schrodinger.application.prime.wrapper module

Classes to assist in preparing prime input files

class schrodinger.application.prime.wrapper.PrimeConfig(kw=None)

Bases: schrodinger.application.inputconfig.InputConfig

Class for reading and writing simplified Prime homology modeling input files.

specs = ["JOB_TYPE                   = string(default='MODEL')", "DIR_NAME                   = string(default='.')", 'QUERY_OFFSET               = integer(default=0)', 'TAILS                      = integer(default=0)', "SIDE_OPT                   = string(default='false')", "MINIMIZE                   = string(default='true')", "BUILD_INSERTIONS           = string(default='true')", 'MAX_INSERTION_SIZE         = integer(default=20)', "BUILD_TRANSITIONS          = string(default='true')", "BUILD_DELETIONS            = string(default='true')", "KEEP_ROTAMERS              = string(default='true')", "KNOWLEDGE_BASED            = string(default='true')", 'NUM_OUTPUT_STRUCT          = integer(default=1)', "TEMPLATE_RESIDUE_NUMBERS   = string(default='false')"]
__init__(kw=None)

Accepts one argument which is either a path or a keyword dictionary.

setAlignment(alignment, ligands=('all',), include_water=False, template_number=1)
Parameters

  • alignment (BasePrimeAlignment) – Alignment.

  • ligands (tuple of str) – Names of ligands to be included in the model.

  • include_water (bool) – Whether to include water molecules in the built model.

  • template_number (int) – Template number

writeConfig(filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/prime.

Parameters

filename (str) – Name of output file.

__contains__(key, /)

True if the dictionary has the specified key, else False.

__len__()

Return len(self).

as_bool(key)

Accepts a key as input. The corresponding value must be a string or the objects (True or 1) or (False or 0). We allow 0 and 1 to retain compatibility with Python 2.2.

If the string is one of True, On, Yes, or 1 it returns True.

If the string is one of False, Off, No, or 0 it returns False.

as_bool is not case sensitive.

Any other input will raise a ValueError.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_bool('a')
Traceback (most recent call last):
ValueError: Value "fish" is neither True nor False
>>> a['b'] = 'True'
>>> a.as_bool('b')
1
>>> a['b'] = 'off'
>>> a.as_bool('b')
0
as_float(key)

A convenience method which coerces the specified value to a float.

If the value is an invalid literal for float, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_float('a')  
Traceback (most recent call last):
ValueError: invalid literal for float(): fish
>>> a['b'] = '1'
>>> a.as_float('b')
1.0
>>> a['b'] = '3.2'
>>> a.as_float('b')  
3.2...
as_int(key)

A convenience method which coerces the specified value to an integer.

If the value is an invalid literal for int, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_int('a')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: 'fish'
>>> a['b'] = '1'
>>> a.as_int('b')
1
>>> a['b'] = '3.2'
>>> a.as_int('b')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: '3.2'
as_list(key)

A convenience method which fetches the specified value, guaranteeing that it is a list.

>>> a = ConfigObj()
>>> a['a'] = 1
>>> a.as_list('a')
[1]
>>> a['a'] = (1,)
>>> a.as_list('a')
[1]
>>> a['a'] = [1]
>>> a.as_list('a')
[1]
clear()

A version of clear that also affects scalars/sections Also clears comments and configspec.

Leaves other attributes alone :

depth/main/parent are not affected

copy() → a shallow copy of D
dict()

Return a deepcopy of self as a dictionary.

All members that are Section instances are recursively turned to ordinary dictionaries - by calling their dict method.

>>> n = a.dict()
>>> n == a
1
>>> n is a
0
fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None)

A version of get that doesn’t bypass string interpolation.

getSpecsString()

Return a string of specifications. One keywords per line. Raises ValueError if this class has no specifications.

items() → list of D’s (key, value) pairs, as 2-tuples
iteritems() → an iterator over the (key, value) items of D
iterkeys() → an iterator over the keys of D
itervalues() → an iterator over the values of D
keys() → list of D’s keys
merge(indict)

A recursive update - useful for merging config files.

>>> a = '''[section1]
...     option1 = True
...     [[subsection]]
...     more_options = False
...     # end of file'''.splitlines()
>>> b = '''# File is user.ini
...     [section1]
...     option1 = False
...     # end of file'''.splitlines()
>>> c1 = ConfigObj(b)
>>> c2 = ConfigObj(a)
>>> c2.merge(c1)
>>> c2
ConfigObj({'section1': {'option1': 'False', 'subsection': {'more_options': 'False'}}})
pop(key, default=<object object>)

‘D.pop(k[,d]) -> v, remove specified key and return the corresponding value. If key is not found, d is returned if given, otherwise KeyError is raised’

popitem()

Pops the first (key,val)

printout()

Print all keywords of this instance to stdout.

