cdxml-toolkit 0.5.0__py3-none-any.whl

cdxml_toolkit/constants.py

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+"""
+constants.py -- Centralized constants for chem-tools v0.3.
+
+All hardcoded magic numbers that were previously scattered across individual
+tool scripts are collected here.  Each constant has a comment noting its
+purpose and original source file(s).
+
+Sections:
+  1. ACS Document 1996 style constants
+  2. ACS_STYLE dict and CDXML_HEADER template string
+  3. LCMS analysis constants
+  4. Mass matching constants
+  5. Layout constants (reaction_cleanup gaps)
+  6. Image / structure constants
+"""
+
+# ============================================================================
+# 1. ACS Document 1996 style constants
+# ============================================================================
+
+# Bond length -- float for geometry calculations
+# Originally in: alignment.py, scheme_polisher_v2.py, coord_normalizer.py,
+#   reaction_from_image.py, reaction_cleanup.py (~line 772), scheme_aligner.py (~line 146)
+ACS_BOND_LENGTH = 14.40
+
+# Bond length -- string for CDXML XML attributes
+# Originally in: cdxml_builder.py, chemscript_bridge.py, eln_enrichment.py,
+#   reactant_heuristic.py, reaction_from_image.py (CDXML header)
+ACS_BOND_LENGTH_STR = "14.40"
+
+# Chain angle -- float for calculations
+# Originally in: cdxml_builder.py, chemscript_bridge.py
+ACS_CHAIN_ANGLE = 120
+
+# Chain angle -- string for CDXML XML attributes
+# Originally in: cdxml_builder.py, chemscript_bridge.py
+ACS_CHAIN_ANGLE_STR = "120"
+
+# Font table ID for Arial (ChemDraw font table index)
+# Originally in: cdxml_builder.py, scheme_polisher_v2.py
+ACS_LABEL_FONT = "3"
+
+# Label size in points (atom labels)
+# Originally in: cdxml_builder.py, scheme_polisher_v2.py
+ACS_LABEL_SIZE = "10"
+
+# Label face: 96 = bold (ChemDraw encoding)
+# Originally in: cdxml_builder.py, scheme_polisher_v2.py
+ACS_LABEL_FACE = "96"
+
+# Caption size in points (reaction conditions text)
+# Originally in: cdxml_builder.py
+ACS_CAPTION_SIZE = "10"
+
+# Caption face: 0 = plain
+# Originally in: cdxml_builder.py, chemscript_bridge.py
+ACS_CAPTION_FACE = "0"
+
+# Line width in points
+# Originally in: cdxml_builder.py, chemscript_bridge.py
+ACS_LINE_WIDTH = "0.60"
+
+# Bold bond width in points
+# Originally in: cdxml_builder.py, chemscript_bridge.py, scheme_polisher_v2.py
+ACS_BOLD_WIDTH = "2"
+
+# Bond spacing (percentage, ChemDraw internal units)
+# Originally in: cdxml_builder.py, scheme_polisher_v2.py
+ACS_BOND_SPACING = "18"
+
+# Hash spacing (dashed bond dash gap) in points
+# Originally in: cdxml_builder.py, chemscript_bridge.py, scheme_polisher_v2.py
+ACS_HASH_SPACING = "2.50"
+
+# Margin width in points
+# Originally in: cdxml_builder.py, chemscript_bridge.py, scheme_polisher_v2.py
+ACS_MARGIN_WIDTH = "1.60"
+
+
+# ============================================================================
+# 2. ACS_STYLE dict and CDXML_HEADER template
+# ============================================================================
+
+# Complete ACS Document 1996 style dict -- all values are strings for direct
+# use as XML attributes.  Superset of chemscript_bridge.ACS_STYLE_ATTRS and
+# scheme_polisher_v2.ACS_SETTINGS.
+# Originally in: chemscript_bridge.py (ACS_STYLE_ATTRS), scheme_polisher_v2.py (ACS_SETTINGS)
+ACS_STYLE = {
+    "BondLength": ACS_BOND_LENGTH_STR,
+    "ChainAngle": ACS_CHAIN_ANGLE_STR,
+    "BoldWidth": ACS_BOLD_WIDTH,
+    "LineWidth": ACS_LINE_WIDTH,
+    "MarginWidth": ACS_MARGIN_WIDTH,
+    "HashSpacing": ACS_HASH_SPACING,
+    "BondSpacing": ACS_BOND_SPACING,
+    "LabelFont": ACS_LABEL_FONT,
+    "LabelSize": ACS_LABEL_SIZE,
+    "LabelFace": ACS_LABEL_FACE,
+    "CaptionFont": ACS_LABEL_FONT,
+    "CaptionSize": ACS_CAPTION_SIZE,
+    "CaptionFace": ACS_CAPTION_FACE,
+}
+
+# Full CDXML document header template with ACS Document 1996 style.
