Add functional groups and update documentation

docs/howto/fgs.nblink

@@ -0,0 +1,3 @@
+{
+  "path": "../../examples/fgs.ipynb"
+}

docs/index.rst

@@ -26,6 +26,7 @@ Welcome to the documentation of GlyLES!
     howto/conversion
     howto/visualization
     howto/filtering
+    howto/fgs
 
 .. toctree::
     :glob:

glyles/glycans/mono/reactor.py

@@ -24,11 +24,14 @@
     "Am": "C(=N)C",
     "Asp": "N[C@@H](CC(=O)O)C(=O)O",
     "Br": "Br",
+    "Cbz": "C(=O)OCc2ccccc2",
     "Cer": "OC[C@H](NC=O)C(O)/C=C/" + "C" * 13,
     "Cho": "OCC[N+](C)(C)C",
     "Cl": "Cl",
+    "ClAc": "C(=O)CCl",
     "Cm": "NC(=O)",
     "Cys": "N[C@@H](CS)C(=O)O",
+    "DCA": "C(=O)C(Cl)Cl",
     "Etn": "OCCN",
     "EtN": "OCCN",
     "F": "F",
@@ -38,51 +41,78 @@
     "I": "I",
     "Lys": "NCCCC[C@H](N)C(=O)O",
     "N": "N",
+    "N3": "N=[N+]=[N-]",
     "NFo": "NC=O",
+    "Ns": "S(=O)(=O)c2ccccc2[N+](=O)[O-]",
+    "oNB": "Cc2ccccc2[N+](=O)[O-]",
     "Orn": "NCCC[C@H](N)C(=O)O",
     "P": "OP(=O)(O)O",
     "PhNO2": "Oc2ccc([N+]([O-])=O)cc2",
+    "Pic": "CC2=CC=CC=N2",
+    "Pico": "C(=O)C2=CC=CC=N2",
     "Pp": "OC(=O)CC",
     "S": "S(=O)(=O)O",
     "Pro": "N2CCCC2C(=O)O",
     "Ser": "OC(=O)[C@H](N)CO",
+    "TBDPS": "[Si](C(C)(C)C)(c2ccccc2)c2ccccc2",
+    "TBS": "[Si](C)(C)C(C)(C)C",
+    "TCA": "C(=O)C(Cl)(Cl)Cl",
+    "TES": "[Si](CC)(CC)CC",
     "Tf": "OS(=O)(=O)C(F)(F)F",
+    "TFA": "C(=O)C(F)(F)F",
+    "TIPS": "[Si](C(C)C)(C(C)C)C(C)C",
+    "TMS": "[Si](C)(C)C",
     "Thr": "N[C@@H](C(=O)O)[C@@H](O)C",
+    "Troc": "C(=O)OCC(Cl)(Cl)Cl",
+    "Ts": "S(=O)(=O)c2ccc(C)cc2",
     "Ulo": "OC(c2ccccc2)(c2ccccc2(Cl))CCN(C)C",
 
     # COH land
     "A": "OC(=O)C",
+    "Al": "CCC=C",
     "Allyl": "CC=C",
     "Ac": "C(=O)C",
-    "Ang": "OC(=O)C/(C)=C\\C",
-    "Bz": "C(=O)c2ccccc2",
+    "Ang": "OC(=O)/C(C)=C\\C",
     "Bn": "Cc2ccccc2",
+    "Boc": "C(=O)OC(C)(C)C",
+    "Bz": "C(=O)c2ccccc2",
     "cdPam": "OC(=O)CCCCCCC/C=C\\CCCCCC",
     "Cet": "CCC(=O)O",
+    "cHx": "C2CCCCC2",
     "Cin": "OC(=O)/C=C/c2ccccc2",
-    "Coum": "OC(=O)/C=C/c1ccc(O)ccc1",
+    "Coum": "OC(=O)/C=C/c2cc(O)ccc2",
     "Dce": "OC(=O)CCCCCCCC=C",
     "Dhp": "OC(=O)C(O)(O)CCC",
     "Dhpa": "OC(=O)C(O)(O)CCC",
+    "DMT": "C(c2ccc(OC)cc2)(c2ccccc2)c2ccccc2",
     "Etg": "OCCO",
     "Fer": "OC(=O)/C=C/c2ccc(O)c(OC)c2",
+    "Fmoc": "C(=O)OCC2c3ccccc3c4c2cccc4",
     "Fo": "OC(=O)",
     "Gc": "C(=O)CO",
     "Gly": "OCC(O)CO",
     "Gro": "OCC(O)CO",
     "He": "C(O)C",
     "Lac": "OC(=O)C(O)C",
+    "Lev": "C(=O)CCC(=O)C",
     "Lin": "OC(=O)CCCCCCC/C=C\\C/C=C\\CCCCC",
     "Mal": "O[C@H](C(=O)O)CC(=O)O",
+    "MMT": "C(c2ccccc2)(c2ccccc2)c2ccc(OC)cc2",
+    "MOM": "COC",
+    "NAP": "CCc2cc3ccccc3cc2",
     "Ole": "OC(=O)CCCCCCC/C=C\\CCCCCCCC",
     "Ph": "c2ccccc2",
     "Phyt": "OCCC(C)CCCC(C)CCCC(C)CCCC(C)C",
+    "Piv": "C(=O)C(C)(C)C",
+    "PMB": "Cc2ccc(OC)cc2",
+    "PMP": "Cc2ccccc2O",
+    "Poc": "C(=O)OCC#C",
     "Pyr": "OC(=O)C(=O)C",
     "Sin": "OC(=O)/C=C/c2cc(OC)c(O)c(OC)c2",
     "Suc": "OC(=O)CCC(=O)O",
-    "Tig": "OC(=O)C/(C)=C/C",
-    "Tr": "C(c2ccccc2)(c3ccccc3)c4ccccc4",
-    "Ts": "OS(=O)(=O)c2ccc(C)cc2",
+    "THP": "C2CCCCO2",
+    "Tig": "OC(=O)/C(C)=C/C",
+    "Tr": "C(c2ccccc2)(c2ccccc2)c2ccccc2",
     "Vac": "OC(=O)CCCCCCCCCC=CCCCCCC",
 
     # Sugar rings
@@ -157,7 +187,7 @@
 
 # list of functional groups that start with an N and might be confused with a nitrogen-bridge
 n_conflict = [
-    "Ner", "Nno", "Non", "Nn"
+    "NAP", "Ner", "Nno", "Non", "Nn"
 ]
 
 # list of functional groups that start with an O and might be confused with an oxygen-bridge
@@ -167,7 +197,7 @@
 
 # list of functional groups that start with a P and might be confused with a phosphate-bridge
 p_conflict = [
-    "Psyllic", "Prop", "Pam", "Pro", "Pyr", "Pe", "Ph", "Pr", "Pp"
+    "PMB", "PMP", "Pic", "Pico", "Psyllic", "Prop", "Pam", "Pro", "Pyr", "Pe", "Ph", "Pr", "Pp"
 ]
 