This method is meant for debugging purposes.

reload()

Reload a ConfigObj from file.

This method raises a ReloadError if the ConfigObj doesn’t have a filename attribute pointing to a file.

rename(oldkey, newkey)

Change a keyname to another, without changing position in sequence.

Implemented so that transformations can be made on keys, as well as on values. (used by encode and decode)

Also renames comments.

reset()

Clear ConfigObj instance and restore to ‘freshly created’ state.

restore_default(key)

Restore (and return) default value for the specified key.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

If there is no default value for this key, KeyError is raised.

restore_defaults()

Recursively restore default values to all members that have them.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

It doesn’t delete or modify entries without default values.

setdefault(key, default=None)

A version of setdefault that sets sequence if appropriate.

update(indict)

A version of update that uses our __setitem__.

validate(validator, preserve_errors=False, copy=False, section=None)

Test the ConfigObj against a configspec.

It uses the validator object from validate.py.

To run validate on the current ConfigObj, call:

test = config.validate(validator)

(Normally having previously passed in the configspec when the ConfigObj was created - you can dynamically assign a dictionary of checks to the configspec attribute of a section though).

It returns True if everything passes, or a dictionary of pass/fails (True/False). If every member of a subsection passes, it will just have the value True. (It also returns False if all members fail).

In addition, it converts the values from strings to their native types if their checks pass (and stringify is set).

If preserve_errors is True (False is default) then instead of a marking a fail with a False, it will preserve the actual exception object. This can contain info about the reason for failure. For example the VdtValueTooSmallError indicates that the value supplied was too small. If a value (or section) is missing it will still be marked as False.

You must have the validate module to use preserve_errors=True.

You can then use the flatten_errors function to turn your nested results dictionary into a flattened list of failures - useful for displaying meaningful error messages.

validateValues(preserve_errors=True, copy=True)

Validate the values read in from the InputConfig file.

Provide values for keywords with validators that have default values.

If a validator for a keyword is specified without a default and the keyword is missing from the input file, a RuntimeError will be raised.

Parameters

  • preserve_errors (bool) –

    If set to False, this method returns True if

    all tests passed, and False if there is a failure. If set to True, then instead of getting False for failed checkes, the actual detailed errors are printed for any validation errors encountered.

    Even if preserve_errors is True, missing keys or sections will still be represented by a False in the results dictionary.

  • copy (bool) – If False, default values (as specified in the ‘specs’ strings in the constructor) will not be copied to object’s “defaults” list, which will cause them to not be written out when writeInputFile() method is called. If True, then all keywords with a default will be written out to the file via the writeInputFile() method. NOTE: Default is True, while in ConfigObj default is False.

values() → list of D’s values
walk(function, raise_errors=True, call_on_sections=False, **keywargs)

Walk every member and call a function on the keyword and value.

Return a dictionary of the return values

If the function raises an exception, raise the errror unless raise_errors=False, in which case set the return value to False.

Any unrecognised keyword arguments you pass to walk, will be pased on to the function you pass in.

Note: if call_on_sections is True then - on encountering a subsection, first the function is called for the whole subsection, and then recurses into it’s members. This means your function must be able to handle strings, dictionaries and lists. This allows you to change the key of subsections as well as for ordinary members. The return value when called on the whole subsection has to be discarded.

See the encode and decode methods for examples, including functions.

caution

You can use walk to transform the names of members of a section but you mustn’t add or delete members.

>>> config = '''[XXXXsection]
... XXXXkey = XXXXvalue'''.splitlines()
>>> cfg = ConfigObj(config)
>>> cfg
ConfigObj({'XXXXsection': {'XXXXkey': 'XXXXvalue'}})
>>> def transform(section, key):
...     val = section[key]
...     newkey = key.replace('XXXX', 'CLIENT1')
...     section.rename(key, newkey)
...     if isinstance(val, (tuple, list, dict)):
...         pass
...     else:
...         val = val.replace('XXXX', 'CLIENT1')
...         section[newkey] = val
>>> cfg.walk(transform, call_on_sections=True)
{'CLIENT1section': {'CLIENT1key': None}}
>>> cfg
ConfigObj({'CLIENT1section': {'CLIENT1key': 'CLIENT1value'}})
write(outfile=None, section=None)

Write the current ConfigObj as a file

tekNico: FIXME: use StringIO instead of real files

>>> filename = a.filename
>>> a.filename = 'test.ini'
>>> a.write()
>>> a.filename = filename
>>> a == ConfigObj('test.ini', raise_errors=True)
1
>>> import os
>>> os.remove('test.ini')
writeInputFile(filename, ignore_none=False, yesno=False, smartsort=False)

Write the configuration to a file in the InputConfig format.