+# Contains {bbox} placeholder for the document bounding box.
+# Originally in: cdxml_builder.py (_CDXML_HEADER), reaction_from_image.py (_CDXML_HEADER)
+CDXML_HEADER = """\
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
+<CDXML
+ CreationProgram="ChemDraw 16.0.0.82"
+ BoundingBox="{bbox}"
+ WindowPosition="-2147483648 -2147483648"
+ WindowSize="-2147483648 -2147483648"
+ FractionalWidths="yes"
+ InterpretChemically="yes"
+ ShowAtomQuery="yes"
+ ShowAtomStereo="no"
+ ShowAtomEnhancedStereo="yes"
+ ShowAtomNumber="no"
+ ShowResidueID="no"
+ ShowBondQuery="yes"
+ ShowBondRxn="yes"
+ ShowBondStereo="no"
+ ShowTerminalCarbonLabels="no"
+ ShowNonTerminalCarbonLabels="no"
+ HideImplicitHydrogens="no"
+ LabelFont="{label_font}"
+ LabelSize="{label_size}"
+ LabelFace="{label_face}"
+ CaptionFont="{label_font}"
+ CaptionSize="{caption_size}"
+ HashSpacing="{hash_spacing}"
+ MarginWidth="{margin_width}"
+ LineWidth="{line_width}"
+ BoldWidth="{bold_width}"
+ BondLength="{bond_length}"
+ BondSpacing="{bond_spacing}"
+ ChainAngle="{chain_angle}"
+ LabelJustification="Auto"
+ CaptionJustification="Left"
+ AminoAcidTermini="HOH"
+ ShowSequenceTermini="yes"
+ ShowSequenceBonds="yes"
+ ResidueWrapCount="40"
+ ResidueBlockCount="10"
+ ResidueZigZag="yes"
+ NumberResidueBlocks="no"
+ PrintMargins="36 36 36 36"
+ ChemPropName=""
+ ChemPropFormula="Chemical Formula: "
+ ChemPropExactMass="Exact Mass: "
+ ChemPropMolWt="Molecular Weight: "
+ ChemPropMOverZ="m/z: "
+ ChemPropAnalysis="Elemental Analysis: "
+ ChemPropBoilingPt="Boiling Point: "
+ ChemPropMeltingPt="Melting Point: "
+ ChemPropCritTemp="Critical Temp: "
+ ChemPropCritPres="Critical Pres: "
+ ChemPropCritVol="Critical Vol: "
+ ChemPropGibbs="Gibbs Energy: "
+ ChemPropLogP="Log P: "
+ ChemPropMR="MR: "
+ ChemPropHenry="Henry&apos;s Law: "
+ ChemPropEForm="Heat of Form: "
+ ChemProptPSA="tPSA: "
+ ChemPropCLogP="CLogP: "
+ ChemPropCMR="CMR: "
+ ChemPropLogS="LogS: "
+ ChemPropPKa="pKa: "
+ ChemPropID=""
+ color="0"
+ bgcolor="1"
+ RxnAutonumberStart="1"
+ RxnAutonumberConditions="no"
+ RxnAutonumberStyle="Roman"
+ RxnAutonumberFormat="(#)"
+><colortable>
+<color r="1" g="1" b="1"/>
+<color r="0" g="0" b="0"/>
+<color r="1" g="0" b="0"/>
+<color r="1" g="1" b="0"/>
+<color r="0" g="1" b="0"/>
+<color r="0" g="1" b="1"/>
+<color r="0" g="0" b="1"/>
+<color r="1" g="0" b="1"/>
+</colortable><fonttable>
+<font id="{label_font}" charset="iso-8859-1" name="Arial"/>
+</fonttable>"""
+
+# Minimal CDXML wrapper for single-fragment operations (ChemScript, etc.)
+# Originally in: alignment.py (sp_fragment_to_cdxml), eln_enrichment.py, reactant_heuristic.py
+CDXML_MINIMAL_HEADER = (
+    '<?xml version="1.0" encoding="UTF-8" ?>\n'
+    '<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >\n'
+    '<CDXML BondLength="' + ACS_BOND_LENGTH_STR + '">'
+)
+
+# CDXML closing tag
+# Originally in: cdxml_builder.py, reaction_from_image.py
+CDXML_FOOTER = "</CDXML>"
+
+
+# ============================================================================
+# 3. LCMS analysis constants
+# ============================================================================
+
+# Default RT matching tolerance in minutes for cross-file peak matching
+# Originally in: multi_lcms_analyzer.py (--rt-tolerance default)
+LCMS_RT_TOLERANCE = 0.02
+
+# Default m/z clustering tolerance in Da for ion merging
+# Originally in: multi_lcms_analyzer.py (--mz-tolerance default)
+LCMS_MZ_TOLERANCE = 0.5
+
+# Fraction change threshold for increasing/decreasing trend classification
+# Originally in: multi_lcms_analyzer.py (--trend-threshold default)
+LCMS_TREND_THRESHOLD = 0.2
+
+# Default minimum area% for a compound to appear in the reaction summary
+# Originally in: multi_lcms_analyzer.py (--min-summary-area default)
+LCMS_MIN_SUMMARY_AREA = 2.0
+
+# Column boundary x-coordinate (half of 612pt letter page width) for
+# two-column MS/UV panel parsing in MassLynx PDF reports.
