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// $Id: MolOps.cpp 1528 2010-09-26 17:04:37Z glandrum $
//
// Copyright (C) 2005-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "RDLib.h"
#include <string>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <DataStructs/BitVects.h>
#include <DataStructs/BitOps.h>
extern "C" {
PG_FUNCTION_INFO_V1(rd_canonsmiles);
Datum rd_canonsmiles(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_molpickle);
Datum rd_molpickle(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_hassubstruct_smi);
Datum rd_hassubstruct_smi(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_hassubstruct_pkl);
Datum rd_hassubstruct_pkl(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_substructcount_smi);
Datum rd_substructcount_smi(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_substructcount_pkl);
Datum rd_substructcount_pkl(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_substructfp);
Datum rd_substructfp(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_substructfp_bits);
Datum rd_substructfp_bits(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_similarityfp);
Datum rd_similarityfp(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_similarityfp_bits);
Datum rd_similarityfp_bits(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_mollogp_smi);
Datum rd_mollogp_smi(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_mollogp_pkl);
Datum rd_mollogp_pkl(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_amw_smi);
Datum rd_amw_smi(PG_FUNCTION_ARGS);
PG_FUNCTION_INFO_V1(rd_amw_pkl);
Datum rd_amw_pkl(PG_FUNCTION_ARGS);
}
Datum rd_canonsmiles(PG_FUNCTION_ARGS)
{
std::string res="";
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
RDKit::RWMol *mol=0;
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try {
res=RDKit::MolToSmiles(*mol,true);
} catch (...) {
ereport(ERROR,(errcode(ERRCODE_INTERNAL_ERROR),
errmsg("molecule constructed from SMILES '%s' could not be converted back to SMILES",
smiS.c_str())));
}
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_canonsmiles function call")));
}
text *textRes;
int totalSz=res.size()+VARHDRSZ;
textRes = (text *)palloc(totalSz);
VARATT_SIZEP(textRes)=totalSz;
memcpy(VARDATA(textRes),res.c_str(),res.size());
PG_RETURN_TEXT_P(textRes);
}
Datum rd_molpickle(PG_FUNCTION_ARGS)
{
StringInfoData buf;
pq_begintypsend(&buf);
std::string pkl="";
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
RDKit::RWMol *mol=0;
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
RDKit::MolPickler::pickleMol(*mol,pkl);
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_molpickle function call")));
}
pq_sendtext(&buf,pkl.c_str(),pkl.size());
PG_RETURN_BYTEA_P(pq_endtypsend(&buf));
}
Datum rd_hassubstruct_smi(PG_FUNCTION_ARGS)
{
if(PG_ARGISNULL(0) || PG_ARGISNULL(1)) {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_hassubstruct_smi function call")));
}
text *sma = PG_GETARG_TEXT_P(0);
text *smi = PG_GETARG_TEXT_P(1);
RDKit::RWMol *probe=0;
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
std::string smaS(VARDATA(sma),VARSIZE(sma)-VARHDRSZ);
bool res = false;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try {
probe=RDKit::SmartsToMol(smaS);
} catch (...) {
probe=0;
}
if(probe){
RDKit::MatchVectType matchVect;
res = RDKit::SubstructMatch(*mol,*probe,matchVect);
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES/SMARTS '%s' could not be converted into a query",
smaS.c_str())));
}
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
PG_RETURN_BOOL(res);
}
Datum rd_hassubstruct_pkl(PG_FUNCTION_ARGS)
{
bool res = false;
if(!PG_ARGISNULL(0) && !PG_ARGISNULL(1)) {
bytea *probePkl=PG_GETARG_BYTEA_P(0);
bytea *refPkl=PG_GETARG_BYTEA_P(1);
RDKit::ROMol *probe=0,*ref=0;
try {