Parameters

  • filename (a file path or an open file handle) – The file to write the configuration to.

  • ignore_none (bool) – If True, keywords with a value of None will not be written to the input file.

  • yesno (bool) – If True, boolean keywords will be written as “yes” and “no”, if False, as “True” and “False”.

  • smartsort (bool) – If True, keywords that are identical except for the numbers at the end will be sorted such that “2” will go before “10”.

class schrodinger.application.prime.wrapper.ConsensusConfig(kw=None)

Bases: schrodinger.application.inputconfig.InputConfig

Class for reading and writing simplified Prime consensus modeling input files.

specs = ["ALIGN_FILE                 = string()SC_OPT                     = string(default='yes')"]
__init__(kw=None)

Accepts one argument which is either a path or a keyword dictionary.

setAlignment(alignment)
writeConfig(filename)

Writes a simplified input file to filename.

This input file needs to be run via $SCHRODINGER/consensus_homology.

Parameters

filename (str) – Name of output file.

__contains__(key, /)

True if the dictionary has the specified key, else False.

__len__()

Return len(self).

as_bool(key)

Accepts a key as input. The corresponding value must be a string or the objects (True or 1) or (False or 0). We allow 0 and 1 to retain compatibility with Python 2.2.

If the string is one of True, On, Yes, or 1 it returns True.

If the string is one of False, Off, No, or 0 it returns False.

as_bool is not case sensitive.

Any other input will raise a ValueError.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_bool('a')
Traceback (most recent call last):
ValueError: Value "fish" is neither True nor False
>>> a['b'] = 'True'
>>> a.as_bool('b')
1
>>> a['b'] = 'off'
>>> a.as_bool('b')
0
as_float(key)

A convenience method which coerces the specified value to a float.

If the value is an invalid literal for float, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_float('a')  
Traceback (most recent call last):
ValueError: invalid literal for float(): fish
>>> a['b'] = '1'
>>> a.as_float('b')
1.0
>>> a['b'] = '3.2'
>>> a.as_float('b')  
3.2...
as_int(key)

A convenience method which coerces the specified value to an integer.

If the value is an invalid literal for int, a ValueError will be raised.

>>> a = ConfigObj()
>>> a['a'] = 'fish'
>>> a.as_int('a')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: 'fish'
>>> a['b'] = '1'
>>> a.as_int('b')
1
>>> a['b'] = '3.2'
>>> a.as_int('b')
Traceback (most recent call last):
ValueError: invalid literal for int() with base 10: '3.2'
as_list(key)

A convenience method which fetches the specified value, guaranteeing that it is a list.

>>> a = ConfigObj()
>>> a['a'] = 1
>>> a.as_list('a')
[1]
>>> a['a'] = (1,)
>>> a.as_list('a')
[1]
>>> a['a'] = [1]
>>> a.as_list('a')
[1]
clear()

A version of clear that also affects scalars/sections Also clears comments and configspec.

Leaves other attributes alone :

depth/main/parent are not affected

copy() → a shallow copy of D
dict()

Return a deepcopy of self as a dictionary.

All members that are Section instances are recursively turned to ordinary dictionaries - by calling their dict method.

>>> n = a.dict()
>>> n == a
1
>>> n is a
0
fromkeys(value=None, /)

Create a new dictionary with keys from iterable and values set to value.

get(key, default=None)

A version of get that doesn’t bypass string interpolation.

getSpecsString()

Return a string of specifications. One keywords per line. Raises ValueError if this class has no specifications.

items() → list of D’s (key, value) pairs, as 2-tuples
iteritems() → an iterator over the (key, value) items of D
iterkeys() → an iterator over the keys of D
itervalues() → an iterator over the values of D
keys() → list of D’s keys
merge(indict)

A recursive update - useful for merging config files.

