From 5fb2726c47d5a6b8410131a06e7ef660b63da0cd Mon Sep 17 00:00:00 2001
From: Aliaksandr Dziarkach
 <18146690+AliaksandrDziarkach@users.noreply.github.com>
Date: Thu, 17 Aug 2023 10:31:24 +0300
Subject: [PATCH] #1224 Different indent after loading reaction from file and
 after layout it (#1227)

Co-authored-by: Aliaksandr Dziarkach <adziarkach@infoblox.com>
---
 api/c/indigo/src/indigo_internal.h            |   4 +-
 api/c/indigo/src/indigo_layout.cpp            |   4 +-
 .../ref/formats/rxn_no_layout.py.out          | 196 ++--
 .../tests/basic/ref/crazystereo.ket           | 888 +++++++++---------
 .../tests/layout/ref/932-agents.ket           | 118 +--
 .../tests/layout/ref/reaction_layout.rdf      |  56 +-
 .../integration/tests/layout/ref/test1.rxn    |  54 +-
 .../tests/layout/ref/test_sgroup.rxn          |  28 +-
 core/indigo-core/layout/molecule_layout.h     |   1 +
 core/indigo-core/layout/reaction_layout.h     |   8 +-
 .../layout/src/reaction_layout.cpp            |  36 +-
 11 files changed, 694 insertions(+), 699 deletions(-)

diff --git a/api/c/indigo/src/indigo_internal.h b/api/c/indigo/src/indigo_internal.h
index cb692e671d..12b6a1c58b 100644
--- a/api/c/indigo/src/indigo_internal.h
+++ b/api/c/indigo/src/indigo_internal.h
@@ -34,6 +34,8 @@
 #include "base_cpp/exception.h"
 #include "base_cpp/io_base.h"
 
+#include "layout/reaction_layout.h"
+
 #include "molecule/molecule_fingerprint.h"
 #include "molecule/molecule_gross_formula.h"
 #include "molecule/molecule_ionize.h"
@@ -329,7 +331,7 @@ class DLLEXPORT Indigo
 
     int layout_max_iterations; // default is zero -- no limit
     bool smart_layout = false;
-    float layout_horintervalfactor = 1.4f;
+    float layout_horintervalfactor = ReactionLayout::DEFAULT_HOR_INTERVAL_FACTOR;
 
     int layout_orientation = 0;
 
diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp
index a9bb9b4b72..d8e7107a51 100644
--- a/api/c/indigo/src/indigo_layout.cpp
+++ b/api/c/indigo/src/indigo_layout.cpp
@@ -56,7 +56,7 @@ CEXPORT int indigoLayout(int object)
             }
 
             ml.max_iterations = self.layout_max_iterations;
-            ml.bond_length = 1.6f;
+            ml.bond_length = MoleculeLayout::DEFAULT_BOND_LENGTH;
             ml.layout_orientation = (layout_orientation_value)self.layout_orientation;
 
