Refinement restraints: contacts with lattice translates are kept, and an atom's own symmetry contact once

Contacts() dropped every pair found in image 0 with a nonzero lattice shift ("the identity term
covers the contact"), but that pair is a contact with a translated copy of j, not with j itself:
in P1 no intermolecular repulsion or B-contact restraint was made at all, and in every group the
contacts along a, b and c were missing (MeasureGeometry's clash count with them). Such a pair is
now kept like a symmetry mate's, from the lower atom of the two.

An atom against its own image x -> T x is also met through T^-1 at the same distance (another
operator, or the same one at another lattice shift for a screw), and both were kept: atoms near
a 3-, 4- or 6-fold or a screw axis were repelled twice. For i == j the image first in fractional
coordinates of T x and T^-1 x is kept; an involution is kept once as before.

Test: in P1 two waters 2.4 A apart across a cell face get one repulsion and one B contact (none
before); a water 1.4 A from a 3-fold axis gets one repulsion with its images (two before).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 0d6e4d0491e655a49d59b709e1398843506d162a)

tests/RefinementTest.cpp

@@ -507,6 +507,36 @@ TEST_CASE("RefinementRestraints_gradient", "[Refinement]") {
 #endif
 }
 
+// Contacts with other copies of the molecule: in P1 two waters 2.4 A apart across the a face (17.6 A apart within
+// the cell) repel each other once, and a water 1.4 A from a 3-fold axis, 2.4 A from its images x -> T x and
+// x -> T^-1 x (one contact per asymmetric unit), repels its image once.
+TEST_CASE("RefinementRestraints_lattice_and_symmetry_contacts", "[Refinement]") {
+    auto oxygens = [](gemmi::Structure &st, const std::vector<gemmi::Fractional> &where) {
+        std::vector<gemmi::Atom *> atoms = atoms_of(st.models[0]);
+        REQUIRE(atoms.size() == where.size());
+        for (size_t i = 0; i < where.size(); i++)
+            atoms[i]->pos = st.cell.orthogonalize(where[i]);
+    };
+    {
+        const gemmi::UnitCell cell(20, 21, 22, 90, 90, 90);
+        gemmi::Structure st = residue_crystal({"HOH", "HOH"}, cell, "P 1", 1);
+        oxygens(st, {gemmi::Fractional(0.01, 0.5, 0.5), gemmi::Fractional(0.89, 0.5, 0.5)});
+        const RefinementTopology topo = BuildRefinementTopology(st);
+        const RestraintSet rep = BuildRepulsions(topo, st.models[0], cell, *st.find_spacegroup(), 0.0);
+        REQUIRE(rep.records.size() == 1);
+        CHECK(rep.records[0].tran[0] == Catch::Approx(-20.0f));
+        CHECK(BuildBContacts(topo, st.models[0], cell, *st.find_spacegroup()).records.size() == 1);
+    }
+    {
+        const gemmi::UnitCell cell(20, 20, 22, 90, 90, 120);
+        gemmi::Structure st = residue_crystal({"HOH"}, cell, "P 3", 1);
+        oxygens(st, {cell.fractionalize(gemmi::Position(1.4, 0.0, 11.0))});
+        const RefinementTopology topo = BuildRefinementTopology(st);
+        const RestraintSet rep = BuildRepulsions(topo, st.models[0], cell, *st.find_spacegroup(), 0.0);
+        CHECK(rep.records.size() == 1);
+    }
+}
+
 // A complete model whose every atom is off by a Gaussian error of sigma_x per axis: D(s) = <cos(2 pi s.dx)> =
 // exp(-2 pi^2 sigma_x^2 s^2) (Luzzati). With a negligible measurement error D comes out at that; with an error of
 // half the rms amplitude of the outermost shell it falls below it there, where the error is a large part of the