oemolistream¶
class oemolistream : public oemolstreambase
The oemolistream class provides a stream-like abstraction for reading molecules from files, strings or standard input. The oemolistream maintains the format and flavor of molecular reading for the stream. It also manages the conversion between multi-conformer molecules and single conformer molecules in cases where the molecule read into is not compatible with the file format (in the sense of a multi-conformer file format being read into a single-conformer molecule, or a single-conformer file format being read into a multi-conformer molecule). The oemolistream is capable of uncompressing gzip files while reading.
The following methods are publicly inherited from oemolstreambase:
Constructors¶
oemolistream()
Default constructor. Creates a new oemolistream object that is connected to the standard input.
oemolistream(const char *fname)
oemolistream(const std::string &fname)
Creates a new oemolistream object and opens the file specified by the given name (‘fname’).
oemolistream(OEPlatform::oeistream *, bool owned=true)
Creates a new oemolistream object from an existing oeistream object. The second optional argument is used to indicate whether the new oemolistream now owns the given oeistream and is therefore responsible for closing and destroying it when it itself is closed and/or destroyed.
Warning
Only in C++ can an oemolistream object own an existing oeistream object.
Usage in Python
i = oechem.oeistream()
owned = True
ifs = oechem.oemolistream(i, not owned)
See also
To associate a file or a stream with an
oemolistream after it has been created, see the
oemolstreambase.open
method.
operator bool¶
operator bool() const
operator OEPlatform::oeistream &¶
operator OEPlatform::oeistream &() const
GetConfTest¶
OEConfTestBase &GetConfTest() const
GetOEMols¶
GetOEMols() -> <generator of OEMol objects>
Returns a generator over all the molecules in the file or stream. Each molecule will be an OEMol object. These are references to the molecules in the file or stream and so calling this method does not create copies of the molecules.
GetOEGraphMols¶
GetOEGraphMols() -> <generator of OEGraphMol objects>
Returns a generator over all the molecules in the
input stream in the current order. Each molecule will be
an OEGraphMol object. If opened on a
multi-conformer .oeb
file, only the first conformer
will be returned for each molecule record.
Note
Unlike OEChem::OEMolDatabase::GetOEGraphMols
, a reference to
each molecule will be used for each iteration to avoid unnecessary
copying of molecules.
GetMCMolBases¶
OESystem::OEIterBase<OEChem::OEMCMolBase> *GetMCMolBases(bool single=false)
GetMolBases¶
OESystem::OEIterBase<OEChem::OEMolBase> *GetMolBases()
GetReadFailureCt¶
unsigned GetReadFailureCt() const
IncrementReadFailureCt¶
void IncrementReadFailureCt()
ResetReadFailureCt¶
void ResetReadFailureCt()
SetConfTest¶
bool SetConfTest(const OEConfTestBase &)
Sets the functor class which is used to compare incoming graphs to determine whether they should be placed as conformers of a multi-conformer molecule or be returned individually as single molecules. The default conformer test never places separate graphs into a multi-conformer molecule (OEDefaultConfTest).
SetFlavor¶
bool SetFlavor(unsigned int format, unsigned int flavor)
Sets the file flavor for a given format associated with the
oemolistream object.
The set of valid formats are defined in the
the OEFormat namespace.
The set of valid bitmasks flavors are defined in the
OEIFlavor
namespace.
The current flavor can be queried using the
oemolstreambase.GetFlavor
method.
Each format has its own specific flavor which must be set
separately.
The oemolistream constructors
call the OESetDefaultFlavors
function
to set the flavors for all of the formats to their default state.
SetFormat¶
bool SetFormat(unsigned int format)
Sets the file format associated with the
oemolistream object.
The set of valid formats are defined in the
the OEFormat namespace.
By default, when reading from standard input, the associated
file format is OEFormat_SMI
.
The file format property of an oemolistream
may be retrieved using the
oemolstreambase.GetFormat
method.
Note
The file format property is also set automatically by
oemolstreambase.open
based upon the file
extension of the specified filename.
SetTracer¶
bool SetTracer(OESystem::OETracerBase *tracer, bool owntracer)
Registers the tracer, tracer
, to report the current progress
of the oemolistream object on reading molecules.
The second optional argument is used to indicate whether the
oemolistream now owns the given
OETracerBase object and is therefore responsible for
closing and destroying it when it itself is closed and/or
destroyed.
Warning
Only in C++ can an oemolistream object own an existing OETracerBase object.
See also
Setgz¶
bool Setgz(bool gz, OEPlatform::oeistream *sptr=0, bool owned=false)
Specifies that the contents of the
oemolistream object are to be treated as compressed
by GNU gzip compressed. The decompression takes place on-the-fly.
Usually the ‘gz’ property of a oemolistream
object is determined implicitly from the file extension used to
open the stream for reading.
The current ‘gz’ property of the oemolistream
object can be retrieved using the
oemolstreambase.Getgz
method.
close¶
void close()
Closes the oemolistream object.
This method may be safely called multiple times.
However oemolistream.close
method is called
from within the oemolistream destructor and
therefore it is not necessary to call this explicitly under most
circumstances.
eof¶
bool eof() const
getbyte¶
int getbyte()
getline¶
bool getline(char *buffer, oesize_t max)
openstring¶
bool openstring(const std::string &str)
bool openstring(const unsigned char *buffer, oesize_t len)
Allows the oemolistream to read from a buffer in memory, instead of from a file or standard input.
Internally, the oemolistream.openstring
method make a copy of the specified file contents, allowing the
oemolistream to continue to function
independently of whether the original buffer is later modified
or deallocated.
Note
Prior to calling oemolistream.openstring
it
is necessary to specify the format and whether or not the format is
compressed with gzip. These can be set with the
oemolistream.SetFormat
and
oemolistream.Setgz
methods respectively.
peekbyte¶
int peekbyte()
read¶
bool read(unsigned char *buffer, oesize_t len)
rewind¶
void rewind()
seek¶
void seek(oefpos_t pos)
Moves the position of the next valid read to the position indicated. This function takes account of gzip streams and molecule caching.
size¶
oefpos_t size()
Returns the size of the input stream if applicable to the current stream. The return type is a portable file-system pointer type.
skip¶
bool skip(oefpos_t len)
skipbyte¶
bool skipbyte()
skipline¶
bool skipline()
tell¶
oefpos_t tell()
Returns the current position of the next read. This function accounts for molecular caching.
Note
If you are reading an .oeb
file that was written as
multi-conformer molecules and is being read with single conformer
molecules, all of the conformers are read into cache at once,
and the pointer will point to the beginning of a multi-conformer
molecule rather than to a conformer inside a molecule.