFP_P(b);
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}
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PGDLLEXPORT Datum sfp_out(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_out);
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Datum
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sfp_out(PG_FUNCTION_ARGS) {
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PG_RETURN_DATUM( DirectFunctionCall1( byteaout, PG_GETARG_DATUM(0) ) );
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}
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PGDLLEXPORT Datum rdkit_version(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(rdkit_version);
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Datum
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rdkit_version(PG_FUNCTION_ARGS) {
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char *ver = "" RDKITVER;
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char buf[1024];
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Assert(strlen(ver) == 6);
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snprintf(buf, sizeof(buf), "%d.%d.%d",
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atoi( pnstrdup(ver, 2) ),
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atoi( pnstrdup(ver + 2 , 2) ),
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atoi( pnstrdup(ver + 4, 2) ));
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PG_RETURN_TEXT_P(cstring_to_text(buf));
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}
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/* chemical reactions */
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PGDLLEXPORT Datum reaction_in(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(reaction_in);
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Datum
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reaction_in(PG_FUNCTION_ARGS) {
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char *data = PG_GETARG_CSTRING(0);
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CChemicalReaction crxn;
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Reaction *rxn;
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crxn = parseChemReactText(data,false,false);
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if(!crxn){
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ereport(ERROR,
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(errcode(ERRCODE_DATA_EXCEPTION),
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errmsg("could not construct chemical reaction")));
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}
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rxn = deconstructChemReact(crxn);
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freeChemReaction(crxn);
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PG_RETURN_REACTION_P(rxn);
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}
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PGDLLEXPORT Datum reaction_recv(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(reaction_recv);
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Datum
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reaction_recv(PG_FUNCTION_ARGS) {
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bytea *data = PG_GETARG_BYTEA_P(0);
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int len=VARSIZE(data)-VARHDRSZ;
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CChemicalReaction crxn;
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Reaction *rxn;
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crxn = parseChemReactBlob(VARDATA(data),len);
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rxn = deconstructChemReact(crxn);
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freeChemReaction(crxn);
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PG_FREE_IF_COPY(data, 0);
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PG_RETURN_REACTION_P(rxn);
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}
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PGDLLEXPORT Datum reaction_out(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(reaction_out);
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Datum
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reaction_out(PG_FUNCTION_ARGS) {
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CChemicalReaction rxn;
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char *str;
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int len;
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fcinfo->flinfo->fn_extra = searchReactionCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(0),
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NULL, &rxn, NULL);
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str = makeChemReactText(rxn, &len,false);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PGDLLEXPORT Datum reaction_send(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(reaction_send);
|
|
Datum
|
|
reaction_send(PG_FUNCTION_ARGS) {
|
|
CChemicalReaction rxn;
|
|
bytea *res;
|
|
char *str;
|
|
int len;
|
|
|
|
fcinfo->flinfo->fn_extra = searchReactionCache(
|
|
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 crxn;
|
|
Reaction *rxn;
|
|
|
|
crxn = parseChemReactCTAB(data,true);
|
|
if (!crxn) {
|
|
PG_RETURN_NULL();
|
|
}
|
|
rxn = deconstructChemReact(crxn);
|
|
freeChemReaction(crxn);
|
|
|
|
PG_RETURN_REACTION_P(rxn);
|
|
}
|
|
|
|
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 crxn;
|
|
Reaction *rxn;
|
|
|
|
crxn = parseChemReactText(data,true,true);
|
|
if (!crxn) {
|
|
PG_RETURN_NULL();
|
|
}
|
|
rxn = deconstructChemReact(crxn);
|
|
freeChemReaction(crxn);
|
|
|
|
PG_RETURN_REACTION_P(rxn);
|
|
}
|
|
|
|
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 crxn;
|
|
Reaction *rxn;
|
|
|
|
crxn = parseChemReactText(data,false,true);
|
|
if (!crxn) {
|
|
PG_RETURN_NULL();
|
|
}
|
|
rxn = deconstructChemReact(crxn);
|
|
freeChemReaction(crxn);
|
|
|
|
PG_RETURN_REACTION_P(rxn);
|
|
}
|
|
|
|
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 = searchReactionCache(
|
|
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 = searchReactionCache(
|
|
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 = searchReactionCache(
|
|
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) );
|
|
}
|
|
|
|
|