- CheckFileExt
-
CheckFileExt(FileName, FileExts)
Check file type based on the specified file extensions delimited by spaces.
Arguments:
FileName (str): Name of a file.
FileExts (str): Space delimited string containing valid file extensions.
Returns:
bool : True, FileName contains a valid file extension; Otherwise, False.
- CheckTextValue
-
CheckTextValue(Value, ValidValues)
Check text value based on the specified valid values delimited by spaces.
Arguments:
Value (str): Text value
ValidValues (str): Space delimited string containing valid values.
Returns:
bool : True, Value is valid; Otherwise, False.
- DoesSMILESFileContainTitleLine
-
DoesSMILESFileContainTitleLine(FileName)
Determine whether the SMILES file contain a title line based on the presence of a string SMILES, Name or ID in the first line.
Arguments:
FileName (str): Name of a file.
Returns:
bool : True, File contains title line; Otherwise, False.
- ExpandFileNames
-
ExpandFileNames(FilesSpec, Delimiter = ",")
Expand files specification using glob module to process any * or ? wild cards in file names and return a list of expanded file names.
Arguments:
FilesSpec (str): Files specifications
Delimiter (str): Delimiter for file specifications
Returns:
list : List of expanded file names
- GetExamplesTextFromDocOptText
-
GetExamplesTextFromDocOptText(DocOptText)
Get script usage example lines from a docopt doc string. The example text line start from a line containing `Examples:` keyword at the beginning of the line.
Arguments:
DocOptText (str): Doc string containing script usage examples lines starting with
a line marked by `Examples:` keyword at the beginning of a line.
Returns:
str : A string containing text lines retrieved from the examples section of
DocOptText parameter.
- GetExcelStyleColumnLabel
-
GetExcelStyleColumnLabel(ColNum)
Return Excel style column label for a colum number.
Arguments:
ColNum (int): Column number
Returns:
str : Excel style column label.
- GetFormattedElapsedTime
-
GetFormattedElapsedTime(StartingWallClockTime, StartingProcessorTime)
Get elapsed wallclock and processor times as a string in the following format: Wallclock: %s days, %d hrs, %d mins, %d secs (Process: %d days, %d hrs, %d mins, %.2f secs).
Arguments:
StartingWallClockTime (float): Starting wallclock time in seconds.
StartingProcessorTime (float): Starting processor time in seconds.
Returns:
str : Elapsed time formatted as:
Wallclock: %s days, %d hrs, %d mins, %d secs (Process: %d days,
%d hrs, %d mins, %.2f secs)
- GetFormattedFileSize
-
GetFormattedFileSize(FileName, Precision = 1)
Get file size as a string in the following format: %.*f <bytes, KB, MB, GB>
Arguments:
FileName (str): File path.
Precision (int): File size precision.
Returns:
str : File size formatted as: %.2f <bytes, KB, MB, GB>
- GetMayaChemToolsLibDataPath
-
GetMayaChemToolsLibDataPath()
Get location of MayaChemTools lib data directory.
Returns:
str : Location of MayaChemTools lib data directory.
The location of MayaChemTools lib data directory is determined relative to MayaChemTools python lib directory name available through sys.path.
- GetMayaChemToolsVersion
-
GetMayaChemToolsVersion()
Get version number for MayaChemTools from PackageInfo.csv file in MayaChemTool lib data directory.
Returns:
str : Version number
- GetTextLines
-
GetTextLines(TextFilePath)
Read text lines from input file, remove new line characters and return a list containing stripped lines.
Arguments:
TextFilePath (str): Text file name including file path.
Returns:
list : A list lines.
- GetTextLinesWords
-
GetTextLinesWords(TextFilePath, Delimiter, QuoteChar, IgnoreHeaderLine)
Parse lines in the specified text file into words in a line and return a list containing list of parsed line words.
Arguments:
TextFilePath (str): Text file name including file path.
Delimiter (str): Delimiter for parsing text lines.
QuoteChar (str): Quote character for line words.
IgnoreHeaderLine (bool): A flag indicating whether to ignore first
valid data line corresponding to header line.
Returns:
list : A list of lists containing parsed words for lines.
The lines starting with # or // are considered comment lines and are ignored during parsing along with any empty lines.
- GetWallClockAndProcessorTime
-
GetWallClockAndProcessorTime()
Get wallclock and processor times in seconds.
Returns:
float : Wallclock time.
float : Processor time.
