pyXLMS.constants package#
Module contents#
Constants used across pyXLMS.
Examples
>>> from pyXLMS.constants import MODIFICATIONS
>>> MODIFICATIONS["Carbamidomethyl"]
57.021464
>>> MODIFICATIONS["BS3"]
138.06808
- pyXLMS.constants.AMINO_ACIDS = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'}#
List of valid amino acids.
List of one-letter codes for all valid amino acids.
Examples
>>> from pyXLMS.constants import AMINO_ACIDS >>> "A" in AMINO_ACIDS True >>> "B" in AMINO_ACIDS True
- pyXLMS.constants.AMINO_ACIDS_1TO3 = {'A': 'ALA', 'B': 'ASX', 'C': 'CYS', 'D': 'ASP', 'E': 'GLU', 'F': 'PHE', 'G': 'GLY', 'H': 'HIS', 'I': 'ILE', 'J': 'XLE', 'K': 'LYS', 'L': 'LEU', 'M': 'MET', 'N': 'ASN', 'O': 'PYL', 'P': 'PRO', 'Q': 'GLN', 'R': 'ARG', 'S': 'SER', 'T': 'THR', 'U': 'SEC', 'V': 'VAL', 'W': 'TRP', 'X': 'XAA', 'Y': 'TYR', 'Z': 'GLX'}#
Mapping of amino acid 1-letter codes to their 3-letter codes.
Mapping of all amino acid 1-letter codes to their corresponding 3-letter codes.
Examples
>>> from pyXLMS.constants import AMINO_ACIDS_1TO3 >>> AMINO_ACIDS_1TO3["G"] 'GLY'
- pyXLMS.constants.AMINO_ACIDS_3TO1 = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'ASX': 'B', 'CYS': 'C', 'GLN': 'Q', 'GLU': 'E', 'GLX': 'Z', 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K', 'MET': 'M', 'PHE': 'F', 'PRO': 'P', 'PYL': 'O', 'SEC': 'U', 'SER': 'S', 'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V', 'XAA': 'X', 'XLE': 'J'}#
Mapping of amino acid 3-letter codes to their 1-letter codes.
Mapping of all amino acid 3-letter codes to their corresponding 1-letter codes.
Examples
>>> from pyXLMS.constants import AMINO_ACIDS_3TO1 >>> AMINO_ACIDS_3TO1["GLY"] 'G'
- pyXLMS.constants.AMINO_ACIDS_REPLACEMENTS = {'B': {'D', 'N'}, 'J': {'I', 'L'}, 'X': {'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y'}, 'Z': {'E', 'Q'}}#
Mapping of placeholder amino acid codes to their respective possible amino acids.
Dictionary mapping placeholder one-letter amino acid codes to their respective possible amino acids
Examples
>>> from pyXLMS.constants import AMINO_ACIDS_REPLACEMENTS >>> AMINO_ACIDS_REPLACEMENTS["B"] {'D', 'N'} >>> AMINO_ACIDS_REPLACEMENTS["Z"] {'E', 'Q'}
- pyXLMS.constants.CROSSLINKERS = {'ADH': 138.09054635, 'BS3': 138.06808, 'DSBSO': 308.03883, 'DSBU': 196.08479231, 'DSG': 96.0211293726, 'DSS': 138.06808, 'DSSO': 158.00376, 'PhoX': 209.97181, 'SDA': 82.041865}#
Dictionary of crosslinkers.
Dictionary of pre-defined crosslinkers that maps crosslinker names to crosslinker delta masses. Currently contains “BS3”, “DSS”, “DSSO”, “DSBU”, “ADH”, “DSBSO”, “PhoX”, “DSG”, “SDA”.
Examples
>>> from pyXLMS.constants import CROSSLINKERS >>> CROSSLINKERS["BS3"] 138.06808
- pyXLMS.constants.MEROX_MODIFICATION_MAPPING = {'B': {'Amino Acid': 'C', 'Modification': ('Carbamidomethyl', 57.021464)}, 'm': {'Amino Acid': 'M', 'Modification': ('Oxidation', 15.994915)}}#
Dictionary that maps MeroX modification symbols to their corresponding amino acids and post-translational-modifications.
Dictionary that maps MeroX modification symbols (e.g. “B”) to their corresponding amino acids and post-translational-modifications (e.g.
