From 92076781ee057faca37a1bd31ed1b09606244cbe Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 5 Jul 2023 09:51:52 +0200
Subject: [PATCH] test charges in PDB reader
---
modules/io/tests/test_io_pdb.cc | 36 +++++++++++++++++++
modules/io/tests/testfiles/pdb/charge.pdb | 7 ++++
.../io/tests/testfiles/pdb/charge_faulty.pdb | 7 ++++
3 files changed, 50 insertions(+)
create mode 100644 modules/io/tests/testfiles/pdb/charge.pdb
create mode 100644 modules/io/tests/testfiles/pdb/charge_faulty.pdb
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 99071118e..0c479a3ca 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -1131,4 +1131,40 @@ BOOST_AUTO_TEST_CASE(test_pqr_write_atom)
BOOST_CHECK_EQUAL(fwriter.IsPQR(), true);
}
+// Charges
+BOOST_AUTO_TEST_CASE(test_parse_charge)
+{
+ Logger::Instance().PushVerbosityLevel(0);
+ String fname("testfiles/pdb/charge.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+ reader.Import(ent);
+
+ BOOST_CHECK(ent.FindAtom("A", 68, "N").GetCharge() == 1.0);
+ BOOST_CHECK(ent.FindAtom("A", 68, "CA").GetCharge() == 0);
+ BOOST_CHECK(ent.FindAtom("A", 68, "CB").GetCharge() == 0);
+ BOOST_CHECK(ent.FindAtom("A", 68, "CG1").GetCharge() == 0);
+ BOOST_CHECK(ent.FindAtom("A", 68, "CG2").GetCharge() == 4);
+ BOOST_CHECK(ent.FindAtom("A", 68, "O").GetCharge() == -1);
+
+}
+BOOST_AUTO_TEST_CASE(faulty_charges)
+{
+ String fname("testfiles/pdb/charge_faulty.pdb");
+ PDBReader reader(fname, IOProfile());
+ mol::EntityHandle ent=mol::CreateEntity();
+ BOOST_CHECK_THROW(reader.Import(ent), IOException);
+// IOProfile profile;
+// profile.fault_tolerant=true;
+// PDBReader reader2(fname, profile);
+// reader2.Import(ent);
+//
+// BOOST_CHECK(ent.FindAtom("A", 68, "N").GetCharge() == 1.0);
+// BOOST_CHECK(ent.FindAtom("A", 68, "CA").GetCharge() == 0);
+// BOOST_CHECK(ent.FindAtom("A", 68, "CB").GetCharge() == 0);
+// BOOST_CHECK(ent.FindAtom("A", 68, "CG1").GetCharge() == 0);
+// BOOST_CHECK(ent.FindAtom("A", 68, "CG2").GetCharge() == 4);
+// BOOST_CHECK(ent.FindAtom("A", 68, "O").GetCharge() == -1);
+}
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/pdb/charge.pdb b/modules/io/tests/testfiles/pdb/charge.pdb
new file mode 100644
index 000000000..50cb4d674
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/charge.pdb
@@ -0,0 +1,7 @@
+ATOM 1 N VAL A 68 -67.790 -2.746 1.520 1.00120.70 1SG 1+
+ATOM 2 CA VAL A 68 -68.907 -2.689 2.484 1.00120.70 1SG
+ATOM 3 CB VAL A 68 -68.374 -2.515 3.872 1.00120.70 1SG 0+
+ATOM 4 CG1 VAL A 68 -67.534 -3.751 4.234 1.00120.70 1SG
+ATOM 5 CG2 VAL A 68 -67.591 -1.194 3.924 1.00120.70 1SG 4+
+ATOM 6 C VAL A 68 -69.796 -1.526 2.177 1.00120.70 1SG
+ATOM 7 O VAL A 68 -69.882 -1.095 1.029 1.00120.70 1SG 1-
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pdb/charge_faulty.pdb b/modules/io/tests/testfiles/pdb/charge_faulty.pdb
new file mode 100644
index 000000000..2fb2446db
--- /dev/null
+++ b/modules/io/tests/testfiles/pdb/charge_faulty.pdb
@@ -0,0 +1,7 @@
+ATOM 1 N VAL A 68 -67.790 -2.746 1.520 1.00120.70 1SG 1+
+ATOM 2 CA VAL A 68 -68.907 -2.689 2.484 1.00120.70 1SG
+ATOM 3 CB VAL A 68 -68.374 -2.515 3.872 1.00120.70 1SG 68
+ATOM 4 CG1 VAL A 68 -67.534 -3.751 4.234 1.00120.70 1SG
+ATOM 5 CG2 VAL A 68 -67.591 -1.194 3.924 1.00120.70 1SG 4+
+ATOM 6 C VAL A 68 -69.796 -1.526 2.177 1.00120.70 1SG
+ATOM 7 O VAL A 68 -69.882 -1.095 1.029 1.00120.70 1SG 1-
\ No newline at end of file
--
GitLab