IoAdapterPy
Python implementation of IoAdapterBase class providing essential read and write methods for mmCIF and BCIF data files -
Source code in mmcif/io/IoAdapterPy.py
class IoAdapterPy(IoAdapterBase):
"""Python implementation of IoAdapterBase class providing essential read and write methods for mmCIF and BCIF data files -"""
# pylint: disable=arguments-differ
def readFile(
self,
inputFilePath,
enforceAscii=False,
selectList=None,
excludeFlag=False,
logFilePath=None,
outDirPath=None,
cleanUp=True,
fmt="mmcif",
timeout=None,
storeStringsAsBytes=False,
defaultStringEncoding="utf-8",
**kwargs
):
"""Parse the data blocks in the input mmCIF or BCIF format data file into list of data or definition containers. The data category
content within each data block is stored a collection of DataCategory objects within each container.
Args:
inputFilePath (string): Input file path
enforceAscii (bool, optional): Flag to require ASCII encoding when reading in 'mmcif' file. See encoding error options. Defaults to False.
selectList (List, optional): List of data category names to be extracted or excluded from the input file (default: select/extract)
excludeFlag (bool, optional): Flag to indicate selectList should be treated as an exclusion list
logFilePath (string, optional): Log file path (if not provided this will be derived from the input file.)
outDirPath (string, optional): Path for translated/re-encoded files and default logfiles.
cleanUp (bool, optional): Flag to automatically remove logs and temporary files on exit.
fmt (string, optional): Format of input file (either "mmcif" or "bcif"). Defaults to "mmcif".
timeout (float, optional): Timeout in seconds for fetching data from remote urls
# BCIF-specific args:
storeStringsAsBytes (bool, optional): Strings are stored as lists of bytes (for BCIF files only). Defaults to False.
defaultStringEncoding (str, optional): Default encoding for string data (for BCIF files only). Defaults to "utf-8".
**kwargs: Placeholder for missing keyword arguments.
Returns:
List of DataContainers: Contents of input file parsed into a list of DataContainer objects.
"""
if kwargs:
logger.warning("Unsupported keyword arguments %s", kwargs.keys())
filePath = str(inputFilePath)
# oPath = outDirPath if outDirPath else '.'
oPath = self._chooseTemporaryPath(inputFilePath, outDirPath=outDirPath)
containerList = []
if enforceAscii:
encoding = "ascii"
else:
encoding = "utf-8"
try:
#
lPath = logFilePath
if not lPath:
lPath = self._getDefaultFileName(filePath, fileType="cif-parser-log", outDirPath=oPath)
#
self._setLogFilePath(lPath)
# ---
if self.__isLocal(filePath) and not self._fileExists(filePath):
return []
#
fmt = fmt.lower()
#
if sys.version_info[0] > 2: # Check if using Python version higher than 2
if fmt == "mmcif":
if self.__isLocal(filePath):
filePath = self._uncompress(filePath, oPath)
with open(filePath, "r", encoding=encoding, errors=self._readEncodingErrors) as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else: # handle files from the internet...
if filePath.endswith(".gz"):
customHeader = {"Accept-Encoding": "gzip"}
with closing(requests.get(filePath, headers=customHeader, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
gzit = gzip.GzipFile(fileobj=io.BytesIO(ifh.content))
it = (line.decode(encoding, "ignore") for line in gzit)
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with closing(requests.get(filePath, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
it = (line.decode(encoding, "ignore") + "\n" for line in ifh.iter_lines())
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
elif fmt == "bcif":
# local vs. remote and gzip business is already done in BinaryCifReader
bcifRd = BinaryCifReader(storeStringsAsBytes=storeStringsAsBytes, defaultStringEncoding=defaultStringEncoding)
containerList = bcifRd.deserialize(filePath)
else:
logger.error("Unsupported fmt %r. Currently only supports 'mmcif' or 'bcif'.", fmt)
else:
logger.warning("Support for Python 2 will be deprecated soon. Please use Python 3.")
if fmt == "bcif":
logger.error("Support for BCIF reading only available in Python 3.")