>>> a = '''[section1]
...     option1 = True
...     [[subsection]]
...     more_options = False
...     # end of file'''.splitlines()
>>> b = '''# File is user.ini
...     [section1]
...     option1 = False
...     # end of file'''.splitlines()
>>> c1 = ConfigObj(b)
>>> c2 = ConfigObj(a)
>>> c2.merge(c1)
>>> c2
ConfigObj({'section1': {'option1': 'False', 'subsection': {'more_options': 'False'}}})
pop(key, default=<object object>)

‘D.pop(k[,d]) -> v, remove specified key and return the corresponding value. If key is not found, d is returned if given, otherwise KeyError is raised’

popitem()

Pops the first (key,val)

printout()

Print all keywords of this instance to stdout.

This method is meant for debugging purposes.

reload()

Reload a ConfigObj from file.

This method raises a ReloadError if the ConfigObj doesn’t have a filename attribute pointing to a file.

rename(oldkey, newkey)

Change a keyname to another, without changing position in sequence.

Implemented so that transformations can be made on keys, as well as on values. (used by encode and decode)

Also renames comments.

reset()

Clear ConfigObj instance and restore to ‘freshly created’ state.

restore_default(key)

Restore (and return) default value for the specified key.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

If there is no default value for this key, KeyError is raised.

restore_defaults()

Recursively restore default values to all members that have them.

This method will only work for a ConfigObj that was created with a configspec and has been validated.

It doesn’t delete or modify entries without default values.

setdefault(key, default=None)

A version of setdefault that sets sequence if appropriate.

update(indict)

A version of update that uses our __setitem__.

validate(validator, preserve_errors=False, copy=False, section=None)

Test the ConfigObj against a configspec.

It uses the validator object from validate.py.

To run validate on the current ConfigObj, call:

test = config.validate(validator)

(Normally having previously passed in the configspec when the ConfigObj was created - you can dynamically assign a dictionary of checks to the configspec attribute of a section though).

It returns True if everything passes, or a dictionary of pass/fails (True/False). If every member of a subsection passes, it will just have the value True. (It also returns False if all members fail).

In addition, it converts the values from strings to their native types if their checks pass (and stringify is set).

If preserve_errors is True (False is default) then instead of a marking a fail with a False, it will preserve the actual exception object. This can contain info about the reason for failure. For example the VdtValueTooSmallError indicates that the value supplied was too small. If a value (or section) is missing it will still be marked as False.

You must have the validate module to use preserve_errors=True.

You can then use the flatten_errors function to turn your nested results dictionary into a flattened list of failures - useful for displaying meaningful error messages.

validateValues(preserve_errors=True, copy=True)

Validate the values read in from the InputConfig file.

Provide values for keywords with validators that have default values.

If a validator for a keyword is specified without a default and the keyword is missing from the input file, a RuntimeError will be raised.

Parameters

  • preserve_errors (bool) –

    If set to False, this method returns True if

    all tests passed, and False if there is a failure. If set to True, then instead of getting False for failed checkes, the actual detailed errors are printed for any validation errors encountered.

    Even if preserve_errors is True, missing keys or sections will still be represented by a False in the results dictionary.

  • copy (bool) – If False, default values (as specified in the ‘specs’ strings in the constructor) will not be copied to object’s “defaults” list, which will cause them to not be written out when writeInputFile() method is called. If True, then all keywords with a default will be written out to the file via the writeInputFile() method. NOTE: Default is True, while in ConfigObj default is False.

values() → list of D’s values
walk(function, raise_errors=True, call_on_sections=False, **keywargs)

Walk every member and call a function on the keyword and value.

Return a dictionary of the return values

If the function raises an exception, raise the errror unless raise_errors=False, in which case set the return value to False.

Any unrecognised keyword arguments you pass to walk, will be pased on to the function you pass in.

Note: if call_on_sections is True then - on encountering a subsection, first the function is called for the whole subsection, and then recurses into it’s members. This means your function must be able to handle strings, dictionaries and lists. This allows you to change the key of subsections as well as for ordinary members. The return value when called on the whole subsection has to be discarded.

See the encode and decode methods for examples, including functions.

caution

You can use walk to transform the names of members of a section but you mustn’t add or delete members.

