🎨 Improve layouting and visual

Use ColorCode for the coloring of the edges + their labels

Author: jsnel

docs/notebooks/kinetic_scheme_visualization.ipynb

@@ -242,11 +242,9 @@
     "from glotaran.io import load_model, load_parameters\n",
     "\n",
     "model = load_model(\n",
-    "    \"../../reference_only/kinetic-scheme-visualizer/example/\"\n",
     "    \"target_rcg_gcrcg_rcgcr_refine.yml\"\n",
     ")\n",
     "params = load_parameters(\n",
-    "    \"../../reference_only/kinetic-scheme-visualizer/example/\"\n",
     "    \"target_rcg_gcrcg_rcgcr_refine-params.yml\"\n",
     ")"
    ]

docs/notebooks/target_rcg_gcrcg_rcgcr_refine-params.yml

@@ -0,0 +1,69 @@
+inputs1:
+  - ["s1", 1, { vary: False }]
+  - ["0", 0, { vary: False }]
+  - ["g_rcg", 0.12, { vary: False }]
+  - ["g_gcrcg", 1, { "expr": "$inputs1.g_rcg*2" }]
+  - ["g_rcgcr", 1, { "expr": "$inputs1.g_rcg*0.5" }]
+
+ratesrcgcr:
+  - ["k55", 0.521E-03, { "vary": False }]
+
+ratesgcrcg:
+  - ["k55", 1.06102962E-03, { "vary": False }]
+  - ["k52", 1, { "expr": "$ratesgcrcg.k51" }]
+  - ["k51", 0.635131359, { "vary": False }]
+  - ["k54", 1, { "expr": "$ratesgcrcg.k53" }]
+  - ["k53", 0.975641429, { "vary": False }]
+  - ["k62", 1, { "expr": "$ratesgcrcg.k61" }]
+  - ["k61", 1, { "expr": "$rates.k61*2" }]
+
+rates:
+  - ["k21", 7.72667789, { "vary": False }]
+  - ["k32", 1.57667196, { "vary": False }]
+  - ["k43", 0.150893405, { "vary": False }]
+  - ["k44", 5.71769197E-04, { "vary": False }]
+  - ["k55", 3.31293675E-04, { "vary": False }]
+  - ["k52", 1, { "expr": "$rates.k51" }]
+  - ["k51", 0.318180293, { "vary": False }]
+  - ["k54", 1, { "expr": "$rates.k53" }]
+  - ["k53", 0.458410978, { "vary": False }]
+  - ["k62", 1, { "expr": "$rates.k61" }]
+  - ["k61", 0.147264779, { "vary": False }]
+  - ["k66", 9.56490561E-02, { "vary": False }]
+
+area:
+  - ["1", 1, { "vary": False }]
+
+rel:
+  - ["r1", 1, { "vary": False }]
+
+scale:
+  - ["rcg_dcm", 1, { "vary": False }]
+  - ["gcrcg_dcm", 1.48898424443862, { "vary": True }]
+  - ["rcgcr_dcm", 0.57328491578764, { "vary": True }]
+  - ["guide_rcg_r1", 1.13646911340376, { "vary": True }]
+  - ["guide_rcg_r2", 1, { "expr": "$scale.guide_rcg_r1" }]
+  - ["guide_rcg_r3", 1, { "expr": "$scale.guide_rcg_r1" }]
+  - ["guide_rcg_r4", 1, { "expr": "$scale.guide_rcg_r1" }]
+  - ["guide_rcg_g", 504.658491592697, { "vary": True }]
+  - ["guide_gcrcg_g", 1, { "expr": "$scale.guide_rcg_g" }]
+  - ["guide_rcgcr_g", 1, { "expr": "$scale.guide_rcg_g" }]
+  - ["guide_gcrcg_r1", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_gcrcg_r2", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_gcrcg_r3", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_gcrcg_r4", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_rcgcr_r1", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_rcgcr_r2", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_rcgcr_r3", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+  - ["guide_rcgcr_r4", 1, { "expr": "$scale.guide_rcg_r1 * 1000" }]
+
+irf:
+  - ["common_dispcenter", 550, { "vary": False }]
+  - ["data1_disp1", -0.840490937, { "vary": False }]
+  - ["data1_disp2", -0.354524136, { "vary": False }]
+  - ["center1", 1.04188406, { "vary": False }]
+  - ["center2", 1.03445363, { "vary": False }]
+  - ["center7", 1.08, { "vary": True }]
+  - ["width1", 5.79295903E-02, { "vary": False }]
+  - ["width2", 5.19465879E-02, { "vary": False }]
+  - ["width7", 7.2146E-02, { "vary": False }]