- IsEmpty
-
IsEmpty(Value)
Determine whether the specified value is empty after converting it in to a string and removing all leading and trailing white spaces. A value of type None is considered empty.
Arguments:
Value (str, int or float): Text or a value
Returns:
bool : True, Text string is empty; Otherwsie, False.
- IsFloat
-
IsFloat(Value)
Determine whether the specified value is a float by converting it into a float.
Arguments:
Value (str, int or float): Text
Returns:
bool : True, Value is a float; Otherwsie, False.
- IsInteger
-
IsInteger(Value)
Determine whether the specified value is an integer by converting it into an int.
Arguments:
Value (str, int or float): Text
Returns:
bool : True, Value is an integer; Otherwsie, False.
- IsNumber
-
IsNumber(Value)
Determine whether the specified value is a number by converting it into a float.
Arguments:
Value (str, int or float): Text
Returns:
bool : True, Value is a number; Otherwsie, False.
- JoinWords
-
JoinWords(Words, Delimiter, Quote = False)
Join words in a list using specified delimiter with optional quotes around words.
Arguments:
Words (list): List containing words to join.
Delimiter (string): Delimiter for joining words.
Quote (bool): Put quotes around words.
Returns:
str : String containing joined words.
- ObjectFromBase64EncodedString
-
ObjectFromBase64EncodedString(EncodedObject)
Generate Python object from a bas64 encoded and pickled object string.
Arguments:
str: Base64 encoded and pickled object string.
Returns:
object : Python object or None.
- ObjectToBase64EncodedString
-
ObjectToBase64EncodedString(Object)
Encode Python object into base64 encoded string. The object is pickled before encoding.
Arguments:
object: Python object.
Returns:
str : Base64 encode object string or None.
- ParseFileName
-
ParseFileName(FilePath)
Parse specified file path and return file dir, file name, and file extension.
Arguments:
FilePath (str): Name of a file with complete file path.
Returns:
str : File directory.
str : File name without file extension.
str : File extension.
- PrintError
-
PrintError(Msg, Status=1)
Print message to stderr along with flushing stderr and exit with a specified status. An `Error` prefix is placed before the message.
Arguments:
Msg (str): Text message.
Status (int): Exit status.
- PrintInfo
-
PrintInfo(Msg='')
Print message to stderr along with flushing stderr.
Arguments:
Msg (str): Text message.
- PrintWarning
-
PrintWarning(msg)
Print message to stderr along with flushing stderr. An `Warning` prefix is placed before the message.
Arguments:
Msg (str): Text message.
- ProcessOptionConformerGenerator
-
ProcessOptionConformerGenerator(OptionName, OptionValue)
Process conformer generator option and return a map containing paramater name and values for generatiing conformers.
Arguments:
ParamOptionName (str): Command line conformer generator option name
ParamOptionValue (str): Command line conformer generator option value
Returns:
dictionary: Conformer generation parameter name and value pairs.
- ProcessOptionConformerParameters
-
ProcessOptionConformerParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None)
Process parameters for conformer generation and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line conformer generation parameters
option name.
ParamsOptionValue (str): Comma delimited list of parameter name and value pairs.
ParamsDefaultInfo (dict): Default values to override for selected parameters.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter name and values specified in ParamsOptionValues are validated before returning them in a dictionary.
- ProcessOptionInfileParameters
-
ProcessOptionInfileParameters(ParamsOptionName, ParamsOptionValue, InfileName = None, OutfileName = None, ParamsDefaultInfo = None)
Process parameters for reading input files and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line input parameters option name.
ParamsOptionValue (str): Comma delimited list of parameter name and value pairs.
InfileName (str): Name of input file.
OutfileName (str): Name of output file.
ParamsDefaultInfo (dict): Default values to override for selected parameters.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter name and values specified in ParamsOptionValue are validated before returning them in a dictionary.
- ProcessOptionMultiprocessingParameters
-
ProcessOptionMultiprocessingParameters(ParamsOptionName, ParamsOptionValue)
Process parameters for multiprocessing and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line multiprocessing parameters option name.
ParamsOptionValue (str): Comma delimited list of parameter name and value pairs.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter name and values specified in ParamsOptionValue are validated before returning them in a dictionary.
- ProcessOptionNameValuePairParameters
-
ProcessOptionNameValuePairParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo)
Process name and value parameter pairs for an option and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line option name for name and value
parameter pairs.
ParamsOptionValue (str): Comma delimited list of parameter name and
value parameter pairs.