{"Amino Acid": "C", "Modification": ("Carbamidomethyl", 57.021464)}).Examples
>>> from pyXLMS.constants import MEROX_MODIFICATION_MAPPING >>> MEROX_MODIFICATION_MAPPING["B"] {'Amino Acid': 'C', 'Modification': ('Carbamidomethyl', 57.021464)}
>>> from pyXLMS.constants import MEROX_MODIFICATION_MAPPING >>> MEROX_MODIFICATION_MAPPING["m"] {'Amino Acid': 'M', 'Modification': ('Oxidation', 15.994915)}
>>> from pyXLMS.constants import MEROX_MODIFICATION_MAPPING >>> MEROX_MODIFICATION_MAPPING {'B': {'Amino Acid': 'C', 'Modification': ('Carbamidomethyl', 57.021464)}, 'm': {'Amino Acid': 'M', 'Modification': ('Oxidation', 15.994915)}}
- pyXLMS.constants.MODIFICATIONS = {'ADH': 138.09054635, 'Acetyl': 42.010565, 'BS3': 138.06808, 'Carbamidomethyl': 57.021464, 'DSBSO': 308.03883, 'DSBU': 196.08479231, 'DSG': 96.0211293726, 'DSS': 138.06808, 'DSSO': 158.00376, 'Oxidation': 15.994915, 'PhoX': 209.97181, 'Phospho': 79.966331, 'SDA': 82.041865}#
Dictionary of post-translational-modifications.
Dictionary of pre-defined post-translational-modifications that maps modification names to modification delta masses. Currently contains “Carbamidomethyl”, “Oxidation”, “Phospho”, “Acetyl” and all crosslinkers.
Examples
>>> from pyXLMS.constants import MODIFICATIONS >>> MODIFICATIONS["Carbamidomethyl"] 57.021464 >>> MODIFICATIONS["BS3"] 138.06808
- pyXLMS.constants.SCOUT_MODIFICATION_MAPPING = {'+15.994900': ('Oxidation', 15.994915), '+57.021460': ('Carbamidomethyl', 57.021464), 'ADH': ('ADH', 138.09054635), 'BS3': ('BS3', 138.06808), 'Carbamidomethyl': ('Carbamidomethyl', 57.021464), 'DSBSO': ('DSBSO', 308.03883), 'DSBU': ('DSBU', 196.08479231), 'DSG': ('DSG', 96.0211293726), 'DSS': ('DSS', 138.06808), 'DSSO': ('DSSO', 158.00376), 'Oxidation of Methionine': ('Oxidation', 15.994915), 'PhoX': ('PhoX', 209.97181), 'SDA': ('SDA', 82.041865)}#
Dictionary that maps sequence elements and modifications from Scout to their corresponding post-translational-modifications.
Dictionary that maps sequence elements (e.g. “+57.021460”) and modifications (e.g. “Carbamidomethyl”) from Scout to their corresponding post-translational-modifications (e.g. (“Carbamidomethyl”, 57.021464)).
Examples
>>> from pyXLMS.constants import SCOUT_MODIFICATION_MAPPING >>> SCOUT_MODIFICATION_MAPPING["+57.021460"] ('Carbamidomethyl', 57.021464) >>> SCOUT_MODIFICATION_MAPPING["Carbamidomethyl"] ('Carbamidomethyl', 57.021464) >>> SCOUT_MODIFICATION_MAPPING["Oxidation of Methionine"] ('Oxidation', 15.994915)
- pyXLMS.constants.XI_MODIFICATION_MAPPING = {'->': ('Substitution', nan), 'bs3_ami': ('BS3 Amidated', 155.094619105), 'bs3_hyd': ('BS3 Hydrolized', 156.0786347), 'bs3_tris': ('BS3 Tris', 259.141973), 'bs3loop': ('BS3 Looplink', 138.06808), 'bs3nh2': ('BS3 Amidated', 155.094619105), 'bs3oh': ('BS3 Hydrolized', 156.0786347), 'cm': ('Carbamidomethyl', 57.021464), 'dsbu_ami': ('DSBU Amidated', 213.111341), 'dsbu_hyd': ('DSBU Hydrolized', 214.095357), 'dsbu_loop': ('DSBU Looplink', 196.08479231), 'dsbu_tris': ('DSBU Tris', 317.158685), 'dsbuloop': ('DSBU Looplink', 196.08479231), 'dsso_ami': ('DSSO Amidated', 175.030313905), 'dsso_hyd': ('DSSO Hydrolized', 176.0143295), 'dsso_loop': ('DSSO Looplink', 158.00376), 'dsso_tris': ('DSSO Tris', 279.077658), 'dssoloop': ('DSSO Looplink', 158.00376), 'ox': ('Oxidation', 15.994915)}#
Dictionary that maps sequence elements from xiSearch and xiFDR to their corresponding post-translational-modifications.
Dictionary that maps sequence elements (e.g. “cm”) from xiSearch and xiFDR to their corresponding post-translational-modifications (e.g. (“Carbamidomethyl”, 57.021464)).
Examples
>>> from pyXLMS.constants import XI_MODIFICATION_MAPPING >>> XI_MODIFICATION_MAPPING["cm"] ('Carbamidomethyl', 57.021464) >>> XI_MODIFICATION_MAPPING["ox"] ('Oxidation', 15.994915)