diff --git a/data/bonds.json b/data/bonds.json
index e6225f2b13ec9789d973328fb99bd497a689dca4..3f91d71a647e7bee74ed1c5b3a1961afc3a681f8 100644
--- a/data/bonds.json
+++ b/data/bonds.json
@@ -3,27 +3,27 @@
"bonds":{
"length":{
"test": "test 100 1.000",
- "sugar-ring": "harmonic 200 1.520",
- "sugar-glyc": "harmonic 1.0 2.600",
"cho-pho": "harmonic 1.506 4.770",
"pho-gly": "harmonic 1.506 4.410",
"gly-est": "harmonic 1.506 4.140",
"est-tail": "harmonic 1.506 4.095",
"tail-tail": "harmonic 1.506 4.050",
"ami-pho": "harmonic 1.506 4.365",
+ "sugar-ring": "harmonic 200 1.520",
+ "sugar-glyc": "harmonic 110 2.458",
"sugar-dum": "harmonic 100 3"
},
"angle":{
- "sugar-ring": "cosine/squared 120 110.0",
- "dipole": "dipole 10 109.0",
"cho-pho-gly": "cosine/squared 3.585 115.0",
"pho-gly-est": "cosine/squared 3.585 90.0",
"tail-sat": "cosine/squared 3.585 180.0",
"tail-unsat": "cosine/squared 3.585 120.0",
"gly-dipole": "dipole 1.195 0.0",
+ "sugar-ring": "cosine/squared 120 110.0",
"sugar-dipole": "dipole/harmonic 1 150",
- "sugar-glyc-1": "cosine/squared x 139",
- "sugar-glyc-2": "cosine/squared x 139"
+ "sugar-glyc-1": "cosine/squared 63 139",
+ "sugar-glyc-2": "cosine/squared 14 115.5",
+ "sugar-glyc-2-C6": "cosine/squared 9.4 134"
},
"dihedral":{
"sugar-dih-1": "fourier 2 1.00 3 0 0.25 1 -120",
@@ -34,18 +34,12 @@
"sugar-dih-30pc-2": "fourier 2 0.75 3 0 -0.10 1 120",
"sugar-dih-80pc-1": "fourier 2 0.75 3 0 -0.32 1 -120",
"sugar-dih-80pc-2": "fourier 2 0.75 3 0 -0.32 1 120",
- "dipole-1": "dipole 50 -60",
- "dipole-2": "dipole 50 60",
"sugar-glyc-ax": "charmm 10.0 1 170 0.0",
"sugar-glyc-ax-ax": "charmm 10.0 1 160 0.0",
"sugar-glyc-ax-eq": "charmm 10.0 1 185 0.0",
"sugar-glyc-eq": "charmm 5.0 1 85 0.0",
"sugar-glyc-eq-ax": "charmm 5.0 1 95 0.0",
"sugar-glyc-eq-eq": "charmm 5.0 1 80 0.0"
- },
- "improper":{
- "dipole-cone-1": "dipole/cone 200 120 60",
- "dipole-cone-2": "dipole/cone 200 -120 60"
}
}
}
diff --git a/data/elba-sugar/mol-allose.json b/data/elba-sugar/mol-allose.json
index 7c43f160a6a4fd6c8e95f5deb7172be537e77ebb..1372be9d158586aed549c6560a39aa38fe534dad 100644
--- a/data/elba-sugar/mol-allose.json
+++ b/data/elba-sugar/mol-allose.json
@@ -12,36 +12,11 @@
{"type": "sugar-dih-2", "atoms":["O5", "C1", "C2", "C3"]}
]
},
- "0NXD":{
- "templates":["0XXD"],
- "dihedrals":[
- {"type": "sugar-dih-1", "atoms":["C1", "C2", "C3", "C4"]},
- {"type": "sugar-dih-2", "atoms":["C2", "C3", "C4", "C5"]},
- {"type": "sugar-dih-1", "atoms":["C3", "C4", "C5", "O5"]},
- {"type": "sugar-dih-2", "atoms":["C4", "C5", "O5", "C1"]},
- {"type": "sugar-dih-1", "atoms":["C5", "O5", "C1", "C2"]},
- {"type": "sugar-dih-2", "atoms":["O5", "C1", "C2", "C3"]}
- ]
- },
"0NA":{
- "templates":["0NX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0NX"]
},
"0NB":{
- "templates":["0NX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0NX"]
},
"1NA":{
"templates":["0NA"],
@@ -102,9 +77,6 @@
"lengths":[
{"type": "sugar-glyc", "atoms":["C1", "+C5"]}
]
- },
- "3NAD":{
- "templates":["0NXD"]
}
}
}
diff --git a/data/elba-sugar/mol-altrose.json b/data/elba-sugar/mol-altrose.json
index 908661f2c91afa832e478ec52bc806a6a7f112c5..d895fdf057fbdde43a44870d5a51c565a9c191b5 100644
