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TolerableError Raised when the structure could not be processed due to a non-fatal error. |
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TooManyGroupsError Raised when the structure could not be processed because it has too many ionizable groups. |
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Fragment Class representing a fragment from the ionizer library. |
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Spec This class represents a specification line in the ionizer data file. |
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Ionizer Class for ionizing structures (part of LigPrep). |
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__doc__ =
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ION_FRAGLIB_DEF = "ionized"
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MYERRHAND = mm.MMERR_DEFAULT_HANDLER
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IND = " "
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IND2 = IND* 2
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IND3 = IND* 3
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IND4 = IND* 4
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ION_FRAG_DEF = "mmfrag-ion.ini"
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SPEC_FILE_DEF = "ionizer.ini"
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COMMENT_CHAR = "#"
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MAX_GROUPS_DEF = 15
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MAX_GROUPS_MAX = 31
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MAX_IONS_DEF = 4
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MAX_ABSTOTQ_DEF = 2
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MAX_OUTCTS_DEF = 512
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PH_DEF = 7.0
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PH_THRESH_DEF = 2.0
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PK_THRESH_DEF = 1000.0
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MIN_FRAG_ATOMS = 2
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PH_PRECISION = 0.01
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PH_DIFF_TOL = PH_PRECISION/ 10.
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RT = 0.001987207* 298.15
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RT_LN_10 = RT* math.log(10.0)
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M2IO_DATA_TOTAL_CHARGE = "i_ionizer_Tot_Q"
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M2IO_DATA_ION_STATE_NUM = "i_ionizer_Ion_state_n"
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M2IO_DATA_CENTER_ATOMS = "s_ionizer_Ion_centers"
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M2IO_DATA_CENTER_TYPES = "s_ionizer_Ion_types"
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M2IO_DATA_CENTERS_ORIG = "s_ionizer_Ion_ctrs_in"
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M2IO_DATA_COST_TOTAL = "r_ionizer_Ionization_penalty"
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M2IO_DATA_COST_CHARGE = "r_ionizer_Ionization_penalty_charging"
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M2IO_DATA_COST_NEUT = "r_ionizer_Ionization_penalty_neutral"
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M2IO_DATA_RETAIN = "i_lp_orig_ion_str"
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MMSHARE_DATA_DIR = "\$MMSHARE_EXEC/../../data"
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MMFILE_PATH_DELIM = ":"
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Return a string representation of the charge. "-" will be prepended for negative numbers, "+" for positive, and nothing for zero. |
Add the given path to the mmfile search path. This makes it possible to search for the mmfrag.ini file in custom locations. |
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__doc__
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