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rdkit/Code/GraphMol/catch_sgroups.cpp
Greg Landrum ab2fc55292 add methods to allow the following properties from SubstanceGroups to be cleared: (#3547) 
- Brackets
- CStates
- AttachPoints
2020-11-03 12:02:25 -05:00

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//
//
// Copyright (C) 2018 Greg Landrum and T5 Informatics GmbH
//
// @@ 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 "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SubstanceGroup.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include "GraphMol/FileParsers/FileParsers.h"
using namespace RDKit;
/* Auxiliary functions */
void testIdxVector(const std::vector<unsigned int> &groupVector,
const std::vector<unsigned int> &reference) {
size_t vecSize = reference.size();
CHECK(groupVector.size() == vecSize);
auto sgItr = groupVector.begin();
for (auto refItr = reference.begin(); refItr != reference.end();
++sgItr, ++refItr) {
CHECK(1 + *sgItr == *refItr);
}
}
void testBrackets(
const std::vector<SubstanceGroup::Bracket> &brackets,
const std::vector<std::array<std::array<double, 3>, 3>> &reference) {
CHECK(brackets.size() == 2);
for (int i = 0; i < 2; ++i) {
for (int j = 0; j < 3; ++j) {
for (int k = 0; k < 3; ++k) {
CHECK(std::abs(brackets[i][j][k] - reference[i][j][k]) < 1.e-6);
}
}
}
}
RWMol buildSampleMolecule() {
// This builds a RDKit::RWMol with all implemented SubstanceGroup features in
// order to test them. SubstanceGroups and features probably do not make any
// sense.
//// Initialize Molecule ////
RWMol mol;
// Add some atoms and bonds
for (unsigned i = 0; i < 6; ++i) {
mol.addAtom(new Atom(6), false, true);
if (i > 0) {
mol.addBond(i - 1, i, Bond::SINGLE);
}
}
//// First SubstanceGroup ////
{
SubstanceGroup sg(&mol, "MUL");
sg.setProp("SUBTYPE", "BLO");
sg.setProp("MULT", "n");
sg.setProp("CONNECT", "HH");
// Add some atoms and bonds
for (unsigned i = 0; i < 3; ++i) {
sg.addAtomWithIdx(i);
sg.addParentAtomWithIdx(i);
sg.addBondWithIdx(i); // add 2 CBONDs + 1 XBOND
}
sg.setProp("COMPNO", 7u);
sg.setProp("ESTATE", "E");
SubstanceGroup::Bracket bracket1 = {{RDGeom::Point3D(1., 3., 0.),
RDGeom::Point3D(5., 7., 0.),
RDGeom::Point3D(0., 0., 0.)}};
sg.addBracket(bracket1);
SubstanceGroup::Bracket bracket2 = {{RDGeom::Point3D(2., 4., 0.),
RDGeom::Point3D(6., 8., 0.),
RDGeom::Point3D(0., 0., 0.)}};
sg.addBracket(bracket2);
// Vector should not be parsed (not a SUP group)
sg.addCState(2, RDGeom::Point3D());
sg.setProp("CLASS", "TEST CLASS");
sg.addAttachPoint(0, 0, "XX");
sg.setProp("BRKTYP", "PAREN");
addSubstanceGroup(mol, sg);
}
//// Second SubstanceGroup ////
{
SubstanceGroup sg(&mol, "SUP");
// Add some atoms and bonds
for (unsigned i = 3; i < 6; ++i) {
sg.addAtomWithIdx(i);
sg.addParentAtomWithIdx(i);
sg.addBondWithIdx(i - 1); // add 1 XBOND + 2 CBONDs
}
sg.setProp("LABEL", "TEST LABEL");
// V2000 has only x and y coords; z value restricted to 0.