--- a/data/elba-sugar/mol-altrose.json
+++ b/data/elba-sugar/mol-altrose.json
@@ -13,24 +13,10 @@
]
},
"0EA":{
- "templates":["0EX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0EX"]
},
"0EB":{
- "templates":["0EX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0EX"]
},
"1EA":{
"templates":["0EA"],
diff --git a/data/elba-sugar/mol-galactose.json b/data/elba-sugar/mol-galactose.json
index 3ec8abb4676dfb7df323f9de770e0d497a0eb6a5..c1020bcd628d7eb68724aa673c2e5d41f88e6124 100644
--- a/data/elba-sugar/mol-galactose.json
+++ b/data/elba-sugar/mol-galactose.json
@@ -13,24 +13,10 @@
]
},
"0LA":{
- "templates":["0LX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0LX"]
},
"0LB":{
- "templates":["0LX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0LX"]
},
"1LA":{
"templates":["0LA"],
diff --git a/data/elba-sugar/mol-glucose.json b/data/elba-sugar/mol-glucose.json
index dbc56aa7a341a15b2e41aa72d725917aa5288ab5..de03693eeb3535a84561f402c5d5193d8ff9422f 100644
--- a/data/elba-sugar/mol-glucose.json
+++ b/data/elba-sugar/mol-glucose.json
@@ -12,36 +12,11 @@
{"type": "sugar-dih-2", "atoms":["O5", "C1", "C2", "C3"]}
]
},
- "0GXD":{
- "templates":["0XXD"],
- "dihedrals":[
- {"type": "sugar-dih-1", "atoms":["C1", "C2", "C3", "C4"]},
- {"type": "sugar-dih-2", "atoms":["C2", "C3", "C4", "C5"]},
- {"type": "sugar-dih-1", "atoms":["C3", "C4", "C5", "O5"]},
- {"type": "sugar-dih-2", "atoms":["C4", "C5", "O5", "C1"]},
- {"type": "sugar-dih-1", "atoms":["C5", "O5", "C1", "C2"]},
- {"type": "sugar-dih-2", "atoms":["O5", "C1", "C2", "C3"]}
- ]
- },
"0GA":{
- "templates":["0GX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0GX"]
},
"0GB":{
- "templates":["0GX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0GX"]
},
"1GA":{
"templates":["0GA"],
@@ -102,20 +77,6 @@
"lengths":[
{"type": "sugar-glyc", "atoms":["C1", "+C5"]}
]
- },
- "0GAD": {
- "templates": [
- "0GXD"
- ]
- },
- "1GAD":{
- "templates":["0GAD"],
- "lengths":[
- {"type": "sugar-glyc", "atoms":["C1", "+C1"]}
- ],
- "angles":[
- {"type": "sugar-glyc-1", "atoms":["C2", "C1", "+C1"]}
- ]
}
}
}
\ No newline at end of file
diff --git a/data/elba-sugar/mol-gulose.json b/data/elba-sugar/mol-gulose.json
index 4e9157f1e4ba20bfaf95b2a46725a2dcbe4ca920..ec61da89794da35eb0c7d18a38bb90b6fecf069d 100644
--- a/data/elba-sugar/mol-gulose.json
+++ b/data/elba-sugar/mol-gulose.json
@@ -13,24 +13,10 @@
]
},
"0KA":{
- "templates":["0KX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0KX"]
},
"0KB":{
- "templates":["0KX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-1", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0KX"]
},
"1KA":{
"templates":["0KA"],
diff --git a/data/elba-sugar/mol-idose.json b/data/elba-sugar/mol-idose.json
index 5f8d23310a333c5cf7af5306956b857be28151b5..7e8ca0b2ccfc6bc72f5f9efccda6e7cd8b3a67aa 100644
--- a/data/elba-sugar/mol-idose.json
+++ b/data/elba-sugar/mol-idose.json
@@ -13,24 +13,10 @@
]
},
"0IA":{
- "templates":["0IX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0IX"]
},
"0IB":{
- "templates":["0IX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-1", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0IX"]
