schrodinger.application.desmond.constants module

Define common numerical constants, CT and atom property names, and keyword values (enums).

Copyright Schrodinger, LLC. All rights reserved.

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.

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)

__init__(name: str, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__contains__

Return key in self.

__len__

Return len(self).

capitalize() → str

Return a capitalized version of S, i.e. make the first character have upper case and the rest lower case.

casefold() → str

Return a version of S suitable for caseless comparisons.

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)

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.

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.

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.

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.

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.

format(*args, **kwargs) → str

Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).

format_map(mapping) → str

Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{‘ and ‘}’).

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.

isalnum() → bool

Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.

isalpha() → bool

Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.

isdecimal() → bool

Return True if there are only decimal characters in S, False otherwise.

isdigit() → bool

Return True if all characters in S are digits and there is at least one character in S, False otherwise.

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”.

islower() → bool

Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.

isnumeric() → bool

Return True if there are only numeric characters in S, False otherwise.

isprintable() → bool

Return True if all characters in S are considered printable in repr() or S is empty, False otherwise.

isspace() → bool

Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.

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.

isupper() → bool

Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.

join(iterable) → str

Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

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).

lower() → str

Return a copy of the string S converted to lowercase.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

swapcase() → str

Return a copy of S with uppercase characters converted to lowercase and vice versa.

title() → str

Return a titlecased version of S, i.e. words start with title case characters, all remaining cased characters have lower case.

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.

upper() → str

Return a copy of S converted to uppercase.

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.

class schrodinger.application.desmond.constants.Conversion

Bases: object

KCAL_TO_JOUL = 4184.0
CAL_CM_TO_MPA = 0.48888
AU_TO_KG = 1.6605655
__init__

Initialize self. See help(type(self)) for accurate signature.

schrodinger.application.desmond.constants.opls_forcefield_names()
class schrodinger.application.desmond.constants.EXISTING_RESTRAINT

Bases: schrodinger.application.desmond.constants.Constants

RETAIN = 'retain'
IGNORE = 'ignore'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.WATER_MODELS

Bases: schrodinger.application.desmond.constants.Constants

SPC = 'SPC'
SPCE = 'SPCE'
TIP3P = 'TIP3P'
TIP3P_CHARMM = 'TIP3P_CHARMM'
TIP4P = 'TIP4P'
TIP4PEW = 'TIP4PEW'
TIP4P2005 = 'TIP4P2005'
TIP5P = 'TIP5P'
TIP4PD = 'TIP4PD'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE

Bases: schrodinger.application.desmond.constants.Constants

KEEP = 'keep'
CLEAR = 'clear'
ASSIGN = 'assign'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.FEP_TYPES

Bases: schrodinger.application.desmond.constants.Constants

PROTEIN_STABILITY = 'prm_stability'
PROTEIN_SELECTIVITY = 'protein_selectivity'
COVALENT_LIGAND = 'covalent_ligand'
SMALL_MOLECULE = 'small_molecule'
METALLOPROTEIN = 'metalloprotein'
LIGAND_SELECTIVITY = 'ligand_selectivity'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.SIMULATION_PROTOCOL

Bases: schrodinger.application.desmond.constants.Constants

DEFAULT = 'default'
CHARGED = 'charge'
FORMALCHARGED = 'charge0'
COREHOPPING = 'core-hopping'
MACROCYCLE_COREHOPPING = 'macrocycle-core-hopping'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.REST_PROPERTIES

Bases: schrodinger.application.desmond.constants.Constants

SOLVENT_HOTREGION = 'i_rest_solvent_hotregion'
COMPLEX_HOTREGION = 'i_rest_complex_hotregion'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.REST_COMPONENT

Bases: schrodinger.application.desmond.constants.Constants

ENVIRONMENT = 'environment'
RECEPTOR = 'receptor'
MEMBRANE = 'membrane'
LIGAND = 'ligand'
COMPLEX = 'complex'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.REST_REGION_RULE

Bases: schrodinger.application.desmond.constants.Constants

DEFAULT = 'default'
ALL = 'all'
__init__

Initialize self. See help(type(self)) for accurate signature.

class schrodinger.application.desmond.constants.ConfRestraintType

Bases: schrodinger.application.desmond.constants.Constants

BACKBONE = 'backbone'
SIDECHAIN = 'sidechain'
CALPHA_RUNG = 'calpha_rung'
__init__

Initialize self. See help(type(self)) for accurate signature.