 # list of functional groups that start with a C and might be confused with a carbon-bridge

glyles/grammar/Glycan.g4

@@ -1,5 +1,4 @@
 grammar Glycan;
-
 start:
     '#' (LBRACK branch RBRACK)* begin '#';
 begin:
@@ -60,16 +59,16 @@ OXYGEN:
 PHOSPHOR:
     'P';
 FG:
-    'Ceroplastic' | 'Lacceroic' | '3oxoMyr' | 'Psyllic' | 'Geddic' | 'Allyl' | 'Phthi'
-    | 'aLnn' | 'gLnn' | 'eSte' | 'Coum' | 'HSer' | 'Prop'
-    | 'Ach' | 'Aep' | 'Ala' | 'Ang' | 'Asp' | 'Beh' | 'But' | 'Cct' | 'Cer' | 'Cet' | 'Cho' | 'Cin' | 'Crt' | 'Cys'
-    | 'Dce' | 'Dco' | 'Dec' | 'Dhp' | 'Dod' | 'Etg' | 'EtN' | 'Etn' | 'Fer' | 'Gro' | 'Glu' | 'Gly' | 'Hpo' | 'Hse'
-    | 'Hxo' | 'Lac' | 'Lau' | 'Leu' | 'Lin' | 'Lys' | 'Mal' | 'Mar' | 'Mel' | 'Mon' | 'Myr' | 'Ner' | 'Nno' | 'Non'
-    | 'Oco' | 'Ole' | 'Orn' | 'Pam' | 'Pro' | 'Pyr' | 'Ser' | 'Sin' | 'Ste' | 'tBu' | 'Thr' | 'Tig' | 'Und' | 'Vac'
-    | 'Udo' | 'Ulo' | 'ulo'
-    | 'Ac' | 'Am' | 'Bn' | 'Br' | 'Bu' | 'Bz' | 'Cl' | 'Cm' | 'DD' | 'DL' | 'Et' | 'Fo' | 'Gc' | 'Hp' | 'Hx'
-    | 'LD' | 'LL' | 'Me' | 'Nn' | 'Oc' | 'Pe' | 'Ph' | 'Pr' | 'Pp' | 'Tf' | 'Tr' | 'Ts' | 'Vl' | 'en'
-    | 'A' | 'F' | 'I' | 'S';
+    '3oxoMyr' | 'A' | 'Ac' | 'Ach' | 'Aep' | 'Al' | 'Ala' | 'Alloc' | 'Allyl' | 'aLnn' | 'Am' | 'Ang' | 'Asp' | 'Beh'
+    | 'Bn' | 'Boc' | 'Br' | 'Bu' | 'But' | 'Bz' | 'Cbz' | 'Cct' | 'Cer' | 'Ceroplastic' | 'Cet' | 'Cho' | 'cHx' | 'Cin'
+    | 'Cl' | 'ClAc' | 'Cm' | 'Coum' | 'Crt' | 'Cys' | 'DCA' | 'Dce' | 'Dco' | 'DD' | 'Dec' | 'Dhp' | 'DL' | 'DMT'
+    | 'Dod' | 'en' | 'eSte' | 'Et' | 'Etg' | 'EtN' | 'Etn' | 'F' | 'Fer' | 'Fmoc' | 'Fo' | 'Gc' | 'Geddic' | 'gLnn'
+    | 'Glu' | 'Gly' | 'Gro' | 'Hp' | 'Hpo' | 'Hse' | 'HSer' | 'Hx' | 'Hxo' | 'I' | 'Lac' | 'Lacceroic' | 'Lau' | 'LD'
+    | 'Leu' | 'Lev' | 'Lin' | 'LL' | 'Lys' | 'Mal' | 'Mar' | 'Me' | 'Mel' | 'MMT' | 'MOM' | 'Mon' | 'Myr' | 'N3'
+    | 'NAP' | 'Ner' | 'Nn' | 'Nno' | 'Non' | 'Ns' | 'Oc' | 'Oco' | 'Ole' | 'oNB' | 'Orn' | 'Pam' | 'Pe' | 'Ph'
+    | 'Phthi' | 'Pic' | 'Pico' | 'Piv' | 'PMB' | 'PMP' | 'Poc' | 'Pp' | 'Pr' | 'Pro' | 'Prop' | 'Psyllic' | 'Pyr'
+    | 'S' | 'Ser' | 'Sin' | 'Ste' | 'TBDPS' | 'TBS' | 'tBu' | 'TCA' | 'TES' | 'Tf' | 'TFA' | 'THP' | 'Thr' | 'Tig'
+    | 'TIPS' | 'TMS' | 'Tr' | 'Troc' | 'Ts' | 'Udo' | 'Ulo' | 'ulo' | 'Und' | 'Vac' | 'Vl';
 ANHYDRO:
     'Anhydro';
 HEAD: