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2017-2 Schrodinger Python API
Package schrodinger :: Package utils :: Module fileutils
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Module fileutils

A module of file utilities to deal with common file issues.

NOTE: This module is used in scripts that need to be able to run without a Schrodinger license, and therefore can't depend on the pymmlibs.

The force_remove and force_rename functions deal with the fact that os.remove() and os.rename() don't work on Windows if write permissions are not enabled.

Classes [hide private]
  chdir
A context manager that carries out commands inside of the specified directory and restores the current directory when done.
  tempfilename
  TempStructureFile
Functions [hide private]
 
force_remove(*args)
Remove each file in 'args' in a platform independent way without an exception, regardless of presence of the file or the lack of write permission.
 
force_rmtree(dirname, ignore_errors=False)
Remove the directory 'dirname', using force_remove to remove any difficult to remove files or sub-directories.
 
force_rename(old, new)
Rename a file, even if a file at the new name exists, and even if that file doesn't have write permission, and even if old and new are on different devices.
a tuple containing two strings
splitext(p)
Split the extension from a pathname.
 
get_structure_file_format(filename)
Return the format of a structure file, based on the filename extension.
bool
is_maestro_file(filename)
Returns True if specified filename represents a Maestro file.
bool
is_sd_file(filename)
Returns True if specified filename represents a SD file.
bool
is_csv_file(filename)
Returns True if specified filename represents a CSV file.
bool
is_smiles_file(filename)
Returns True if specified filename represents a Smiles file.
bool
is_poseviewer_file(filename)
Returns True if specified filename represents a Maestro PoseViewer file.
bool
is_hypothesis_file(filename)
Returns True if specified filename represents a Phase hypothesis file.
 
get_basename(filename)
Returns the final component of specified path name minus the extension.
 
is_valid_jobname(jobname)
Returns True if specified job name is valid, does not contain any illegal characters, and does not start with ".".
 
get_jobname(filename)
Returns a job name derived from the specified filename.
 
get_next_filename_prefix(path, midfix, zfill_width=0)
Return next filename prefix in series <root><midfix><number>.
 
get_next_filename(path, midfix, zfill_width=0)
Return next filename in series <root><midfix><number>.<ext>.
 
remote_mmshare_dir()
 
remote_scripts_dir()
str
get_mmshare_dir()
Return the path to the local $SCHRODINGER/mmshare-*/ directory
str
get_mmshare_data_dir()
Return the path of the local $SCHRODINGER/mmshare-*/data/ directory.
str
get_mmshare_scripts_dir()
Return the path of the $SCHRODINGER/mmshare-*/python/scripts/ directory.
str
get_mmshare_common_dir()
Return the path of the $SCHRODINGER/mmshare-*/python/common/ directory.
str
get_directory_path(which_directory)
This function returns the schrodinger specific directory.
 
_deprecated_get_dir_warning()
Issue a deprecation warning which redirects users to call get_directory_path instead of the deprecated functions below.
 
get_directory(which_directory)
 
get_home_dir()
 
get_appdata_dir()
 
get_local_appdata_dir()
 
get_desktop_dir()
 
get_mydocuments_dir()
 
get_mynetworkplaces_dir()
 
get_userdata_dir()
 
get_schrodinger_temp_dir()
str or None
_check_for_pymol_by_platform(path)
Check for platform-specific executable file or script in the directory path provided.
str
_locate_pymol_in_registry(root_key, keypath, valuename=None)
Find out pymol installation path under given keypath and keyname.
str or None
locate_pymol()
Find the executable or script we use to launch PyMOL.
list
get_pymol_cmd(use_x11=False)
Get a cmd list for launching Pymol.
 
create_hard_link(source, link_name)
Create a hard link pointing to source named link_name.
 
mkdir_p(path, *mode)
Like os.makedirs, create a directory, including intermediate-level directories if necessary.
 
cat(source_filenames, dest_filename)
Concatenate the contents of the source files, writing them to a destination file.
Variables [hide private]
  _winreg = None
hash(x)
  fsenc = 'ANSI_X3.4-1968'
  MAESTRO_STRICT = 'maestro_strict'
  _MAE_EXTS = ['.mae', '.mae.gz', '.maegz']
  EXTENSIONS = {'cif': ['.cif'], 'maestro': ['.bld', '.cms', '.c...
  APPDATA = 2
  CIF = 'cif'
  DESKTOP = 6
  DOCUMENTS = 7
  HOME = 1
  LOCAL_APPDATA = 3
hash(x)
  MAESTRO = 'maestro'
  MOL2 = 'mol2'
  NETWORK = 8
  PDB = 'pdb'
  PHASE_HYPO = 'phasehypo'
  SD = 'sd'
  SMILES = 'smiles'
  SMILESCSV = 'smilescsv'
  TEMP = 5
  USERDATA = 4
  __package__ = 'schrodinger.utils'
Function Details [hide private]

force_remove(*args)

 

Remove each file in 'args' in a platform independent way without an exception, regardless of presence of the file or the lack of write permission.

