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Add cxsmiles query atoms to CTAB parsers and writers (#3261)

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* allow CXSMILES generic query atoms to be parsed from mol;
need more tests here

* remove vestigial directory

* Add d_queryType to Query
This opens up additional flexibility with customizing the way queries are handled
Also includes some assorted cleanups in the Query directory

* remove the MolFileSymbol hack added in #3235
We don't need it anymore

* Add support for additional ChemAxon extensions and document them

Signed-off-by: greg landrum <greg.landrum@gmail.com>

* bump pickle version

* add an additional test
This commit is contained in:
Greg Landrum
2020-07-03 18:51:19 +02:00
committed by GitHub
parent f4a85cf9cb
commit 1630540ef0
26 changed files with 415 additions and 227 deletions
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220
Code/Query/test.cpp
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@@ -1,6 +1,5 @@
// $Id$
//
// Copyright (c) 2003-2006 Greg Landrum and Rational Discovery LLC
// Copyright (c) 2003-2020 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
@@ -22,31 +21,33 @@ void test1() {
cout << "Float" << endl;
EqualityQuery<double> q(1.0);
CHECK_INVARIANT(!q.Match(0.0), "");
CHECK_INVARIANT(q.Match(1.0), "");
CHECK_INVARIANT(!q.Match(1.001), "");
CHECK_INVARIANT(!q.Match(1.1), "");
CHECK_INVARIANT(!q.Match(-2), "");
TEST_ASSERT(!q.Match(0.0));
TEST_ASSERT(q.Match(1.0));
TEST_ASSERT(!q.Match(1.001));
TEST_ASSERT(!q.Match(1.1));
TEST_ASSERT(!q.Match(-2));
cout << "With Tolerance" << endl;
q.setTol(0.002);
CHECK_INVARIANT(!q.Match(0.0), "");
CHECK_INVARIANT(q.Match(1.0), "");
CHECK_INVARIANT(q.Match(1.001), "");
CHECK_INVARIANT(!q.Match(1.1), "");
CHECK_INVARIANT(!q.Match(-2), "");
TEST_ASSERT(!q.Match(0.0));
TEST_ASSERT(q.Match(1.0));
TEST_ASSERT(q.Match(1.001));
TEST_ASSERT(!q.Match(1.1));
TEST_ASSERT(!q.Match(-2));
TEST_ASSERT(q.getTypeLabel().empty());
q.setTypeLabel("FloatEquality");
Query<double> *newQ;
newQ = q.copy();
CHECK_INVARIANT(!newQ->Match(0.0), "");
CHECK_INVARIANT(newQ->Match(1.0), "");
CHECK_INVARIANT(newQ->Match(1.001), "");
CHECK_INVARIANT(!newQ->Match(1.1), "");
CHECK_INVARIANT(!newQ->Match(-2), "");
TEST_ASSERT(!newQ->Match(0.0));
TEST_ASSERT(newQ->Match(1.0));
TEST_ASSERT(newQ->Match(1.001));
TEST_ASSERT(!newQ->Match(1.1));
TEST_ASSERT(!newQ->Match(-2));
TEST_ASSERT(newQ->getTypeLabel() == "FloatEquality");
delete newQ;
}
void test2() {
cout << "Set" << endl;
SetQuery<int> q;
@@ -54,17 +55,17 @@ void test2() {
