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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
414 lines
12 KiB
C
414 lines
12 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 <postgres.h>
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#include <fmgr.h>
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#include "rdkit.h"
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#include "guc.h"
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#include "cache.h"
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static int
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sfpcmp(Sfp *a, Sfp *b) {
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int res;
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res = memcmp(VARDATA(a), VARDATA(b), Min(VARSIZE(a), VARSIZE(b)) - VARHDRSZ);
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if (res) {
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return res;
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}
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if (VARSIZE(a) == VARSIZE(b)) {
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return 0;
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}
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return (VARSIZE(a) > VARSIZE(b)) ? 1 : -1;
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}
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#define sfpCMPFUNC( type, action, ret ) \
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PGDLLEXPORT Datum sfp_##type(PG_FUNCTION_ARGS); \
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PG_FUNCTION_INFO_V1(sfp_##type); \
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Datum \
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sfp_##type(PG_FUNCTION_ARGS) \
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{ \
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Sfp *a, *b; \
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int res; \
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\
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fcinfo->flinfo->fn_extra = searchSfpCache( \
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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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&a, NULL, NULL); \
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fcinfo->flinfo->fn_extra = searchSfpCache( \
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fcinfo->flinfo->fn_extra, \
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fcinfo->flinfo->fn_mcxt, \
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PG_GETARG_DATUM(1), \
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&b, NULL, NULL); \
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res = sfpcmp(a, b); \
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PG_RETURN_##ret( res action 0 ); \
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} \
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/* keep compiler quiet - no extra ; */ \
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extern int no_such_variable
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sfpCMPFUNC(lt, <, BOOL);
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sfpCMPFUNC(le, <=, BOOL);
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sfpCMPFUNC(eq, ==, BOOL);
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sfpCMPFUNC(ge, >=, BOOL);
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sfpCMPFUNC(gt, >, BOOL);
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sfpCMPFUNC(ne, !=, BOOL);
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sfpCMPFUNC(cmp, +, INT32);
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PGDLLEXPORT Datum sfp_tanimoto_sml(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_tanimoto_sml);
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Datum
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sfp_tanimoto_sml(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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double res;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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res = calcSparseTanimotoSml(asfp, bsfp);
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PG_RETURN_FLOAT8(res);
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}
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PGDLLEXPORT Datum sfp_tanimoto_sml_op(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_tanimoto_sml_op);
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Datum
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sfp_tanimoto_sml_op(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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double res;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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res = calcSparseTanimotoSml(asfp, bsfp);
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PG_RETURN_BOOL( res >= getTanimotoLimit() );
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}
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#ifdef USE_SFP_OBJECTS
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PGDLLEXPORT Datum sfp_dice_sml(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_dice_sml);
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Datum
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sfp_dice_sml(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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double res;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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res = calcSparseDiceSml(asfp, bsfp);
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PG_RETURN_FLOAT8(res);
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}
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PGDLLEXPORT Datum sfp_dice_sml_op(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_dice_sml_op);
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Datum
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sfp_dice_sml_op(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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double res;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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res = calcSparseDiceSml(asfp, bsfp);
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PG_RETURN_BOOL( res >= getDiceLimit() );
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}
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#else
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PGDLLEXPORT Datum sfp_dice_sml(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_dice_sml);
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Datum
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sfp_dice_sml(PG_FUNCTION_ARGS) {
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const char *a,*b;
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unsigned int sza,szb;
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double res;
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bytea *ba=PG_GETARG_BYTEA_P(0);
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bytea *bb=PG_GETARG_BYTEA_P(1);
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a = VARDATA(ba);
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sza=VARSIZE(ba)-VARHDRSZ;
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b = VARDATA(bb);
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szb=VARSIZE(bb)-VARHDRSZ;
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res = calcSparseStringDiceSml(a,sza,b,szb);
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PG_RETURN_FLOAT8(res);
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}
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PGDLLEXPORT Datum sfp_dice_sml_op(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_dice_sml_op);
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Datum
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sfp_dice_sml_op(PG_FUNCTION_ARGS) {
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const char *a,*b;
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unsigned int sza,szb;
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double res;
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bytea *ba=PG_GETARG_BYTEA_P(0);
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bytea *bb=PG_GETARG_BYTEA_P(1);
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a = VARDATA(ba);
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sza=VARSIZE(ba)-VARHDRSZ;
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b = VARDATA(bb);
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szb=VARSIZE(bb)-VARHDRSZ;
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res = calcSparseStringDiceSml(a,sza,b,szb);
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PG_RETURN_BOOL(res >= getDiceLimit() );
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}
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PGDLLEXPORT Datum sfp_allvals_gt(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_allvals_gt);
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Datum
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sfp_allvals_gt(PG_FUNCTION_ARGS) {
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const char *a;
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unsigned int sza;
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bool res;
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bytea *ba=PG_GETARG_BYTEA_P(0);
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int tgt=PG_GETARG_INT32(1);
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a = VARDATA(ba);
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sza=VARSIZE(ba)-VARHDRSZ;
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res = calcSparseStringAllValsGT(a,sza,tgt);
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PG_RETURN_BOOL(res);
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}
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PGDLLEXPORT Datum sfp_allvals_lt(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_allvals_lt);
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Datum
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sfp_allvals_lt(PG_FUNCTION_ARGS) {
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const char *a;
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unsigned int sza;
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bool res;
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bytea *ba=PG_GETARG_BYTEA_P(0);
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int tgt=PG_GETARG_INT32(1);
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a = VARDATA(ba);
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sza=VARSIZE(ba)-VARHDRSZ;
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res = calcSparseStringAllValsLT(a,sza,tgt);
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PG_RETURN_BOOL(res);
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}
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#endif // USE_SFP_OBJECTS
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PGDLLEXPORT Datum sfp_add(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_add);
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Datum
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sfp_add(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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CSfp fp;
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Sfp *sfp;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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fp = addSFP(asfp, bsfp);
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum sfp_subtract(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(sfp_subtract);
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Datum
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sfp_subtract(PG_FUNCTION_ARGS) {
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CSfp asfp, bsfp;
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CSfp fp;
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Sfp *sfp;
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fcinfo->flinfo->fn_extra = searchSfpCache(
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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, &asfp, NULL);
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fcinfo->flinfo->fn_extra = searchSfpCache(
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fcinfo->flinfo->fn_extra,
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fcinfo->flinfo->fn_mcxt,
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PG_GETARG_DATUM(1),
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NULL, &bsfp, NULL);
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fp = subtractSFP(asfp, bsfp);
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum morgan_fp(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(morgan_fp);
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Datum
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morgan_fp(PG_FUNCTION_ARGS) {
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CROMol mol;
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CSfp fp;
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Sfp *sfp;
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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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fp = makeMorganSFP(mol, PG_GETARG_INT32(1) /* radius */ );
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum featmorgan_fp(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(featmorgan_fp);
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Datum
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featmorgan_fp(PG_FUNCTION_ARGS) {
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CROMol mol;
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CSfp fp;
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Sfp *sfp;
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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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fp = makeFeatMorganSFP(mol, PG_GETARG_INT32(1) /* radius */ );
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum atompair_fp(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(atompair_fp);
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Datum
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atompair_fp(PG_FUNCTION_ARGS) {
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CROMol mol;
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CSfp fp;
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Sfp *sfp;
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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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fp = makeAtomPairSFP(mol);
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum torsion_fp(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(torsion_fp);
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Datum
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torsion_fp(PG_FUNCTION_ARGS) {
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CROMol mol;
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CSfp fp;
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Sfp *sfp;
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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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fp = makeTopologicalTorsionSFP(mol);
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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PGDLLEXPORT Datum reaction_difference_fp(PG_FUNCTION_ARGS);
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PG_FUNCTION_INFO_V1(reaction_difference_fp);
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Datum
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reaction_difference_fp(PG_FUNCTION_ARGS) {
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CChemicalReaction rxn;
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CSfp fp;
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Sfp *sfp;
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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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fp = makeReactionDifferenceSFP(rxn, getReactionDifferenceFpSize(),
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PG_GETARG_INT32(1) /* Fingerprinttype */ );
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sfp = deconstructCSfp(fp);
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freeCSfp(fp);
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PG_RETURN_SFP_P(sfp);
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}
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