probe = new RDKit::ROMol(std::string(VARDATA(probePkl),VARSIZE(probePkl)-VARHDRSZ));
} catch (...) {
probe=0;
}
try {
ref = new RDKit::ROMol(std::string(VARDATA(refPkl),VARSIZE(refPkl)-VARHDRSZ));
} catch (...) {
ref=0;
}
if(probe && ref){
RDKit::MatchVectType matchVect;
res = RDKit::SubstructMatch(*ref,*probe,matchVect);
} else {
if(!probe){
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument 1 to a molecule")));
}
if(!ref){
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument 2 to a molecule")));
}
}
if(probe) delete probe;
if(ref) delete ref;
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_hassubstruct_pkl function call")));
}
//elog(INFO,"%d %s",res,smiS.c_str());
PG_RETURN_BOOL(res);
}
Datum rd_substructcount_smi(PG_FUNCTION_ARGS)
{
if(PG_ARGISNULL(0) || PG_ARGISNULL(1)) {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_substructcount_smi function call")));
}
text *sma = PG_GETARG_TEXT_P(0);
text *smi = PG_GETARG_TEXT_P(1);
RDKit::RWMol *probe=0;
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
std::string smaS(VARDATA(sma),VARSIZE(sma)-VARHDRSZ);
int res = 0;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try {
probe=RDKit::SmartsToMol(smaS);
} catch (...) {
probe=0;
}
if(probe){
std::vector<RDKit::MatchVectType> matchVect;
res = RDKit::SubstructMatch(*mol,*probe,matchVect,true);
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES/SMARTS '%s' could not be converted into a query",
smaS.c_str())));
}
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
PG_RETURN_INT32(res);
}
Datum rd_substructcount_pkl(PG_FUNCTION_ARGS)
{
int res = 0;
if(!PG_ARGISNULL(0) && !PG_ARGISNULL(1)) {
bytea *probePkl=PG_GETARG_BYTEA_P(0);
bytea *refPkl=PG_GETARG_BYTEA_P(1);
RDKit::ROMol *probe=0,*ref=0;
try {
probe = new RDKit::ROMol(std::string(VARDATA(probePkl),VARSIZE(probePkl)-VARHDRSZ));
} catch (...) {
probe=0;
}
try {
ref = new RDKit::ROMol(std::string(VARDATA(refPkl),VARSIZE(refPkl)-VARHDRSZ));
} catch (...) {
ref=0;
}
if(probe && ref){
std::vector<RDKit::MatchVectType> matchVect;
res = RDKit::SubstructMatch(*ref,*probe,matchVect,true);
} else {
if(!probe){
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument 1 to a molecule")));
}
if(!ref){
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument 2 to a molecule")));
}
}
if(probe) delete probe;
if(ref) delete ref;
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_substructcount_pkl function call")));
}
//elog(INFO,"%d %s",res,smiS.c_str());
PG_RETURN_INT32(res);
}
Datum rd_substructfp(PG_FUNCTION_ARGS)
{
StringInfoData buf;
pq_begintypsend(&buf);
ExplicitBitVect *bv=0;
int fpSize=2048;
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try{
bv = RDKFingerprintMol(*mol,1,7,fpSize);
} catch (...) {
bv = new ExplicitBitVect(fpSize);
}
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_substructfp function call")));
}
std::string pkl=bv->toString();
delete bv;
pq_sendtext(&buf,pkl.c_str(),pkl.size());
PG_RETURN_BYTEA_P(pq_endtypsend(&buf));
}
Datum rd_substructfp_bits(PG_FUNCTION_ARGS)
{
int fpSize=2048;
ExplicitBitVect *bv=0;
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try{
bv = RDKFingerprintMol(*mol,1,7,fpSize);
} catch (...) {
bv = 0;
}
delete mol;
} else {
bv = 0;
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_substructfp_bits function call")));
}
// BVToVarBits handles null pointers w/o problems so we can go ahead and
// call it directly:
VarBit *result = BVToVarBits(bv,fpSize);
if(bv){
delete bv;
}
PG_RETURN_VARBIT_P(result);
}
Datum rd_similarityfp(PG_FUNCTION_ARGS)
{
StringInfoData buf;
pq_begintypsend(&buf);
ExplicitBitVect *bv=0;
int fpSize=2048;
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
double tgtDensity=0.3;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try{
bv = RDKFingerprintMol(*mol,1,7,fpSize);