>>> config = '''[XXXXsection]
... XXXXkey = XXXXvalue'''.splitlines()
>>> cfg = ConfigObj(config)
>>> cfg
ConfigObj({'XXXXsection': {'XXXXkey': 'XXXXvalue'}})
>>> def transform(section, key):
...     val = section[key]
...     newkey = key.replace('XXXX', 'CLIENT1')
...     section.rename(key, newkey)
...     if isinstance(val, (tuple, list, dict)):
...         pass
...     else:
...         val = val.replace('XXXX', 'CLIENT1')
...         section[newkey] = val
>>> cfg.walk(transform, call_on_sections=True)
{'CLIENT1section': {'CLIENT1key': None}}
>>> cfg
ConfigObj({'CLIENT1section': {'CLIENT1key': 'CLIENT1value'}})
write(outfile=None, section=None)

Write the current ConfigObj as a file

tekNico: FIXME: use StringIO instead of real files

>>> filename = a.filename
>>> a.filename = 'test.ini'
>>> a.write()
>>> a.filename = filename
>>> a == ConfigObj('test.ini', raise_errors=True)
1
>>> import os
>>> os.remove('test.ini')
writeInputFile(filename, ignore_none=False, yesno=False, smartsort=False)

Write the configuration to a file in the InputConfig format.

Parameters

  • filename (a file path or an open file handle) – The file to write the configuration to.

  • ignore_none (bool) – If True, keywords with a value of None will not be written to the input file.

  • yesno (bool) – If True, boolean keywords will be written as “yes” and “no”, if False, as “True” and “False”.

  • smartsort (bool) – If True, keywords that are identical except for the numbers at the end will be sorted such that “2” will go before “10”.

class schrodinger.application.prime.wrapper.PrimeTemplate(pdb_id='')

Bases: schrodinger.application.prime.wrapper._WorkingDirectoryMixin

This class encapsulates Prime template structure. A template includes a single chain.

WATER_NAMES = {'HOH', 'WAT'}
FIND_LIGANDS_KWARGS = {'allow_ion_only_molecules': True, 'excluded_residue_names': {'HOH', 'WAT'}, 'min_heavy_atom_count': 1}
__init__(pdb_id='')
property file_name
property st
property ligands

Returns a list of ligands found in the template structure.

Return type

list of schrodinger.structuils.analyze.Ligand objects

Returns

List of ligands in current template structure.

property waters
writePDB()

Writes template structure to PDB file.

Return type

bool

Returns

True on successful write.

prependWorkingDirectory(path)

If it’s set, prepend the working directory to the given path.

Parameters

path (str) – Path to modify

Returns

Modified path

Return type

str

setWorkingDirectory(wd)

Set directory used to write files

Parameters

wd (str) – Path of the working directory

class schrodinger.application.prime.wrapper.BasePrimeAlignment(name, query_seq)

Bases: schrodinger.application.prime.wrapper._WorkingDirectoryMixin

Encapsulates pairwise query-template alignment. Allows writing alignment files in Prime format.

__init__(name, query_seq)
Parameters

  • name (str) – Alignment name.

  • query_seq (str) – Text of prealigned query sequence.

property name
property query_sequence
property template
property template_sequence
setTemplate(template, sequence=None)

Adds a pre-aligned template sequence to the alignment.

Parameters

  • template (PrimeTemplate) – Template.

  • sequence (str) – Template sequence aligned to query (i.e. including gaps).

setWorkingDirectory(wd)

Propagate change in working directory to template

getAlnFilename()

Get the filename of the aln written by writeInputForPrime.

writeInputForPrime()

Writes Prime alignment to external file.

writeInputForConsensus(file_name, append=False)

Writes out FASTA alignment for consensus homology modeling. The alignment needs to include chain name and secondary structure definition for each template sequence.

Parameters

  • append (bool) – Whether to append to existing file.

  • file_name (str) – Name of output file.

getSSA(st, chain_id='')

Gets a secondary structure annotation string for structure st chain chain_id.

Parameters
prependWorkingDirectory(path)

If it’s set, prepend the working directory to the given path.

Parameters

path (str) – Path to modify

Returns

Modified path

Return type

str

schrodinger.application.prime.wrapper.basename_no_ext(file_name)

Returns file basename without extension.

schrodinger.application.prime.wrapper.convert_gaps_to_dots(sequence)

Replaces gap symbols with dots to make a sequence compatible with Prime.

Parameters

sequence (str) – Input gapped sequence.

Return type

str

Returns

Converted sequence.

schrodinger.application.prime.wrapper.convert_gaps_to_tildes(sequence)

Replaces gap symbols with tildes to make a sequence compatible with consensus modeling.

Parameters

sequence (str) – Input gapped sequence.

Return type

str

Returns

Converted sequence.