From 236a99ac1c26bcc056fb08c8c79f9abfda71ba55 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Fri, 19 Jun 2026 21:27:15 +0200
Subject: [PATCH 01/10] chore: add SMILEIDX for PAPC

---
 .../membrane/PAPC/mappingPAPCcharmm.yaml      | 56 ++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml b/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
index 90f44af2b..aab52b128 100644
--- a/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
+++ b/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
@@ -1,6 +1,7 @@
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 23
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -10,16 +11,20 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
+  SMILEIDX: 24
 # sn-1 
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
+  SMILEIDX: 25
 M_G1C2O1_M:
   ATOMNAME: O32
   FRAGMENT: sn-1
+  SMILEIDX: 26
 M_G1C3_M:
   ATOMNAME: C32
   FRAGMENT: sn-1
+  SMILEIDX: 27
 M_G1C3H1_M:
   ATOMNAME: H2X
   FRAGMENT: sn-1
@@ -28,7 +33,8 @@ M_G1C3H2_M:
   FRAGMENT: sn-1
 M_G1C4_M:
   ATOMNAME: C33
-  FRAGMENT: sn-1
+  FRAGMENT: s8n-1
+  SMILEIDX: 28
 M_G1C4H1_M:
   ATOMNAME: H3X
   FRAGMENT: sn-1
@@ -38,6 +44,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C34
   FRAGMENT: sn-1
+  SMILEIDX: 29
 M_G1C5H1_M:
   ATOMNAME: H4X
   FRAGMENT: sn-1
@@ -47,6 +54,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C35
   FRAGMENT: sn-1
+  SMILEIDX: 30
 M_G1C6H1_M:
   ATOMNAME: H5X
   FRAGMENT: sn-1
@@ -56,6 +64,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C36
   FRAGMENT: sn-1
+  SMILEIDX: 31
 M_G1C7H1_M:
   ATOMNAME: H6X
   FRAGMENT: sn-1
@@ -65,6 +74,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C37
   FRAGMENT: sn-1
+  SMILEIDX: 32
 M_G1C8H1_M:
   ATOMNAME: H7X
   FRAGMENT: sn-1
@@ -74,6 +84,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C38
   FRAGMENT: sn-1
+  SMILEIDX: 33
 M_G1C9H1_M:
   ATOMNAME: H8X
   FRAGMENT: sn-1
@@ -83,6 +94,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C39
   FRAGMENT: sn-1
+  SMILEIDX: 34
 M_G1C10H1_M:
   ATOMNAME: H9X
   FRAGMENT: sn-1
@@ -92,6 +104,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C310
   FRAGMENT: sn-1
+  SMILEIDX: 35
 M_G1C11H1_M:
   ATOMNAME: H10X
   FRAGMENT: sn-1
@@ -101,6 +114,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C311
   FRAGMENT: sn-1
+  SMILEIDX: 36
 M_G1C12H1_M:
   ATOMNAME: H11X
   FRAGMENT: sn-1
@@ -110,6 +124,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C312
   FRAGMENT: sn-1
+  SMILEIDX: 37
 M_G1C13H1_M:
   ATOMNAME: H12X
   FRAGMENT: sn-1
@@ -119,6 +134,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C313
   FRAGMENT: sn-1
+  SMILEIDX: 38
 M_G1C14H1_M:
   ATOMNAME: H13X
   FRAGMENT: sn-1
@@ -128,6 +144,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C314
   FRAGMENT: sn-1
+  SMILEIDX: 39
 M_G1C15H1_M:
   ATOMNAME: H14X
   FRAGMENT: sn-1
@@ -137,6 +154,7 @@ M_G1C15H2_M:
 M_G1C16_M:
   ATOMNAME: C315
   FRAGMENT: sn-1
+  SMILEIDX: 40
 M_G1C16H1_M:
   ATOMNAME: H15X
   FRAGMENT: sn-1
@@ -146,6 +164,7 @@ M_G1C16H2_M:
 M_G1C17_M:
   ATOMNAME: C316
   FRAGMENT: sn-1
+  SMILEIDX: 31
 M_G1C17H1_M:
   ATOMNAME: H16X
   FRAGMENT: sn-1
@@ -159,21 +178,26 @@ M_G1C17H3_M:
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 22
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 21
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 20
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 19
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 18
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -183,6 +207,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 17
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -192,6 +217,7 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 16
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
@@ -201,18 +227,21 @@ M_G2C5H2_M:
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 15
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 14
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 13
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
@@ -222,18 +251,21 @@ M_G2C8H2_M:
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 12
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 11
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 10
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
@@ -243,18 +275,21 @@ M_G2C11H2_M:
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 9
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 8
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 7
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
@@ -264,18 +299,21 @@ M_G2C14H2_M:
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 6
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 5
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 4
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
@@ -285,6 +323,7 @@ M_G2C17H2_M:
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 3
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
@@ -294,6 +333,7 @@ M_G2C18H2_M:
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 2
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -303,6 +343,7 @@ M_G2C19H2_M:
 M_G2C20_M:
   ATOMNAME: C219
   FRAGMENT: sn-2
+  SMILEIDX: 1
 M_G2C20H1_M:
   ATOMNAME: H19R
   FRAGMENT: sn-2
@@ -312,6 +353,7 @@ M_G2C20H2_M:
 M_G2C21_M:
   ATOMNAME: C220
   FRAGMENT: sn-2
+  SMILEIDX: 0
 M_G2C21H1_M:
   ATOMNAME: H20R
   FRAGMENT: sn-2
@@ -325,6 +367,7 @@ M_G2C21H3_M:
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 32
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -334,22 +377,28 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
+  SMILEIDX: 33
 # headgroup
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 34
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 35
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 36
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 37
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 38
 M_G3C4H1_M:
   ATOMNAME: H11A
   FRAGMENT: headgroup
@@ -359,6 +408,7 @@ M_G3C4H2_M:
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 39
 M_G3C5H1_M:
   ATOMNAME: H12A
   FRAGMENT: headgroup
@@ -368,9 +418,11 @@ M_G3C5H2_M:
 M_G3N6_M:
   ATOMNAME: N
   FRAGMENT: headgroup
+  SMILEIDX: 40
 M_G3N6C1_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 41
 M_G3N6C1H1_M:
   ATOMNAME: H13A
   FRAGMENT: headgroup
@@ -383,6 +435,7 @@ M_G3N6C1H3_M:
 M_G3N6C2_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 42
 M_G3N6C2H1_M:
   ATOMNAME: H14A
   FRAGMENT: headgroup
@@ -395,6 +448,7 @@ M_G3N6C2H3_M:
 M_G3N6C3_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 43
 M_G3N6C3H1_M:
   ATOMNAME: H15A
   FRAGMENT: headgroup

From ce80132f0bc2f80ec3cb0fb6bdf3c994ee6cb47e Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Fri, 19 Jun 2026 21:28:41 +0200
Subject: [PATCH 02/10] fix: typo in PAPC mapping

---
 Molecules/membrane/PAPC/mappingPAPCcharmm.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml b/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
index aab52b128..8ea9a08f3 100644
--- a/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
+++ b/Molecules/membrane/PAPC/mappingPAPCcharmm.yaml
@@ -33,7 +33,7 @@ M_G1C3H2_M:
   FRAGMENT: sn-1
 M_G1C4_M:
   ATOMNAME: C33
-  FRAGMENT: s8n-1
+  FRAGMENT: sn-1
   SMILEIDX: 28
 M_G1C4H1_M:
   ATOMNAME: H3X

From e11bec4d8ea3da0596e42d478864648ee01df9ee Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 09:57:37 +0200
Subject: [PATCH 03/10] fix: add PSF,PDB,DCD to gitignore

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.gitignore b/.gitignore
index e1116694c..0c8a6e4a8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,7 @@
+# All
+Simulations/**/*.psf
+Simulations/**/*.dcd
+Simulations/**/*.pdb
 # macOS
 .DS_Store
 .AppleDouble

From 0e2b233cd89ce41db73be434dfef3da42d3be299 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 09:58:05 +0200
Subject: [PATCH 04/10] feat: add SMILEIDX to PDPC and PILPC (automatic)

---
 .../membrane/PDPC/mappingPDPCcharmm.yaml      | 60 +++++++++++++++++--
 .../membrane/PILPC/mappingPiLPCcharmm.yaml    | 52 ++++++++++++++++
 2 files changed, 108 insertions(+), 4 deletions(-)

diff --git a/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml b/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml
index 39682dc5d..b7affdd39 100644
--- a/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml
+++ b/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml
@@ -1,6 +1,7 @@
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 18
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -10,16 +11,19 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
-# sn-1 
+  SMILEIDX: 17
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
+  SMILEIDX: 15
 M_G1C2O1_M:
   ATOMNAME: O32
   FRAGMENT: sn-1
+  SMILEIDX: 16
 M_G1C3_M:
   ATOMNAME: C32
   FRAGMENT: sn-1
+  SMILEIDX: 14
 M_G1C3H1_M:
   ATOMNAME: H2X
   FRAGMENT: sn-1
@@ -29,6 +33,7 @@ M_G1C3H2_M:
 M_G1C4_M:
   ATOMNAME: C33
   FRAGMENT: sn-1
+  SMILEIDX: 13
 M_G1C4H1_M:
   ATOMNAME: H3X
   FRAGMENT: sn-1
@@ -38,6 +43,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C34
   FRAGMENT: sn-1
+  SMILEIDX: 12
 M_G1C5H1_M:
   ATOMNAME: H4X
   FRAGMENT: sn-1
@@ -47,6 +53,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C35
   FRAGMENT: sn-1
+  SMILEIDX: 11
 M_G1C6H1_M:
   ATOMNAME: H5X
   FRAGMENT: sn-1
@@ -56,6 +63,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C36
   FRAGMENT: sn-1
+  SMILEIDX: 10
 M_G1C7H1_M:
   ATOMNAME: H6X
   FRAGMENT: sn-1
@@ -65,6 +73,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C37
   FRAGMENT: sn-1
+  SMILEIDX: 9
 M_G1C8H1_M:
   ATOMNAME: H7X
   FRAGMENT: sn-1
@@ -74,6 +83,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C38
   FRAGMENT: sn-1
+  SMILEIDX: 8
 M_G1C9H1_M:
   ATOMNAME: H8X
   FRAGMENT: sn-1
@@ -83,6 +93,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C39
   FRAGMENT: sn-1
+  SMILEIDX: 7
 M_G1C10H1_M:
   ATOMNAME: H9X
   FRAGMENT: sn-1
@@ -92,6 +103,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C310
   FRAGMENT: sn-1
+  SMILEIDX: 6
 M_G1C11H1_M:
   ATOMNAME: H10X
   FRAGMENT: sn-1
@@ -101,6 +113,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C311
   FRAGMENT: sn-1
+  SMILEIDX: 5
 M_G1C12H1_M:
   ATOMNAME: H11X
   FRAGMENT: sn-1
@@ -110,6 +123,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C312
   FRAGMENT: sn-1
+  SMILEIDX: 4
 M_G1C13H1_M:
   ATOMNAME: H12X
   FRAGMENT: sn-1
@@ -119,6 +133,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C313
   FRAGMENT: sn-1
+  SMILEIDX: 3
 M_G1C14H1_M:
   ATOMNAME: H13X
   FRAGMENT: sn-1
@@ -128,6 +143,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C314
   FRAGMENT: sn-1
+  SMILEIDX: 2
 M_G1C15H1_M:
   ATOMNAME: H14X
   FRAGMENT: sn-1
@@ -137,6 +153,7 @@ M_G1C15H2_M:
 M_G1C16_M:
   ATOMNAME: C315
   FRAGMENT: sn-1
+  SMILEIDX: 1
 M_G1C16H1_M:
   ATOMNAME: H15X
   FRAGMENT: sn-1
@@ -146,6 +163,7 @@ M_G1C16H2_M:
 M_G1C17_M:
   ATOMNAME: C316
   FRAGMENT: sn-1
+  SMILEIDX: 0
 M_G1C17H1_M:
   ATOMNAME: H16X
   FRAGMENT: sn-1
@@ -155,25 +173,29 @@ M_G1C17H2_M:
 M_G1C17H3_M:
   ATOMNAME: H16Z
   FRAGMENT: sn-1
-# sn-2
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 19
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 32
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 33
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 34
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 35
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -183,6 +205,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 36
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -192,18 +215,21 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 37
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 38
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 39
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
@@ -213,18 +239,21 @@ M_G2C7H2_M:
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 40
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 41
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 42
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
@@ -234,18 +263,21 @@ M_G2C10H2_M:
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 43
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 44
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 45
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
@@ -255,18 +287,21 @@ M_G2C13H2_M:
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 46
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 47
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 48
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
@@ -276,18 +311,21 @@ M_G2C16H2_M:
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 49
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 50
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 51
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -297,18 +335,21 @@ M_G2C19H2_M:
 M_G2C20_M:
   ATOMNAME: C219
   FRAGMENT: sn-2
+  SMILEIDX: 52
 M_G2C20H1_M:
   ATOMNAME: H19R
   FRAGMENT: sn-2
 M_G2C21_M:
   ATOMNAME: C220
   FRAGMENT: sn-2
+  SMILEIDX: 53
 M_G2C21H1_M:
   ATOMNAME: H20R
   FRAGMENT: sn-2
 M_G2C22_M:
   ATOMNAME: C221
   FRAGMENT: sn-2
+  SMILEIDX: 54
 M_G2C22H1_M:
   ATOMNAME: H21R
   FRAGMENT: sn-2
@@ -318,6 +359,7 @@ M_G2C22H2_M:
 M_G2C23_M:
   ATOMNAME: C222
   FRAGMENT: sn-2
+  SMILEIDX: 55
 M_G2C23H1_M:
   ATOMNAME: H22R
   FRAGMENT: sn-2
@@ -327,10 +369,10 @@ M_G2C23H2_M:
 M_G2C23H3_M:
   ATOMNAME: H22T
   FRAGMENT: sn-2
-# bb
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 20
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -340,22 +382,27 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
-# headgroup
+  SMILEIDX: 21
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 22
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 24
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 23
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 25
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 26
 M_G3C4H1_M:
   ATOMNAME: H11A
   FRAGMENT: headgroup
@@ -365,6 +412,7 @@ M_G3C4H2_M:
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 27
 M_G3C5H1_M:
   ATOMNAME: H12A
   FRAGMENT: headgroup
@@ -374,9 +422,11 @@ M_G3C5H2_M:
 M_G3N6_M:
   ATOMNAME: N
   FRAGMENT: headgroup
+  SMILEIDX: 28
 M_G3N6C1_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 29
 M_G3N6C1H1_M:
   ATOMNAME: H13A
   FRAGMENT: headgroup
@@ -389,6 +439,7 @@ M_G3N6C1H3_M:
 M_G3N6C2_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 30
 M_G3N6C2H1_M:
   ATOMNAME: H14A
   FRAGMENT: headgroup
@@ -401,6 +452,7 @@ M_G3N6C2H3_M:
 M_G3N6C3_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 31
 M_G3N6C3H1_M:
   ATOMNAME: H15A
   FRAGMENT: headgroup
diff --git a/Molecules/membrane/PILPC/mappingPiLPCcharmm.yaml b/Molecules/membrane/PILPC/mappingPiLPCcharmm.yaml
index c211eea36..1e5c77d89 100644
--- a/Molecules/membrane/PILPC/mappingPiLPCcharmm.yaml
+++ b/Molecules/membrane/PILPC/mappingPiLPCcharmm.yaml
@@ -1,6 +1,7 @@
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 18
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -10,15 +11,19 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
+  SMILEIDX: 17
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
+  SMILEIDX: 15
 M_G1C2O1_M:
   ATOMNAME: O32
   FRAGMENT: sn-1
+  SMILEIDX: 16
 M_G1C3_M:
   ATOMNAME: C32
   FRAGMENT: sn-1
+  SMILEIDX: 14
 M_G1C3H1_M:
   ATOMNAME: H2X
   FRAGMENT: sn-1
@@ -28,6 +33,7 @@ M_G1C3H2_M:
 M_G1C4_M:
   ATOMNAME: C33
   FRAGMENT: sn-1
+  SMILEIDX: 13
 M_G1C4H1_M:
   ATOMNAME: H3X
   FRAGMENT: sn-1
@@ -37,6 +43,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C34
   FRAGMENT: sn-1
+  SMILEIDX: 12
 M_G1C5H1_M:
   ATOMNAME: H4X
   FRAGMENT: sn-1
@@ -46,6 +53,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C35
   FRAGMENT: sn-1
+  SMILEIDX: 11
 M_G1C6H1_M:
   ATOMNAME: H5X
   FRAGMENT: sn-1
@@ -55,6 +63,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C36
   FRAGMENT: sn-1
+  SMILEIDX: 10
 M_G1C7H1_M:
   ATOMNAME: H6X
   FRAGMENT: sn-1
@@ -64,6 +73,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C37
   FRAGMENT: sn-1
+  SMILEIDX: 9
 M_G1C8H1_M:
   ATOMNAME: H7X
   FRAGMENT: sn-1
@@ -73,6 +83,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C38
   FRAGMENT: sn-1
+  SMILEIDX: 8
 M_G1C9H1_M:
   ATOMNAME: H8X
   FRAGMENT: sn-1
@@ -82,6 +93,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C39
   FRAGMENT: sn-1
+  SMILEIDX: 7
 M_G1C10H1_M:
   ATOMNAME: H9X
   FRAGMENT: sn-1
@@ -91,6 +103,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C310
   FRAGMENT: sn-1
+  SMILEIDX: 6
 M_G1C11H1_M:
   ATOMNAME: H10X
   FRAGMENT: sn-1
@@ -100,6 +113,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C311
   FRAGMENT: sn-1
+  SMILEIDX: 5
 M_G1C12H1_M:
   ATOMNAME: H11X
   FRAGMENT: sn-1
@@ -109,6 +123,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C312
   FRAGMENT: sn-1
+  SMILEIDX: 4
 M_G1C13H1_M:
   ATOMNAME: H12X
   FRAGMENT: sn-1
@@ -118,6 +133,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C313
   FRAGMENT: sn-1
+  SMILEIDX: 3
 M_G1C14H1_M:
   ATOMNAME: H13X
   FRAGMENT: sn-1
@@ -127,6 +143,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C314
   FRAGMENT: sn-1
+  SMILEIDX: 2
 M_G1C15H1_M:
   ATOMNAME: H14X
   FRAGMENT: sn-1
@@ -136,6 +153,7 @@ M_G1C15H2_M:
 M_G1C16_M:
   ATOMNAME: C315
   FRAGMENT: sn-1
+  SMILEIDX: 1
 M_G1C16H1_M:
   ATOMNAME: H15X
   FRAGMENT: sn-1
@@ -145,6 +163,7 @@ M_G1C16H2_M:
 M_G1C17_M:
   ATOMNAME: C316
   FRAGMENT: sn-1
+  SMILEIDX: 0
 M_G1C17H1_M:
   ATOMNAME: H16X
   FRAGMENT: sn-1
@@ -157,21 +176,26 @@ M_G1C17H3_M:
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 19
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 32
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 33
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 34
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 35
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -181,6 +205,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 36
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -190,6 +215,7 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 37
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
@@ -199,6 +225,7 @@ M_G2C5H2_M:
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 38
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
@@ -208,18 +235,21 @@ M_G2C6H2_M:
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 39
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 40
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 41
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
@@ -229,18 +259,21 @@ M_G2C9H2_M:
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 42
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 43
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 44
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
@@ -250,6 +283,7 @@ M_G2C12H2_M:
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 45
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
@@ -259,6 +293,7 @@ M_G2C13H2_M:
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 46
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
@@ -268,6 +303,7 @@ M_G2C14H2_M:
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 47
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
@@ -277,6 +313,7 @@ M_G2C15H2_M:
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 48
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
@@ -286,6 +323,7 @@ M_G2C16H2_M:
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 49
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
@@ -295,6 +333,7 @@ M_G2C17H2_M:
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 50
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
@@ -304,6 +343,7 @@ M_G2C18H2_M:
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 51
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -316,6 +356,7 @@ M_G2C19H3_M:
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 20
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -325,21 +366,27 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
+  SMILEIDX: 21
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 22
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 23
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 24
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 25
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 26
 M_G3C4H1_M:
   ATOMNAME: H11A
   FRAGMENT: headgroup
@@ -349,6 +396,7 @@ M_G3C4H2_M:
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 27
 M_G3C5H1_M:
   ATOMNAME: H12A
   FRAGMENT: headgroup
@@ -358,9 +406,11 @@ M_G3C5H2_M:
 M_G3N6_M:
   ATOMNAME: N
   FRAGMENT: headgroup
+  SMILEIDX: 28
 M_G3N6C1_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 29
 M_G3N6C1H1_M:
   ATOMNAME: H13A
   FRAGMENT: headgroup
@@ -373,6 +423,7 @@ M_G3N6C1H3_M:
 M_G3N6C2_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 30
 M_G3N6C2H1_M:
   ATOMNAME: H14A
   FRAGMENT: headgroup
@@ -385,6 +436,7 @@ M_G3N6C2H3_M:
 M_G3N6C3_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 31
 M_G3N6C3H1_M:
   ATOMNAME: H15A
   FRAGMENT: headgroup