RDGeom::Point3D vector(3., 4., 0.);
sg.addCState(2, vector); // Vector should be parsed now!
sg.addAttachPoint(3, -1, "YY");
addSubstanceGroup(mol, sg);
}
//// Third SubstanceGroup ////
{
SubstanceGroup sg(&mol, "DAT");
sg.setProp("FIELDNAME", "SAMPLE FIELD NAME"); // 30 char max
// Field Type is ignored in V3000
sg.setProp("FIELDINFO", "SAMPLE FIELD INFO"); // 20 char max
sg.setProp("QUERYTYPE", "PQ"); // 2 char max
sg.setProp("QUERYOP", "SAMPLE QUERY OP"); // 15 char max (rest of line)
// This should be properly formatted, but format is not checked
sg.setProp("FIELDDISP", "SAMPLE FIELD DISP");
STR_VECT dataFields = {"SAMPLE DATA FIELD 1", "SAMPLE DATA FIELD 2",
"SAMPLE DATA FIELD 3"};
sg.setProp("DATAFIELDS", dataFields);
addSubstanceGroup(mol, sg);
}
// Set a parent with higher index
const auto &sgroups = getSubstanceGroups(mol);
sgroups.at(0).setProp<unsigned int>("PARENT", 3);
return mol;
}
/* End Auxiliary functions */
TEST_CASE("Basic Sgroup creation", "[Sgroups]") {
// Create two SubstanceGroups and add them to a molecule
RWMol mol;
{
SubstanceGroup sg0(&mol, "DAT");
SubstanceGroup sg1(&mol, "SUP");
addSubstanceGroup(mol, sg0);
addSubstanceGroup(mol, sg1);
}
const auto &sgroups = getSubstanceGroups(mol);
REQUIRE(sgroups.size() == 2);
CHECK(sgroups.at(0).getProp<std::string>("TYPE") == "DAT");
CHECK(sgroups.at(1).getProp<std::string>("TYPE") == "SUP");
}
TEST_CASE("Build and test sample molecule", "[Sgroups]") {
auto mol = buildSampleMolecule();
const auto &sgroups = getSubstanceGroups(mol);
CHECK(sgroups.size() == 3);
SECTION("first sgroup") {
const auto &sg = sgroups.at(0);
CHECK(sg.getProp<std::string>("TYPE") == "MUL");
CHECK(sg.getProp<std::string>("SUBTYPE") == "BLO");
CHECK(sg.getProp<std::string>("MULT") == "n");
CHECK(sg.getProp<std::string>("CONNECT") == "HH");
std::vector<unsigned int> atoms_reference = {1, 2, 3};
auto atoms = sg.getAtoms();
testIdxVector(atoms, atoms_reference);
std::vector<unsigned int> patoms_reference = {1, 2, 3};
testIdxVector(sg.getParentAtoms(), patoms_reference);
std::vector<unsigned int> bonds_reference = {1, 2, 3};
auto bonds = sg.getBonds();
// bonds are not sorted in V3000; sort them here
std::sort(bonds.begin(), bonds.end());
testIdxVector(bonds, bonds_reference);
CHECK(sg.getBondType(bonds[0]) == SubstanceGroup::BondType::CBOND);
CHECK(sg.getBondType(bonds[1]) == SubstanceGroup::BondType::CBOND);
CHECK(sg.getBondType(bonds[2]) == SubstanceGroup::BondType::XBOND);
CHECK(sg.getProp<unsigned int>("COMPNO") == 7u);
CHECK(sg.getProp<std::string>("ESTATE") == "E");
std::vector<std::array<std::array<double, 3>, 3>> brackets_reference = {
{{{{1., 3., 0.}}, {{5., 7., 0.}}, {{0., 0., 0.}}}},
{{{{2., 4., 0.}}, {{6., 8., 0.}}, {{0., 0., 0.}}}},
};
testBrackets(sg.getBrackets(), brackets_reference);
auto cstates = sg.getCStates();
CHECK(cstates.size() == 1);
CHECK(cstates[0].bondIdx == bonds[2]);
CHECK(cstates[0].vector.x == 0.);
CHECK(cstates[0].vector.y == 0.);
CHECK(cstates[0].vector.z == 0.);