             TimeoutCancellationHandler cancellation(self.cancellation_timeout);
@@ -105,7 +105,7 @@ CEXPORT int indigoLayout(int object)
                 ReactionLayout rl(rxn, self.smart_layout);
                 rl.max_iterations = self.layout_max_iterations;
                 rl.layout_orientation = (layout_orientation_value)self.layout_orientation;
-                rl.bond_length = 1.6f;
+                rl.bond_length = MoleculeLayout::DEFAULT_BOND_LENGTH;
                 rl.horizontal_interval_factor = self.layout_horintervalfactor;
                 rl.make();
                 try
diff --git a/api/tests/integration/ref/formats/rxn_no_layout.py.out b/api/tests/integration/ref/formats/rxn_no_layout.py.out
index 8419bece36..17697cf853 100644
--- a/api/tests/integration/ref/formats/rxn_no_layout.py.out
+++ b/api/tests/integration/ref/formats/rxn_no_layout.py.out
@@ -29,7 +29,7 @@
             {
                 "type": "plus",
                 "location": [
-                    5.2510833740234379,
+                    9.501733779907227,
                     0.0,
                     0.0
                 ]
@@ -37,7 +37,7 @@
             {
                 "type": "plus",
                 "location": [
-                    12.91125774383545,
+                    19.503467559814454,
                     0.0,
                     0.0
                 ]
@@ -45,7 +45,7 @@
             {
                 "type": "plus",
                 "location": [
-                    18.638530731201173,
+                    23.103466033935548,
                     0.0,
                     0.0
                 ]
@@ -53,7 +53,7 @@
             {
                 "type": "plus",
                 "location": [
-                    24.1688289642334,
+                    26.70346450805664,
                     0.0,
                     0.0
                 ]
@@ -61,7 +61,7 @@
             {
                 "type": "plus",
                 "location": [
-                    28.737014770507814,
+                    31.90349578857422,
                     0.0,
                     0.0
                 ]
@@ -69,7 +69,7 @@
             {
                 "type": "plus",
                 "location": [
-                    38.702880859375,
+                    48.909507751464847,
                     0.0,
                     0.0
                 ]
@@ -80,12 +80,12 @@
                     "mode": "open-angle",
                     "pos": [
                         {
-                            "x": 32.09308624267578,
+                            "x": 36.30352783203125,
                             "y": 0.0,
                             "z": 0.0
                         },
                         {
-                            "x": 33.19913864135742,
+                            "x": 40.50352478027344,
                             "y": 0.0,
                             "z": 0.0
                         }
@@ -100,80 +100,80 @@
             {
                 "label": "C",
                 "location": [
-                    1.5023635625839234,
-                    0.8676860332489014,
+                    3.7037816047668459,
+                    1.3882975578308106,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    3.0010616779327394,
-                    0.0030012130737304689,
+                    6.101698875427246,
+                    0.004801750183105469,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    2.5030517578125,
-                    0.8673515319824219,
+                    5.304883003234863,
+                    1.3877620697021485,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    2.500718593597412,
-                    -0.8640168309211731,
+                    5.301149368286133,
+                    -1.3824270963668824,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    1.0000206232070926,
-                    -0.002666711807250977,
+                    2.900032997131348,
+                    -0.004266738891601563,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    1.50503146648407,
-                    -0.8656835556030273,
+                    3.708050489425659,
+                    -1.3850938081741334,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    1.0023539066314698,
-                    1.7337028980255128,
+                    2.90376615524292,
+                    2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    1.0083551406860352,
-                    -1.7337028980255128,
+                    2.9133682250976564,
+                    -2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    0.0,
-                    -0.005331993103027344,
+                    1.2999999523162842,
+                    -0.008531332015991211,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    4.0010833740234379,
-                    0.002666711807250977,
+                    7.701733589172363,
+                    0.004266738891601563,
                     0.0
                 ]
             }
@@ -257,80 +257,80 @@
             {
                 "label": "C",
                 "location": [
-                    8.003446578979493,
-                    0.8676860332489014,
+                    13.70551586151123,
+                    1.3882975578308106,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    9.502144813537598,
-                    0.0030012130737304689,
+                    16.10343360900879,
+                    0.004801750183105469,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    9.004135131835938,
-                    0.8673515319824219,
+                    15.306617736816408,
+                    1.3877620697021485,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    9.001802444458008,
-                    -0.8640168309211731,
+                    15.30288314819336,
+                    -1.3824270963668824,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    7.50110387802124,
-                    -0.002666711807250977,
+                    12.901766777038576,
+                    -0.004266738891601563,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    8.006114959716797,
-                    -0.8656835556030273,
+                    13.709784507751465,
+                    -1.3850938081741334,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    7.503437042236328,
-                    1.7337028980255128,
+                    12.905500411987305,
+                    2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    7.509438514709473,
-                    -1.7337028980255128,
+                    12.915102005004885,
+                    -2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    6.5010833740234379,
-                    -0.005331993103027344,
+                    11.30173397064209,
