schrodinger.application.desmond.constants module¶
Define common numerical constants, CT and atom property names, and keyword values (enums).
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.desmond.constants.
Constants
¶ Bases:
object
Related constants can inherit from
Constants
to make them iterable in the order of their declarations.-
__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
MaePropertyName
(name: str, **kwargs)¶ Bases:
str
This class defines a container for structure or atom level properties. The property key can be accessed directly, while enum values are accessed via the
VAL
attribute.Example usage: CT_TYPE = MaePropertyName(‘s_ffio_ct_type’, FULL_SYSTEM=’full_system’)
ct.property[CT_TYPE] = CT_TYPE.VAL.FULL_SYSTEM valid_ct_types = list(CT_TYPE.VAL)
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__init__
(name: str, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
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__contains__
¶ Return key in self.
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__len__
¶ Return len(self).
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capitalize
() → str¶ Return a capitalized version of S, i.e. make the first character have upper case and the rest lower case.
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casefold
() → str¶ Return a version of S suitable for caseless comparisons.
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center
(width[, fillchar]) → str¶ Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)
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count
(sub[, start[, end]]) → int¶ Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.
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encode
(encoding='utf-8', errors='strict') → bytes¶ Encode S using the codec registered for encoding. Default encoding is ‘utf-8’. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.
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endswith
(suffix[, start[, end]]) → bool¶ Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.
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expandtabs
(tabsize=8) → str¶ Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.
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find
(sub[, start[, end]]) → int¶ Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return -1 on failure.
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format
(*args, **kwargs) → str¶ Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).
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format_map
(mapping) → str¶ Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{‘ and ‘}’).
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index
(sub[, start[, end]]) → int¶ Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Raises ValueError when the substring is not found.
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isalnum
() → bool¶ Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.
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isalpha
() → bool¶ Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.
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isdecimal
() → bool¶ Return True if there are only decimal characters in S, False otherwise.
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isdigit
() → bool¶ Return True if all characters in S are digits and there is at least one character in S, False otherwise.
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isidentifier
() → bool¶ Return True if S is a valid identifier according to the language definition.
Use keyword.iskeyword() to test for reserved identifiers such as “def” and “class”.
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islower
() → bool¶ Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.
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isnumeric
() → bool¶ Return True if there are only numeric characters in S, False otherwise.
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isprintable
() → bool¶ Return True if all characters in S are considered printable in repr() or S is empty, False otherwise.
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isspace
() → bool¶ Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.
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istitle
() → bool¶ Return True if S is a titlecased string and there is at least one character in S, i.e. upper- and titlecase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.
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isupper
() → bool¶ Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.
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join
(iterable) → str¶ Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.
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ljust
(width[, fillchar]) → str¶ Return S left-justified in a Unicode string of length width. Padding is done using the specified fill character (default is a space).
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lower
() → str¶ Return a copy of the string S converted to lowercase.
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lstrip
([chars]) → str¶ Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead.
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static
maketrans
()¶ Return a translation table usable for str.translate().
If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.
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partition
(sep) -> (head, sep, tail)¶ Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.
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replace
(old, new[, count]) → str¶ Return a copy of S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.
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rfind
(sub[, start[, end]]) → int¶ Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Return -1 on failure.
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rindex
(sub[, start[, end]]) → int¶ Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.
Raises ValueError when the substring is not found.
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rjust
(width[, fillchar]) → str¶ Return S right-justified in a string of length width. Padding is done using the specified fill character (default is a space).
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rpartition
(sep) -> (head, sep, tail)¶ Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.
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rsplit
(sep=None, maxsplit=-1) → list of strings¶ Return a list of the words in S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified, any whitespace string is a separator.
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rstrip
([chars]) → str¶ Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead.
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split
(sep=None, maxsplit=-1) → list of strings¶ Return a list of the words in S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.
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splitlines
([keepends]) → list of strings¶ Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.
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startswith
(prefix[, start[, end]]) → bool¶ Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.
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strip
([chars]) → str¶ Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead.
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swapcase
() → str¶ Return a copy of S with uppercase characters converted to lowercase and vice versa.
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title
() → str¶ Return a titlecased version of S, i.e. words start with title case characters, all remaining cased characters have lower case.
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translate
(table) → str¶ Return a copy of the string S in which each character has been mapped through the given translation table. The table must implement lookup/indexing via __getitem__, for instance a dictionary or list, mapping Unicode ordinals to Unicode ordinals, strings, or None. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.
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upper
() → str¶ Return a copy of S converted to uppercase.
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zfill
(width) → str¶ Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.
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class
schrodinger.application.desmond.constants.
Conversion
¶ Bases:
object
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KCAL_TO_JOUL
= 4184.0¶
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CAL_CM_TO_MPA
= 0.48888¶
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AU_TO_KG
= 1.6605655¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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schrodinger.application.desmond.constants.
opls_forcefield_names
()¶
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class
schrodinger.application.desmond.constants.
EXISTING_RESTRAINT
¶ Bases:
schrodinger.application.desmond.constants.Constants
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RETAIN
= 'retain'¶
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IGNORE
= 'ignore'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
WATER_MODELS
¶ Bases:
schrodinger.application.desmond.constants.Constants
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SPC
= 'SPC'¶
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SPCE
= 'SPCE'¶
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TIP3P
= 'TIP3P'¶
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TIP3P_CHARMM
= 'TIP3P_CHARMM'¶
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TIP4P
= 'TIP4P'¶
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TIP4PEW
= 'TIP4PEW'¶
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TIP4P2005
= 'TIP4P2005'¶
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TIP5P
= 'TIP5P'¶
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TIP4PD
= 'TIP4PD'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
CUSTOM_CHARGE_MODE
¶ Bases:
schrodinger.application.desmond.constants.Constants
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KEEP
= 'keep'¶
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CLEAR
= 'clear'¶
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ASSIGN
= 'assign'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
FEP_TYPES
¶ Bases:
schrodinger.application.desmond.constants.Constants
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PROTEIN_STABILITY
= 'prm_stability'¶
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PROTEIN_SELECTIVITY
= 'protein_selectivity'¶
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COVALENT_LIGAND
= 'covalent_ligand'¶
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SMALL_MOLECULE
= 'small_molecule'¶
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METALLOPROTEIN
= 'metalloprotein'¶
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LIGAND_SELECTIVITY
= 'ligand_selectivity'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
SIMULATION_PROTOCOL
¶ Bases:
schrodinger.application.desmond.constants.Constants
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DEFAULT
= 'default'¶
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CHARGED
= 'charge'¶
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FORMALCHARGED
= 'charge0'¶
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COREHOPPING
= 'core-hopping'¶
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MACROCYCLE_COREHOPPING
= 'macrocycle-core-hopping'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
REST_PROPERTIES
¶ Bases:
schrodinger.application.desmond.constants.Constants
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SOLVENT_HOTREGION
= 'i_rest_solvent_hotregion'¶
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COMPLEX_HOTREGION
= 'i_rest_complex_hotregion'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
REST_COMPONENT
¶ Bases:
schrodinger.application.desmond.constants.Constants
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ENVIRONMENT
= 'environment'¶
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RECEPTOR
= 'receptor'¶
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MEMBRANE
= 'membrane'¶
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LIGAND
= 'ligand'¶
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COMPLEX
= 'complex'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.constants.
REST_REGION_RULE
¶ Bases:
schrodinger.application.desmond.constants.Constants
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DEFAULT
= 'default'¶
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ALL
= 'all'¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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