ParamsDefaultInfo (dict): A dictionary containing a list of parameter
type and default value pairs keyed by parameter name. Supported
parameter types: bool, int, float, file, and str.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter names and values specified in ParamsOptionValue are validated before returning them in a dictionary.
Example(s):
ParamsDefaultInfo = {"Cleanup": ["bool", True], "RemoveFragments":
["bool", True], "Neutralize": ["bool", True],
"CanonicalizeTautomer": ["bool", True]}
ProcessOptionNameValuePairParameters("--methodologyParams",
Options["--methodologyParams"], ParamsDefaultInfo)
- ProcessOptionOutfileParameters
-
ProcessOptionOutfileParameters(ParamsOptionName, ParamsOptionValue, InfileName = None, OutfileName = None, ParamsDefaultInfo = None)
Process parameters for writing output files and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line input parameters option name.
ParamsOptionValue (str): Comma delimited list of parameter name and value pairs.
InfileName (str): Name of input file.
OutfileName (str): Name of output file.
ParamsDefaultInfo (dict): Default values to override for selected parameters.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter name and values specified in ParamsOptionValue are validated before returning them in a dictionary.
The default value of some parameters may depend on type of input file. Consequently, the input file name is also needed.
- ProcessOptionPyMOLCubeFileViewParameters
-
ProcessOptionPyMOLCubeFileViewParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None)
Process PyMOl parameters for cube file views and return a map containing processed parameter names and values.
ParamsOptionValue is a comma delimited list of parameter name and value pairs for setting up PyMOL views.
The supported parameter names along with their default and possible values are shown below:
ContourColor1, red, ContourColor2, blue,
ContourLevel1, -0.02, ContourLevel2, 0.02,
ContourLevel, 0.02,
ContourLevelAutoAt, 0.5,
ESPRampValues, -1.0 0 1.0,
ESPRampColors, red white blue,
HideHydrogens, yes, DisplayESP, OnSurface,
DisplayMolecule, BallAndStick,
DisplaySphereScale, 0.3, DisplayStickRadius, 0.2,
MeshQuality,2, MeshWidth, 0.5,
SurfaceQualuty, 2, SurfaceTransparency, 0.25,
VolumeColorRamp, auto, VolumeColorRampOpacity, 0.2,
VolumeContourWindowFactor, 0.05
Arguments:
ParamsOptionName (str): Command line PyMOL view option name.
ParamsOptionValues (str): Comma delimited list of parameter name and value pairs.
ParamsDefaultInfo (dict): Default values to override for selected parameters.
Returns:
dictionary: Processed parameter name and value pairs.
- ProcessOptionSeabornPlotParameters
-
ProcessOptionSeabornPlotParameters(ParamsOptionName, ParamsOptionValue, ParamsDefaultInfo = None)
Process parameters for generating Seaborn plots and return a map containing processed parameter names and values.
Arguments:
ParamsOptionName (str): Command line seaborn parameters option name.
ParamsOptionValue (str): Comma delimited list of parameter name and value pairs.
ParamsDefaultValues (dict): Default values for selected parameters.
Returns:
dictionary: Processed parameter name and value pairs.
The parameter name and values specified in ParamsOptionValue are validated before returning them in a dictionary.
- ReplaceHTMLEntitiesInText
-
ReplaceHTMLEntitiesInText(Text)
Check and replace the followng HTML entities to their respective code for display in a browser: < (less than), > (greater than), & (ampersand), " (double quote), and ' (single quote).
Arguments:
Text (str): Text value.
Returns:
str : Modifed text value.
- TruncateText
-
TruncateText(Text, Width, TrailingChars = "...")
Truncate text using specified width along with appending any trailing characters.
Arguments:
Text (string): Input text.
Width (int): Max number of characters before truncating text.
Delimiter (string): Trailing characters to append or None.
Returns:
str : Truncated text
- ValidateOptionFileExt
-
ValidateOptionFileExt(OptionName, FileName, FileExts)
Validate file type based on the specified file extensions delimited by spaces.
Arguments:
OptionName (str): Command line option name.
FileName (str): Name of a file.
FileExts (str): Space delimited string containing valid file extensions.
The function exits with an error message for a file name containing invalid file extension.
- ValidateOptionFilePath
-
ValidateOptionFilePath(OptionName, FilePath)
Validate presence of the file.
Arguments:
OptionName (str): Command line option name.
FilePath (str): Name of a file with complete path.
The function exits with an error message for a file path that doesn't exist.
- ValidateOptionFloatValue
-
ValidateOptionFloatValue(OptionName, OptionValue, CmpOpValueMap)
Validate option value using comparison operater and value pairs in specified in a map.
Arguments:
OptionName (str): Command line option name.
OptionValue (float or str): Command line option value.
CmpOpValueMap (dictionary): Comparison operator key and value pairs to
validate values specified in OptionValue.
The function exits with an error message for an invalid option values specified in OptionValue.
Example(s):
ValidateOptionNumberValue("-b, --butinaSimilarityCutoff",
Options["--butinaSimilarityCutoff"],
{">": 0.0, "<=" : 1.0})
- ValidateOptionIntegerValue
-
ValidateOptionIntegerValue(OptionName, OptionValue, CmpOpValueMap)
Validate option value using comparison operater and value pairs in specified in a map.
Arguments:
OptionName (str): Command line option name.
OptionValue (int or str): Command line option value.
CmpOpValueMap (dictionary): Comparison operator key and value pairs to
validate values specified in OptionValue.
The function exits with an error message for an invalid option values specified in OptionValue.
Example(s):
ValidateOptionIntegerValue("--maxConfs", Options["--maxConfs"],
{">": 0})
- ValidateOptionNumberValue
-
ValidateOptionNumberValue(OptionName, OptionValue, CmpOpValueMap)
Validate option value using comparison operater and value pairs in specified in a map.
Arguments:
OptionName (str): Command line option name.
OptionValue (int or float): Command line option value.
CmpOpValueMap (dictionary): Comparison operator key and value pairs to
validate values specified in OptionValue.
The function exits with an error message for an invalid option values specified in OptionValue.
Example(s):
ValidateOptionNumberValue("--maxConfs", int(Options["--maxConfs"]),
{">": 0})
ValidateOptionNumberValue("-b, --butinaSimilarityCutoff",
float(Options["--butinaSimilarityCutoff"]),
{">": 0.0, "<=" : 1.0})
- ValidateOptionNumberValues
-
ValidateOptionNumberValues(OptionName, OptionValueString, OptionValueCount, OptionValueDelimiter, OptionValueType, CmpOpValueMap)
Validate numerical option values using option value string, delimiter, value type, and a specified map containing comparison operator and value pairs.
Arguments:
OptionName (str): Command line option name.
OptionValueString (str): Command line option value.
OptionValueCount (int): Number of values in OptionValueString.
OptionValueDelimiter (str): Delimiter used for values in OptionValueString.
OptionValueType (str): Valid number types (integer or float)
CmpOpValueMap (dictionary): Comparison operator key and value pairs to
validate values specified in OptionValueString.
The function exits with an error message for invalid option values specified in OptionValueString
Example(s):
ValidateOptionNumberValues("-m, --molImageSize",
Options["--molImageSize"], 2, ",", "integer", {">": 0})
- ValidateOptionTextValue
-
ValidateOptionTextValue(OptionName, OptionValue, ValidValues)
Validate option value based on the valid specified values separated by spaces.
Arguments:
OptionName (str): Command line option name.
OptionValue (str): Command line option value.
ValidValues (str): Space delimited string containing valid values.
The function exits with an error message for an invalid option value.
- ValidateOptionsDistinctFileNames
-
ValidateOptionsDistinctFileNames(OptionName1, FilePath1, OptionName2, FilePath2)
Validate two distinct file names.
Arguments:
OptionName1 (str): Command line option name.
FilePath1 (str): Name of a file with complete file path.
OptionName2 (str): Command line option name.
FilePath2 (str): Name of a file with complete file path.
The function exits with an error message for two non distinct file names.
- ValidateOptionsOutputFileOverwrite
-
ValidateOptionsOutputFileOverwrite(OptionName, FilePath, OverwriteOptionName, OverwriteStatus)
Validate overwriting of output file.
Arguments:
OptionName (str): Command line option name.
FilePath (str): Name of a file with complete file path.
OverwriteOptionName (str): Overwrite command line option name.
OverwriteStatus (bool): True, overwrite
The function exits with an error message for a file that is present and is not allowed to be written as indicated by value of OverwriteStatus.
- WrapText
-
WrapText(Text, Delimiter, Width)
Wrap text using specified delimiter and width.
Arguments:
Text (string): Input text
Delimiter (string): Delimiter for wrapping text
Width (int): Max number of characters before wrapping text
Returns:
str : Wrapped text
