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MolDraw2D: first pass at rendering atom lists (#3804)

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* first pass at rendering atom lists

* a bit of additional cleanup
This commit is contained in:
Greg Landrum
2021-02-17 15:25:53 +01:00
committed by GitHub
parent 8ebf50f2d2
commit 009e593b5c
5 changed files with 165 additions and 58 deletions
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67
Code/GraphMol/QueryOps.cpp
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@@ -11,6 +11,7 @@
#include <algorithm>
#include <RDGeneral/types.h>
#include <GraphMol/QueryAtom.h>
#include <boost/range/iterator_range.hpp>
namespace RDKit {
@@ -601,6 +602,7 @@ ATOM_NULL_QUERY *makeAtomNullQuery() {
}
bool isComplexQuery(const Bond *b) {
PRECONDITION(b, "bad bond");
if (!b->hasQuery()) {
return false;
}
@@ -638,6 +640,7 @@ bool isComplexQuery(const Bond *b) {
return true;
}
namespace {
bool _complexQueryHelper(Atom::QUERYATOM_QUERY const *query, bool &hasAtNum) {
if (!query) {
return false;
@@ -665,7 +668,70 @@ bool _complexQueryHelper(Atom::QUERYATOM_QUERY const *query, bool &hasAtNum) {
}
return false;
}
template <typename T>
bool _atomListQueryHelper(const T query) {
PRECONDITION(query, "no query");
if (query->getNegation()) {
return false;
}
if (query->getDescription() == "AtomAtomicNum") {
return true;
}
if (query->getDescription() == "AtomOr") {
for (const auto child : boost::make_iterator_range(query->beginChildren(),
query->endChildren())) {
if (!_atomListQueryHelper(child)) {
return false;
}
}
}
return true;
}
} // namespace
bool isAtomListQuery(const Atom *a) {
PRECONDITION(a, "bad atom");
if (!a->hasQuery()) {
return false;
}
if (a->getQuery()->getDescription() == "AtomOr") {
for (const auto child : boost::make_iterator_range(
a->getQuery()->beginChildren(), a->getQuery()->endChildren())) {
if (!_atomListQueryHelper(child)) {
return false;
}
}
return true;
}
return false;
}
void getAtomListQueryVals(const Atom::QUERYATOM_QUERY *q,
std::vector<int> &vals) {
// list queries are series of nested ors of AtomAtomicNum queries
PRECONDITION(q, "bad query");
auto descr = q->getDescription();
PRECONDITION(descr == "AtomOr", "bad query");
if (descr == "AtomOr") {
for (const auto child :
boost::make_iterator_range(q->beginChildren(), q->endChildren())) {
auto descr = child->getDescription();
if (child->getNegation() ||
(descr != "AtomOr" && descr != "AtomAtomicNum")) {
throw ValueErrorException("bad query type");
}
// we don't allow negation of any children of the query:
if (descr == "AtomOr") {
getAtomListQueryVals(child.get(), vals);
} else if (descr == "AtomAtomicNum") {
vals.push_back(static_cast<ATOM_EQUALS_QUERY *>(child.get())->getVal());
}
}
}
}
bool isComplexQuery(const Atom *a) {
PRECONDITION(a, "bad atom");
if (!a->hasQuery()) {
return false;
}
@@ -697,6 +763,7 @@ bool isComplexQuery(const Atom *a) {
return true;
}
bool isAtomAromatic(const Atom *a) {
PRECONDITION(a, "bad atom");
bool res = false;
if (!a->hasQuery()) {
res = a->getIsAromatic();