CHECK(sg.getProp<std::string>("CLASS") == "TEST CLASS");
auto ap = sg.getAttachPoints();
CHECK(ap.size() == 1);
CHECK(ap[0].aIdx == atoms[0]);
CHECK(ap[0].lvIdx == static_cast<int>(atoms[0]));
CHECK(ap[0].id == "XX");
CHECK(sg.getProp<std::string>("BRKTYP") == "PAREN");
CHECK(sg.getProp<unsigned int>("PARENT") == 3u);
}
SECTION("second sgroup") {
const auto &sg = sgroups.at(1);
CHECK(sg.getProp<std::string>("TYPE") == "SUP");
std::vector<unsigned int> atoms_reference = {4, 5, 6};
auto atoms = sg.getAtoms();
testIdxVector(atoms, atoms_reference);
std::vector<unsigned int> patoms_reference = {4, 5, 6};
testIdxVector(sg.getParentAtoms(), patoms_reference);
std::vector<unsigned int> bonds_reference = {3, 4, 5};
auto bonds = sg.getBonds();
// bonds are not sorted in V3000; sort them here
std::sort(bonds.begin(), bonds.end());
testIdxVector(bonds, bonds_reference);
CHECK(sg.getBondType(bonds[0]) == SubstanceGroup::BondType::XBOND);
CHECK(sg.getBondType(bonds[1]) == SubstanceGroup::BondType::CBOND);
CHECK(sg.getBondType(bonds[2]) == SubstanceGroup::BondType::CBOND);
CHECK(sg.getProp<std::string>("LABEL") == "TEST LABEL");
auto cstates = sg.getCStates();
CHECK(cstates.size() == 1);
CHECK(cstates[0].bondIdx == bonds[0]);
CHECK(cstates[0].vector.x == 3.);
CHECK(cstates[0].vector.y == 4.);
CHECK(cstates[0].vector.z == 0.);
auto ap = sg.getAttachPoints();
CHECK(ap.size() == 1);
CHECK(ap[0].aIdx == atoms[0]);
CHECK(ap[0].lvIdx == -1);
CHECK(ap[0].id == "YY");
}
SECTION("third sgroup") {
const auto &sg = sgroups.at(2);
CHECK(sg.getProp<std::string>("TYPE") == "DAT");
CHECK(sg.getProp<std::string>("FIELDNAME") == "SAMPLE FIELD NAME");
CHECK(sg.getProp<std::string>("FIELDINFO") == "SAMPLE FIELD INFO");
CHECK(sg.getProp<std::string>("QUERYTYPE") == "PQ");
CHECK(sg.getProp<std::string>("QUERYOP") == "SAMPLE QUERY OP");
CHECK(sg.getProp<std::string>("FIELDDISP") == "SAMPLE FIELD DISP");
auto dataFields = sg.getProp<STR_VECT>("DATAFIELDS");
CHECK(dataFields.size() == 3);
CHECK(dataFields[0] == "SAMPLE DATA FIELD 1");
CHECK(dataFields[1] == "SAMPLE DATA FIELD 2");
CHECK(dataFields[2] == "SAMPLE DATA FIELD 3");
}
}
TEST_CASE("Removing sgroups", "[Sgroups]") {
SECTION("basics") {
auto m1 = R"CTAB(
Mrv2014 07312005252D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 7 6 3 0 0
M V30 BEGIN ATOM
M V30 1 * -12.75 11.5 0 0
M V30 2 O -11.4163 12.27 0 0
M V30 3 C -10.0826 11.5 0 0
M V30 4 C -8.749 12.27 0 0
M V30 5 O -10.0826 9.96 0 0
M V30 6 N -7.4153 11.5 0 0
M V30 7 C -6.0816 12.27 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 2 3 5
M V30 5 1 4 6
M V30 6 1 6 7
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 0 ATOMS=(3 2 3 5) XBONDS=(2 1 3) BRKXYZ=(9 -9.9955 12.6173 0 -
M V30 -9.0715 11.0169 0 0 0 0) BRKXYZ=(9 -11.5035 11.1527 0 -12.4275 12.7531 -
M V30 0 0 0 0) CONNECT=HT LABEL=n
M V30 2 DAT 0 ATOMS=(1 6) FIELDNAME=foo_data -
M V30 FIELDDISP=" -7.4153 11.5000 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=bar
M V30 3 DAT 0 ATOMS=(1 7) FIELDNAME=bar_data -