q.insert(3);
q.insert(5);
CHECK_INVARIANT(!q.Match(0), "");
CHECK_INVARIANT(q.Match(1), "");
CHECK_INVARIANT(q.Match(3), "");
CHECK_INVARIANT(!q.Match(-3), "");
TEST_ASSERT(!q.Match(0));
TEST_ASSERT(q.Match(1));
TEST_ASSERT(q.Match(3));
TEST_ASSERT(!q.Match(-3));
Query<int> *newQ;
newQ = q.copy();
CHECK_INVARIANT(!newQ->Match(0), "");
CHECK_INVARIANT(newQ->Match(1), "");
CHECK_INVARIANT(newQ->Match(3), "");
CHECK_INVARIANT(!newQ->Match(-3), "");
TEST_ASSERT(!newQ->Match(0));
TEST_ASSERT(newQ->Match(1));
TEST_ASSERT(newQ->Match(3));
TEST_ASSERT(!newQ->Match(-3));
delete newQ;
}
@@ -79,17 +80,17 @@ void test3() {
q->addChild(Query<int>::CHILD_TYPE(l));
q->addChild(Query<int>::CHILD_TYPE(g));
CHECK_INVARIANT(!q->Match(0), "");
CHECK_INVARIANT(q->Match(1), "");
CHECK_INVARIANT(q->Match(3), "");
CHECK_INVARIANT(!q->Match(-3), "");
TEST_ASSERT(!q->Match(0));
TEST_ASSERT(q->Match(1));
TEST_ASSERT(q->Match(3));
TEST_ASSERT(!q->Match(-3));
Query<int> *newQ;
newQ = q->copy();
CHECK_INVARIANT(!newQ->Match(0), "");
CHECK_INVARIANT(newQ->Match(1), "");
CHECK_INVARIANT(newQ->Match(3), "");
CHECK_INVARIANT(!newQ->Match(-3), "");
TEST_ASSERT(!newQ->Match(0));
TEST_ASSERT(newQ->Match(1));
TEST_ASSERT(newQ->Match(3));
TEST_ASSERT(!newQ->Match(-3));
delete newQ;
delete q;
@@ -106,17 +107,17 @@ void test4() {
q->addChild(Query<int>::CHILD_TYPE(l));
q->addChild(Query<int>::CHILD_TYPE(g));
CHECK_INVARIANT(q->Match(0), "");
CHECK_INVARIANT(q->Match(1), "");
CHECK_INVARIANT(q->Match(3), "");
CHECK_INVARIANT(q->Match(-3), "");
TEST_ASSERT(q->Match(0));
TEST_ASSERT(q->Match(1));
TEST_ASSERT(q->Match(3));
TEST_ASSERT(q->Match(-3));
Query<int> *newQ;
newQ = q->copy();
CHECK_INVARIANT(newQ->Match(0), "");
CHECK_INVARIANT(newQ->Match(1), "");
CHECK_INVARIANT(newQ->Match(3), "");
CHECK_INVARIANT(newQ->Match(-3), "");
TEST_ASSERT(newQ->Match(0));
TEST_ASSERT(newQ->Match(1));
TEST_ASSERT(newQ->Match(3));
TEST_ASSERT(newQ->Match(-3));
delete newQ;
delete q;
@@ -133,19 +134,19 @@ void test5() {
q->addChild(Query<int>::CHILD_TYPE(l));
q->addChild(Query<int>::CHILD_TYPE(g));
CHECK_INVARIANT(q->Match(-1), "");
CHECK_INVARIANT(q->Match(0), "");
CHECK_INVARIANT(!q->Match(1), "");
CHECK_INVARIANT(!q->Match(3), "");
CHECK_INVARIANT(q->Match(-3), "");
TEST_ASSERT(q->Match(-1));
TEST_ASSERT(q->Match(0));
TEST_ASSERT(!q->Match(1));
TEST_ASSERT(!q->Match(3));
TEST_ASSERT(q->Match(-3));
Query<int> *newQ;
newQ = q->copy();
CHECK_INVARIANT(newQ->Match(-1), "");
CHECK_INVARIANT(newQ->Match(0), "");
CHECK_INVARIANT(!newQ->Match(1), "");
CHECK_INVARIANT(!newQ->Match(3), "");
