Improve SMILEidx for PUFA molecules

.gitignore

@@ -1,3 +1,7 @@
+# All
+Simulations/**/*.psf
+Simulations/**/*.dcd
+Simulations/**/*.pdb
 # macOS
 .DS_Store
 .AppleDouble

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