double density=static_cast<double>(bv->getNumOnBits())/bv->getNumBits();
while(density<tgtDensity && bv->getNumBits()>8){
ExplicitBitVect *tmp=FoldFingerprint(*bv,2);
delete bv;
bv = tmp;
density=static_cast<double>(bv->getNumOnBits())/bv->getNumBits();
}
} catch (...) {
bv = new ExplicitBitVect(fpSize);
}
delete mol;
} else {
bv = new ExplicitBitVect(fpSize);
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_similarityfp function call")));
}
std::string pkl=bv->toString();
delete bv;
pq_sendtext(&buf,pkl.c_str(),pkl.size());
PG_RETURN_BYTEA_P(pq_endtypsend(&buf));
}
Datum rd_similarityfp_bits(PG_FUNCTION_ARGS)
{
int fpSize=2048;
ExplicitBitVect *bv=0;
if(!PG_ARGISNULL(0)){
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
double tgtDensity=0.3;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
try{
bv = RDKFingerprintMol(*mol,1,7,fpSize);
double density=static_cast<double>(bv->getNumOnBits())/bv->getNumBits();
while(density<tgtDensity && bv->getNumBits()>8){
ExplicitBitVect *tmp=FoldFingerprint(*bv,2);
delete bv;
bv = tmp;
density=static_cast<double>(bv->getNumOnBits())/bv->getNumBits();
}
} catch (...) {
bv = new ExplicitBitVect(fpSize);
}
delete mol;
} else {
bv = new ExplicitBitVect(fpSize);
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty SMILES in rd_similarityfp_bits function call")));
}
// BVToVarBits handles null pointers w/o problems so we can go ahead and
// call it directly:
if(bv) fpSize=bv->getNumBits();
VarBit *result = BVToVarBits(bv,fpSize);
if(bv){
delete bv;
}
PG_RETURN_VARBIT_P(result);
}
Datum rd_mollogp_smi(PG_FUNCTION_ARGS)
{
//elog(NOTICE,"rd_mollogp_smi");
if(PG_ARGISNULL(0)){
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_mollogp_smi function call")));
}
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
double res = 0.0;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
double tmp;
RDKit::Descriptors::CalcCrippenDescriptors(*mol,res,tmp);
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
PG_RETURN_FLOAT8(res);
}
Datum rd_mollogp_pkl(PG_FUNCTION_ARGS)
{
//elog(NOTICE,"rd_mollogp_pkl");
double res=0;
if(!PG_ARGISNULL(0)){
bytea *molPkl=PG_GETARG_BYTEA_P(0);
RDKit::ROMol *mol=0;
try {
mol = new RDKit::ROMol(std::string(VARDATA(molPkl),VARSIZE(molPkl)-VARHDRSZ));
} catch (...) {
mol=0;
}
if(mol){
//elog(NOTICE," numatoms: %d",mol->getNumAtoms());
double tmp;
RDKit::Descriptors::CalcCrippenDescriptors(*mol,res,tmp);
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument to a molecule in rd_mollogp_pkl")));
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_mollogp_pkl function call")));
}
PG_RETURN_FLOAT8(res);
}
Datum rd_amw_smi(PG_FUNCTION_ARGS)
{
if(PG_ARGISNULL(0)){
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_amw_smi function call")));
}
text *smi = PG_GETARG_TEXT_P(0);
std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
double res = 0.0;
RDKit::RWMol *mol;
try {
mol=RDKit::SmilesToMol(smiS);
} catch (...) {
mol=0;
}
if(mol) {
res = RDKit::Descriptors::CalcAMW(*mol);
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("SMILES '%s' could not be converted into a molecule",
smiS.c_str())));
}
PG_RETURN_FLOAT8(res);
}
Datum rd_amw_pkl(PG_FUNCTION_ARGS)
{
double res=0;
if(!PG_ARGISNULL(0)){
bytea *molPkl=PG_GETARG_BYTEA_P(0);
RDKit::ROMol *mol=0;
try {
mol = new RDKit::ROMol(std::string(VARDATA(molPkl),VARSIZE(molPkl)-VARHDRSZ));
} catch (...) {
mol=0;
}
if(mol){
res = RDKit::Descriptors::CalcAMW(*mol);
delete mol;
} else {
ereport(ERROR,(errcode(ERRCODE_INVALID_PARAMETER_VALUE),
errmsg("problems converting argument to a molecule in rd_amw_pkl")));
}
} else {
ereport(ERROR,(errcode(ERRCODE_NULL_VALUE_NOT_ALLOWED),
errmsg("missing or empty argument in rd_amw_pkl function call")));
}
PG_RETURN_FLOAT8(res);
}
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