schrodinger.application.ligprep.ionizer module

Ionizer module. Ported from ionizer.pl on February 2014.

Copyright (c) Schrodinger, LLC. All rights reserved.

schrodinger.application.ligprep.ionizer.format_charge(charge)

Return a string representation of the charge. “-” will be prepended for negative numbers, “+” for positive, and nothing for zero.

schrodinger.application.ligprep.ionizer.get_bonded_hydrogens(atom)

Return a list of atom numbers of all Hydrogens bonded to given atom.

schrodinger.application.ligprep.ionizer.prepend_mmfile_path(pdir)

Add the given path to the mmfile search path. This makes it possible to search for the mmfrag.ini file in custom locations.

schrodinger.application.ligprep.ionizer.free_energy_costs(x)

For a given pKa - pH difference X, this function calculates and returns RT.ln(10^X + 1) and RT.ln(10^(-X) + 1)

exception schrodinger.application.ligprep.ionizer.TolerableError

Bases: Exception

Raised when the structure could not be processed due to a non-fatal error.

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.ligprep.ionizer', '__doc__': '\n Raised when the structure could not be processed due to a non-fatal error.\n ', '__weakref__': <attribute '__weakref__' of 'TolerableError' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.ligprep.ionizer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.application.ligprep.ionizer.TooManyGroupsError

Bases: Exception

Raised when the structure could not be processed because it has too many ionizable groups.

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.ligprep.ionizer', '__doc__': '\n Raised when the structure could not be processed because it has too many\n ionizable groups.\n ', '__weakref__': <attribute '__weakref__' of 'TooManyGroupsError' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

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

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.ligprep.ionizer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.ligprep.ionizer.Fragment(st, connect_to, chargef)

Bases: object

Class representing a fragment from the ionizer library.

__init__(st, connect_to, chargef)

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.ligprep.ionizer', '__doc__': '\n Class representing a fragment from the ionizer library.\n ', '__init__': <function Fragment.__init__>, '__dict__': <attribute '__dict__' of 'Fragment' objects>, '__weakref__': <attribute '__weakref__' of 'Fragment' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.ligprep.ionizer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.ligprep.ionizer.Spec(cmd, linenum, mmsubs_pattern, mmsubs_handle)

Bases: object

This class represents a specification line in the ionizer data file.

__init__(cmd, linenum, mmsubs_pattern, mmsubs_handle)

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

__del__()
getMatches(st)

Run a substracture search for this pattern in the specified structure.

Return type:list of int lists.
Returns:A list of matches, where each list is a list of atom indices.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.ligprep.ionizer', '__doc__': '\n This class represents a specification line in the ionizer data file.\n ', '__init__': <function Spec.__init__>, '__del__': <function Spec.__del__>, 'getMatches': <function Spec.getMatches>, '__dict__': <attribute '__dict__' of 'Spec' objects>, '__weakref__': <attribute '__weakref__' of 'Spec' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.ligprep.ionizer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.ligprep.ionizer.Ionizer(loglevel=0, specfile=None, ph=None, ph_thresh=None, pk_thresh=None)

Bases: object

Class for ionizing structures (part of LigPrep).

To ionize a structure, do:

i = Ionizer() out_sts = i.ionizeStructure(st)

These options can be adjusted after instantiating the class:

Variables:
  • max_ions – Maximum number of ionizations.
  • max_abstotq – Maximum absolute value of total charge.
  • max_groups – Maximum ionizational groups to handle (up to MAX_GROUPS_MAX).
  • max_outcts – Maximum output CTs per input CT.
  • retain – Whether to retain the input structure in the output.
  • retain_lab – Retain the input structure that has “i_lp_orig_ion_str” property set.
  • show_match_atoms – Whether to report substructure pattern matches to the logger (log file).
  • show_skips – Whether to show skipped state generations. Applies only to log levels 1 and up.
  • keep_props – Whether to keep any structure-based properties from the input CT in the output CTs.
  • retitle_with – Prefix for adding ion state numbers to output CT titles.
  • logger – Logger instance. When processing CTs, any info, warning, and error messages will be redirected here.
  • show_final_list – Report final ionization candidate list to logger.
__init__(loglevel=0, specfile=None, ph=None, ph_thresh=None, pk_thresh=None)
Parameters:
  • logleve – Reporting log level. Use 0 for quietest (default); use 1 to log state generations; use 2 to log ion frag fusions also.
  • specfile (str or None) – Path to the non-standard patterns spec file to use.
  • ph (float or None) – Effective pH of active site. Does not apply to pK-only mode.
  • ph_thresh (float or None) – De-protonated |pKa-pH| difference limit. Does not apply to pK-only mode.
  • pk_thresh (float or None) – Strong/weak pK threshold (no default). Overrides pH-based rejection mode and activates pK-only mode. Reject on pKa values only (no pH).
__del__()
initializeMmlibs()

Initialize the mmlibs libraries.

readFragmentLibrary(flib_name)

Read the ionized frag library and populate self.frags dictionary.

The ionized frag lib contains a fairly small number of fragments, all or most of which will be fused in a typical run; therefore we just collect information on all of them now.

readSpecFile()

Put cwd and $HOME/.schrodinger/mmshare at the front of the mmfile search path, to allow user “ionizer.ini” in either of those dirs to override installed data file in the mmshare data dir.

Note: We wait as late as possible to do this, to prevent any similar override of the mmfrag data files, which we currently consider to be inviolate, that is, the user must not be allowed to override them, even accidentally.

ionizeCommandParser(linenum, cmd, subs_patt, frag_name, pka)

Validate mmsubs pattern spec; if all goes well, will store compiled pattern matcher below

Parses both Acid and Base specs.

Parameters:
  • linenum (int) – Line number that is being parsed
  • cmd (str) – Spec command that is being parsed. Either “acid” or “base”.
  • subs_patt (str) – Substructure pattern for this specification.
  • frag_name (str) – Name of the fragment to use (from the “ionized” fragment library).
  • pka (str) – String representation of the pKa for this ionizable group.
Return type:

Spec
Returns:

The Spec instance representing this ionizable group.
excludeCommandParser(linenum, subs_patt)

Validate an “exclude” mmsubs pattern spec.

Parameters:
  • linenum (int) – Line number that is being parsed
  • subs_patt (str) – Substructure pattern for this specification.
collectIonCandidates(st)

Check CT for matches to Acid/Base/Exclude patterns, in same order as supplied in control spec file; for non-Excluded, final Acid/Base matches, store specs in hash indexed on ion center atom number; also get ordered list of candidate atom numbers.

generateStateCT(st, total_charge, state_num, state_fuse_atoms, ion_candidates, ycost_total, zcost_total)

Generate the CT for the specificed ionization state.

Parameters:
  • st (structure.Structure) – Input structure.
  • total_charge (int) – Total charge of this ionization state.
  • state_num (int) – The number of this state (0-indexed)
  • state_fuse_atoms (list of ints) – List of atoms to which the new fragment will be attached to.
  • ion_candidates (dict; key: atom index; value: Spec) – Specifications for this state change.
  • ycost_total (float) – Charging ionization penalty for this state
  • zcost_total (float) – Neutral ionization penalty for this state
fuseIonFragment(output_st, fuse_atom_orig, pre_fuse_center, renumbered_fuse_atoms, cand)

This function coordinates the ionization of one ionizable group, via mmbuild_fuse() of the appropriate ionizing fragment onto the group’s ionization center atom (same method as Maestro builder uses for Place onto non-terminal atom); function also takes care of various property adjustments in the modified CT.

saveIonCenterProps(st, center_anum)

Save certain properties of an ion center atom before the ionizing fuse.

restoreIonCenterProps(st, iatom)

Restores the atom properties saved by the method above. Also sets the default display color property based on the atom’s new (i.e., post-fuse) atom type. Pass in post-fuse atom number (new ionized group center or bonded H).