+# Originally in: lcms_analyzer.py (computed as page_width / 2.0)
+LCMS_COLUMN_BOUNDARY = 306.0
+
+# MS axis tick values to exclude when extracting m/z labels
+# Originally in: lcms_analyzer.py (_MS_AXIS_TICKS)
+LCMS_MS_AXIS_TICKS = {500.0, 1000.0}
+
+# UV axis tick values to exclude when extracting wavelength labels
+# Originally in: lcms_analyzer.py (_UV_AXIS_TICKS)
+LCMS_UV_AXIS_TICKS = {150.0, 200.0, 250.0, 300.0, 350.0, 400.0}
+
+# UV wavelength valid range (nm) for lambda-max extraction
+# Originally in: lcms_analyzer.py (_parse_uv_from_words, line ~408)
+LCMS_UV_WAVELENGTH_MIN = 150.0
+LCMS_UV_WAVELENGTH_MAX = 400.0
+
+
+# ============================================================================
+# 4. Mass matching constants
+# ============================================================================
+
+# MW tolerance in Da for matching CSV reagents to scheme fragments
+# Originally in: eln_enrichment.py (best_delta threshold, lines ~306 and ~347)
+MW_MATCH_TOLERANCE = 2.0
+
+# Loose MW tolerance in Da for matching substrate fragment to CSV row
+# Originally in: eln_enrichment.py (substrate MW match, line ~689)
+MW_MATCH_TOLERANCE_LOOSE = 5.0
+
+# MW tolerance in Da for matching species to CSV rows in procedure_writer
+# Originally in: procedure_writer.py (MASS_TOLERANCE, line ~69)
+MASS_TOLERANCE = 1.5
+
+# Minimum area% for a peak to be reported in LCMS characterization/notes
+# Originally in: procedure_writer.py (MIN_REPORT_AREA_PCT, line ~70)
+MIN_REPORT_AREA_PCT = 20.0
+
+# Minimum area% for an unidentified compound to be counted as "significant"
+# Originally in: procedure_writer.py (hardcoded 2.0 in tracking summary, line ~1990)
+MIN_SIGNIFICANT_AREA = 2.0
+
+
+# ============================================================================
+# 5. Layout constants (from reaction_cleanup.py)
+# ============================================================================
+
+# Gap in points from arrow to bottom of above-arrow objects (base case)
+# Originally in: reaction_cleanup.py (ABOVE_GAP in most approaches, line ~457)
+LAYOUT_ABOVE_GAP = 8.0
+
+# Gap in points from arrow to top of below-arrow objects
+# Originally in: reaction_cleanup.py (BELOW_GAP in all approaches, line ~458)
+LAYOUT_BELOW_GAP = 4.0
+
+# Extra gap for fragments with hanging NH/PH labels (N or P at bottom with <=2 bonds)
+# Originally in: reaction_cleanup.py (HANGING_GAP, line ~899)
+LAYOUT_HANGING_LABEL_GAP = 16.0
+
+# Gap in points between multiple fragments on the same side (arrow_driven approach)
+# Originally in: reaction_cleanup.py (INTER_GAP, line ~523)
+LAYOUT_INTER_FRAGMENT_GAP = 8.0
+
+# Gap between molecule edge and arrow tip, in multiples of bond length (chemdraw_mimic)
+# Originally in: reaction_cleanup.py (FRAG_GAP_BONDS, line ~774)
+LAYOUT_FRAG_GAP_BONDS = 1.0
+
+# Gap between multiple reactants, in multiples of bond length (chemdraw_mimic)
+# Originally in: reaction_cleanup.py (INTER_GAP_BONDS, line ~775)
+LAYOUT_INTER_GAP_BONDS = 0.8
+
+
+# ============================================================================
+# 6. Image / structure constants
+# ============================================================================
+
+# Reduced bond length for condition structures rendered above/below the arrow
+# (smaller than ACS_BOND_LENGTH so they don't overwhelm the scheme)
+# Originally in: reaction_from_image.py (EXPAND_SCALE_BOND, line ~420)
+EXPAND_SCALE_BOND = 10.0