From a1d40857aa1439468de4ddecd5d35d10c0a635e1 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 10:02:43 +0200
Subject: [PATCH 05/10] feat: add SMILEIDX to CER180 and SDPC

---
 .../membrane/CER180/mappingCER180charmm.yaml  | 40 ++++++++++++
 .../membrane/SDPC/mappingSDPCcharmm.yaml      | 63 +++++++++++++++++--
 2 files changed, 98 insertions(+), 5 deletions(-)

diff --git a/Molecules/membrane/CER180/mappingCER180charmm.yaml b/Molecules/membrane/CER180/mappingCER180charmm.yaml
index 749379f5b..ceda46697 100644
--- a/Molecules/membrane/CER180/mappingCER180charmm.yaml
+++ b/Molecules/membrane/CER180/mappingCER180charmm.yaml
@@ -1,30 +1,35 @@
 M_G1_M:
   ATOMNAME: C3S
   FRAGMENT: backbone
+  SMILEIDX: 23
 M_G1H2_M:
   ATOMNAME: H3S
   FRAGMENT: backbone
 M_G1O1_M:
   ATOMNAME: O3
   FRAGMENT: backbone
+  SMILEIDX: 39
 M_G1O1H1_M:
   ATOMNAME: HO3
   FRAGMENT: backbone
 M_G1C1_M:
   ATOMNAME: C4S
   FRAGMENT: sn-1
+  SMILEIDX: 24
 M_G1C1H1_M:
   ATOMNAME: H4S
   FRAGMENT: sn-1
 M_G1C2_M:
   ATOMNAME: C5S
   FRAGMENT: sn-1
+  SMILEIDX: 25
 M_G1C2H1_M:
   ATOMNAME: H5S
   FRAGMENT: sn-1
 M_G1C3_M:
   ATOMNAME: C6S
   FRAGMENT: sn-1
+  SMILEIDX: 26
 M_G1C3H1_M:
   ATOMNAME: H6S
   FRAGMENT: sn-1
@@ -34,6 +39,7 @@ M_G1C3H2_M:
 M_G1C4_M:
   ATOMNAME: C7S
   FRAGMENT: sn-1
+  SMILEIDX: 27
 M_G1C4H1_M:
   ATOMNAME: H7S
   FRAGMENT: sn-1
@@ -43,6 +49,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C8S
   FRAGMENT: sn-1
+  SMILEIDX: 28
 M_G1C5H1_M:
   ATOMNAME: H8S
   FRAGMENT: sn-1
@@ -52,6 +59,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C9S
   FRAGMENT: sn-1
+  SMILEIDX: 29
 M_G1C6H1_M:
   ATOMNAME: H9S
   FRAGMENT: sn-1
@@ -61,6 +69,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C10S
   FRAGMENT: sn-1
+  SMILEIDX: 30
 M_G1C7H1_M:
   ATOMNAME: H10S
   FRAGMENT: sn-1
@@ -70,6 +79,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C11S
   FRAGMENT: sn-1
+  SMILEIDX: 31
 M_G1C8H1_M:
   ATOMNAME: H11S
   FRAGMENT: sn-1
@@ -79,6 +89,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C12S
   FRAGMENT: sn-1
+  SMILEIDX: 32
 M_G1C9H1_M:
   ATOMNAME: H12S
   FRAGMENT: sn-1
@@ -88,6 +99,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C13S
   FRAGMENT: sn-1
+  SMILEIDX: 33
 M_G1C10H1_M:
   ATOMNAME: H13S
   FRAGMENT: sn-1
@@ -97,6 +109,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C14S
   FRAGMENT: sn-1
+  SMILEIDX: 34
 M_G1C11H1_M:
   ATOMNAME: H14S
   FRAGMENT: sn-1
@@ -106,6 +119,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C15S
   FRAGMENT: sn-1
+  SMILEIDX: 35
 M_G1C12H1_M:
   ATOMNAME: H15S
   FRAGMENT: sn-1
@@ -115,6 +129,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C16S
   FRAGMENT: sn-1
+  SMILEIDX: 36
 M_G1C13H1_M:
   ATOMNAME: H16S
   FRAGMENT: sn-1
@@ -124,6 +139,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C17S
   FRAGMENT: sn-1
+  SMILEIDX: 37
 M_G1C14H1_M:
   ATOMNAME: H17S
   FRAGMENT: sn-1
@@ -133,6 +149,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C18S
   FRAGMENT: sn-1
+  SMILEIDX: 38
 M_G1C15H1_M:
   ATOMNAME: H18S
   FRAGMENT: sn-1
@@ -145,24 +162,29 @@ M_G1C15H3_M:
 M_G2_M:
   ATOMNAME: C2S
   FRAGMENT: backbone
+  SMILEIDX: 20
 M_G2H1_M:
   ATOMNAME: H2S
   FRAGMENT: backbone
 M_G2N1_M:
   ATOMNAME: NF
   FRAGMENT: backbone
+  SMILEIDX: 19
 M_G2N1H1_M:
   ATOMNAME: HNF
   FRAGMENT: backbone
 M_G2C2_M:
   ATOMNAME: C1F
   FRAGMENT: sn-2
+  SMILEIDX: 17
 M_G2C2O1_M:
   ATOMNAME: OF
   FRAGMENT: sn-2
+  SMILEIDX: 18
 M_G2C3_M:
   ATOMNAME: C2F
   FRAGMENT: sn-2
+  SMILEIDX: 16
 M_G2C3H1_M:
   ATOMNAME: H2F
   FRAGMENT: sn-2
@@ -172,6 +194,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C3F
   FRAGMENT: sn-2
+  SMILEIDX: 15
 M_G2C4H1_M:
   ATOMNAME: H3F
   FRAGMENT: sn-2
@@ -181,6 +204,7 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C4F
   FRAGMENT: sn-2
+  SMILEIDX: 14
 M_G2C5H1_M:
   ATOMNAME: H4F
   FRAGMENT: sn-2
@@ -190,6 +214,7 @@ M_G2C5H2_M:
 M_G2C6_M:
   ATOMNAME: C5F
   FRAGMENT: sn-2
+  SMILEIDX: 13
 M_G2C6H1_M:
   ATOMNAME: H5F
   FRAGMENT: sn-2
@@ -199,6 +224,7 @@ M_G2C6H2_M:
 M_G2C7_M:
   ATOMNAME: C6F
   FRAGMENT: sn-2
+  SMILEIDX: 12
 M_G2C7H1_M:
   ATOMNAME: H6F
   FRAGMENT: sn-2
@@ -208,6 +234,7 @@ M_G2C7H2_M:
 M_G2C8_M:
   ATOMNAME: C7F
   FRAGMENT: sn-2
+  SMILEIDX: 11
 M_G2C8H1_M:
   ATOMNAME: H7F
   FRAGMENT: sn-2
@@ -217,6 +244,7 @@ M_G2C8H2_M:
 M_G2C9_M:
   ATOMNAME: C8F
   FRAGMENT: sn-2
+  SMILEIDX: 10
 M_G2C9H1_M:
   ATOMNAME: H8F
   FRAGMENT: sn-2
@@ -226,6 +254,7 @@ M_G2C9H2_M:
 M_G2C10_M:
   ATOMNAME: C9F
   FRAGMENT: sn-2
+  SMILEIDX: 9
 M_G2C10H1_M:
   ATOMNAME: H9F
   FRAGMENT: sn-2
@@ -235,6 +264,7 @@ M_G2C10H2_M:
 M_G2C11_M:
   ATOMNAME: C10F
   FRAGMENT: sn-2
+  SMILEIDX: 8
 M_G2C11H1_M:
   ATOMNAME: H10F
   FRAGMENT: sn-2
@@ -244,6 +274,7 @@ M_G2C11H2_M:
 M_G2C12_M:
   ATOMNAME: C11F
   FRAGMENT: sn-2
+  SMILEIDX: 7
 M_G2C12H1_M:
   ATOMNAME: H11F
   FRAGMENT: sn-2
@@ -253,6 +284,7 @@ M_G2C12H2_M:
 M_G2C13_M:
   ATOMNAME: C12F
   FRAGMENT: sn-2
+  SMILEIDX: 6
 M_G2C13H1_M:
   ATOMNAME: H12F
   FRAGMENT: sn-2
@@ -262,6 +294,7 @@ M_G2C13H2_M:
 M_G2C14_M:
   ATOMNAME: C13F
   FRAGMENT: sn-2
+  SMILEIDX: 5
 M_G2C14H1_M:
   ATOMNAME: H13F
   FRAGMENT: sn-2
@@ -271,6 +304,7 @@ M_G2C14H2_M:
 M_G2C15_M:
   ATOMNAME: C14F
   FRAGMENT: sn-2
+  SMILEIDX: 4
 M_G2C15H1_M:
   ATOMNAME: H14F
   FRAGMENT: sn-2
@@ -280,6 +314,7 @@ M_G2C15H2_M:
 M_G2C16_M:
   ATOMNAME: C15F
   FRAGMENT: sn-2
+  SMILEIDX: 3
 M_G2C16H1_M:
   ATOMNAME: H15F
   FRAGMENT: sn-2
@@ -289,6 +324,7 @@ M_G2C16H2_M:
 M_G2C17_M:
   ATOMNAME: C16F
   FRAGMENT: sn-2
+  SMILEIDX: 2
 M_G2C17H1_M:
   ATOMNAME: H16F
   FRAGMENT: sn-2
@@ -298,6 +334,7 @@ M_G2C17H2_M:
 M_G2C18_M:
   ATOMNAME: C17F
   FRAGMENT: sn-2
+  SMILEIDX: 1
 M_G2C18H1_M:
   ATOMNAME: H17F
   FRAGMENT: sn-2
@@ -307,6 +344,7 @@ M_G2C18H2_M:
 M_G2C19_M:
   ATOMNAME: C18F
   FRAGMENT: sn-2
+  SMILEIDX: 0
 M_G2C19H1_M:
   ATOMNAME: H18F
   FRAGMENT: sn-2
@@ -319,6 +357,7 @@ M_G2C19H3_M:
 M_G3_M:
   ATOMNAME: C1S
   FRAGMENT: backbone
+  SMILEIDX: 21
 M_G3H1_M:
   ATOMNAME: H1S
   FRAGMENT: backbone
@@ -328,6 +367,7 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O1
   FRAGMENT: headgroup
+  SMILEIDX: 22
 M_G3O1H1_M:
   ATOMNAME: HO1
   FRAGMENT: headgroup
diff --git a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml
index 8c31f7d2e..5f595b78e 100644
--- a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml
+++ b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml
@@ -1,19 +1,23 @@
-# headgroup
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 24
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 26
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 25
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 27
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 28
 M_G3C4H1_M:
   ATOMNAME: H11A
   FRAGMENT: headgroup
@@ -23,6 +27,7 @@ M_G3C4H2_M:
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 29
 M_G3C5H1_M:
   ATOMNAME: H12A
   FRAGMENT: headgroup
@@ -32,9 +37,11 @@ M_G3C5H2_M:
 M_G3N6_M:
   ATOMNAME: N
   FRAGMENT: headgroup
+  SMILEIDX: 30
 M_G3N6C1_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 31
 M_G3N6C1H1_M:
   ATOMNAME: H13A
   FRAGMENT: headgroup
@@ -47,6 +54,7 @@ M_G3N6C1H3_M:
 M_G3N6C2_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 32
 M_G3N6C2H1_M:
   ATOMNAME: H14A
   FRAGMENT: headgroup
@@ -59,6 +67,7 @@ M_G3N6C2H3_M:
 M_G3N6C3_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 33
 M_G3N6C3H1_M:
   ATOMNAME: H15A
   FRAGMENT: headgroup
@@ -68,10 +77,10 @@ M_G3N6C3H2_M:
 M_G3N6C3H3_M:
   ATOMNAME: H15C
   FRAGMENT: headgroup
-# bb
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 20
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -81,18 +90,22 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
+  SMILEIDX: 19
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 21
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 34
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 22
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -102,16 +115,19 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
-# sn-1
+  SMILEIDX: 23
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
+  SMILEIDX: 17
 M_G1C2O1_M:
   ATOMNAME: O32
   FRAGMENT: sn-1
+  SMILEIDX: 18
 M_G1C3_M:
   ATOMNAME: C32
   FRAGMENT: sn-1
+  SMILEIDX: 16
 M_G1C3H1_M:
   ATOMNAME: H2X
   FRAGMENT: sn-1
@@ -121,6 +137,7 @@ M_G1C3H2_M:
 M_G1C4_M:
   ATOMNAME: C33
   FRAGMENT: sn-1
+  SMILEIDX: 15
 M_G1C4H1_M:
   ATOMNAME: H3X
   FRAGMENT: sn-1
@@ -130,6 +147,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C34
   FRAGMENT: sn-1
+  SMILEIDX: 14
 M_G1C5H1_M:
   ATOMNAME: H4X
   FRAGMENT: sn-1
@@ -139,6 +157,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C35
   FRAGMENT: sn-1
+  SMILEIDX: 13
 M_G1C6H1_M:
   ATOMNAME: H5X
   FRAGMENT: sn-1
@@ -148,6 +167,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C36
   FRAGMENT: sn-1
+  SMILEIDX: 12
 M_G1C7H1_M:
   ATOMNAME: H6X
   FRAGMENT: sn-1
@@ -157,6 +177,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C37
   FRAGMENT: sn-1
+  SMILEIDX: 11
 M_G1C8H1_M:
   ATOMNAME: H7X
   FRAGMENT: sn-1
@@ -166,6 +187,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C38
   FRAGMENT: sn-1
+  SMILEIDX: 10
 M_G1C9H1_M:
   ATOMNAME: H8X
   FRAGMENT: sn-1
@@ -175,6 +197,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C39
   FRAGMENT: sn-1
+  SMILEIDX: 9
 M_G1C10H1_M:
   ATOMNAME: H9X
   FRAGMENT: sn-1
@@ -184,6 +207,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C310
   FRAGMENT: sn-1
+  SMILEIDX: 8
 M_G1C11H1_M:
   ATOMNAME: H10X
   FRAGMENT: sn-1
@@ -193,6 +217,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C311
   FRAGMENT: sn-1
+  SMILEIDX: 7
 M_G1C12H1_M:
   ATOMNAME: H11X
   FRAGMENT: sn-1
@@ -202,6 +227,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C312
   FRAGMENT: sn-1
+  SMILEIDX: 6
 M_G1C13H1_M:
   ATOMNAME: H12X
   FRAGMENT: sn-1
@@ -211,6 +237,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C313
   FRAGMENT: sn-1
+  SMILEIDX: 5
 M_G1C14H1_M:
   ATOMNAME: H13X
   FRAGMENT: sn-1
@@ -220,6 +247,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C314
   FRAGMENT: sn-1
+  SMILEIDX: 4
 M_G1C15H1_M:
   ATOMNAME: H14X
   FRAGMENT: sn-1
@@ -229,6 +257,7 @@ M_G1C15H2_M:
 M_G1C16_M:
   ATOMNAME: C315
   FRAGMENT: sn-1
+  SMILEIDX: 3
 M_G1C16H1_M:
   ATOMNAME: H15X
   FRAGMENT: sn-1
@@ -238,6 +267,7 @@ M_G1C16H2_M:
 M_G1C17_M:
   ATOMNAME: C316
   FRAGMENT: sn-1
+  SMILEIDX: 2
 M_G1C17H1_M:
   ATOMNAME: H16X
   FRAGMENT: sn-1
@@ -247,6 +277,7 @@ M_G1C17H2_M:
 M_G1C18_M:
   ATOMNAME: C317
   FRAGMENT: sn-1
+  SMILEIDX: 1
 M_G1C18H1_M:
   ATOMNAME: H17X
   FRAGMENT: sn-1
@@ -256,6 +287,7 @@ M_G1C18H2_M:
 M_G1C19_M:
   ATOMNAME: C318
   FRAGMENT: sn-1
+  SMILEIDX: 0
 M_G1C19H1_M:
   ATOMNAME: H18X
   FRAGMENT: sn-1
@@ -265,16 +297,18 @@ M_G1C19H2_M:
 M_G1C19H3_M:
   ATOMNAME: H18Z
   FRAGMENT: sn-1
-# sn-2
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 35
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 36
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 37
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -284,6 +318,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 38
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -293,18 +328,21 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 39
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 40
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 41
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
@@ -314,18 +352,21 @@ M_G2C7H2_M:
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 42
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 43
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 44
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
@@ -335,18 +376,21 @@ M_G2C10H2_M:
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 45
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 46
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 47
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
@@ -356,18 +400,21 @@ M_G2C13H2_M:
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 48
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 49
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 50
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
@@ -377,18 +424,21 @@ M_G2C16H2_M:
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 51
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 52
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 53
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -398,18 +448,21 @@ M_G2C19H2_M:
 M_G2C20_M:
   ATOMNAME: C219
   FRAGMENT: sn-2
+  SMILEIDX: 54
 M_G2C20H1_M:
   ATOMNAME: H19R
   FRAGMENT: sn-2
 M_G2C21_M:
   ATOMNAME: C220
   FRAGMENT: sn-2
+  SMILEIDX: 55
 M_G2C21H1_M:
   ATOMNAME: H20R
   FRAGMENT: sn-2
 M_G2C22_M:
   ATOMNAME: C221
   FRAGMENT: sn-2
+  SMILEIDX: 56
 M_G2C22H1_M:
   ATOMNAME: H21R
   FRAGMENT: sn-2
@@ -419,6 +472,7 @@ M_G2C22H2_M:
 M_G2C23_M:
   ATOMNAME: C222
   FRAGMENT: sn-2
+  SMILEIDX: 57
 M_G2C23H1_M:
   ATOMNAME: H22R
   FRAGMENT: sn-2
@@ -428,4 +482,3 @@ M_G2C23H2_M:
 M_G2C23H3_M:
   ATOMNAME: H22T
   FRAGMENT: sn-2
-