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.ligprep.ionizer', '__doc__': '\n Class for ionizing structures (part of LigPrep).\n\n To ionize a structure, do:\n\n i = Ionizer()\n out_sts = i.ionizeStructure(st)\n\n\n These options can be adjusted after instantiating the class:\n\n :ivar max_ions: Maximum number of ionizations.\n\n :ivar max_abstotq: Maximum absolute value of total charge.\n\n :ivar max_groups: Maximum ionizational groups to handle (up to MAX_GROUPS_MAX).\n\n :ivar max_outcts: Maximum output CTs per input CT.\n\n :ivar retain: Whether to retain the input structure in the output.\n\n :ivar retain_lab: Retain the input structure that has "i_lp_orig_ion_str"\n property set.\n\n :ivar show_match_atoms: Whether to report substructure pattern matches to\n the logger (log file).\n\n :ivar show_skips: Whether to show skipped state generations. Applies only to\n log levels 1 and up.\n\n :ivar keep_props: Whether to keep any structure-based properties from\n the input CT in the output CTs.\n\n :ivar retitle_with: Prefix for adding ion state numbers to output CT\n titles.\n\n :ivar logger: Logger instance. When processing CTs, any info, warning,\n and error messages will be redirected here.\n\n :ivar show_final_list: Report final ionization candidate list to logger.\n ', '__init__': <function Ionizer.__init__>, '__del__': <function Ionizer.__del__>, 'initializeMmlibs': <function Ionizer.initializeMmlibs>, 'readFragmentLibrary': <function Ionizer.readFragmentLibrary>, 'readSpecFile': <function Ionizer.readSpecFile>, 'ionizeCommandParser': <function Ionizer.ionizeCommandParser>, 'excludeCommandParser': <function Ionizer.excludeCommandParser>, '_treatStructure': <function Ionizer._treatStructure>, 'collectIonCandidates': <function Ionizer.collectIonCandidates>, '_expandCT': <function Ionizer._expandCT>, 'generateStateCT': <function Ionizer.generateStateCT>, 'fuseIonFragment': <function Ionizer.fuseIonFragment>, 'saveIonCenterProps': <function Ionizer.saveIonCenterProps>, 'restoreIonCenterProps': <function Ionizer.restoreIonCenterProps>, 'reviseIonizedGroup': <function Ionizer.reviseIonizedGroup>, 'addIonProperties': <function Ionizer.addIonProperties>, 'addCostProperties': <function Ionizer.addCostProperties>, 'ionizeStructure': <function Ionizer.ionizeStructure>, '__dict__': <attribute '__dict__' of 'Ionizer' objects>, '__weakref__': <attribute '__weakref__' of 'Ionizer' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.ligprep.ionizer'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

reviseIonizedGroup(st, center_atom)

Function to apply above reset function to all atoms of newly ionized group. Pass in post-fuse ionized group center atom number Collect list of newly ionized group’s atoms (new ionized center + all Hydrogens bonded to it); revise certain atom properties to match original ion center

addIonProperties(st, state_num, total_charge, center_atoms_string, center_types_string, center_atoms_orig_string)

This function writes CT-level properties recording several details of a particular ionization state; it’s intended to be used on CTs generated for output; the values expressed in the properties must be calculated beforehand; all of these properties get marked as dependent on CONNECTIVITY.

addCostProperties(st, ycost_total, zcost_total)

For use in pH mode only, this function adds CT-level properties recording the free energy costs associated with this particular ionization state.

ionizeStructure(st)

This is the public interface method. The specified CT will be ionized, and the output structures will be returned as a list.

Parameters:

st (structure.Structure object) – Structure to ionize.
Return type:

List of structures.
Returns:

Returns a list of ionized output structures.
Raises: