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

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Module ionizer

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

Classes

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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

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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

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__doc__ = ...

ION_FRAGLIB_DEF = 'ionized'

MYERRHAND = -1

IND = ' '

IND2 = ' '

IND3 = ' '

IND4 = ' '

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 = 0.001

RT = 0.59248576705

RT_LN_10 = 1.36424889502

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 = ':'

__package__ = 'schrodinger.application.ligprep'

Function Details

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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

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doc

Value:

"""

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

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