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539
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1 """
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2 Helpers to parse reaction strings into structured dictionaries.
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3
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4 Features:
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5 - Reaction direction detection (forward, backward, reversible)
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6 - Parsing of custom reaction strings into stoichiometric maps
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7 - Conversion of a dict of raw reactions into a directional reactions dict
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8 - Loading custom reactions from a tabular file (TSV)
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9 """
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10 from enum import Enum
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11 import utils.general_utils as utils
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12 from typing import Dict
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13 import re
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14
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15 # Reaction direction encoding:
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16 class ReactionDir(Enum):
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17 """
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18 A reaction can go forward, backward, or be reversible (both directions).
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19 Cobrapy-style formulas encode direction using specific arrows handled here.
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20 """
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21 FORWARD = "-->"
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22 BACKWARD = "<--"
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23 REVERSIBLE = "<=>"
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24
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25 @classmethod
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26 def fromReaction(cls, reaction :str) -> 'ReactionDir':
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27 """
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28 Takes a whole reaction formula string and looks for one of the arrows, returning the
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29 corresponding reaction direction.
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30
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31 Args:
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32 reaction : the reaction's formula.
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33
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34 Raises:
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35 ValueError : if no valid arrow is found.
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36
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37 Returns:
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38 ReactionDir : the corresponding reaction direction.
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39 """
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40 for member in cls:
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41 if member.value in reaction: return member
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42
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43 raise ValueError("No valid arrow found within reaction string.")
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44
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45 ReactionsDict = Dict[str, Dict[str, float]]
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46
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47
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48 def add_custom_reaction(reactionsDict :ReactionsDict, rId :str, reaction :str) -> None:
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49 """
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50 Add one reaction entry to reactionsDict.
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51
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52 The entry maps each substrate ID to its stoichiometric coefficient.
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53 If a substrate appears without an explicit coefficient, 1.0 is assumed.
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54
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55 Args:
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56 reactionsDict: Dict to update in place.
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57 rId: Unique reaction ID.
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58 reaction: Reaction formula string.
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59
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60 Returns:
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61 None
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62
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63 Side effects: updates reactionsDict in place.
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64 """
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65 reaction = reaction.strip()
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66 if not reaction: return
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67
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68 reactionsDict[rId] = {}
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69 # Assumes ' + ' is spaced to avoid confusion with charge symbols.
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70 for word in reaction.split(" + "):
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71 metabId, stoichCoeff = word, 1.0
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72 # Coefficient can be integer or float (dot decimal) and must be space-separated.
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73 foundCoeff = re.search(r"\d+(\.\d+)? ", word)
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74 if foundCoeff:
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75 wholeMatch = foundCoeff.group(0)
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76 metabId = word[len(wholeMatch):].strip()
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77 stoichCoeff = float(wholeMatch.strip())
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78
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79 reactionsDict[rId][metabId] = stoichCoeff
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80
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81 if not reactionsDict[rId]: del reactionsDict[rId] # Empty reactions are removed.
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82
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83
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84 def create_reaction_dict(unparsed_reactions: Dict[str, str]) -> ReactionsDict:
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85 """
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86 Parse a dict of raw reaction strings into a directional reactions dict.
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87
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88 Args:
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89 unparsed_reactions: Mapping reaction ID -> raw reaction string.
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90
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91 Returns:
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92 ReactionsDict: Parsed dict. Reversible reactions produce two entries with _F and _B suffixes.
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93 """
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94 reactionsDict :ReactionsDict = {}
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95 for rId, reaction in unparsed_reactions.items():
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96 reactionDir = ReactionDir.fromReaction(reaction)
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97 left, right = reaction.split(f" {reactionDir.value} ")
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98
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99 # Reversible reactions are split into two: forward (_F) and backward (_B).
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100 reactionIsReversible = reactionDir is ReactionDir.REVERSIBLE
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101 if reactionDir is not ReactionDir.BACKWARD:
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102 add_custom_reaction(reactionsDict, rId + "_F" * reactionIsReversible, left)
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103
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104 if reactionDir is not ReactionDir.FORWARD:
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105 add_custom_reaction(reactionsDict, rId + "_B" * reactionIsReversible, right)
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106
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107 return reactionsDict
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108
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109
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110 def parse_custom_reactions(customReactionsPath :str) -> ReactionsDict:
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111 """
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112 Load custom reactions from a tabular file and parse into a reactions dict.
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113
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114 Args:
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115 customReactionsPath: Path to the reactions file (TSV or CSV-like).
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116
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117 Returns:
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118 ReactionsDict: Parsed reactions dictionary.
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119 """
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120 try:
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121 rows = utils.readCsv(utils.FilePath.fromStrPath(customReactionsPath), delimiter = "\t", skipHeader=False)
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122 if len(rows) <= 1:
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123 raise ValueError("The custom reactions file must contain at least one reaction.")
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124
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125 id_idx, idx_formula = utils.findIdxByName(rows[0], "Formula")
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126
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127 except Exception as e:
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128 # Fallback re-read with same settings; preserves original behavior
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129 rows = utils.readCsv(utils.FilePath.fromStrPath(customReactionsPath), delimiter = "\t", skipHeader=False)
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130 if len(rows) <= 1:
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131 raise ValueError("The custom reactions file must contain at least one reaction.")
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132
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133 id_idx, idx_formula = utils.findIdxByName(rows[0], "Formula")
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134
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135 reactionsData = {row[id_idx] : row[idx_formula] for row in rows[1:]}
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136
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137 return create_reaction_dict(reactionsData)
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138
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