+                    -0.008531332015991211,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    10.502166748046877,
-                    0.002666711807250977,
+                    17.703468322753908,
+                    0.004266738891601563,
                     0.0
                 ]
             }
@@ -414,7 +414,7 @@
             {
                 "label": "O",
                 "location": [
-                    15.320348739624024,
+                    21.303466796875,
                     0.0,
                     0.0
                 ]
@@ -428,7 +428,7 @@
             {
                 "label": "O",
                 "location": [
-                    21.95671272277832,
+                    24.903465270996099,
                     0.0,
                     0.0
                 ]
@@ -442,7 +442,7 @@
             {
                 "label": "O",
                 "location": [
-                    26.38094520568848,
+                    28.503463745117189,
                     0.0,
                     0.0
                 ],
@@ -451,7 +451,7 @@
             {
                 "label": "O",
                 "location": [
-                    27.38096427917481,
+                    30.10349464416504,
                     0.0,
                     0.0
                 ]
@@ -473,7 +473,7 @@
             {
                 "label": "O",
                 "location": [
-                    30.093067169189458,
+                    33.703495025634769,
                     0.0,
                     0.0
                 ]
@@ -481,7 +481,7 @@
             {
                 "label": "O",
                 "location": [
-                    31.09308624267578,
+                    35.30352783203125,
                     0.0,
                     0.0
                 ]
@@ -503,88 +503,88 @@
             {
                 "label": "C",
                 "location": [
-                    36.20417785644531,
-                    0.8676860332489014,
+                    44.71158981323242,
+                    1.3882975578308106,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    37.702880859375,
-                    0.0030012130737304689,
+                    47.1095085144043,
+                    0.004801750183105469,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    37.20486831665039,
-                    0.8673515319824219,
+                    46.31269073486328,
+                    1.3877620697021485,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    37.20253372192383,
-                    -0.8640168309211731,
+                    46.3089599609375,
+                    -1.3824270963668824,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    35.70183944702149,
-                    -0.002666711807250977,
+                    43.90784454345703,
+                    -0.004266738891601563,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    36.20684814453125,
-                    -0.8656835556030273,
+                    44.715858459472659,
+                    -1.3850938081741334,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    35.71017074584961,
-                    -1.7337028980255128,
+                    43.921180725097659,
+                    -2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    34.70181655883789,
-                    -0.005331993103027344,
+                    42.30780792236328,
+                    -0.008531332015991211,
                     0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    34.19913864135742,
-                    0.859018087387085,
+                    41.50352478027344,
+                    1.3744287490844729,
                     0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    34.20413589477539,
-                    -0.873016893863678,
+                    41.51152420043945,
+                    -1.3968271017074586,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    35.70417022705078,
-                    1.7337028980255128,
+                    43.91157531738281,
+                    2.773924827575684,
                     0.0
                 ]
             }
@@ -675,88 +675,88 @@
             {
                 "label": "C",
                 "location": [
-                    41.70792007446289,
-                    0.8676860332489014,
+                    53.917572021484378,
+                    1.3882975578308106,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    43.20661926269531,
-                    0.0030012130737304689,
+                    56.31549072265625,
+                    0.004801750183105469,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    42.70861053466797,
-                    0.8673515319824219,
+                    55.51867294311524,
+                    1.3877620697021485,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    42.706275939941409,
-                    -0.8640168309211731,
+                    55.51494216918945,
+                    -1.3824270963668824,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    41.20558166503906,
-                    -0.002666711807250977,
+                    53.113826751708987,
+                    -0.004266738891601563,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    41.71059036254883,
-                    -0.8656835556030273,
+                    53.92184066772461,
+                    -1.3850938081741334,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    41.21391296386719,
-                    -1.7337028980255128,
+                    53.12716293334961,
+                    -2.773924827575684,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    40.20555877685547,
-                    -0.005331993103027344,
+                    51.51379013061524,
+                    -0.008531332015991211,
                     0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    39.702880859375,
-                    0.859018087387085,
+                    50.70950698852539,
+                    1.3744287490844729,
                     0.0
                 ]
             },
             {
                 "label": "O",
                 "location": [
-                    39.70787811279297,
-                    -0.873016893863678,
+                    50.717506408691409,
+                    -1.3968271017074586,
                     0.0
                 ]
             },
             {
                 "label": "C",
                 "location": [
-                    41.20791244506836,
-                    1.7337028980255128,
+                    53.117557525634769,
+                    2.773924827575684,
                     0.0
                 ]
             }
diff --git a/api/tests/integration/tests/basic/ref/crazystereo.ket b/api/tests/integration/tests/basic/ref/crazystereo.ket
index fe4a79bc83..021d14692f 100644
--- a/api/tests/integration/tests/basic/ref/crazystereo.ket
+++ b/api/tests/integration/tests/basic/ref/crazystereo.ket
@@ -1,445 +1,445 @@
-{
-    "root": {
-        "nodes": [
-            {
-                "$ref": "mol0"
-            },
-            {
-                "$ref": "mol1"
-            },
-            {
-                "type": "arrow",
-                "data": {
-                    "mode": "open-angle",
-                    "pos": [
-                        {
-                            "x": 4.464198589324951,
-                            "y": 0.0,
-                            "z": 0.0
-                        },
-                        {
-                            "x": 5.464198589324951,
-                            "y": 0.0,
-                            "z": 0.0
-                        }
-                    ]
-                }
-            }
-        ]
-    },
-    "mol0": {
-        "type": "molecule",
-        "atoms": [
-            {
-                "label": "C",
-                "location": [
-                    1.7320992946624756,
-                    0.49999362230300906,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    0.8660491108894348,
-                    0.9999874234199524,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    0.0,
-                    0.49999362230300906,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    0.0,
-                    -0.4999937117099762,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    0.8660491108894348,
-                    -0.9999874234199524,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    1.7320992946624756,
-                    -0.4999937117099762,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    2.5980277061462404,
-                    -0.9999874234199524,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    3.464198589324951,
-                    -0.4999937117099762,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    3.464198589324951,
-                    0.49999362230300906,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    2.5980277061462404,
-                    0.9999874234199524,
-                    0.0
-                ]
-            }
-        ],
-        "bonds": [
-            {
-                "type": 1,
-                "atoms": [
-                    0,
-                    1
-                ]
-            },
-            {
-                "type": 2,
-                "atoms": [
-                    1,
-                    2
-                ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    2,
-                    3
-                ]
-            },
-            {
-                "type": 2,
-                "atoms": [
-                    3,
-                    4
-                ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    4,
-                    5
-                ]
-            },
-            {
-                "type": 2,
-                "atoms": [
-                    6,
-                    7
-                ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    7,
-                    8
-                ]
-            },
-            {
-                "type": 2,
-                "atoms": [
-                    8,
-                    9
-                ]
-            },
-            {
-                "type": 2,
-                "atoms": [
-                    0,
-                    5
-                ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    0,
-                    9
-                ]
-            },
-            {
-                "type": 1,
-                "atoms": [
-                    5,
-                    6
-                ]
-            }
-        ]
-    },
-    "mol1": {
-        "type": "molecule",
-        "atoms": [
-            {
-                "label": "C",
-                "location": [
-                    9.92827606201172,
-                    2.249971866607666,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    9.062226295471192,
-                    1.7499775886535645,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    9.062226295471192,
-                    0.7499902248382568,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    9.92827606201172,
-                    0.2499966621398926,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    10.794326782226565,
-                    0.7499902248382568,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    10.794326782226565,
-                    1.7499775886535645,
-                    0.0
-                ]
-            },
-            {
-                "label": "C",
-                "location": [
-                    8.196298599243164,
-                    0.2499966621398926,
-                    0.0
-                ],
-                "stereoLabel": "&1"
-            },
-            {
-                "label": "C",
-                "location": [
-                    7.3302483558654789,
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diff --git a/api/tests/integration/tests/layout/ref/932-agents.ket b/api/tests/integration/tests/layout/ref/932-agents.ket
index 27b827673f..a579fbfeb9 100644
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diff --git a/api/tests/integration/tests/layout/ref/reaction_layout.rdf b/api/tests/integration/tests/layout/ref/reaction_layout.rdf
index b1bbfeebe5..46f3e0097b 100644
--- a/api/tests/integration/tests/layout/ref/reaction_layout.rdf
+++ b/api/tests/integration/tests/layout/ref/reaction_layout.rdf
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   8  7  0  0  0  0  0  0  0  0999 V2000
-    0.0000    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.3856    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.7713    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    4.1569    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    5.5426    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.9282    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    8.3138    1.2000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
-    4.1569   -1.2000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3000    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6856    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.0713    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4569    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.8426    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.2282    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.6138    1.2000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4569   -1.2000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0
@@ -30,12 +30,12 @@ $MOL
   -INDIGO-01000000002D
 