From dd50e1a4ecd1e460420a24e230990d316209a471 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 10:03:13 +0200
Subject: [PATCH 06/10] fix: change CER1 to CER180 as it is named in PSF

---
 .../7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml b/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml
index 401408d90..2484cccfc 100644
--- a/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml
+++ b/Simulations/7ee/0dd/7ee0dd27df2a8d15323124198450c6b1f1642702/7ee0dd27df2a8d15323124198450c6b1f1642702/README.yaml
@@ -43,7 +43,7 @@ COMPOSITION:
     - 13
     - 13
   CER180:
-    NAME: CER1
+    NAME: CER180
     MAPPING: mappingCER180charmm.yaml
     COUNT:
     - 5

From bf0d735d9694b0b45b0ede9bdb97cea890b586c8 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 10:16:37 +0200
Subject: [PATCH 07/10] fix: SMILEIDX and neutralized smiles for SAPI24

---
 .../membrane/SAPI24/mappingSAPI24charmm.yaml  | 69 +++++++++++++++++++
 Molecules/membrane/SAPI24/metadata.yaml       |  4 +-
 2 files changed, 71 insertions(+), 2 deletions(-)

diff --git a/Molecules/membrane/SAPI24/mappingSAPI24charmm.yaml b/Molecules/membrane/SAPI24/mappingSAPI24charmm.yaml
index 2763a94ca..4d56b987f 100644
--- a/Molecules/membrane/SAPI24/mappingSAPI24charmm.yaml
+++ b/Molecules/membrane/SAPI24/mappingSAPI24charmm.yaml
@@ -1,6 +1,7 @@
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 20
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -10,15 +11,19 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
+  SMILEIDX: 19
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
+  SMILEIDX: 17
 M_G1C2O1_M:
   ATOMNAME: O32
   FRAGMENT: sn-1
+  SMILEIDX: 18
 M_G1C3_M:
   ATOMNAME: C32
   FRAGMENT: sn-1
+  SMILEIDX: 16
 M_G1C3H1_M:
   ATOMNAME: H2X
   FRAGMENT: sn-1
@@ -28,6 +33,7 @@ M_G1C3H2_M:
 M_G1C4_M:
   ATOMNAME: C33
   FRAGMENT: sn-1
+  SMILEIDX: 15
 M_G1C4H1_M:
   ATOMNAME: H3X
   FRAGMENT: sn-1
@@ -37,6 +43,7 @@ M_G1C4H2_M:
 M_G1C5_M:
   ATOMNAME: C34
   FRAGMENT: sn-1
+  SMILEIDX: 14
 M_G1C5H1_M:
   ATOMNAME: H4X
   FRAGMENT: sn-1
@@ -46,6 +53,7 @@ M_G1C5H2_M:
 M_G1C6_M:
   ATOMNAME: C35
   FRAGMENT: sn-1
+  SMILEIDX: 13
 M_G1C6H1_M:
   ATOMNAME: H5X
   FRAGMENT: sn-1
@@ -55,6 +63,7 @@ M_G1C6H2_M:
 M_G1C7_M:
   ATOMNAME: C36
   FRAGMENT: sn-1
+  SMILEIDX: 12
 M_G1C7H1_M:
   ATOMNAME: H6X
   FRAGMENT: sn-1
@@ -64,6 +73,7 @@ M_G1C7H2_M:
 M_G1C8_M:
   ATOMNAME: C37
   FRAGMENT: sn-1
+  SMILEIDX: 11
 M_G1C8H1_M:
   ATOMNAME: H7X
   FRAGMENT: sn-1
@@ -73,6 +83,7 @@ M_G1C8H2_M:
 M_G1C9_M:
   ATOMNAME: C38
   FRAGMENT: sn-1
+  SMILEIDX: 10
 M_G1C9H1_M:
   ATOMNAME: H8X
   FRAGMENT: sn-1
@@ -82,6 +93,7 @@ M_G1C9H2_M:
 M_G1C10_M:
   ATOMNAME: C39
   FRAGMENT: sn-1
+  SMILEIDX: 9
 M_G1C10H1_M:
   ATOMNAME: H9X
   FRAGMENT: sn-1
@@ -91,6 +103,7 @@ M_G1C10H2_M:
 M_G1C11_M:
   ATOMNAME: C310
   FRAGMENT: sn-1
+  SMILEIDX: 8
 M_G1C11H1_M:
   ATOMNAME: H10X
   FRAGMENT: sn-1
@@ -100,6 +113,7 @@ M_G1C11H2_M:
 M_G1C12_M:
   ATOMNAME: C311
   FRAGMENT: sn-1
+  SMILEIDX: 7
 M_G1C12H1_M:
   ATOMNAME: H11X
   FRAGMENT: sn-1
@@ -109,6 +123,7 @@ M_G1C12H2_M:
 M_G1C13_M:
   ATOMNAME: C312
   FRAGMENT: sn-1
+  SMILEIDX: 6
 M_G1C13H1_M:
   ATOMNAME: H12X
   FRAGMENT: sn-1
@@ -118,6 +133,7 @@ M_G1C13H2_M:
 M_G1C14_M:
   ATOMNAME: C313
   FRAGMENT: sn-1
+  SMILEIDX: 5
 M_G1C14H1_M:
   ATOMNAME: H13X
   FRAGMENT: sn-1
@@ -127,6 +143,7 @@ M_G1C14H2_M:
 M_G1C15_M:
   ATOMNAME: C314
   FRAGMENT: sn-1
+  SMILEIDX: 4
 M_G1C15H1_M:
   ATOMNAME: H14X
   FRAGMENT: sn-1
@@ -136,6 +153,7 @@ M_G1C15H2_M:
 M_G1C16_M:
   ATOMNAME: C315
   FRAGMENT: sn-1
+  SMILEIDX: 3
 M_G1C16H1_M:
   ATOMNAME: H15X
   FRAGMENT: sn-1
@@ -145,6 +163,7 @@ M_G1C16H2_M:
 M_G1C17_M:
   ATOMNAME: C316
   FRAGMENT: sn-1
+  SMILEIDX: 2
 M_G1C17H1_M:
   ATOMNAME: H16X
   FRAGMENT: sn-1
@@ -154,6 +173,7 @@ M_G1C17H2_M:
 M_G1C18_M:
   ATOMNAME: C317
   FRAGMENT: sn-1
+  SMILEIDX: 1
 M_G1C18H1_M:
   ATOMNAME: H17X
   FRAGMENT: sn-1
@@ -163,6 +183,7 @@ M_G1C18H2_M:
 M_G1C19_M:
   ATOMNAME: C318
   FRAGMENT: sn-1
+  SMILEIDX: 0
 M_G1C19H1_M:
   ATOMNAME: H18X
   FRAGMENT: sn-1
@@ -175,21 +196,26 @@ M_G1C19H3_M:
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 21
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 47
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 48
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 49
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 50
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -199,6 +225,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 51
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -208,6 +235,7 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 52
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
@@ -217,18 +245,21 @@ M_G2C5H2_M:
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 53
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 54
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 55
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
@@ -238,18 +269,21 @@ M_G2C8H2_M:
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 56
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 57
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 58
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