M V30 FIELDDISP=" -6.0816 12.2700 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=baz
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m1);
auto &sgs = getSubstanceGroups(*m1);
CHECK(sgs.size() == 3);
sgs.erase(++sgs.begin());
CHECK(sgs.size() == 2);
CHECK(getSubstanceGroups(*m1).size() == 2);
auto molb = MolToV3KMolBlock(*m1);
CHECK(molb.find("foo_data") == std::string::npos);
CHECK(molb.find("M V30 2 DAT 0 ATOMS=(1 7) FIELDNAME=bar_data") !=
std::string::npos);
}
}
TEST_CASE(
"Github #3315: SubstanceGroups should not be written with quotes around "
"missing fields",
"[Sgroups][bug]") {
SECTION("basics") {
auto m1 = R"CTAB(
Mrv2014 07312012022D
2 1 0 0 0 0 999 V2000
1.4295 0.1449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4266 -0.6801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M STY 1 1 DAT
M SAL 1 1 1
M SDT 1 test sgroup
M SDD 1 0.5348 -0.3403 DRU ALL 0 0
M SED 1 sgroupval
M END
)CTAB"_ctab;
REQUIRE(m1);
auto molb = MolToV3KMolBlock(*m1);
CHECK(molb.find("FIELDINFO") == std::string::npos);
CHECK(molb.find("QUERYTYPE") == std::string::npos);
CHECK(molb.find("QUERYOP") == std::string::npos);
CHECK(molb.find("FIELDNAME") != std::string::npos);
}
}
TEST_CASE("Allow brackets, cstates, and attachment points to be removed",
"[Sgroups]") {
auto m1 = R"CTAB(example
-ISIS- 10171405052D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 15 1 0 0
M V30 BEGIN ATOM
M V30 1 C 6.4292 -1.1916 0 0 CFG=3
M V30 2 C 7.0125 -0.6042 0 0
M V30 3 N 6.4292 -0.0250999 0 0
M V30 4 C 5.8416 -0.6042 0 0
M V30 5 C 5.8416 -1.7708 0 0
M V30 6 N 6.4292 -2.3584 0 0 CFG=3
M V30 7 C 7.0125 -1.7708 0 0
M V30 8 O 5.7166 -3.5875 0 0
M V30 9 C 5.7166 -4.4125 0 0 CFG=3
M V30 10 C 4.8875 -4.4125 0 0
M V30 11 C 6.5376 -4.4166 0 0
M V30 12 C 5.7166 -5.2376 0 0
M V30 13 C 6.4292 -3.175 0 0
M V30 14 O 7.1375 -3.5875 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 1
M V30 5 1 1 5
M V30 6 1 5 6
M V30 7 1 6 7
M V30 8 1 7 1
M V30 9 1 6 13
M V30 10 1 8 9
M V30 11 1 9 10
M V30 12 1 9 11
M V30 13 1 9 12
M V30 14 2 13 14
M V30 15 1 8 13
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SUP 0 ATOMS=(7 8 9 10 11 12 13 14) XBONDS=(1 9) BRKXYZ=(9 6.24 -2.9 0 -
M V30 6.24 -2.9 0 0 0 0) CSTATE=(4 9 0 0.82 0) LABEL=Boc SAP=(3 13 6 1)
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m1);
SECTION("brackets") {
REQUIRE(m1);
auto &sgs = getSubstanceGroups(*m1);
REQUIRE(sgs.size() == 1);
CHECK(sgs[0].getBrackets().size() == 1);
sgs[0].clearBrackets();
CHECK(sgs[0].getBrackets().size() == 0);
}
SECTION("cstates") {
auto &sgs = getSubstanceGroups(*m1);
REQUIRE(sgs.size() == 1);
CHECK(sgs[0].getCStates().size() == 1);
sgs[0].clearCStates();
CHECK(sgs[0].getCStates().size() == 0);
}
SECTION("attachpts") {
auto &sgs = getSubstanceGroups(*m1);
REQUIRE(sgs.size() == 1);
CHECK(sgs[0].getAttachPoints().size() == 1);
sgs[0].clearAttachPoints();
CHECK(sgs[0].getAttachPoints().size() == 0);
}
}
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