mirror of
https://github.com/rdkit/rdkit.git
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374 lines
11 KiB
C
374 lines
11 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 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 "rdkit.h"
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#include "fmgr.h"
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#if PG_VERSION_NUM>=90000
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#include "utils/bytea.h"
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#endif
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#include "utils/builtins.h"
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PG_MODULE_MAGIC;
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PG_FUNCTION_INFO_V1(mol_in);
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Datum mol_in(PG_FUNCTION_ARGS);
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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);
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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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PG_FUNCTION_INFO_V1(mol_recv);
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Datum mol_recv(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(mol_out);
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Datum mol_out(PG_FUNCTION_ARGS);
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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);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PG_FUNCTION_INFO_V1(mol_send);
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Datum mol_send(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(mol_from_ctab);
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Datum mol_from_ctab(PG_FUNCTION_ARGS);
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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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CROMol mol;
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Mol *res;
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mol = parseMolCTAB(data,false,true);
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if(!mol) PG_RETURN_NULL();
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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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PG_FUNCTION_INFO_V1(mol_from_smarts);
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Datum mol_from_smarts(PG_FUNCTION_ARGS);
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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);
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if(!mol) PG_RETURN_NULL();
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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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PG_FUNCTION_INFO_V1(mol_from_smiles);
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Datum mol_from_smiles(PG_FUNCTION_ARGS);
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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);
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if(!mol) PG_RETURN_NULL();
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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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PG_FUNCTION_INFO_V1(mol_to_smiles);
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Datum mol_to_smiles(PG_FUNCTION_ARGS);
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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);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PG_FUNCTION_INFO_V1(mol_to_smarts);
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Datum mol_to_smarts(PG_FUNCTION_ARGS);
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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);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PG_FUNCTION_INFO_V1(mol_from_pkl);
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Datum mol_from_pkl(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(mol_to_pkl);
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Datum mol_to_pkl(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(qmol_in);
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Datum qmol_in(PG_FUNCTION_ARGS);
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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);
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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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PG_FUNCTION_INFO_V1(qmol_out);
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Datum qmol_out(PG_FUNCTION_ARGS);
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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);
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PG_RETURN_CSTRING( pnstrdup(str, len) );
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}
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PG_FUNCTION_INFO_V1(bfp_in);
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Datum bfp_in(PG_FUNCTION_ARGS);
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Datum
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bfp_in(PG_FUNCTION_ARGS) {
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MolBitmapFingerPrint fp;
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BitmapFingerPrint *b = DatumGetBitmapFingerPrintP(DirectFunctionCall1(
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byteain,
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PG_GETARG_DATUM(0)
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));
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/* check correctness */
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fp = constructMolBitmapFingerPrint(b);
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freeMolBitmapFingerPrint(fp);
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PG_RETURN_BITMAPFINGERPRINT_P(b);
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}
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PG_FUNCTION_INFO_V1(bfp_out);
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Datum bfp_out(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(bfp_from_binary_text);
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Datum bfp_from_binary_text(PG_FUNCTION_ARGS);
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Datum
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bfp_from_binary_text(PG_FUNCTION_ARGS) {
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MolBitmapFingerPrint fp;
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BitmapFingerPrint *b =PG_GETARG_BYTEA_P(0);
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fp = constructMolBitmapFingerPrint(b);
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freeMolBitmapFingerPrint(fp);
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PG_RETURN_BITMAPFINGERPRINT_P(b);
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}
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PG_FUNCTION_INFO_V1(bfp_to_binary_text);
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Datum bfp_to_binary_text(PG_FUNCTION_ARGS);
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Datum
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bfp_to_binary_text(PG_FUNCTION_ARGS) {
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MolBitmapFingerPrint abfp;
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fcinfo->flinfo->fn_extra = SearchBitmapFPCache(
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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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BitmapFingerPrint *b=deconstructMolBitmapFingerPrint(abfp);
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PG_RETURN_BYTEA_P( b );
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}
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PG_FUNCTION_INFO_V1(sfp_in);
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Datum sfp_in(PG_FUNCTION_ARGS);
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Datum
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sfp_in(PG_FUNCTION_ARGS) {
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MolSparseFingerPrint fp;
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SparseFingerPrint *b = DatumGetSparseFingerPrintP(DirectFunctionCall1(
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byteain,
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PG_GETARG_DATUM(0)
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));
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/* check correctness */
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fp = constructMolSparseFingerPrint(b);
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freeMolSparseFingerPrint(fp);
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PG_RETURN_SPARSEFINGERPRINT_P(b);
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}
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PG_FUNCTION_INFO_V1(sfp_out);
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Datum sfp_out(PG_FUNCTION_ARGS);
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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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PG_FUNCTION_INFO_V1(rdkit_version);
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Datum rdkit_version(PG_FUNCTION_ARGS);
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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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