From 9e42eac70df58b463d81ef4b3f606d954992668e Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 19 Jun 2013 13:20:06 +0200
Subject: [PATCH] remember PDBize residue number
this is a follow up to 76b079d7a, in which part of the problem, but not
the complete one was fixed.
---
modules/io/tests/test_io_mmcif.py | 13 +++++++++++++
modules/mol/alg/src/pdbize.cc | 7 +++----
modules/mol/alg/src/pdbize.hh | 4 +++-
3 files changed, 19 insertions(+), 5 deletions(-)
diff --git a/modules/io/tests/test_io_mmcif.py b/modules/io/tests/test_io_mmcif.py
index a11811f59..d5dcf651c 100644
--- a/modules/io/tests/test_io_mmcif.py
+++ b/modules/io/tests/test_io_mmcif.py
@@ -136,6 +136,19 @@ class TestMMCifInfo(unittest.TestCase):
self.assertEquals(tr_ol[0][0], 0)
self.assertEquals(tr_ol[0][1], 1)
+ def test_mmcifinfo_biounit_pdbize_with_multiple_transforms(self):
+ ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/multiple_transforms.cif.gz",
+ seqres=True,
+ info=True)
+ pdb_ent = info.GetBioUnits()[0].PDBize(ent)
+ pdb_seqres_ent = info.GetBioUnits()[0].PDBize(ent, seqres)
+ chains = pdb_ent.chains
+ self.assertEquals([c.name for c in chains],
+ ['A', '_', '-', 'B', 'C', 'D'])
+ ligand_chain = chains[1]
+ ligand_residues = ligand_chain.residues
+ self.assertEquals([r.number for r in ligand_residues],
+ [mol.ResNum(1), mol.ResNum(2), mol.ResNum(3), mol.ResNum(4)])
def test_mmcifinfo_biounit_pdbize(self):
ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
seqres=True,
diff --git a/modules/mol/alg/src/pdbize.cc b/modules/mol/alg/src/pdbize.cc
index 4b6fd0d57..9e3638358 100644
--- a/modules/mol/alg/src/pdbize.cc
+++ b/modules/mol/alg/src/pdbize.cc
@@ -70,7 +70,6 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
{
XCSEditor edi = ent_.EditXCS(BUFFERED_EDIT);
- int last_rnum = 0;
for (geom::Mat4List::const_iterator i = transforms.begin(),
e = transforms.end(); i != e; ++i) {
for (ChainViewList::const_iterator j = asu.GetChainList().begin(),
@@ -125,14 +124,14 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
// deal with ligands...
if (!ligand_chain_) {
ligand_chain_ = edi.InsertChain(LIGAND_CHAIN_NAME);
- last_rnum = 0;
+ last_rnum_ = 0;
}
char ins_code = chain.GetResidueCount()>1 ? 'A' : '\0';
for (ResidueViewList::const_iterator k = chain.GetResidueList().begin(),
e3 = chain.GetResidueList().end(); k != e3; ++k) {
ResidueHandle new_res = edi.AppendResidue(ligand_chain_, k->GetName(),
- ResNum(last_rnum+1, ins_code));
+ ResNum(last_rnum_+1, ins_code));
transfer_residue_properties(*k, new_res);
new_res.SetStringProp("type", StringFromChainType(chain.GetType()));
new_res.SetStringProp("description", chain.GetDescription());
@@ -144,7 +143,7 @@ void PDBize::Add(EntityView asu, const geom::Mat4List& transforms,
ins_code += 1;
needs_adjustment_ |= copy_atoms(*k, new_res, edi, *i);
}
- last_rnum+=1;
+ last_rnum_+=1;
}
}
}
diff --git a/modules/mol/alg/src/pdbize.hh b/modules/mol/alg/src/pdbize.hh
index 00534a4cf..f3afec693 100644
--- a/modules/mol/alg/src/pdbize.hh
+++ b/modules/mol/alg/src/pdbize.hh
@@ -36,7 +36,8 @@ class DLLEXPORT_OST_MOL_ALG PDBize {
public:
explicit PDBize(int min_polymer_size=10):
min_polymer_size_(min_polymer_size), ent_(mol::CreateEntity()),
- curr_chain_name_(POLYPEPTIDE_CHAIN_NAMES), needs_adjustment_(false)
+ curr_chain_name_(POLYPEPTIDE_CHAIN_NAMES), needs_adjustment_(false),
+ last_rnum_(0)
{}
void Add(mol::EntityView asu, const geom::Mat4List& transforms,
@@ -50,6 +51,7 @@ private:
ChainHandle water_chain_;
const char* curr_chain_name_;
bool needs_adjustment_;
+ int last_rnum_;
std::map<ResidueHandle,ResidueHandle> dst_to_src_map_;
};
--
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