From 4514c413ccaa68d0361ec431985abdfdfb77ffb9 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Sat, 3 Apr 2010 08:20:14 +0000
Subject: [PATCH] add JOIN_SPREAD_ATOM_RECORDS flag to PDBReader
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1916 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/__init__.py | 9 ++++++++-
modules/io/pymod/export_pdb_io.cc | 1 +
modules/io/src/mol/pdb_io.hh | 23 +++++++++++++++++++++++
modules/io/src/mol/pdb_reader.cc | 17 ++++++++++++-----
4 files changed, 44 insertions(+), 6 deletions(-)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index a0fc73cc9..82ab97c27 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -20,7 +20,8 @@ from _io import *
from ost import mol,conop
def LoadPDB(filename, restrict_chains="", no_hetatms=False,
- fault_tolerant=False, load_multi=False):
+ fault_tolerant=False, load_multi=False,
+ join_spread_atom_records=False):
"""
Load PDB file from disk.
@@ -35,6 +36,10 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
If load_multi is set to true, a list of entities will be returned instead
of only the first.
+
+ If join_spread_atom_records is set to true, atom records belonging to the
+ same residue are joined, even if they do not appear sequentially in the PDB
+ file.
"""
conop_inst=conop.Conopology.Instance()
builder=conop_inst.GetBuilder("DEFAULT")
@@ -45,6 +50,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
flags=PDB.SKIP_FAULTY_RECORDS
if no_hetatms:
flags|=PDB.NO_HETATMS
+ if join_spread_atom_records:
+ flags|=PDB.JOIN_SPREAD_ATOM_RECORDS
reader.SetFlags(flags)
if load_multi:
ent_list=[]
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index e984697ee..5f252d318 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -37,6 +37,7 @@ void export_pdb_io()
.value("NO_HETATMS", PDB::NO_HETATMS)
.value("SKIP_FAULTY_RECORDS", PDB::SKIP_FAULTY_RECORDS)
.value("WRITE_MULTIPLE_MODELS", PDB::WRITE_MULTIPLE_MODELS)
+ .value("JOIN_SPREAD_ATOM_RECORDS", PDB::JOIN_SPREAD_ATOM_RECORDS)
;
class_<PDBReader, boost::noncopyable>("PDBReader", init<String>())
.def("HasNext", &PDBReader::HasNext)
diff --git a/modules/io/src/mol/pdb_io.hh b/modules/io/src/mol/pdb_io.hh
index 5bc34e106..e14cfb2d4 100644
--- a/modules/io/src/mol/pdb_io.hh
+++ b/modules/io/src/mol/pdb_io.hh
@@ -35,6 +35,29 @@ struct PDB {
WRITE_MULTIPLE_MODELS=4,
/// \brief enable for PQR
PQR_FORMAT=8,
+ /// \brief Join atom records into one residue, even if the atom records
+ /// are not sequential.
+ ///
+ /// This is useful in the following case:
+ ///
+ /// \verbatim
+ /// ATOM 43 N AALA P 4
+ /// ATOM 45 CA AALA P 4
+ /// ATOM 47 C AALA P 4
+ /// ATOM 48 O AALA P 4
+ /// ATOM 49 N APRO P 5
+ /// ATOM 50 CD APRO P 5
+ /// ATOM 53 CA APRO P 5
+ /// ATOM 55 CB APRO P 5
+ /// ATOM 58 CG APRO P 5
+ /// ATOM 61 C APRO P 5
+ /// ATOM 62 O APRO P 5
+ /// ATOM 550 CB AALA P 4
+ /// \endverbatim
+ ///
+ /// By default, the atom 550 will start a new residue instead of being
+ /// joined with atoms 43-48 into one residue.
+ JOIN_SPREAD_ATOM_RECORDS=16
} Type;
};
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 5c8f137f7..c59be53a6 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -446,14 +446,21 @@ void PDBReader::ParseAndAddAtom(const String& line, int line_num,
++chain_count_;
}
}
-
if(update_residue) {
- LOGN_DUMP("new residue " << rkey << " " << rnum);
- curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
+ if (flags_ & PDB::JOIN_SPREAD_ATOM_RECORDS) {
+ curr_residue_=curr_chain_.FindResidue(rnum);
+ if (!curr_residue_.IsValid()) {
+ LOGN_DUMP("new residue " << rkey << " " << rnum);
+ curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
+ ++residue_count_;
+ }
+ } else {
+ LOGN_DUMP("new residue " << rkey << " " << rnum);
+ curr_residue_=editor.AppendResidue(curr_chain_, rkey, rnum);
+ ++residue_count_;
+ }
assert(curr_residue_.IsValid());
- ++residue_count_;
}
-
// finally add atom
LOGN_DUMP("adding atom " << aname << " (" << s_ele << ") @" << apos);
mol::AtomProp aprop;
--
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