@@ -259,18 +293,21 @@ M_G2C11H2_M:
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 59
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 60
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 61
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
@@ -280,18 +317,21 @@ M_G2C14H2_M:
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 62
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 63
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 64
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
@@ -301,6 +341,7 @@ M_G2C17H2_M:
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 65
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
@@ -310,6 +351,7 @@ M_G2C18H2_M:
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 66
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -319,6 +361,7 @@ M_G2C19H2_M:
 M_G2C20_M:
   ATOMNAME: C219
   FRAGMENT: sn-2
+  SMILEIDX: 67
 M_G2C20H1_M:
   ATOMNAME: H19R
   FRAGMENT: sn-2
@@ -328,6 +371,7 @@ M_G2C20H2_M:
 M_G2C21_M:
   ATOMNAME: C220
   FRAGMENT: sn-2
+  SMILEIDX: 68
 M_G2C21H1_M:
   ATOMNAME: H20R
   FRAGMENT: sn-2
@@ -340,6 +384,7 @@ M_G2C21H3_M:
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 22
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -349,102 +394,126 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
+  SMILEIDX: 23
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 24
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 25
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 26
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 27
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 28
 M_G3C4H1_M:
   ATOMNAME: H1
   FRAGMENT: headgroup
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 29
 M_G3C5H1_M:
   ATOMNAME: H2
   FRAGMENT: headgroup
 M_G3C5O1_M:
   ATOMNAME: O2
   FRAGMENT: headgroup
+  SMILEIDX: 46
 M_G3C5O1H1_M:
   ATOMNAME: HO2
   FRAGMENT: headgroup
 M_G3C6_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 30
 M_G3C6H1_M:
   ATOMNAME: H3
   FRAGMENT: headgroup
 M_G3C6O1_M:
   ATOMNAME: O3
   FRAGMENT: headgroup
+  SMILEIDX: 45
 M_G3C6O1H1_M:
   ATOMNAME: HO3
   FRAGMENT: headgroup
 M_G3C7_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 31
 M_G3C7H1_M:
   ATOMNAME: H4
   FRAGMENT: headgroup
 M_G3C7O1_M:
   ATOMNAME: O4
   FRAGMENT: headgroup
+  SMILEIDX: 40
 M_G3C7P2_M:
   ATOMNAME: P4
   FRAGMENT: headgroup
+  SMILEIDX: 41
 M_G3C7O3_M:
   ATOMNAME: OP42
   FRAGMENT: headgroup
+  SMILEIDX: 43
 M_G3C7O3H1_M:
   ATOMNAME: HP42
   FRAGMENT: headgroup
 M_G3C7P2O1_M:
   ATOMNAME: OP43
   FRAGMENT: headgroup
+  SMILEIDX: 44
 M_G3C7P2O2_M:
   ATOMNAME: OP44
   FRAGMENT: headgroup
+  SMILEIDX: 42
 M_G3C8_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 32
 M_G3C8H1_M:
   ATOMNAME: H5
   FRAGMENT: headgroup
 M_G3C8O1_M:
   ATOMNAME: O5
   FRAGMENT: headgroup
+  SMILEIDX: 35
 M_G3C8P2_M:
   ATOMNAME: P5
   FRAGMENT: headgroup
+  SMILEIDX: 36
 M_G3C8P2O1_M:
   ATOMNAME: OP52
   FRAGMENT: headgroup
+  SMILEIDX: 37
 M_G3C8P2O2_M:
   ATOMNAME: OP53
   FRAGMENT: headgroup
+  SMILEIDX: 38
 M_G3C8P2O3_M:
   ATOMNAME: OP54
   FRAGMENT: headgroup
+  SMILEIDX: 39
 M_G3C9_M:
   ATOMNAME: C16
   FRAGMENT: headgroup
+  SMILEIDX: 33
 M_G3C9H1_M:
   ATOMNAME: H6
   FRAGMENT: headgroup
 M_G3C9O1_M:
   ATOMNAME: O6
   FRAGMENT: headgroup
+  SMILEIDX: 34
 M_G3C9O1H1_M:
   ATOMNAME: HO6
   FRAGMENT: headgroup
diff --git a/Molecules/membrane/SAPI24/metadata.yaml b/Molecules/membrane/SAPI24/metadata.yaml
index fc3db5052..aba3a1c58 100644
--- a/Molecules/membrane/SAPI24/metadata.yaml
+++ b/Molecules/membrane/SAPI24/metadata.yaml
@@ -9,11 +9,11 @@ bioschema_properties:
     phosphate'
   iupacName: '[(1R,2S,3R,4R,5S,6R)-2,3,5-trihydroxy-4-[[2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyl]oxy-3-octadecanoyloxypropoxy]-oxidophosphoryl]oxy-6-phosphonatooxycyclohexyl]
     phosphate'
-  molecularFormula: C47H80O19P3-5
+  molecularFormula: C47H85O19P3
   molecularWeight: 1042.0
   inChI: InChI=1S/C47H85O19P3/c1-3-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-36-41(49)63-39(37-61-40(48)35-33-31-29-27-25-23-21-18-16-14-12-10-8-6-4-2)38-62-69(59,60)66-45-42(50)43(51)46(64-67(53,54)55)47(44(45)52)65-68(56,57)58/h11,13,17,19,22,24,28,30,39,42-47,50-52H,3-10,12,14-16,18,20-21,23,25-27,29,31-38H2,1-2H3,(H,59,60)(H2,53,54,55)(H2,56,57,58)/p-5/b13-11-,19-17-,24-22-,30-28-/t39?,42-,43+,44+,45-,46-,47-/m1/s1
   inChIKey: CNWINRVXAYPOMW-WJUYXORRSA-I
-  smiles: CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)([O-])O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)OP(=O)([O-])[O-])OP(=O)([O-])[O-])O)O)OC(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\CCCCC
+  smiles: CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)OP(=O)(O)O)OP(=O)(O)O)O)O)OC(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\CCCCC
   image: https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=24742074&t=l
   alternateName:
   - BDBM15235

From 488f0c907780253d26ba2be034f9e9c24ecade5e Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 10:34:00 +0200
Subject: [PATCH 08/10] fix: automatic SMILEIDX for SD5PC

---
 .../membrane/SD5PC/mappingSD5PCcharmm.yaml    | 44 ++++++++++++++++---
 1 file changed, 39 insertions(+), 5 deletions(-)

diff --git a/Molecules/membrane/SD5PC/mappingSD5PCcharmm.yaml b/Molecules/membrane/SD5PC/mappingSD5PCcharmm.yaml
index 52e11b746..54efcef37 100644
--- a/Molecules/membrane/SD5PC/mappingSD5PCcharmm.yaml
+++ b/Molecules/membrane/SD5PC/mappingSD5PCcharmm.yaml
@@ -1,19 +1,23 @@
-# headgroup
 M_G3P2_M:
   ATOMNAME: P
   FRAGMENT: headgroup
+  SMILEIDX: 24
 M_G3P2O1_M:
   ATOMNAME: O14
   FRAGMENT: headgroup
+  SMILEIDX: 26
 M_G3P2O2_M:
   ATOMNAME: O13
   FRAGMENT: headgroup
+  SMILEIDX: 25
 M_G3O3_M:
   ATOMNAME: O12
   FRAGMENT: headgroup
+  SMILEIDX: 27
 M_G3C4_M:
   ATOMNAME: C11
   FRAGMENT: headgroup
+  SMILEIDX: 28
 M_G3C4H1_M:
   ATOMNAME: H11A
   FRAGMENT: headgroup
@@ -23,6 +27,7 @@ M_G3C4H2_M:
 M_G3C5_M:
   ATOMNAME: C12
   FRAGMENT: headgroup
+  SMILEIDX: 29
 M_G3C5H1_M:
   ATOMNAME: H12A
   FRAGMENT: headgroup
@@ -32,9 +37,11 @@ M_G3C5H2_M:
 M_G3N6_M:
   ATOMNAME: N
   FRAGMENT: headgroup
+  SMILEIDX: 30
 M_G3N6C1_M:
   ATOMNAME: C13
   FRAGMENT: headgroup
+  SMILEIDX: 31
 M_G3N6C1H1_M:
   ATOMNAME: H13A
   FRAGMENT: headgroup
@@ -47,6 +54,7 @@ M_G3N6C1H3_M:
 M_G3N6C2_M:
   ATOMNAME: C14
   FRAGMENT: headgroup
+  SMILEIDX: 32
 M_G3N6C2H1_M:
   ATOMNAME: H14A
   FRAGMENT: headgroup
@@ -59,6 +67,7 @@ M_G3N6C2H3_M:
 M_G3N6C3_M:
   ATOMNAME: C15
   FRAGMENT: headgroup
+  SMILEIDX: 33
 M_G3N6C3H1_M:
   ATOMNAME: H15A
   FRAGMENT: headgroup
@@ -68,10 +77,10 @@ M_G3N6C3H2_M:
 M_G3N6C3H3_M:
   ATOMNAME: H15C
   FRAGMENT: headgroup
-# bb
 M_G1_M:
   ATOMNAME: C3
   FRAGMENT: glycerol backbone
+  SMILEIDX: 20
 M_G1H1_M:
   ATOMNAME: HX
   FRAGMENT: glycerol backbone
@@ -81,18 +90,22 @@ M_G1H2_M:
 M_G1O1_M:
   ATOMNAME: O31
   FRAGMENT: glycerol backbone
+  SMILEIDX: 19
 M_G2_M:
   ATOMNAME: C2
   FRAGMENT: glycerol backbone
+  SMILEIDX: 21
 M_G2H1_M:
   ATOMNAME: HS
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
   FRAGMENT: glycerol backbone
+  SMILEIDX: 34
 M_G3_M:
   ATOMNAME: C1
   FRAGMENT: glycerol backbone
+  SMILEIDX: 22
 M_G3H1_M:
   ATOMNAME: HA
   FRAGMENT: glycerol backbone
@@ -102,7 +115,7 @@ M_G3H2_M:
 M_G3O1_M:
   ATOMNAME: O11
   FRAGMENT: glycerol backbone
-# sn-1
+  SMILEIDX: 23
 M_G1C2_M:
   ATOMNAME: C31
   FRAGMENT: sn-1
@@ -284,16 +297,18 @@ M_G1C19H2_M:
 M_G1C19H3_M:
   ATOMNAME: H18Z
   FRAGMENT: sn-1
-# sn-2
 M_G2C2_M:
   ATOMNAME: C21
   FRAGMENT: sn-2
+  SMILEIDX: 35
 M_G2C2O1_M:
   ATOMNAME: O22
   FRAGMENT: sn-2
+  SMILEIDX: 36
 M_G2C3_M:
   ATOMNAME: C22
   FRAGMENT: sn-2
+  SMILEIDX: 37
 M_G2C3H1_M:
   ATOMNAME: H2R
   FRAGMENT: sn-2
@@ -303,6 +318,7 @@ M_G2C3H2_M:
 M_G2C4_M:
   ATOMNAME: C23
   FRAGMENT: sn-2
+  SMILEIDX: 38
 M_G2C4H1_M:
   ATOMNAME: H3R
   FRAGMENT: sn-2
@@ -312,18 +328,21 @@ M_G2C4H2_M:
 M_G2C5_M:
   ATOMNAME: C24
   FRAGMENT: sn-2
+  SMILEIDX: 39
 M_G2C5H1_M:
   ATOMNAME: H4R
   FRAGMENT: sn-2
 M_G2C6_M:
   ATOMNAME: C25
   FRAGMENT: sn-2
+  SMILEIDX: 40
 M_G2C6H1_M:
   ATOMNAME: H5R
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C26
   FRAGMENT: sn-2
+  SMILEIDX: 41
 M_G2C7H1_M:
   ATOMNAME: H6R
   FRAGMENT: sn-2
@@ -333,18 +352,21 @@ M_G2C7H2_M:
 M_G2C8_M:
   ATOMNAME: C27
   FRAGMENT: sn-2
+  SMILEIDX: 42
 M_G2C8H1_M:
   ATOMNAME: H7R
   FRAGMENT: sn-2
 M_G2C9_M:
   ATOMNAME: C28
   FRAGMENT: sn-2
+  SMILEIDX: 43
 M_G2C9H1_M:
   ATOMNAME: H8R
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C29
   FRAGMENT: sn-2
+  SMILEIDX: 44
 M_G2C10H1_M:
   ATOMNAME: H9R
   FRAGMENT: sn-2
@@ -354,18 +376,21 @@ M_G2C10H2_M:
 M_G2C11_M:
   ATOMNAME: C210
   FRAGMENT: sn-2
+  SMILEIDX: 45
 M_G2C11H1_M:
   ATOMNAME: H10R
   FRAGMENT: sn-2
 M_G2C12_M:
   ATOMNAME: C211
   FRAGMENT: sn-2
+  SMILEIDX: 46
 M_G2C12H1_M:
   ATOMNAME: H11R
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C212
   FRAGMENT: sn-2
+  SMILEIDX: 47
 M_G2C13H1_M:
   ATOMNAME: H12R
   FRAGMENT: sn-2
@@ -375,18 +400,21 @@ M_G2C13H2_M:
 M_G2C14_M:
   ATOMNAME: C213
   FRAGMENT: sn-2
+  SMILEIDX: 48
 M_G2C14H1_M:
   ATOMNAME: H13R
   FRAGMENT: sn-2
 M_G2C15_M:
   ATOMNAME: C214
   FRAGMENT: sn-2
+  SMILEIDX: 49
 M_G2C15H1_M:
   ATOMNAME: H14R
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C215
   FRAGMENT: sn-2
+  SMILEIDX: 50
 M_G2C16H1_M:
   ATOMNAME: H15R
   FRAGMENT: sn-2
@@ -396,18 +424,21 @@ M_G2C16H2_M:
 M_G2C17_M:
   ATOMNAME: C216
   FRAGMENT: sn-2
+  SMILEIDX: 51
 M_G2C17H1_M:
   ATOMNAME: H16R
   FRAGMENT: sn-2
 M_G2C18_M:
   ATOMNAME: C217
   FRAGMENT: sn-2
+  SMILEIDX: 52
 M_G2C18H1_M:
   ATOMNAME: H17R
   FRAGMENT: sn-2
 M_G2C19_M:
   ATOMNAME: C218
   FRAGMENT: sn-2
+  SMILEIDX: 53
 M_G2C19H1_M:
   ATOMNAME: H18R
   FRAGMENT: sn-2
@@ -417,6 +448,7 @@ M_G2C19H2_M:
 M_G2C20_M:
   ATOMNAME: C219
   FRAGMENT: sn-2
+  SMILEIDX: 54
 M_G2C20H1_M:
   ATOMNAME: H19R
   FRAGMENT: sn-2
@@ -426,6 +458,7 @@ M_G2C20H2_M:
 M_G2C21_M:
   ATOMNAME: C220
   FRAGMENT: sn-2
+  SMILEIDX: 55
 M_G2C21H1_M:
   ATOMNAME: H20R
   FRAGMENT: sn-2
@@ -435,6 +468,7 @@ M_G2C21H2_M:
 M_G2C22_M:
   ATOMNAME: C221
   FRAGMENT: sn-2
+  SMILEIDX: 56
 M_G2C22H1_M:
   ATOMNAME: H21R
   FRAGMENT: sn-2
@@ -444,6 +478,7 @@ M_G2C22H2_M:
 M_G2C23_M:
   ATOMNAME: C222
   FRAGMENT: sn-2
+  SMILEIDX: 57
 M_G2C23H1_M:
   ATOMNAME: H22R
   FRAGMENT: sn-2
@@ -453,4 +488,3 @@ M_G2C23H2_M:
 M_G2C23H3_M:
   ATOMNAME: H22T
   FRAGMENT: sn-2
-

From 5b9f69ae89e1f6978e222b697e568a3b871fad43 Mon Sep 17 00:00:00 2001
From: comcon1 <comcon1@protonmail.com>
Date: Sat, 20 Jun 2026 12:09:54 +0200
Subject: [PATCH 09/10] fix: remove clumpy mapping SMILEIDX for SDG, add NOTES
 for sdg molecule (prlty fixes #427)