   6  6  0  0  0  0  0  0  0  0999 V2000
-   12.4995    1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.1138    0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.1138   -0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   12.4995   -1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   13.8851   -0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   13.8851    0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.5995    1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.2138    0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.2138   -0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.5995   -1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.9851   -0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.9851    0.8000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  2  0  0  0  0
   3  4  1  0  0  0  0
@@ -48,13 +48,13 @@ $MOL
   -INDIGO-01000000002D
 
   7  6  0  0  0  0  0  0  0  0999 V2000
-   17.4851    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   18.8708    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   20.2564    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   21.6420    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   23.0277    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   24.4133    1.2000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
-   20.2564   -1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.1851    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.5708    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.9564    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.3420    1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   27.7277    0.4000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   29.1133    1.2000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
+   24.9564   -1.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0
@@ -67,13 +67,13 @@ $MOL
   -INDIGO-01000000002D
 
   7  7  0  0  0  0  0  0  0  0999 V2000
-   26.4133    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   27.2133    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   28.8133    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   29.6133    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   28.8133   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   27.2133   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   31.2133    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   32.7133    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.5133    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.1133    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.9133    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.1133   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   33.5133   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   37.5133    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  2  0  0  0  0
   3  4  1  0  0  0  0
diff --git a/api/tests/integration/tests/layout/ref/test1.rxn b/api/tests/integration/tests/layout/ref/test1.rxn
index c7b54a78e8..38bf3dff3a 100644
--- a/api/tests/integration/tests/layout/ref/test1.rxn
+++ b/api/tests/integration/tests/layout/ref/test1.rxn
@@ -8,11 +8,11 @@ $MOL
   -INDIGO-01000000002D
 
   5  5  0  0  0  0  0  0  0  0999 V2000
-    0.0000   -1.0928    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-    0.8000    0.2928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.4000    0.2928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.7856   -0.5072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.7856    1.0928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3000   -1.0928    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    2.1000    0.2928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7000    0.2928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.0856   -0.5072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.0856    1.0928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0
@@ -24,28 +24,28 @@ $MOL
   -INDIGO-01000000002D
 
  22 22  0  0  0  0  0  0  0  0999 V2000
-   11.7569   -2.3391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.7569   -0.7391    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-   10.3713    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    8.9856   -0.7391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    8.1856   -2.1247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.3856   -0.7391    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   13.1426    0.0609    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
-   12.3426    1.4465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   13.9426   -1.3247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   14.5282    0.8609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   15.1405    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   13.9159    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   15.9138    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   15.3016   -1.4173    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   16.5261   -1.4173    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   17.2995    0.8609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   17.9118    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   16.6872    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   18.6851    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   18.6851   -1.5391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   20.0708    0.8609    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   20.0708   -0.7391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   15.6569   -2.3391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.6569   -0.7391    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   14.2713    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8856   -0.7391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.0856   -2.1247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.2856   -0.7391    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   17.0426    0.0609    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+   16.2426    1.4465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   17.8426   -1.3247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   18.4282    0.8609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.0405    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   17.8159    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   19.8138    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.2016   -1.4173    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   20.4261   -1.4173    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   21.1995    0.8609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.8118    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   20.5872    2.3391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   22.5851    0.0609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.5851   -1.5391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   23.9708    0.8609    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   23.9708   -0.7391    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  1  0  0  0  0
   2  3  1  0  0  0  0
   3  4  1  0  0  0  0
diff --git a/api/tests/integration/tests/layout/ref/test_sgroup.rxn b/api/tests/integration/tests/layout/ref/test_sgroup.rxn
index 29d5a803c0..8ccdbbdb32 100644
--- a/api/tests/integration/tests/layout/ref/test_sgroup.rxn
+++ b/api/tests/integration/tests/layout/ref/test_sgroup.rxn
@@ -8,12 +8,12 @@ $MOL
   -INDIGO-01000000002D
 