Parameters:
  • args (str) - the pathname for the files to remove

force_rmtree(dirname, ignore_errors=False)

 

Remove the directory 'dirname', using force_remove to remove any difficult to remove files or sub-directories.

Parameters:
  • dirname (str) - the directory to remove

force_rename(old, new)

 

Rename a file, even if a file at the new name exists, and even if that file doesn't have write permission, and even if old and new are on different devices.

Parameters:
  • old (str) - Path to the file source.
  • new (str) - Path to the file destination.

Note: Renaming may not be an atomic operation. If the 'new' file exists then it is first removed then renamed in two operations. Similarly, if old and new are not on the same device then the file is copied to 'new' then the 'old' file is removed.

splitext(p)

 

Split the extension from a pathname. Returns "(root, ext)". Equivalent to os.path.splitext(), except that for gzip compressed files, such as *.mae.gz files, ".mae.gz" is split off instead of ".gz". *.sdf.gz, *.sd.gz, *.mol.gz

Parameters:
  • p (str) - a pathname
Returns: a tuple containing two strings
The root filename and the file extension.

get_structure_file_format(filename)

 

Return the format of a structure file, based on the filename extension. None is returned if the file extension is not recognized.

is_maestro_file(filename)

 

Returns True if specified filename represents a Maestro file.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename a maestro file?

is_sd_file(filename)

 

Returns True if specified filename represents a SD file.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename an SD file?

is_csv_file(filename)

 

Returns True if specified filename represents a CSV file.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename a csv file?

is_smiles_file(filename)

 

Returns True if specified filename represents a Smiles file.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename a smiles file?

is_poseviewer_file(filename)

 

Returns True if specified filename represents a Maestro PoseViewer file. Checks if the filename ends with *_pv.mae, *_pv.maegz, *_pv.mae.gz, etc.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename a PV file?

is_hypothesis_file(filename)

 

Returns True if specified filename represents a Phase hypothesis file. The *.phypo extension corresponds to a gzipped Maestro file containing a single ct which is a Phase hypothesis.

Parameters:
  • filename (string) - a filename
Returns: bool
Is this filename a Phase hypothesis file?

get_basename(filename)

 

Returns the final component of specified path name minus the extension. Suffixes such as "_pv" and "_epv" are also stripped.

get_jobname(filename)

 

Returns a job name derived from the specified filename. Same as get_basename(), except that illegal characters are removed.

get_next_filename_prefix(path, midfix, zfill_width=0)

 

Return next filename prefix in series <root><midfix><number>.

Given a path (absolute or relative) to a filename or filename prefix, return the next prefix in the sequence implied by path and midfix. For example, with a path of /full/path/to/foo.mae, path/to/foo.mae or foo.mae, or /full/path/to/foo, path/to/foo or foo, and a midifix of '-', this function will return "foo-3" if any file whose prefix foo-2 (and no higher-numbered foo-*) is present. It will return foo-1 if no file whose prefix is foo-<number> is present. The net effect is that any file-name extension in the path argument will be ignored.

This function differs from next_filename() in that here, all files sharing the prefix contained in the path are searched, regardless of extension, and the next filename prefix is returned.

The search is case sensitive or not depending on the semantics of the file system. The leading directory of the path, if any, is included in the return value.

Usage note: you might use this when the filename prefix could be exhibited by many files and you don't want to overwrite any of them. For example, you are starting up a job which will create many files with the same prefix.

get_next_filename(path, midfix, zfill_width=0)

 

Return next filename in series <root><midfix><number>.<ext>.

Given a path (absolute or relative) to a filename, return the next filename in the sequence implied by path and midfix. For example, with a path of /full/path/to/foo.mae, path/to/foo.mae or foo.mae and a midifix of '-', this function will return "foo-3.mae" if file foo-2.mae (and no higher-numbered foo-*.mae )is present. It will return foo-1.mae if no file named foo-<number>.mae is present.

This function differs from next_filename_prefix() in that here, only files with the specified extension are searched, and the next full filename is retured.