},
"1IA":{
"templates":["0IA"],
diff --git a/data/elba-sugar/mol-mannose.json b/data/elba-sugar/mol-mannose.json
index b57febd193dade0c616b63d809a26cb0bec0d364..48d82808d066578c08fce1806a3d7e85b1a313a9 100644
--- a/data/elba-sugar/mol-mannose.json
+++ b/data/elba-sugar/mol-mannose.json
@@ -13,24 +13,10 @@
]
},
"0MA":{
- "templates":["0MX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0MX"]
},
"0MB":{
- "templates":["0MX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-1", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0MX"]
},
"1MA":{
"templates":["0MA"],
diff --git a/data/elba-sugar/mol-talose.json b/data/elba-sugar/mol-talose.json
index 58d86635715db484efc2bcea8fa40e5a7a84b7d0..ad4795af856d6b8a2b849367994ccf20aa4bb1ec 100644
--- a/data/elba-sugar/mol-talose.json
+++ b/data/elba-sugar/mol-talose.json
@@ -13,24 +13,10 @@
]
},
"0TA":{
- "templates":["0TX"],
- "impropers":[
- {"type": "dipole-cone-1", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0TX"]
},
"0TB":{
- "templates":["0TX"],
- "impropers":[
- {"type": "dipole-cone-2", "atoms":["C1", "C2", "O5", "C1"]},
- {"type": "dipole-cone-2", "atoms":["C2", "C3", "C1", "C2"]},
- {"type": "dipole-cone-2", "atoms":["C3", "C4", "C2", "C3"]},
- {"type": "dipole-cone-2", "atoms":["C4", "C5", "C3", "C4"]},
- {"type": "dipole-cone-2", "atoms":["C5", "O5", "C4", "C5"]}
- ]
+ "templates":["0TX"]
},
"1TA":{
"templates":["0TA"],
diff --git a/data/mol-elba-sugar.json b/data/mol-elba-sugar.json
index bbd66f251db9cf78d879fd21b8b1d239bf31d5bf..78a1bbd804b84845bac3c4a549c2c129ff45db26 100644
--- a/data/mol-elba-sugar.json
+++ b/data/mol-elba-sugar.json
@@ -25,33 +25,6 @@
]
},
"0XX":{
- "polymer_type":["sugar"],
- "atoms":[
- {"name": "C1", "type": "MEOH"},
- {"name": "C2", "type": "MEOH"},
- {"name": "C3", "type": "MEOH"},
- {"name": "C4", "type": "MEOH"},
- {"name": "C5", "type": "ETOH"},
- {"name": "O5", "type": "OXY"}
- ],
- "lengths":[
- {"type": "sugar-ring", "atoms":["C1", "C2"]},
- {"type": "sugar-ring", "atoms":["C2", "C3"]},
- {"type": "sugar-ring", "atoms":["C3", "C4"]},
- {"type": "sugar-ring", "atoms":["C4", "C5"]},
- {"type": "sugar-ring", "atoms":["C5", "O5"]},
- {"type": "sugar-ring", "atoms":["O5", "C1"]}
- ],
- "angles":[
- {"type": "sugar-ring", "atoms":["C1", "C2", "C3"]},
- {"type": "sugar-ring", "atoms":["C2", "C3", "C4"]},
- {"type": "sugar-ring", "atoms":["C3", "C4", "C5"]},
- {"type": "sugar-ring", "atoms":["C4", "C5", "O5"]},
- {"type": "sugar-ring", "atoms":["C5", "O5", "C1"]},
- {"type": "sugar-ring", "atoms":["O5", "C1", "C2"]}
- ]
- },
- "0XXD":{
"polymer_type":["sugar"],
"atoms":[
{"name": "C1", "type": "MEOH"},
diff --git a/data/schema.json b/data/schema.json
index 43bdf2f42c21ae647211c4c9aebdb7a1018999af..fb33ec0146cda31a30a32aa2169bc63facbe4b5a 100644
--- a/data/schema.json
+++ b/data/schema.json
@@ -25,11 +25,12 @@
{"required": ["templates"]},
{"required": ["atoms"]}
],
+ "additionalProperties": false,
"properties": {
"comment": {"type": "string"},
"templates": {
"type": "array",
- "minLength": 1,
+ "minLength": 0,
"items": {"type": "string"}
},
"polymer_type": {