elif fmt == "mmcif":
if self.__isLocal(filePath):
filePath = self._uncompress(filePath, oPath)
if enforceAscii:
with io.open(filePath, "r", encoding=encoding, errors=self._readEncodingErrors) as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with open(filePath, "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
if filePath.endswith(".gz"):
customHeader = {"Accept-Encoding": "gzip"}
with closing(requests.get(filePath, headers=customHeader, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
gzit = gzip.GzipFile(fileobj=io.BytesIO(ifh.content))
it = (line.decode(encoding, "ignore") for line in gzit)
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with closing(requests.get(filePath, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
it = (line.decode(encoding, "ignore") + "\n" for line in ifh.iter_lines())
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
logger.error("Unsupported fmt %r for Python2 installation of mmcif.io.IoAdapterPy. Currently only 'mmcif' is supported. Upgrade to Python3 for 'bcif' support", fmt)
if cleanUp:
self._cleanupFile(lPath, lPath)
self._cleanupFile(filePath != str(inputFilePath), filePath)
self._setContainerProperties(containerList, locator=str(inputFilePath), load_date=self._getTimeStamp(), uid=uuid.uuid4().hex)
except (PdbxError, PdbxSyntaxError) as ex:
msg = "File %r with %s" % (filePath, str(ex))
self._appendToLog([msg])
self._cleanupFile(lPath and cleanUp, lPath)
if self._raiseExceptions:
raise_from(ex, None)
# raise ex from None
except Exception as e:
msg = "File %r with %s" % (filePath, str(e))
self._appendToLog([msg])
self._cleanupFile(lPath and cleanUp, lPath)
if self._raiseExceptions:
raise e
else:
logger.error("Failing read for %s with %s", filePath, str(e))
return containerList
def getReadDiags(self):
"""Return diagnostics from last readFile operation. This will NOT be an exhaustive list but
rather the particular failure that raised a parsing exception.
"""
return self._readLogRecords()
def writeFile(
self,
outputFilePath,
containerList,
maxLineLength=900,
enforceAscii=True,
lastInOrder=None,
selectOrder=None,
columnAlignFlag=True,
useStopTokens=False,
formattingStep=None,
fmt="mmcif",
storeStringsAsBytes=False,
defaultStringEncoding="utf-8",
applyTypes=True,
dictionaryApi=None,
useStringTypes=False,
useFloat64=False,
copyInputData=False,
ignoreCastErrors=False,
**kwargs
):
"""Write input list of data containers to the specified output file path in mmCIF or BCIF format.
Args:
outputFilePath (string): output file path
containerList (list DataContainer objects, optional)
maxLineLength (int, optional): Maximum length of output line (content is wrapped beyond this length)
enforceAscii (bool, optional): Enforce ASCII encoding when writing out 'mmcif' file. Defaults to True.
lastInOrder (list of category names, optional): Move data categories in this list to end of each data block
selectOrder (list of category names, optional): Write only data categories on this list.
columnAlignFlag (bool, optional): Format the output in aligned columns (default=True) (Native Python Only)
useStopTokens (bool, optional): Include terminating 'stop_' tokens at the end of mmCIF categories (loop_'s) (Native Python only)
formattingStep (int, optional): The number row samples within each category used to estimate maximum column width for data alignment (Native Python only)
fmt (string, optional): Format of output file (either "mmcif" or "bcif"). Defaults to "mmcif".
# BCIF-specific args:
storeStringsAsBytes (bool, optional): Strings are stored as lists of bytes (for BCIF files only). Defaults to False.
defaultStringEncoding (str, optional): Default encoding for string data (for BCIF files only). Defaults to "utf-8".
applyTypes (bool, optional): apply explicit data typing before encoding (for BCIF files only; requires dictionaryApi to be passed too). Defaults to True.
dictionaryApi (object, optional): DictionaryApi object instance (needed for BCIF files, only when applyTypes is True). Defaults to None.
useStringTypes (bool, optional): assume all types are string (for BCIF files only). Defaults to False.
useFloat64 (bool, optional): store floats with 64 bit precision (for BCIF files only). Defaults to False.
copyInputData (bool, optional): make a new copy input data (for BCIF files only). Defaults to False.
ignoreCastErrors (bool, optional): suppress errors when casting attribute types with dictionaryApi. Defaults to False.