The search is case sensitive or not depending on the semantics of the file system. The leading directory of the path, if any, is included in the return value.

Usage note: You might use this when you are expecting to update only a single file: the one whose filename is given in the path. For example, you are exporting structures to a .mae file and you want to pick a non-conflicting name based on a user's filename specification.

get_mmshare_dir()

 

Return the path to the local $SCHRODINGER/mmshare-*/ directory

Returns: str
Path to the "mmshare" directory.

get_mmshare_data_dir()

 

Return the path of the local $SCHRODINGER/mmshare-*/data/ directory.

Returns: str
Path to the "data" directory.

get_mmshare_scripts_dir()

 

Return the path of the $SCHRODINGER/mmshare-*/python/scripts/ directory.

Returns: str
Path to the "scripts" directory.

get_mmshare_common_dir()

 

Return the path of the $SCHRODINGER/mmshare-*/python/common/ directory.

Returns: str
Path to the "common" directory.

get_directory_path(which_directory)

 

This function returns the schrodinger specific directory.

If an invalid which_directory is specified, then a TypeError is thrown.

Parameters:
  • which_directory (constant) - value should be one of following...
    • HOME : To get user's home dir
    • APPDATA : To get the Schrodinger application shared data dir
    • LOCAL_APPDATA : To get the Schrodinger application local data dir
    • USERDATA : To get user's data dir
    • TEMP : To get default temporary data dir
    • DESKTOP : To get user's desktop dir
    • DOCUMENTS : To get user's 'My Documents' dir
    • NETWORK : To get user's 'My Network places' dir (only for Windows)
Returns: str
Directory path.

get_directory(which_directory)

 

Deprecated: Because this function behaves in a non-standard way by returning an mmlib status, get_directory_path is preferred.

get_home_dir()

 

Deprecated: get_directory_path should be used instead.

get_appdata_dir()

 

Deprecated: get_directory_path should be used instead.

get_local_appdata_dir()

 

Deprecated: get_directory_path should be used instead.

get_desktop_dir()

 

Deprecated: get_directory_path should be used instead.

get_mydocuments_dir()

 

Deprecated: get_directory_path should be used instead.

get_mynetworkplaces_dir()

 

Deprecated: get_directory_path should be used instead.

get_userdata_dir()

 

Deprecated: get_directory_path should be used instead.

get_schrodinger_temp_dir()

 

Deprecated: get_directory_path should be used instead.

_check_for_pymol_by_platform(path)

 

Check for platform-specific executable file or script in the directory path provided.

Parameters:
  • path (str) - The path to modify
Returns: str or None
The path to the PyMOL executable file, or None if PyMOL was not found in the given path

_locate_pymol_in_registry(root_key, keypath, valuename=None)

 

Find out pymol installation path under given keypath and keyname. Check for standard pymol programs and return pymol_launch_command path.

Parameters:
  • root_key (_winreg key) - root registry key
  • keypath (str) - registry keypath
  • valuename (None) - valuename of the key - is always None for this module
Returns: str
the path to the Pymol executable, or None if not found

Note: Any exception encountered during registry lookup results in None being returned

locate_pymol()

 

Find the executable or script we use to launch PyMOL.

Returns: str or None
The pymol launch command or None if PyMOL was not found

get_pymol_cmd(use_x11=False)

 

Get a cmd list for launching Pymol. This may include extra platform- specific arguments.

Parameters:
  • use_x11 (bool) - if True causes -m to be added to the launch command on Mac
Returns: list
a cmd list with the executable as first element and any other options following it.

create_hard_link(source, link_name)

 

Create a hard link pointing to source named link_name.

On Windows, uses CreateHardLinkA() and will raise RuntimeError() on failure.

On other OSes uses os.link(), and will raise OSError on failure.

mkdir_p(path, *mode)

 

Like os.makedirs, create a directory, including intermediate-level directories if necessary. But unlike os.makedirs, don't complain if the directory already exists. The name of this function comes from the POSIX "mkdir -p" shell utility, which behaves the same way.

cat(source_filenames, dest_filename)

 

Concatenate the contents of the source files, writing them to a destination file. All files are specified by name. If source_filenames is an empty list, an empty file is produced.

Parameters:
  • source_filenames (sequence of str) - input files
  • dest_filename (str) - destination file

Variables Details [hide private]

EXTENSIONS

Value:
{'cif': ['.cif'],
 'maestro': ['.bld',
             '.cms',
             '.cms.gz',
             '.cmsgz',
             '.mae',
             '.mae.gz',
             '.maegz'],
...

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2017-2 Schrodinger Python API
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