From beef185276b812aea97f4e91ff2b43dc6f1f2403 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 28 Mar 2011 17:53:27 +0200
Subject: [PATCH] improve SEQRES import and AlignToSEQRES
This is based on exhaustive testing on the complete files of the PDB.
There are still a few unresolved issues. However it is not clear to me,
whether the problems are due to errors in the PDB files or our
misunderstanding.
---
modules/io/src/mol/pdb_reader.cc | 9 ++++++---
modules/seq/alg/pymod/__init__.py | 11 +++++------
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index bf2e50bd8..1ea2c56b8 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -151,9 +151,12 @@ void PDBReader::ParseSeqRes(const StringRef& line, int line_num)
conop::CompoundPtr compound=comp_lib->FindCompound(trimmed.str(),
conop::Compound::PDB);
if (!compound) {
- LOG_WARNING("unknown residue '" << trimmed << "' in SEQRES record. "
- "Setting one-letter-code to X");
- curr_seq.Append('X');
+ if (rname!=StringRef("UNK", 3)) {
+
+ LOG_WARNING("unknown residue '" << trimmed << "' in SEQRES record. "
+ "Setting one-letter-code to '?'");
+ }
+ curr_seq.Append('?');
continue;
}
curr_seq.Append(compound->GetOneLetterCode());
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index bb1ea4e82..1862fc812 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -17,14 +17,13 @@ def AlignToSEQRES(chain, seqres):
"""
from ost import seq
from ost import mol
- residues=chain.residues
+ view=chain.Select('ligand=false and peptide=true')
+ residues=view.residues
if len(residues)==0:
- return None
+ return seq.CreateAlignment()
fragments=[residues[0].one_letter_code]
for r1, r2 in zip(residues[:-2], residues[1:]):
- if not r2.IsPeptideLinking() or r2.IsLigand():
- continue
- if not mol.InSequence(r1, r2):
+ if not mol.InSequence(r1.handle, r2.handle):
fragments.append('')
fragments[-1]+=r2.one_letter_code
ss=str(seqres)
@@ -41,4 +40,4 @@ def AlignToSEQRES(chain, seqres):
seq.CreateSequence('atoms', aln_seq))
-
\ No newline at end of file
+
--
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