Package schrodinger :: Package application :: Package ligprep :: Module ionizer
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Module ionizer

Classes [hide private]
  TolerableError
Raised when the structure could not be processed due to a non-fatal error.
  TooManyGroupsError
Raised when the structure could not be processed because it has too many ionizable groups.
  Fragment
Class representing a fragment from the ionizer library.
  Spec
This class represents a specification line in the ionizer data file.
  Ionizer
Class for ionizing structures (part of LigPrep).
Functions [hide private]
 
format_charge(charge)
Return a string representation of the charge.
 
get_bonded_hydrogens(atom)
Return a list of atom numbers of all Hydrogens bonded to given atom.
 
prepend_mmfile_path(pdir)
Add the given path to the mmfile search path.
 
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)
Variables [hide private]
  __doc__ = ...
  ION_FRAGLIB_DEF = "ionized"
  MYERRHAND = mm.MMERR_DEFAULT_HANDLER
  IND = " "
  IND2 = IND* 2
  IND3 = IND* 3
  IND4 = IND* 4
  ION_FRAG_DEF = "mmfrag-ion.ini"
  SPEC_FILE_DEF = "ionizer.ini"
  COMMENT_CHAR = "#"
  MAX_GROUPS_DEF = 15
  MAX_GROUPS_MAX = 31
  MAX_IONS_DEF = 4
  MAX_ABSTOTQ_DEF = 2
  MAX_OUTCTS_DEF = 512
  PH_DEF = 7.0
  PH_THRESH_DEF = 2.0
  PK_THRESH_DEF = 1000.0
  MIN_FRAG_ATOMS = 2
  PH_PRECISION = 0.01
  PH_DIFF_TOL = PH_PRECISION/ 10.
  RT = 0.001987207* 298.15
  RT_LN_10 = RT* math.log(10.0)
  M2IO_DATA_TOTAL_CHARGE = "i_ionizer_Tot_Q"
  M2IO_DATA_ION_STATE_NUM = "i_ionizer_Ion_state_n"
  M2IO_DATA_CENTER_ATOMS = "s_ionizer_Ion_centers"
  M2IO_DATA_CENTER_TYPES = "s_ionizer_Ion_types"
  M2IO_DATA_CENTERS_ORIG = "s_ionizer_Ion_ctrs_in"
  M2IO_DATA_COST_TOTAL = "r_ionizer_Ionization_penalty"
  M2IO_DATA_COST_CHARGE = "r_ionizer_Ionization_penalty_charging"
  M2IO_DATA_COST_NEUT = "r_ionizer_Ionization_penalty_neutral"
  M2IO_DATA_RETAIN = "i_lp_orig_ion_str"
  MMSHARE_DATA_DIR = "\$MMSHARE_EXEC/../../data"
  MMFILE_PATH_DELIM = ":"
Function Details [hide private]

format_charge(charge)

 

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

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.


Variables Details [hide private]

__doc__

Value:
"""

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

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