CHECK_INVARIANT(newQ->Match(-3), "");
TEST_ASSERT(newQ->Match(-1));
TEST_ASSERT(newQ->Match(0));
TEST_ASSERT(!newQ->Match(1));
TEST_ASSERT(!newQ->Match(3));
TEST_ASSERT(newQ->Match(-3));
delete newQ;
delete q;
@@ -158,26 +159,26 @@ void test6() {
EqualityQuery<int, double, true> q;
q.setDataFunc(foofun);
q.setVal(6);
CHECK_INVARIANT(q.Match(6.0), "");
CHECK_INVARIANT(q.Match(6.1), "");
CHECK_INVARIANT(!q.Match(5.0), "");
TEST_ASSERT(q.Match(6.0));
TEST_ASSERT(q.Match(6.1));
TEST_ASSERT(!q.Match(5.0));
Query<int, double, true> *newQ;
newQ = q.copy();
CHECK_INVARIANT(newQ->Match(6.0), "");
CHECK_INVARIANT(newQ->Match(6.1), "");
CHECK_INVARIANT(!newQ->Match(5.0), "");
TEST_ASSERT(newQ->Match(6.0));
TEST_ASSERT(newQ->Match(6.1));
TEST_ASSERT(!newQ->Match(5.0));
Query<int, double, true> *newQ2 = &q;
CHECK_INVARIANT(newQ2->Match(6.0), "");
CHECK_INVARIANT(newQ2->Match(6.1), "");
CHECK_INVARIANT(!newQ2->Match(5.0), "");
TEST_ASSERT(newQ2->Match(6.0));
TEST_ASSERT(newQ2->Match(6.1));
TEST_ASSERT(!newQ2->Match(5.0));
Query<int, double, true> *newQ3;
newQ3 = newQ2->copy();
CHECK_INVARIANT(newQ3->Match(6.0), "");
CHECK_INVARIANT(newQ3->Match(6.1), "");
CHECK_INVARIANT(!newQ3->Match(5.0), "");
TEST_ASSERT(newQ3->Match(6.0));
TEST_ASSERT(newQ3->Match(6.1));
TEST_ASSERT(!newQ3->Match(5.0));
delete newQ;
delete newQ3;
@@ -195,10 +196,10 @@ void basics1() {
q.setMatchFunc(matchF);
q.setDataFunc(dataF);
CHECK_INVARIANT(!q.Match(0.0), "");
CHECK_INVARIANT(q.Match(1.0), "");
CHECK_INVARIANT(q.Match(1.1), "");
CHECK_INVARIANT(!q.Match(-2.0), "");
TEST_ASSERT(!q.Match(0.0));
TEST_ASSERT(q.Match(1.0));
TEST_ASSERT(q.Match(1.1));
TEST_ASSERT(!q.Match(-2.0));
TEST_ASSERT(!q.getMatchFunc()(0));
TEST_ASSERT(q.getMatchFunc()(3));
@@ -207,66 +208,66 @@ void basics1() {
cout << "Query2" << endl;
Query<bool, int, true> q2;
q2.setDataFunc(cmp);
CHECK_INVARIANT(q2.Match(0), "");
CHECK_INVARIANT(q2.Match(1), "");
CHECK_INVARIANT(!q2.Match(3), "");
CHECK_INVARIANT(!q2.Match(4), "");
CHECK_INVARIANT(!q2.Match(4.0), "");
TEST_ASSERT(q2.Match(0));
TEST_ASSERT(q2.Match(1));
TEST_ASSERT(!q2.Match(3));
TEST_ASSERT(!q2.Match(4));
TEST_ASSERT(!q2.Match(4.0));
}
void basics2() {
cout << "Equality" << endl;
EqualityQuery<int> q2;
q2.setVal(3);
CHECK_INVARIANT(!q2.Match(0), "");
CHECK_INVARIANT(!q2.Match(1), "");
CHECK_INVARIANT(q2.Match(3), "");
CHECK_INVARIANT(!q2.Match(-3), "");
TEST_ASSERT(!q2.Match(0));
TEST_ASSERT(!q2.Match(1));
TEST_ASSERT(q2.Match(3));
TEST_ASSERT(!q2.Match(-3));
cout << "Greater" << endl;
GreaterQuery<int> q3;
q3.setVal(3);