**kwargs: Placeholder for unsupported key value pairs
Returns:
bool: Completion status
"""
lastInOrder = lastInOrder if lastInOrder else ["pdbx_nonpoly_scheme", "pdbx_poly_seq_scheme", "atom_site", "atom_site_anisotrop"]
if kwargs:
logger.warning("Unsupported keyword arguments %s", kwargs.keys())
try:
if enforceAscii:
encoding = "ascii"
else:
encoding = "utf-8"
#
fmt = fmt.lower()
#
if sys.version_info[0] > 2: # Check if using Python version higher than 2
if fmt == "mmcif":
with open(outputFilePath, "w", encoding=encoding) as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
elif fmt == "bcif":
bcifW = BinaryCifWriter(
dictionaryApi=dictionaryApi,
storeStringsAsBytes=storeStringsAsBytes,
defaultStringEncoding=defaultStringEncoding,
applyTypes=applyTypes,
useStringTypes=useStringTypes,
useFloat64=useFloat64,
copyInputData=copyInputData,
ignoreCastErrors=ignoreCastErrors,
)
bcifW.serialize(outputFilePath, containerList)
else:
logger.error("Unsupported fmt %r. Currently only supports 'mmcif' or 'bcif'.", fmt)
return False
else:
logger.warning("Support for Python 2 will be deprecated soon. Please use Python 3.")
if fmt == "bcif":
logger.error("Support for BCIF writing only available in Python 3.")
return False
elif fmt == "mmcif":
if enforceAscii:
with io.open(outputFilePath, "w", encoding=encoding) as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
else:
with open(outputFilePath, "wb") as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
else:
logger.error("Unsupported fmt %r for Python2 installation of mmcif.io.IoAdapterPy. Currently only 'mmcif' is supported. Upgrade to Python3 for 'bcif' support", fmt)
return False
return True
except Exception as ex:
if self._raiseExceptions:
raise_from(ex, None)
else:
logger.exception("Failing write for %s with %s", outputFilePath, str(ex))
logger.error("Failing write for %s with %s", outputFilePath, str(ex))
return False
def __writeFile(
self,
ofh,
containerList,
maxLineLength=900,
columnAlignFlag=True,
lastInOrder=None,
selectOrder=None,
useStopTokens=False,
formattingStep=None,
enforceAscii=False,
cnvCharRefs=False,
):
"""Internal method mapping arguments to PDBxWriter API."""
#
pdbxW = PdbxWriter(ofh)
pdbxW.setUseStopTokens(flag=useStopTokens)
pdbxW.setMaxLineLength(numChars=maxLineLength)
pdbxW.setAlignmentFlag(flag=columnAlignFlag)
pdbxW.setRowPartition(numParts=formattingStep)
pdbxW.setConvertCharRefs(flag=cnvCharRefs)
pdbxW.setSetEnforceAscii(enforceAscii)
pdbxW.write(containerList, lastInOrder=lastInOrder, selectOrder=selectOrder)
def __isLocal(self, locator):
try:
locSp = urlsplit(locator)
return locSp.scheme in ["", "file"]
except Exception as e:
logger.exception("For locator %r failing with %s", locator, str(e))
return None
getReadDiags(self)
Return diagnostics from last readFile operation. This will NOT be an exhaustive list but rather the particular failure that raised a parsing exception.
Source code in mmcif/io/IoAdapterPy.py
def getReadDiags(self):
"""Return diagnostics from last readFile operation. This will NOT be an exhaustive list but
rather the particular failure that raised a parsing exception.
"""
return self._readLogRecords()
readFile(self, inputFilePath, enforceAscii=False, selectList=None, excludeFlag=False, logFilePath=None, outDirPath=None, cleanUp=True, fmt='mmcif', timeout=None, storeStringsAsBytes=False, defaultStringEncoding='utf-8', **kwargs)
Parse the data blocks in the input mmCIF or BCIF format data file into list of data or definition containers. The data category content within each data block is stored a collection of DataCategory objects within each container.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
inputFilePath |
string |
Input file path |
required |
enforceAscii |
bool |
Flag to require ASCII encoding when reading in 'mmcif' file. See encoding error options. Defaults to False. |
False |
selectList |
List |
List of data category names to be extracted or excluded from the input file (default: select/extract) |
None |
excludeFlag |
bool |
Flag to indicate selectList should be treated as an exclusion list |
False |
logFilePath |
string |
Log file path (if not provided this will be derived from the input file.) |
None |
outDirPath |
string |
Path for translated/re-encoded files and default logfiles. |
None |
cleanUp |
bool |
Flag to automatically remove logs and temporary files on exit. |
True |
fmt |
string |
Format of input file (either "mmcif" or "bcif"). Defaults to "mmcif". |
'mmcif' |
timeout |
float |
Timeout in seconds for fetching data from remote urls |
None |
# |
BCIF-specific args |
required | |
storeStringsAsBytes |
bool |
Strings are stored as lists of bytes (for BCIF files only). Defaults to False. |
False |
defaultStringEncoding |
str |
Default encoding for string data (for BCIF files only). Defaults to "utf-8". |
'utf-8' |
**kwargs |
Placeholder for missing keyword arguments. |
{} |
Returns:
| Type | Description |
|---|---|
List of DataContainers |
Contents of input file parsed into a list of DataContainer objects. |
Source code in mmcif/io/IoAdapterPy.py
def readFile(
self,
inputFilePath,
enforceAscii=False,
selectList=None,
excludeFlag=False,
logFilePath=None,
outDirPath=None,
cleanUp=True,
fmt="mmcif",
timeout=None,
storeStringsAsBytes=False,
defaultStringEncoding="utf-8",
**kwargs
):
"""Parse the data blocks in the input mmCIF or BCIF format data file into list of data or definition containers. The data category
content within each data block is stored a collection of DataCategory objects within each container.