docs/notebooks/target_rcg_gcrcg_rcgcr_refine.yml

@@ -0,0 +1,271 @@
+default_megacomplex: decay
+dataset_groups:
+  default:
+    residual_function: variable_projection
+    link_clp: True
+    # residual_function: non_negative_least_squares
+
+dataset:
+  tas_rcg_dcm:
+    megacomplex: [artifact_rcg_dcm, complex_rcg_dcm]
+    initial_concentration: input_rcg
+    irf: irf_rcg
+    scale: scale.rcg_dcm
+  tas_gcrcg_dcm:
+    megacomplex: [artifact_gcrcg_dcm, complex_gcrcg_dcm]
+    initial_concentration: input_gcrcg
+    irf: irf_gcrcg
+    scale: scale.gcrcg_dcm
+  tas_rcgcr_dcm:
+    megacomplex: [artifact_rcgcr_dcm, complex_rcgcr_dcm]
+    initial_concentration: input_rcgcr
+    irf: irf_rcgcr
+    scale: scale.rcgcr_dcm
+  guide_rcg_r1:
+    megacomplex: [complex_guide_rcg_r1]
+    scale: scale.guide_rcg_r1
+  guide_rcg_r2:
+    megacomplex: [complex_guide_rcg_r2]
+    scale: scale.guide_rcg_r2
+  guide_rcg_r3:
+    megacomplex: [complex_guide_rcg_r3]
+    scale: scale.guide_rcg_r3
+  guide_rcg_r4:
+    megacomplex: [complex_guide_rcg_r4]
+    scale: scale.guide_rcg_r4
+  guide_rcg_g:
+    megacomplex: [complex_guide_rcg_g]
+    scale: scale.guide_rcg_g
+  guide_gcrcg_r1:
+    megacomplex: [complex_guide_gcrcg_r1]
+    scale: scale.guide_gcrcg_r1
+  guide_gcrcg_r2:
+    megacomplex: [complex_guide_gcrcg_r2]
+    scale: scale.guide_gcrcg_r2
+  guide_gcrcg_r3:
+    megacomplex: [complex_guide_gcrcg_r3]
+    scale: scale.guide_gcrcg_r3
+  guide_gcrcg_r4:
+    megacomplex: [complex_guide_gcrcg_r4]
+    scale: scale.guide_gcrcg_r4
+  guide_gcrcg_g:
+    megacomplex: [complex_guide_gcrcg_g]
+    scale: scale.guide_gcrcg_g
+  guide_rcgcr_r1:
+    megacomplex: [complex_guide_rcgcr_r1]
+    scale: scale.guide_rcgcr_r1
+  guide_rcgcr_r2:
+    megacomplex: [complex_guide_rcgcr_r2]
+    scale: scale.guide_rcgcr_r2
+  guide_rcgcr_r3:
+    megacomplex: [complex_guide_rcgcr_r3]
+    scale: scale.guide_rcgcr_r3
+  guide_rcgcr_r4:
+    megacomplex: [complex_guide_rcgcr_r4]
+    scale: scale.guide_rcgcr_r4
+  guide_rcgcr_g:
+    megacomplex: [complex_guide_rcgcr_g]
+    scale: scale.guide_rcgcr_g
+
+megacomplex:
+  complex_rcg_dcm:
+    k_matrix: [km_rcg_common, kmrcg, kmg]
+  artifact_rcg_dcm:
+    type: coherent-artifact
+    order: 3
+  complex_gcrcg_dcm:
+    k_matrix: [km_gcrcg_common, km_gcrcg_rcg, km_gcrcg_g]
+  artifact_gcrcg_dcm:
+    type: coherent-artifact
+    order: 3
+  complex_rcgcr_dcm:
+    k_matrix: [km_rcgcr_common, km_rcgcr_rcg, km_rcgcr_g]
+  artifact_rcgcr_dcm:
+    type: coherent-artifact
+    order: 3
+  complex_guide_rcg_r1:
+    dimension: time
+    target: rcg_r1
+    type: clp-guide
+  complex_guide_rcg_r2:
+    dimension: time
+    target: rcg_r2
+    type: clp-guide
+  complex_guide_rcg_r3:
+    dimension: time
+    target: rcg_r3
+    type: clp-guide
+  complex_guide_rcg_r4:
+    dimension: time
+    target: rcg_r4
+    type: clp-guide
+  complex_guide_rcg_g:
+    dimension: time
+    target: rcg_g
+    type: clp-guide
+  complex_guide_gcrcg_r1:
+    dimension: time
+    target: gcrcg_r1
+    type: clp-guide
+  complex_guide_gcrcg_r2:
+    dimension: time
+    target: gcrcg_r2
+    type: clp-guide
+  complex_guide_gcrcg_r3:
+    dimension: time
+    target: gcrcg_r3
+    type: clp-guide
+  complex_guide_gcrcg_r4:
+    dimension: time
+    target: gcrcg_r4
+    type: clp-guide
+  complex_guide_gcrcg_g:
+    dimension: time
+    target: gcrcg_g
+    type: clp-guide
+  complex_guide_rcgcr_r1:
+    dimension: time
+    target: rcgcr_r1
+    type: clp-guide
+  complex_guide_rcgcr_r2:
+    dimension: time
+    target: rcgcr_r2
+    type: clp-guide
+  complex_guide_rcgcr_r3:
+    dimension: time
+    target: rcgcr_r3
+    type: clp-guide
+  complex_guide_rcgcr_r4:
+    dimension: time
+    target: rcgcr_r4
+    type: clp-guide
+  complex_guide_rcgcr_g:
+    dimension: time
+    target: rcgcr_g
+    type: clp-guide
+
+k_matrix:
+  km_rcg_common:
+    matrix:
+      (rcg_r2, rcg_r1): rates.k21
+      (rcg_r3, rcg_r2): rates.k32
+      (rcg_r4, rcg_r3): rates.k43
+      (rcg_r4, rcg_r4): rates.k44
+  kmg:
+    matrix:
+      (rcg_g, rcg_g): rates.k55
+  kmrcg:
+    matrix:
+      (rcg_g, rcg_r1): rates.k51
+      (rcg_g, rcg_r2): rates.k52
+      (rcg_g, rcg_r3): rates.k53
+      (rcg_g, rcg_r4): rates.k54
+      (rcg_s6, rcg_r1): rates.k61
+      (rcg_s6, rcg_r2): rates.k62
+      (rcg_s6, rcg_s6): rates.k66
+  km_rcgcr_common:
+    matrix:
+      (rcgcr_r2, rcgcr_r1): rates.k21
+      (rcgcr_r3, rcgcr_r2): rates.k32
+      (rcgcr_r4, rcgcr_r3): rates.k43
+      (rcgcr_r4, rcgcr_r4): rates.k44
+  km_rcgcr_g:
+    matrix:
+      (rcgcr_g, rcgcr_g): ratesrcgcr.k55
+  km_rcgcr_rcg:
+    matrix:
+      (rcgcr_g, rcgcr_r1): rates.k51
+      (rcgcr_g, rcgcr_r2): rates.k52
+      (rcgcr_g, rcgcr_r3): rates.k53
+      (rcgcr_g, rcgcr_r4): rates.k54
+      (rcgcr_s6, rcgcr_r1): rates.k61
+      (rcgcr_s6, rcgcr_r2): rates.k62
+      (rcgcr_s6, rcgcr_s6): rates.k66
+  km_gcrcg_common:
+    matrix:
+      (gcrcg_r2, gcrcg_r1): rates.k21
+      (gcrcg_r3, gcrcg_r2): rates.k32
+      (gcrcg_r4, gcrcg_r3): rates.k43
+      (gcrcg_r4, gcrcg_r4): rates.k44
+  km_gcrcg_g:
+    matrix:
+      (gcrcg_g, gcrcg_g): ratesgcrcg.k55
+  km_gcrcg_rcg:
+    matrix:
+      (gcrcg_g, gcrcg_r1): ratesgcrcg.k51
+      (gcrcg_g, gcrcg_r2): ratesgcrcg.k52
+      (gcrcg_g, gcrcg_r3): ratesgcrcg.k53
+      (gcrcg_g, gcrcg_r4): ratesgcrcg.k54
+      (gcrcg_s6, gcrcg_r1): ratesgcrcg.k61
+      (gcrcg_s6, gcrcg_r2): ratesgcrcg.k62
+      (gcrcg_s6, gcrcg_s6): rates.k66
+
+initial_concentration:
+  input_rcg:
+    compartments: [rcg_r1, rcg_r2, rcg_r3, rcg_r4, rcg_g, rcg_s6]
+    parameters:
+      [inputs1.s1, inputs1.0, inputs1.0, inputs1.0, inputs1.g_rcg, inputs1.0]
+  input_gcrcg:
+    compartments: [gcrcg_r1, gcrcg_r2, gcrcg_r3, gcrcg_r4, gcrcg_g, gcrcg_s6]
+    parameters:
+      [inputs1.s1, inputs1.0, inputs1.0, inputs1.0, inputs1.g_gcrcg, inputs1.0]
+  input_rcgcr:
+    compartments: [rcgcr_r1, rcgcr_r2, rcgcr_r3, rcgcr_r4, rcgcr_g, rcgcr_s6]
+    parameters:
+      [inputs1.s1, inputs1.0, inputs1.0, inputs1.0, inputs1.g_rcgcr, inputs1.0]
+    # exclude_from_normalize: [s7]
+# 6 needed ! why is it called compartment here and source with equal_area? does this mean that s2=s1*rel.r1 ?
+clp_relations:
+  - source: rcg_s6
+    target: rcgcr_s6
+    parameter: rel.r1
+    interval: [[0, 1000]]
+  - source: rcg_s6
+    target: gcrcg_s6
+    parameter: rel.r1
+    interval: [[0, 1000]]
+
+irf:
+  irf_rcg:
+    type: spectral-gaussian
+    center: irf.center1
+    width: irf.width1
+    dispersion_center: irf.common_dispcenter
+    center_dispersion_coefficients: [irf.data1_disp1, irf.data1_disp2]
+    model_dispersion_with_wavenumber: true
+  irf_gcrcg:
+    type: spectral-gaussian
+    center: irf.center2
+    width: irf.width2
+    dispersion_center: irf.common_dispcenter
+    center_dispersion_coefficients: [irf.data1_disp1, irf.data1_disp2]
+    model_dispersion_with_wavenumber: true
+  irf_rcgcr:
+    type: spectral-gaussian
+    center: irf.center7
+    width: irf.width7
+    dispersion_center: irf.common_dispcenter
+    center_dispersion_coefficients: [irf.data1_disp1, irf.data1_disp2]
+    model_dispersion_with_wavenumber: true
+weights:
+  - datasets: [tas_rcg_dcm, tas_gcrcg_dcm, tas_rcgcr_dcm]
+    global_interval: [520, 535]
+    value: 0.4
+  - datasets: [tas_rcg_dcm, tas_gcrcg_dcm, tas_rcgcr_dcm]
+    global_interval: [1, 420]
+    value: 0.2
+  - datasets:
+      [
+        guide_rcg_g,
+        guide_gcrcg_r1,
+        guide_gcrcg_r2,
+        guide_gcrcg_r3,
+        guide_gcrcg_r4,
+        guide_gcrcg_g,
+        guide_rcgcr_r1,
+        guide_rcgcr_r2,
+        guide_rcgcr_r3,
+        guide_rcgcr_r4,
+        guide_rcgcr_g,
+      ]
+    value: 0.001

pyglotaran_extras/inspect/kinetic_scheme/_constants.py

@@ -18,7 +18,7 @@
 # Default edge styling
 DEFAULT_EDGE_COLOR: str = "#555555"
 DEFAULT_EDGE_LINEWIDTH: float = 1.5
-DEFAULT_ARROWSTYLE: str = "->,head_length=0.4,head_width=0.2"
+DEFAULT_ARROWSTYLE: str = "-|>,head_length=8,head_width=5"
 DEFAULT_RATE_FONTSIZE: int = 9
 
 # Ground state bar styling
@@ -28,8 +28,9 @@
 
 # Layout defaults
 DEFAULT_FIGSIZE: tuple[float, float] = (10.0, 8.0)
-DEFAULT_HORIZONTAL_SPACING: float = 2.0
-DEFAULT_VERTICAL_SPACING: float = 1.5
+DEFAULT_HORIZONTAL_SPACING: float = 0.0
+"""Sentinel: when 0, computed as 3 × node_width at render time (200% gap)."""
+DEFAULT_VERTICAL_SPACING: float = 2.0
 DEFAULT_GROUND_STATE_OFFSET: float = 1.2
 DEFAULT_COMPONENT_GAP: float = 3.0
 """Horizontal gap between disconnected graph components in side-by-side layout."""