diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 95ea418b344a21910a925f463151d34af4a8eb22..aeb29423d858acb258440670110cb5ab3502565b 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -109,7 +109,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
:param join_spread_atom_records: If set, overrides the value of
:attr:`IOProfile.join_spread_atom_records`.
- :param remote: If set to true, the method tries to load the pdb from the
+ :param remote: If set to True, the method tries to load the pdb from the
remote pdb repository www.pdb.org. The filename is then interpreted as the
pdb id.
@@ -119,7 +119,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
:param dialect: Specifies the particular dialect to use. If set, overrides
the value of :attr:`IOProfile.dialect`
- :param seqres: Whether to read SEQRES records. If set to true, the loaded
+ :param seqres: Whether to read SEQRES records. If set to True, the loaded
entity and seqres entry will be returned as a tuple.
:type dialect: :class:`str`
@@ -238,7 +238,7 @@ LoadMapList=LoadImageList
def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
lazy_load=False, stride=1,
- dialect=None):
+ dialect=None, detect_swap=True,swap_bytes=False):
"""
Load CHARMM trajectory file.
@@ -257,6 +257,10 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
set, overrides the value of the profile
:param profile: The IO profile to use for loading the PDB file. See
:doc:`profile`.
+ :param detect_swap: if True (the default), then automatic detection of endianess
+ is attempted, otherwise the swap_bytes parameter is used
+ :param swap_bytes: is detect_swap is False, this flag determines whether bytes
+ are swapped upon loading or not
"""
if not isinstance(crd, mol.EntityHandle):
if dcd_file==None:
@@ -266,7 +270,7 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
else:
if not dcd_file:
raise ValueError("No DCD filename given")
- return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load)
+ return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load, detect_swap, swap_bytes)
def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=None, profile='DEFAULT', remote=False, strict_hydrogens=None, seqres=False, info=False):
"""
@@ -282,7 +286,7 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
the value of :attr:`IOProfile.fault_tolerant`.
- :param remote: If set to true, the method tries to load the pdb from the
+ :param remote: If set to True, the method tries to load the pdb from the
remote pdb repository www.pdb.org. The filename is then interpreted as the
pdb id.
@@ -291,7 +295,7 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
:param strict_hydrogens: If set, overrides the value of
:attr:`IOProfile.strict_hydrogens`.
- :param seqres: Whether to read SEQRES records. If set to true, the loaded
+ :param seqres: Whether to read SEQRES records. If set to True, the loaded
entity and seqres entry will be returned as second item.
:param info: Whether to return an info container with the other output.
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index bc10f6f6a32fc6c9e6c3031e5abd94031f367d2e..87e4c66185d6096ffa35ae0bff4bdfbeb0a33159 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -112,7 +112,9 @@ BOOST_PYTHON_MODULE(_ost_io)
def("LoadCRD", &LoadCRD);
def("LoadCHARMMTraj_", &LoadCHARMMTraj, (arg("ent"), arg("trj_filename"),
- arg("stride")=1, arg("lazy_load")=false));
+ arg("stride")=1, arg("lazy_load")=false,
+ arg("detect_swap")=true,arg("swap_bytes")=false))
+;
def("LoadMAE", &LoadMAE);
export_pdb_io();
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index 7ec81f5ed190a9f68aed306199e56cc5cd4d9cf5..86da0ebcb3fe40b7fe37ff8a72bf0caaf80ec310 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -67,31 +67,41 @@ bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
}
bool read_dcd_header(std::istream& istream, DCDHeader& header, bool& swap_flag,
- bool& ucell_flag, bool& gap_flag)
+ bool& ucell_flag, bool& gap_flag, bool detect_swap, bool byte_swap)
{
if (!istream) {
return false;
}
char dummy[4];
gap_flag=true;
- swap_flag=false;
+ swap_flag = detect_swap ? false : byte_swap;
+
ucell_flag=false;
if(gap_flag) istream.read(dummy,sizeof(dummy));
istream.read(header.hdrr,sizeof(char)*4);
if(header.hdrr[0]!='C' || header.hdrr[1]!='O' || header.hdrr[2]!='R' || header.hdrr[3]!='D') {
throw IOException("LoadCHARMMTraj: missing CORD magic in header");
}
+
istream.read(reinterpret_cast<char*>(header.icntrl),sizeof(int)*20);
- if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
- // nonsense atom count, try swapping
- swap_int(header.icntrl,20);
- if(header.icntrl[1]<0 || header.icntrl[1]>1e6) {
- std::ostringstream msg;
- msg << "LoadCHARMMTraj: nonsense atom count (" << header.icntrl[1] << ") in header";
- throw IOException(msg.str());
- } else {
- LOG_VERBOSE("LoadCHARMMTraj: byte-swapping");
- swap_flag=true;
+
+ if(detect_swap) {
+ if(header.icntrl[1]<0 || header.icntrl[1]>1e7) {
+ // nonsense atom count, try byte swapping
+ swap_int(header.icntrl,20);
+ if(header.icntrl[1]<0 || header.icntrl[1]>1e7) {
+ // still weird? swap back and keep fingers crossed
+ LOG_WARNING("LoadCHARMMTraj: byte swap detection failed, trying to continue");
+ swap_int(header.icntrl,20);
+ swap_flag=false;
+ } else {
+ LOG_VERBOSE("LoadCHARMMTraj: byte-swapping (auto-detected)");
+ swap_flag=true;
+ }
+ }
+ } else {
+ if(byte_swap) {
+ LOG_VERBOSE("LoadCHARMMTraj: byte-swapping (manually set)");
}
}
@@ -241,7 +251,9 @@ bool read_frame(std::istream& istream, const DCDHeader& header,
mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom list is already sorted!
