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support BinaryCIF (bcif) input format

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rdk
2023-11-17 04:25:38 +01:00
parent 5ee5a7361e
commit b265874d6c
5 changed files with 14 additions and 1 deletions
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distro/test_data/1fbl.bcif Normal file
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distro/test_data/2W83.bcif.gz Normal file
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2
src/main/groovy/cz/siret/prank/utils/PdbUtils.groovy
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@@ -61,7 +61,7 @@ class PdbUtils {
String ext = Futils.realExtension(file)
if (ext == "cif") {
if (ext == "cif" || ext == "bcif" ) {
return loadFromCifFile(file)
} else { // pdb / ent
return loadFromPdbFile(file)

9
src/test/groovy/cz/siret/prank/StructureParsingTest.groovy
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@@ -15,14 +15,17 @@ import static org.junit.jupiter.api.Assertions.assertEquals
*/
@CompileStatic
class StructureParsingTest {
Path installDir = Paths.get("distro").toAbsolutePath()
Path dataDir = path installDir, "test_data"
Path pdb_1fbl = path dataDir, "1fbl.pdb.gz"
Path cif_1fbl = path dataDir, "1fbl.cif"
Path bcif_1fbl = path dataDir, "1fbl.bcif"
Path pdb_2W83 = path dataDir, "2W83.pdb"
Path cif_2W83 = path dataDir, "2W83.cif"
Path bcif_2W83 = path dataDir, "2W83.bcif.gz"
@Test
void pdbVsCifEquality() throws Exception {
@@ -30,6 +33,12 @@ class StructureParsingTest {
doTestPdbVsCifEquality(pdb_2W83, cif_2W83)
}
@Test
void cifVsBcifEquality() throws Exception {
doTestPdbVsCifEquality(cif_1fbl, bcif_1fbl)
doTestPdbVsCifEquality(cif_2W83, bcif_2W83)
}
void doTestPdbVsCifEquality(Path pdbFile, Path cifFile) {
Protein pdb = Protein.load(pdbFile.toString())
Protein cif = Protein.load(cifFile.toString())

4
src/test/groovy/cz/siret/prank/program/api/impl/DafaultPrankPredictorTest.groovy
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@@ -37,15 +37,19 @@ class DafaultPrankPredictorTest {
Path pdb_1fbl = path dataDir, "1fbl.pdb.gz"
Path cif_1fbl = path dataDir, "1fbl.cif"
Path bcif_1fbl = path dataDir, "1fbl.bcif"
Path pdb_2W83 = path dataDir, "2W83.pdb"
Path cif_2W83 = path dataDir, "2W83.cif.zst"
Path bcif_2W83 = path dataDir, "2W83.bcif.gz"
List<Path> testFiles = [ //should be liganated proteins with easily predictable binding sites
pdb_1fbl,
cif_1fbl,
bcif_1fbl,
pdb_2W83,
cif_2W83,
bcif_2W83,
path(dataDir, "liganated", "1a82a.pdb"),
path(dataDir, "liganated", "1aaxa.pdb"),
path(dataDir, "liganated", "1nlu.pdb"),