From 71cd5abcb4abb58e23d74402ee897037a99efc13 Mon Sep 17 00:00:00 2001
From: tobias <tobias@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 12 Aug 2010 10:25:18 +0000
Subject: [PATCH] DCD io: increased max number of atoms; implemented stride
option (thanks marco)
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2647 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/mol/dcd_io.cc | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index 29cbb7bd2..778e86ce4 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -89,11 +89,10 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
if(gap_flag) ff.read(dummy,sizeof(dummy));
ff.read(header.hdrr,sizeof(char)*4);
ff.read(reinterpret_cast<char*>(header.icntrl),sizeof(int)*20);
-
- if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
+ if(header.icntrl[1]<0 || header.icntrl[1]>1e8) {
// nonsense atom count, try swapping
swap_int(header.icntrl,20);
- if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
+ if(header.icntrl[1]<0 || header.icntrl[1]>1e8) {
throw(IOException("LoadCHARMMTraj: nonsense atom count in header"));
} else {
LOGN_MESSAGE("LoadCHARMMTraj: byte-swapping");
@@ -147,8 +146,17 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
std::vector<geom::Vec3> clist(header.t_atom_count);
std::vector<float> xlist(header.t_atom_count);
+ size_t frame_size=0;
+ if (skip_flag) {
+ frame_size+=14*4;
+ }
+ if (gap_flag) {
+ frame_size+=6*sizeof(dummy);
+ }
+ frame_size+=3*sizeof(float)*xlist.size();
+
int i=0;
- for(;i<header.num;++i) {
+ for(;i<header.num;i+=stride) {
if(skip_flag) ff.seekg(14*4,std::ios_base::cur);
// read each frame
if(!ff) {
@@ -186,6 +194,8 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist2,
cg.AddFrame(clist);
+ // skip frames (defined by stride)
+ if(stride>1) ff.seekg(frame_size*(stride-1),std::ios_base::cur);
}
ff.get();
--
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