From e05c81aa1068544ebad8f0fb96eae95ddccdc973 Mon Sep 17 00:00:00 2001
From: Marco Biasini <mvbiasini@gmail.com>
Date: Fri, 9 Aug 2013 09:59:54 +0200
Subject: [PATCH] use insertion codes for water chain
---
modules/mol/alg/src/pdbize.cc | 9 ++++-
modules/mol/alg/src/pdbize.hh | 1 +
modules/mol/alg/tests/CMakeLists.txt | 1 +
modules/mol/alg/tests/test_pdbize.py | 51 ++++++++++++++++++++++++++++
4 files changed, 61 insertions(+), 1 deletion(-)
create mode 100644 modules/mol/alg/tests/test_pdbize.py
diff --git a/modules/mol/alg/src/pdbize.cc b/modules/mol/alg/src/pdbize.cc
index d6371e639..e99366831 100644
--- a/modules/mol/alg/src/pdbize.cc
+++ b/modules/mol/alg/src/pdbize.cc
@@ -106,13 +106,20 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
}
if (chain.GetType() == CHAINTYPE_WATER) {
if (!water_chain_) {
+ last_water_rnum_ = ResNum(0, 'Z');
water_chain_ = edi.InsertChain(WATER_CHAIN_NAME);
edi.SetChainDescription(water_chain_, chain.GetDescription());
edi.SetChainType(water_chain_, chain.GetType());
}
for (ResidueViewList::const_iterator k = chain.GetResidueList().begin(),
e3 = chain.GetResidueList().end(); k != e3; ++k) {
- ResidueHandle new_res = edi.AppendResidue(water_chain_, k->GetName());
+ if (last_water_rnum_.GetInsCode() == 'Z') {
+ last_water_rnum_ = ResNum(last_water_rnum_.GetNum()+1, 'A');
+ } else {
+ last_water_rnum_.SetInsCode(last_water_rnum_.GetInsCode()+1);
+ }
+ ResidueHandle new_res = edi.AppendResidue(water_chain_, k->GetName(),
+ last_water_rnum_);
transfer_residue_properties(*k, new_res);
new_res.SetStringProp("type", StringFromChainType(chain.GetType()));
new_res.SetStringProp("description", chain.GetDescription());
diff --git a/modules/mol/alg/src/pdbize.hh b/modules/mol/alg/src/pdbize.hh
index f3afec693..b344cfca4 100644
--- a/modules/mol/alg/src/pdbize.hh
+++ b/modules/mol/alg/src/pdbize.hh
@@ -52,6 +52,7 @@ private:
const char* curr_chain_name_;
bool needs_adjustment_;
int last_rnum_;
+ ResNum last_water_rnum_;
std::map<ResidueHandle,ResidueHandle> dst_to_src_map_;
};
diff --git a/modules/mol/alg/tests/CMakeLists.txt b/modules/mol/alg/tests/CMakeLists.txt
index 758bbbe10..8258cb3d1 100644
--- a/modules/mol/alg/tests/CMakeLists.txt
+++ b/modules/mol/alg/tests/CMakeLists.txt
@@ -2,6 +2,7 @@ set(OST_MOL_ALG_UNIT_TESTS
test_superposition.cc
tests.cc
test_consistency_checks.cc
+ test_pdbize.py
test_convenient_superpose.py
)
diff --git a/modules/mol/alg/tests/test_pdbize.py b/modules/mol/alg/tests/test_pdbize.py
new file mode 100644
index 000000000..abf2bc892
--- /dev/null
+++ b/modules/mol/alg/tests/test_pdbize.py
@@ -0,0 +1,51 @@
+from ost import io, mol, geom, seq
+import unittest
+import os
+import random
+
+class TestPDBize(unittest.TestCase):
+
+ def test_numbers_water_molecules_with_ins_codes(self):
+ m = mol.CreateEntity()
+ e = m.EditXCS(mol.BUFFERED_EDIT)
+ c = e.InsertChain("A");
+ e.SetChainType(c, mol.CHAINTYPE_WATER)
+ for i in range(27):
+ e.AppendResidue(c, "HOH")
+ pdbizer = mol.alg.PDBize()
+ transformations = geom.Mat4List()
+ transformations.append(geom.Mat4())
+ seqs = seq.CreateSequenceList()
+ pdbizer.Add(m.Select(''), transformations, seqs)
+ pdbized = pdbizer.Finish()
+ self.assertEquals([c.name for c in pdbized.chains], ["-"])
+ residues = pdbized.residues
+ for i in range(26):
+ self.assertEquals(residues[i].number.num, 1)
+ self.assertEquals(residues[i].number.ins_code, chr(ord('A')+i))
+ self.assertEquals(residues[26].number.num, 2)
+ self.assertEquals(residues[26].number.ins_code, 'A')
+ def test_starts_from_last_water_rnum(self):
+ m = mol.CreateEntity()
+ e = m.EditXCS(mol.BUFFERED_EDIT)
+ c = e.InsertChain("A");
+ e.SetChainType(c, mol.CHAINTYPE_WATER)
+ e.AppendResidue(c, "HOH")
+ pdbizer = mol.alg.PDBize()
+ transformations = geom.Mat4List()
+ transformations.append(geom.Mat4())
+ seqs = seq.CreateSequenceList()
+ pdbizer.Add(m.Select(''), transformations,seqs)
+ pdbizer.Add(m.Select(''), transformations,seqs)
+ pdbized = pdbizer.Finish()
+ self.assertEquals([c.name for c in pdbized.chains], ["-"])
+ residues = pdbized.residues
+ self.assertEquals([r.number for r in residues],
+ [mol.ResNum(1, 'A'), mol.ResNum(1, 'B')])
+
+
+
+
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
--
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