---
 Molecules/membrane/SDG/NOTES.md               |   2 +
 Molecules/membrane/SDG/mappingSDGlipid17.yaml | 151 ------------------
 2 files changed, 2 insertions(+), 151 deletions(-)
 create mode 100644 Molecules/membrane/SDG/NOTES.md

diff --git a/Molecules/membrane/SDG/NOTES.md b/Molecules/membrane/SDG/NOTES.md
new file mode 100644
index 000000000..5a6de2843
--- /dev/null
+++ b/Molecules/membrane/SDG/NOTES.md
@@ -0,0 +1,2 @@
+SDG for lipid17 is broken as atomnames are indistinguishable for sn-1 and sn-2.
+This topology **SHOULD NOT** be used in future simulations.
diff --git a/Molecules/membrane/SDG/mappingSDGlipid17.yaml b/Molecules/membrane/SDG/mappingSDGlipid17.yaml
index a43242a6a..5ea384b5b 100644
--- a/Molecules/membrane/SDG/mappingSDGlipid17.yaml
+++ b/Molecules/membrane/SDG/mappingSDGlipid17.yaml
@@ -1,511 +1,360 @@
 M_G1_M:
   ATOMNAME: C1
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
-  SMILEIDX: 20
 M_G1H1_M:
   ATOMNAME: HS
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
 M_G1H2_M:
   ATOMNAME: HR
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
 M_G1O1_M:
   ATOMNAME: O11
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 19
 M_G1C2_M:
   ATOMNAME: C11
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 17
 M_G1C2O1_M:
   ATOMNAME: O12
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 18
 M_G1C3_M:
   ATOMNAME: C12
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 27
 M_G1C3H1_M:
   ATOMNAME: H2R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C3H2_M:
   ATOMNAME: H2S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C4_M:
   ATOMNAME: C13
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 28
 M_G1C4H1_M:
   ATOMNAME: H3R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C4H2_M:
   ATOMNAME: H3S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C5_M:
   ATOMNAME: C14
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 29
 M_G1C5H1_M:
   ATOMNAME: H4R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C5H2_M:
   ATOMNAME: H4S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C6_M:
   ATOMNAME: C15
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 30
 M_G1C6H1_M:
   ATOMNAME: H5R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C6H2_M:
   ATOMNAME: H5S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C7_M:
   ATOMNAME: C16
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 31
 M_G1C7H1_M:
   ATOMNAME: H6R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C7H2_M:
   ATOMNAME: H6S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C8_M:
   ATOMNAME: C17
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 32
 M_G1C8H1_M:
   ATOMNAME: H7R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C8H2_M:
   ATOMNAME: H7S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C9_M:
   ATOMNAME: C18
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 33
 M_G1C9H1_M:
   ATOMNAME: H8R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C9H2_M:
   ATOMNAME: H8S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C10_M:
   ATOMNAME: C19
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 34
 M_G1C10H1_M:
   ATOMNAME: H9R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C10H2_M:
   ATOMNAME: H9S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C11_M:
   ATOMNAME: C110
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 35
 M_G1C11H1_M:
   ATOMNAME: H10R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C11H2_M:
   ATOMNAME: H10S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C12_M:
   ATOMNAME: C111
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 36
 M_G1C12H1_M:
   ATOMNAME: H11R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C12H2_M:
   ATOMNAME: H11S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C13_M:
   ATOMNAME: C112
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 37
 M_G1C13H1_M:
   ATOMNAME: H12S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C13H2_M:
   ATOMNAME: H12R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C14_M:
   ATOMNAME: C113
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 38
 M_G1C14H1_M:
   ATOMNAME: H13R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C14H2_M:
   ATOMNAME: H13S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C15_M:
   ATOMNAME: C114
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 39
 M_G1C15H1_M:
   ATOMNAME: H14R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C15H2_M:
   ATOMNAME: H14S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C16_M:
   ATOMNAME: C115
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 40
 M_G1C16H1_M:
   ATOMNAME: H15R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C16H2_M:
   ATOMNAME: H15S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C17_M:
   ATOMNAME: C116
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 41
 M_G1C17H1_M:
   ATOMNAME: H16R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C17H2_M:
   ATOMNAME: H16S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C18_M:
   ATOMNAME: C117
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 42
 M_G1C18H1_M:
   ATOMNAME: H17R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C18H2_M:
   ATOMNAME: H17S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C19_M:
   ATOMNAME: C118
-  RESIDUE: SDG
   FRAGMENT: sn-1
-  SMILEIDX: 43
 M_G1C19H1_M:
   ATOMNAME: H18R
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C19H2_M:
   ATOMNAME: H18S
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G1C19H3_M:
   ATOMNAME: H18T
-  RESIDUE: SDG
   FRAGMENT: sn-1
 M_G2_M:
   ATOMNAME: C2
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
-  SMILEIDX: 21
 M_G2H1_M:
   ATOMNAME: HX
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
 M_G2O1_M:
   ATOMNAME: O21
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 24
 M_G2C2_M:
   ATOMNAME: C21
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 25
 M_G2C2O1_M:
   ATOMNAME: O22
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 26
 M_G2C3_M:
   ATOMNAME: C12
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C3H1_M:
   ATOMNAME: H2R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C3H2_M:
   ATOMNAME: H2S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C4_M:
   ATOMNAME: C13
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C4H1_M:
   ATOMNAME: H3R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C4H2_M:
   ATOMNAME: H3S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C5_M:
   ATOMNAME: C14
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C5H1_M:
   ATOMNAME: H4R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C6_M:
   ATOMNAME: C15
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C6H1_M:
   ATOMNAME: H5R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C7_M:
   ATOMNAME: C16
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C7H1_M:
   ATOMNAME: H6R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C7H2_M:
   ATOMNAME: H6S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C8_M:
   ATOMNAME: C17
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C8H1_M:
   ATOMNAME: H7R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C9_M:
   ATOMNAME: C18
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C9H1_M:
   ATOMNAME: H8R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C10_M:
   ATOMNAME: C19
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C10H1_M:
   ATOMNAME: H9R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C10H2_M:
   ATOMNAME: H9S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C11_M:
   ATOMNAME: C110
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C11H1_M:
   ATOMNAME: H10R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C12_M:
   ATOMNAME: C111
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C12H1_M:
   ATOMNAME: H11R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C13_M:
   ATOMNAME: C112
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C13H1_M:
   ATOMNAME: H12R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C13H2_M:
   ATOMNAME: H12S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C14_M:
   ATOMNAME: C113
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C14H1_M:
   ATOMNAME: H13R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C15_M:
   ATOMNAME: C114
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C15H1_M:
   ATOMNAME: H14R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C16_M:
   ATOMNAME: C115
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C16H1_M:
   ATOMNAME: H15R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C16H2_M:
   ATOMNAME: H15S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C17_M:
   ATOMNAME: C116
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C17H1_M:
   ATOMNAME: H16R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C18_M:
   ATOMNAME: C117
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C18H1_M:
   ATOMNAME: H17R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C19_M:
   ATOMNAME: C118
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C19H1_M:
   ATOMNAME: H18R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C19H2_M:
   ATOMNAME: H18S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C20_M:
   ATOMNAME: C119
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 44
 M_G2C20H1_M:
   ATOMNAME: H19R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C21_M:
   ATOMNAME: C120
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 45
 M_G2C21H1_M:
   ATOMNAME: H20R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C22_M:
   ATOMNAME: C121
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 46
 M_G2C22H1_M:
   ATOMNAME: H21R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C22H2_M:
   ATOMNAME: H21S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C23_M:
   ATOMNAME: C122
-  RESIDUE: SDG
   FRAGMENT: sn-2
-  SMILEIDX: 47
 M_G2C23H1_M:
   ATOMNAME: H22R
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C23H2_M:
   ATOMNAME: H22S
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G2C23H3_M:
   ATOMNAME: H22T
-  RESIDUE: SDG
   FRAGMENT: sn-2
 M_G3_M:
   ATOMNAME: C3
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
-  SMILEIDX: 22
 M_G3H1_M:
   ATOMNAME: HA
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
 M_G3H2_M:
   ATOMNAME: HB
-  RESIDUE: SDG
   FRAGMENT: glycerol backbone
 M_G3O1_M:
   ATOMNAME: O31
-  RESIDUE: SDG
   FRAGMENT: headgroup
-  SMILEIDX: 23
 M_G3O1H1_M:
   ATOMNAME: H31
-  RESIDUE: SDG
   FRAGMENT: headgroup

From 974c860f0f7b21891cb1b698f902e9e0effae784 Mon Sep 17 00:00:00 2001
From: Alexey Nesterenko <comcon1@protonmail.com>
Date: Sun, 21 Jun 2026 22:00:14 +0200
Subject: [PATCH 10/10] Update Molecules/membrane/SAPI24/metadata.yaml

---
 Molecules/membrane/SAPI24/metadata.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Molecules/membrane/SAPI24/metadata.yaml b/Molecules/membrane/SAPI24/metadata.yaml
index aba3a1c58..98e3a26fe 100644
--- a/Molecules/membrane/SAPI24/metadata.yaml
+++ b/Molecules/membrane/SAPI24/metadata.yaml
@@ -4,6 +4,7 @@ NMRlipids:
   charge: -4
 sameAs:
   pubchem.compound: 24742074
+  ChEBI: CHEBI:232300
 bioschema_properties:
   name: '[(1R,2S,3R,4R,5S,6R)-2,3,5-trihydroxy-4-[[2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyl]oxy-3-octadecanoyloxypropoxy]-oxidophosphoryl]oxy-6-phosphonatooxycyclohexyl]
     phosphate'