From 7951fac56df0ee03b2691345a2f473a784196edf Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Wed, 1 Dec 2010 14:09:19 -0500
Subject: [PATCH] tweaks to gfx trace connectivity; fixed dcd loader error
message
---
modules/gfx/src/impl/backbone_trace.cc | 2 ++
modules/io/src/mol/dcd_io.cc | 10 ++++++++--
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index 2a0315380..e3a14b7a7 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -38,6 +38,8 @@ bool in_sequence(const mol::ResidueHandle& r1, const mol::ResidueHandle& r2)
if(n2.GetInsCode()!='\0') {
if(n1.NextInsertionCode()==n2) return true;
}
+ if(mol::InSequence(r1,r2)) return true;
+ // perhaps this fallback is not so good...
if(n1.GetNum()+1==n2.GetNum()) return true;
return false;
}
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index bc36cb93f..15e056daf 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -188,12 +188,18 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
const String& trj_fn,
unsigned int stride)
{
+ std::ifstream istream(trj_fn.c_str(), std::ios::binary);
+ if(!istream) {
+ std::ostringstream msg;
+ msg << "LoadCHARMMTraj: cannot open " << trj_fn;
+ throw(IOException(msg.str()));
+ }
Profile profile_load("LoadCHARMMTraj");
mol::AtomHandleList alist(alist2);
std::sort(alist.begin(),alist.end(),less_index);
- std::ifstream istream(trj_fn.c_str(), std::ios::binary);
+
DCDHeader header;
bool swap_flag=false, skip_flag=false, gap_flag=false;
read_dcd_header(istream, header, swap_flag, skip_flag, gap_flag);
@@ -315,7 +321,7 @@ mol::CoordGroupHandle LoadCHARMMTraj(const mol::EntityHandle& ent,
DCDCoordSource* source=new DCDCoordSource(alist, trj_fn, stride);
return mol::CoordGroupHandle(DCDCoordSourcePtr(source));
}
- LOG_INFO("Importing CHARMM trajectory with lazy_load=false");
+ LOG_INFO("Importing CHARMM trajectory with lazy_load=false");
return load_dcd(alist, trj_fn, stride);
}
--
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