const String& trj_fn,
- unsigned int stride)
+ unsigned int stride,
+ bool detect_swap,
+ bool byte_swap)
{
std::ifstream istream(trj_fn.c_str(), std::ios::binary);
if(!istream) {
@@ -253,7 +265,7 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom li
DCDHeader header;
bool swap_flag=false, ucell_flag=false, gap_flag=false;
- read_dcd_header(istream, header, swap_flag, ucell_flag, gap_flag);
+ read_dcd_header(istream, header, swap_flag, ucell_flag, gap_flag, detect_swap, byte_swap);
if(alist.size() != static_cast<size_t>(header.t_atom_count)) {
LOG_ERROR("LoadCHARMMTraj: atom count missmatch: " << alist.size()
<< " in coordinate file, " << header.t_atom_count
@@ -296,9 +308,10 @@ mol::CoordGroupHandle load_dcd(const mol::AtomHandleList& alist, // this atom li
class DCDCoordSource : public mol::CoordSource {
public:
DCDCoordSource(const mol::AtomHandleList& atoms, const String& filename,
- uint stride):
+ uint stride, bool detect_swap, bool byte_swap):
mol::CoordSource(atoms), filename_(filename),
- stream_(filename.c_str(), std::ios::binary), loaded_(false), stride_(stride)
+ stream_(filename.c_str(), std::ios::binary), loaded_(false), stride_(stride),
+ detect_swap_(detect_swap), byte_swap_(byte_swap)
{
frame_count_=0;
this->SetMutable(false);
@@ -334,6 +347,7 @@ private:
uint frame_count_;
uint curr_frame_;
uint stride_;
+ bool detect_swap_, byte_swap_;
size_t frame_start_;
mol::CoordFramePtr frame_;
};
@@ -342,7 +356,7 @@ private:
void DCDCoordSource::FetchFrame(uint frame)
{
if (!loaded_) {
- read_dcd_header(stream_, header_, swap_flag_, ucell_flag_, gap_flag_);
+ read_dcd_header(stream_, header_, swap_flag_, ucell_flag_, gap_flag_, detect_swap_,byte_swap_);
frame_start_=stream_.tellg();
loaded_=true;
frame_count_=header_.num/stride_;
@@ -365,17 +379,20 @@ typedef boost::shared_ptr<DCDCoordSource> DCDCoordSourcePtr;
mol::CoordGroupHandle LoadCHARMMTraj(const mol::EntityHandle& ent,
const String& trj_fn,
- unsigned int stride, bool lazy_load)
+ unsigned int stride,
+ bool lazy_load,
+ bool detect_swap,
+ bool byte_swap)
{
mol::AtomHandleList alist(ent.GetAtomList());
std::sort(alist.begin(),alist.end(),less_index);
if (lazy_load) {
LOG_VERBOSE("LoadCHARMMTraj: importing with lazy_load=true");
- DCDCoordSourcePtr source(new DCDCoordSource(alist, trj_fn, stride));
+ DCDCoordSourcePtr source(new DCDCoordSource(alist, trj_fn, stride, detect_swap, byte_swap));
return mol::CoordGroupHandle(source);
}
LOG_VERBOSE("LoadCHARMMTraj: importing with lazy_load=false");
- return load_dcd(alist, trj_fn, stride);
+ return load_dcd(alist, trj_fn, stride, detect_swap, byte_swap);
}
namespace {
diff --git a/modules/io/src/mol/dcd_io.hh b/modules/io/src/mol/dcd_io.hh
index 5915de6f16b62f44621356b0fbc145dbcfaccb5f..dded28a462727caeffb9d396092c2334819d667a 100644
--- a/modules/io/src/mol/dcd_io.hh
+++ b/modules/io/src/mol/dcd_io.hh
@@ -36,9 +36,11 @@ namespace ost { namespace io {
atom layout of the entity must match the trajectory file
*/
mol::CoordGroupHandle DLLEXPORT_OST_IO LoadCHARMMTraj(const mol::EntityHandle& ent,
- const String& trj_filename,
- unsigned int stride=1,
- bool lazy_load=false);
+ const String& trj_filename,
+ unsigned int stride=1,
+ bool lazy_load=false,
+ bool detect_swap=true,
+ bool byte_swap=false);
/*! \brief export coord group as PDB file and DCD trajectory