   6  6  0  0  0  0  0  0  0  0999 V2000
-    2.4000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.8000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.8000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.4000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.2000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.1000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  2  0  0  0  0
   2  3  1  0  0  0  0
   3  4  2  0  0  0  0
@@ -24,7 +24,7 @@ M  STY  1   1 DAT
 M  SLB  1   1   1
 M  SAL   1  6   1   2   3   4   5   6
 M  SDT   1 asd                                                                  
-M  SDD   1     2.7571   -0.8839    DA    ALL  1       1  
+M  SDD   1     4.0571   -0.8839    DA    ALL  1       1  
 M  SED   1 asd
 M  END
 $MOL
@@ -32,12 +32,12 @@ $MOL
   -INDIGO-01000000002D
 
   6  6  0  0  0  0  0  0  0  0999 V2000
-    9.2000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.6000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.8000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.6000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.2000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   10.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.1000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.5000    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.7000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.5000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.1000   -1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.9000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1  2  2  0  0  0  0
   2  3  1  0  0  0  0
   3  4  2  0  0  0  0
@@ -48,6 +48,6 @@ M  STY  1   1 DAT
 M  SLB  1   1   1
 M  SAL   1  6   1   2   3   4   5   6
 M  SDT   1 AAA                                                                  
-M  SDD   1     6.3376   -2.0277    DAU   ALL  1       1  
+M  SDD   1    10.2376   -2.0277    DAU   ALL  1       1  
 M  SED   1 BBBBB
 M  END
diff --git a/core/indigo-core/layout/molecule_layout.h b/core/indigo-core/layout/molecule_layout.h
index ce1f71ecf1..d52920acce 100644
--- a/core/indigo-core/layout/molecule_layout.h
+++ b/core/indigo-core/layout/molecule_layout.h
@@ -40,6 +40,7 @@ namespace indigo
         {
             LAYOUT_MAX_ITERATION = 20
         };
+        static constexpr float DEFAULT_BOND_LENGTH = 1.6f;
 
         explicit MoleculeLayout(BaseMolecule& molecule, bool smart_layout = false);
 
diff --git a/core/indigo-core/layout/reaction_layout.h b/core/indigo-core/layout/reaction_layout.h
index c33b6eb4e8..b6488c7a58 100644
--- a/core/indigo-core/layout/reaction_layout.h
+++ b/core/indigo-core/layout/reaction_layout.h
@@ -17,6 +17,7 @@
  ***************************************************************************/
 
 #ifndef __reaction_layout__
+#define __reaction_layout__
 
 #include "layout/metalayout.h"
 #include "reaction/base_reaction.h"
@@ -33,9 +34,12 @@ namespace indigo
     public:
         explicit ReactionLayout(BaseReaction& r, bool smart_layout = false);
 
+        static constexpr float DEFAULT_HOR_INTERVAL_FACTOR = 1.4f;
+
         void make();
 
         float bond_length;
+        float atom_label_width;
         float plus_interval_factor;
         float arrow_interval_factor;
         float horizontal_interval_factor;
@@ -45,8 +49,8 @@ namespace indigo
         layout_orientation_value layout_orientation;
 
     private:
-        Metalayout::LayoutItem& _pushMol(Metalayout::LayoutLine& line, int id, bool is_agent = false);
-        Metalayout::LayoutItem& _pushSpace(Metalayout::LayoutLine& line, float size);
+        void _pushMol(Metalayout::LayoutLine& line, int id, bool is_agent = false);
+        void _pushSpace(Metalayout::LayoutLine& line, float size);
         BaseMolecule& _getMol(int id);
         void _shiftMol(const Metalayout::LayoutItem& item, const Vec2f& pos);
         void _make();
diff --git a/core/indigo-core/layout/src/reaction_layout.cpp b/core/indigo-core/layout/src/reaction_layout.cpp
index 0578f0a9ef..34eb55eda6 100644
--- a/core/indigo-core/layout/src/reaction_layout.cpp
+++ b/core/indigo-core/layout/src/reaction_layout.cpp
@@ -20,12 +20,13 @@
 #include "layout/molecule_layout.h"
 #include "molecule/molecule.h"
 #include "reaction/reaction.h"
+#include <stdio.h>
 
 using namespace indigo;
 