CHECK_INVARIANT(q3.Match(0), "");
CHECK_INVARIANT(q3.Match(1), "");
CHECK_INVARIANT(!q3.Match(3), "");
CHECK_INVARIANT(!q3.Match(5), "");
TEST_ASSERT(q3.Match(0));
TEST_ASSERT(q3.Match(1));
TEST_ASSERT(!q3.Match(3));
TEST_ASSERT(!q3.Match(5));
cout << "GreaterEqual" << endl;
GreaterEqualQuery<int> q4(3);
CHECK_INVARIANT(q4.Match(0), "");
CHECK_INVARIANT(q4.Match(1), "");
CHECK_INVARIANT(q4.Match(3), "");
CHECK_INVARIANT(!q4.Match(5), "");
TEST_ASSERT(q4.Match(0));
TEST_ASSERT(q4.Match(1));
TEST_ASSERT(q4.Match(3));
TEST_ASSERT(!q4.Match(5));
cout << "Less" << endl;
LessQuery<int> q5;
q5.setVal(3);
CHECK_INVARIANT(!q5.Match(0), "");
CHECK_INVARIANT(!q5.Match(1), "");
CHECK_INVARIANT(!q5.Match(3), "");
CHECK_INVARIANT(q5.Match(5), "");
TEST_ASSERT(!q5.Match(0));
TEST_ASSERT(!q5.Match(1));
TEST_ASSERT(!q5.Match(3));
TEST_ASSERT(q5.Match(5));
cout << "LessEqual" << endl;
LessEqualQuery<int> q6(3);
CHECK_INVARIANT(!q6.Match(0), "");
CHECK_INVARIANT(!q6.Match(1), "");
CHECK_INVARIANT(q6.Match(3), "");
CHECK_INVARIANT(q6.Match(5), "");
TEST_ASSERT(!q6.Match(0));
TEST_ASSERT(!q6.Match(1));
TEST_ASSERT(q6.Match(3));
TEST_ASSERT(q6.Match(5));
cout << "Open Range" << endl;
RangeQuery<int> q7(0, 3);
CHECK_INVARIANT(!q7.Match(0), "");
CHECK_INVARIANT(q7.Match(1), "");
CHECK_INVARIANT(!q7.Match(3), "");
CHECK_INVARIANT(!q7.Match(5), "");
TEST_ASSERT(!q7.Match(0));
TEST_ASSERT(q7.Match(1));
TEST_ASSERT(!q7.Match(3));
TEST_ASSERT(!q7.Match(5));
cout << "Closed Range" << endl;
q7.setEndsOpen(false, false);
CHECK_INVARIANT(q7.Match(0), "");
CHECK_INVARIANT(q7.Match(1), "");
CHECK_INVARIANT(q7.Match(3), "");
CHECK_INVARIANT(!q7.Match(5), "");
TEST_ASSERT(q7.Match(0));
TEST_ASSERT(q7.Match(1));
TEST_ASSERT(q7.Match(3));
TEST_ASSERT(!q7.Match(5));
}
int convFunc(const char *arg) { return boost::lexical_cast<int>(arg); };
@@ -279,17 +280,17 @@ void test7() {
q.insert(3);
q.insert(5);
CHECK_INVARIANT(!q.Match("0"), "");
CHECK_INVARIANT(q.Match("1"), "");
CHECK_INVARIANT(q.Match("3"), "");
CHECK_INVARIANT(!q.Match("-3"), "");
TEST_ASSERT(!q.Match("0"));
TEST_ASSERT(q.Match("1"));
TEST_ASSERT(q.Match("3"));
TEST_ASSERT(!q.Match("-3"));
Query<int, const char *, true> *newQ;
newQ = q.copy();
CHECK_INVARIANT(!newQ->Match("0"), "");
CHECK_INVARIANT(newQ->Match("1"), "");
CHECK_INVARIANT(newQ->Match("3"), "");
CHECK_INVARIANT(!newQ->Match("-3"), "");
TEST_ASSERT(!newQ->Match("0"));
TEST_ASSERT(newQ->Match("1"));
TEST_ASSERT(newQ->Match("3"));
TEST_ASSERT(!newQ->Match("-3"));
delete newQ;
}
@@ -305,5 +306,4 @@ int main() {
test5();
test6();
test7();
return 0;
}