Args:
inputFilePath (string): Input file path
enforceAscii (bool, optional): Flag to require ASCII encoding when reading in 'mmcif' file. See encoding error options. Defaults to False.
selectList (List, optional): List of data category names to be extracted or excluded from the input file (default: select/extract)
excludeFlag (bool, optional): Flag to indicate selectList should be treated as an exclusion list
logFilePath (string, optional): Log file path (if not provided this will be derived from the input file.)
outDirPath (string, optional): Path for translated/re-encoded files and default logfiles.
cleanUp (bool, optional): Flag to automatically remove logs and temporary files on exit.
fmt (string, optional): Format of input file (either "mmcif" or "bcif"). Defaults to "mmcif".
timeout (float, optional): Timeout in seconds for fetching data from remote urls
# BCIF-specific args:
storeStringsAsBytes (bool, optional): Strings are stored as lists of bytes (for BCIF files only). Defaults to False.
defaultStringEncoding (str, optional): Default encoding for string data (for BCIF files only). Defaults to "utf-8".
**kwargs: Placeholder for missing keyword arguments.
Returns:
List of DataContainers: Contents of input file parsed into a list of DataContainer objects.
"""
if kwargs:
logger.warning("Unsupported keyword arguments %s", kwargs.keys())
filePath = str(inputFilePath)
# oPath = outDirPath if outDirPath else '.'
oPath = self._chooseTemporaryPath(inputFilePath, outDirPath=outDirPath)
containerList = []
if enforceAscii:
encoding = "ascii"
else:
encoding = "utf-8"
try:
#
lPath = logFilePath
if not lPath:
lPath = self._getDefaultFileName(filePath, fileType="cif-parser-log", outDirPath=oPath)
#
self._setLogFilePath(lPath)
# ---
if self.__isLocal(filePath) and not self._fileExists(filePath):
return []
#
fmt = fmt.lower()
#
if sys.version_info[0] > 2: # Check if using Python version higher than 2
if fmt == "mmcif":
if self.__isLocal(filePath):
filePath = self._uncompress(filePath, oPath)
with open(filePath, "r", encoding=encoding, errors=self._readEncodingErrors) as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else: # handle files from the internet...
if filePath.endswith(".gz"):
customHeader = {"Accept-Encoding": "gzip"}
with closing(requests.get(filePath, headers=customHeader, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
gzit = gzip.GzipFile(fileobj=io.BytesIO(ifh.content))
it = (line.decode(encoding, "ignore") for line in gzit)
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with closing(requests.get(filePath, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
it = (line.decode(encoding, "ignore") + "\n" for line in ifh.iter_lines())
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
elif fmt == "bcif":
# local vs. remote and gzip business is already done in BinaryCifReader
bcifRd = BinaryCifReader(storeStringsAsBytes=storeStringsAsBytes, defaultStringEncoding=defaultStringEncoding)
containerList = bcifRd.deserialize(filePath)
else:
logger.error("Unsupported fmt %r. Currently only supports 'mmcif' or 'bcif'.", fmt)
else:
logger.warning("Support for Python 2 will be deprecated soon. Please use Python 3.")
if fmt == "bcif":
logger.error("Support for BCIF reading only available in Python 3.")
elif fmt == "mmcif":
if self.__isLocal(filePath):
filePath = self._uncompress(filePath, oPath)
if enforceAscii:
with io.open(filePath, "r", encoding=encoding, errors=self._readEncodingErrors) as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with open(filePath, "r") as ifh:
pRd = PdbxReader(ifh)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
if filePath.endswith(".gz"):
customHeader = {"Accept-Encoding": "gzip"}
with closing(requests.get(filePath, headers=customHeader, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
gzit = gzip.GzipFile(fileobj=io.BytesIO(ifh.content))
it = (line.decode(encoding, "ignore") for line in gzit)
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
with closing(requests.get(filePath, timeout=timeout)) as ifh:
if self._raiseExceptions:
ifh.raise_for_status()
it = (line.decode(encoding, "ignore") + "\n" for line in ifh.iter_lines())
pRd = PdbxReader(it)
pRd.read(containerList, selectList, excludeFlag=excludeFlag)
else:
logger.error("Unsupported fmt %r for Python2 installation of mmcif.io.IoAdapterPy. Currently only 'mmcif' is supported. Upgrade to Python3 for 'bcif' support", fmt)
if cleanUp:
self._cleanupFile(lPath, lPath)
self._cleanupFile(filePath != str(inputFilePath), filePath)
self._setContainerProperties(containerList, locator=str(inputFilePath), load_date=self._getTimeStamp(), uid=uuid.uuid4().hex)
except (PdbxError, PdbxSyntaxError) as ex:
msg = "File %r with %s" % (filePath, str(ex))
self._appendToLog([msg])
self._cleanupFile(lPath and cleanUp, lPath)
if self._raiseExceptions:
raise_from(ex, None)
# raise ex from None
except Exception as e:
msg = "File %r with %s" % (filePath, str(e))
self._appendToLog([msg])
self._cleanupFile(lPath and cleanUp, lPath)
if self._raiseExceptions:
raise e
else:
logger.error("Failing read for %s with %s", filePath, str(e))
return containerList
writeFile(self, outputFilePath, containerList, maxLineLength=900, enforceAscii=True, lastInOrder=None, selectOrder=None, columnAlignFlag=True, useStopTokens=False, formattingStep=None, fmt='mmcif', storeStringsAsBytes=False, defaultStringEncoding='utf-8', applyTypes=True, dictionaryApi=None, useStringTypes=False, useFloat64=False, copyInputData=False, ignoreCastErrors=False, **kwargs)
Write input list of data containers to the specified output file path in mmCIF or BCIF format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
outputFilePath |
string |
output file path |
required |
maxLineLength |
int |
Maximum length of output line (content is wrapped beyond this length) |
900 |
enforceAscii |
bool |
Enforce ASCII encoding when writing out 'mmcif' file. Defaults to True. |
True |
lastInOrder |
list of category names |
Move data categories in this list to end of each data block |
None |
selectOrder |
list of category names |
Write only data categories on this list. |
None |
columnAlignFlag |
bool |
Format the output in aligned columns (default=True) (Native Python Only) |
True |
useStopTokens |
bool |
Include terminating 'stop_' tokens at the end of mmCIF categories (loop_'s) (Native Python only) |
False |
formattingStep |
int |
The number row samples within each category used to estimate maximum column width for data alignment (Native Python only) |
None |
fmt |
string |
Format of output file (either "mmcif" or "bcif"). Defaults to "mmcif". |
'mmcif' |
# |
BCIF-specific args |
required | |
storeStringsAsBytes |
bool |
Strings are stored as lists of bytes (for BCIF files only). Defaults to False. |
False |
defaultStringEncoding |
str |
Default encoding for string data (for BCIF files only). Defaults to "utf-8". |
'utf-8' |
applyTypes |
bool |
apply explicit data typing before encoding (for BCIF files only; requires dictionaryApi to be passed too). Defaults to True. |
True |
dictionaryApi |
object |
DictionaryApi object instance (needed for BCIF files, only when applyTypes is True). Defaults to None. |
None |
useStringTypes |
bool |
assume all types are string (for BCIF files only). Defaults to False. |
False |
useFloat64 |
bool |
store floats with 64 bit precision (for BCIF files only). Defaults to False. |
False |
copyInputData |
bool |
make a new copy input data (for BCIF files only). Defaults to False. |
False |
ignoreCastErrors |
bool |
suppress errors when casting attribute types with dictionaryApi. Defaults to False. |
False |
**kwargs |
Placeholder for unsupported key value pairs |
{} |
Returns:
| Type | Description |
|---|---|
bool |
Completion status |
Source code in mmcif/io/IoAdapterPy.py
def writeFile(
self,
outputFilePath,
containerList,
maxLineLength=900,
enforceAscii=True,
lastInOrder=None,
selectOrder=None,
columnAlignFlag=True,
useStopTokens=False,
formattingStep=None,
fmt="mmcif",
storeStringsAsBytes=False,
defaultStringEncoding="utf-8",
applyTypes=True,
dictionaryApi=None,
useStringTypes=False,
useFloat64=False,
copyInputData=False,
ignoreCastErrors=False,
**kwargs
):
"""Write input list of data containers to the specified output file path in mmCIF or BCIF format.