 ReactionLayout::ReactionLayout(BaseReaction& r, bool smart_layout)
-    : bond_length(1), plus_interval_factor(2), arrow_interval_factor(2), preserve_molecule_layout(false), _r(r), _smart_layout(smart_layout),
-      horizontal_interval_factor(0.5f)
+    : bond_length(MoleculeLayout::DEFAULT_BOND_LENGTH), plus_interval_factor(1), arrow_interval_factor(2), preserve_molecule_layout(false), _r(r),
+      _smart_layout(smart_layout), horizontal_interval_factor(DEFAULT_HOR_INTERVAL_FACTOR), atom_label_width(1.3f)
 {
     max_iterations = 0;
 }
@@ -53,7 +54,7 @@ void ReactionLayout::make()
     {
         bool single_atom = _getMol(i).vertexCount() == 1;
         if (i != _r.reactantBegin())
-            _pushSpace(line, plus_interval_factor + (single_atom ? bond_length : kHalfBondLength));
+            _pushSpace(line, plus_interval_factor);
         _pushMol(line, i);
     }
 
@@ -78,7 +79,7 @@ void ReactionLayout::make()
     {
         bool single_atom = _getMol(i).vertexCount() == 1;
         if (i != _r.productBegin())
-            _pushSpace(line, plus_interval_factor + (single_atom ? bond_length : 0));
+            _pushSpace(line, plus_interval_factor);
         _pushMol(line, i);
     }
 
@@ -93,10 +94,11 @@ void ReactionLayout::make()
     _ml.process();
 }
 
-Metalayout::LayoutItem& ReactionLayout::_pushMol(Metalayout::LayoutLine& line, int id, bool is_agent)
+void ReactionLayout::_pushMol(Metalayout::LayoutLine& line, int id, bool is_agent)
 {
-    const int kMaxSymbols = 3;
-    const auto kMinHeight = bond_length / 8;
+    // Molecule label alligned to atom center by non-hydrogen
+    // Hydrogen may be at left or at right H2O, PH3 - so add space before and after molecule
+    _pushSpace(line, atom_label_width);
     Metalayout::LayoutItem& item = line.items.push();
     item.type = 0;
     item.fragment = true;
@@ -108,32 +110,18 @@ Metalayout::LayoutItem& ReactionLayout::_pushMol(Metalayout::LayoutLine& line, i
     }
 
     Rect2f bbox;
-    if (mol.vertexCount() == 1)
-    {
-        int max_h = mol.getAtomMaxH(0);
-        int mult = max_h + 1;
-        if (mult > kMaxSymbols)
-            mult = kMaxSymbols;
-        item.minScaledSize.set(0, kMinHeight);
-        mol.getBoundingBox(bbox, Vec2f(bond_length * mult, bond_length));
-    }
-    else
-    {
-        mol.getBoundingBox(bbox, Vec2f(bond_length, bond_length));
-        item.minScaledSize.set(bond_length, bond_length);
-    }
+    mol.getBoundingBox(bbox);
     item.min.copy(bbox.leftBottom());
     item.max.copy(bbox.rightTop());
-    return item;
+    _pushSpace(line, atom_label_width);
 }
 
-Metalayout::LayoutItem& ReactionLayout::_pushSpace(Metalayout::LayoutLine& line, float size)
+void ReactionLayout::_pushSpace(Metalayout::LayoutLine& line, float size)
 {
     Metalayout::LayoutItem& item = line.items.push();
     item.type = 1;
     item.fragment = false;
     item.scaledSize.set(size, 0);
-    return item;
 }
 
 BaseMolecule& ReactionLayout::_getMol(int id)