Args:
outputFilePath (string): output file path
containerList (list DataContainer objects, optional)
maxLineLength (int, optional): Maximum length of output line (content is wrapped beyond this length)
enforceAscii (bool, optional): Enforce ASCII encoding when writing out 'mmcif' file. Defaults to True.
lastInOrder (list of category names, optional): Move data categories in this list to end of each data block
selectOrder (list of category names, optional): Write only data categories on this list.
columnAlignFlag (bool, optional): Format the output in aligned columns (default=True) (Native Python Only)
useStopTokens (bool, optional): Include terminating 'stop_' tokens at the end of mmCIF categories (loop_'s) (Native Python only)
formattingStep (int, optional): The number row samples within each category used to estimate maximum column width for data alignment (Native Python only)
fmt (string, optional): Format of output file (either "mmcif" or "bcif"). Defaults to "mmcif".
# BCIF-specific args:
storeStringsAsBytes (bool, optional): Strings are stored as lists of bytes (for BCIF files only). Defaults to False.
defaultStringEncoding (str, optional): Default encoding for string data (for BCIF files only). Defaults to "utf-8".
applyTypes (bool, optional): apply explicit data typing before encoding (for BCIF files only; requires dictionaryApi to be passed too). Defaults to True.
dictionaryApi (object, optional): DictionaryApi object instance (needed for BCIF files, only when applyTypes is True). Defaults to None.
useStringTypes (bool, optional): assume all types are string (for BCIF files only). Defaults to False.
useFloat64 (bool, optional): store floats with 64 bit precision (for BCIF files only). Defaults to False.
copyInputData (bool, optional): make a new copy input data (for BCIF files only). Defaults to False.
ignoreCastErrors (bool, optional): suppress errors when casting attribute types with dictionaryApi. Defaults to False.
**kwargs: Placeholder for unsupported key value pairs
Returns:
bool: Completion status
"""
lastInOrder = lastInOrder if lastInOrder else ["pdbx_nonpoly_scheme", "pdbx_poly_seq_scheme", "atom_site", "atom_site_anisotrop"]
if kwargs:
logger.warning("Unsupported keyword arguments %s", kwargs.keys())
try:
if enforceAscii:
encoding = "ascii"
else:
encoding = "utf-8"
#
fmt = fmt.lower()
#
if sys.version_info[0] > 2: # Check if using Python version higher than 2
if fmt == "mmcif":
with open(outputFilePath, "w", encoding=encoding) as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
elif fmt == "bcif":
bcifW = BinaryCifWriter(
dictionaryApi=dictionaryApi,
storeStringsAsBytes=storeStringsAsBytes,
defaultStringEncoding=defaultStringEncoding,
applyTypes=applyTypes,
useStringTypes=useStringTypes,
useFloat64=useFloat64,
copyInputData=copyInputData,
ignoreCastErrors=ignoreCastErrors,
)
bcifW.serialize(outputFilePath, containerList)
else:
logger.error("Unsupported fmt %r. Currently only supports 'mmcif' or 'bcif'.", fmt)
return False
else:
logger.warning("Support for Python 2 will be deprecated soon. Please use Python 3.")
if fmt == "bcif":
logger.error("Support for BCIF writing only available in Python 3.")
return False
elif fmt == "mmcif":
if enforceAscii:
with io.open(outputFilePath, "w", encoding=encoding) as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
else:
with open(outputFilePath, "wb") as ofh:
self.__writeFile(
ofh,
containerList,
maxLineLength=maxLineLength,
columnAlignFlag=columnAlignFlag,
lastInOrder=lastInOrder,
selectOrder=selectOrder,
useStopTokens=useStopTokens,
formattingStep=formattingStep,
enforceAscii=enforceAscii,
cnvCharRefs=self._useCharRefs,
)
else:
logger.error("Unsupported fmt %r for Python2 installation of mmcif.io.IoAdapterPy. Currently only 'mmcif' is supported. Upgrade to Python3 for 'bcif' support", fmt)
return False
return True
except Exception as ex:
if self._raiseExceptions:
raise_from(ex, None)
else:
logger.exception("Failing write for %s with %s", outputFilePath, str(ex))
logger.error("Failing write for %s with %s", outputFilePath, str(ex))
return False