diff --git a/README.md b/README.md
index c174a475f054d207c9bcf3c6d33396968dde95b3..eff30acec7db29e173290f071ce01b9e2b8ddd03 100644
--- a/README.md
+++ b/README.md
@@ -9,8 +9,11 @@ This program uses a library of pre-defined molecule, atom, and bond types to con
## Use
To use the program, execute:
+
`python pdb2lmp.py <PDB/GRO input> <output name>`
+
e.g.:
+
`python pdb2lmp.py data/water.pdb water`
- Output DATA and FF files are created using the output name specified appended with the prefixes `.data` and `.ff` respectively. For the conversion to be successful the molecule names in the import PDB/GRO must match an entry in the PDB2LMP molecule file. If a molecule is missing it may be added to `data/mol.dat`.
+Output DATA and FF files are created using the output name specified appended with the prefixes `.data` and `.ff` respectively. For the conversion to be successful the molecule names in the import PDB/GRO must match an entry in the PDB2LMP molecule file. If a molecule is missing it may be added to `data/mol-elba.json`.
diff --git a/data/bonds.json b/data/bonds.json
index 60629a77e2bf6225c0d3a2e2fa9ac7cdd8d8f152..948424c20965419b5035d36b05657fe0ffc29b67 100644
--- a/data/bonds.json
+++ b/data/bonds.json
@@ -36,15 +36,15 @@
"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",
- "sugar-glyc-d1-3": "charmm -0.1801345 1 -123.0662189 0.0",
- "sugar-glyc-d1-4": "charmm -0.8522 1 -146.907595 0.0",
- "sugar-glyc-d1-6": "charmm 0.4714055 1 0.8067885 0.0",
- "sugar-glyc-d2-a-34": "charmm -0.819724 1 -65.408620 0.0",
- "sugar-glyc-d2-a-6": "charmm 1.312271 1 13.593349 0.0",
- "sugar-glyc-d2-b-34": "charmm -0.2683885 1 -83.0853785 0.0",
- "sugar-glyc-d2-b-6": "charmm -0.542714 1 -26.391433 0.0",
- "sugar-glyc-d3-a": "charmm -6.74014666 1 -83.661744 0.0",
- "sugar-glyc-d3-b": "charmm -0.05605633 1 -42.276276 0.0"
+ "sugar-glyc-d1-3": "charmm -0.1801345 1 -123 0.0",
+ "sugar-glyc-d1-4": "charmm -0.8522 1 -147 0.0",
+ "sugar-glyc-d1-6": "charmm 0.4714055 1 1 0.0",
+ "sugar-glyc-d2-a-34": "charmm -0.819724 1 -65 0.0",
+ "sugar-glyc-d2-a-6": "charmm 1.312271 1 14 0.0",
+ "sugar-glyc-d2-b-34": "charmm -0.2683885 1 -83 0.0",
+ "sugar-glyc-d2-b-6": "charmm -0.542714 1 -26 0.0",
+ "sugar-glyc-d3-a": "charmm -6.74014666 1 -84 0.0",
+ "sugar-glyc-d3-b": "charmm -0.05605633 1 -42 0.0"
},
"improper":{
"dipole-cone-1": "dipole/cone 200 120 60",
diff --git a/data/mol-elba-sugar.json b/data/mol-elba-sugar.json
index aa4fdff147e42ae31d05dabe01ad454268872bc5..47d53f538b56af1a01e7abc891f214d9dfcf298c 100644
--- a/data/mol-elba-sugar.json
+++ b/data/mol-elba-sugar.json
@@ -101,6 +101,13 @@
"angles":[
{"type": "sugar-glyc-1", "atoms":["C2", "C3", "+C1"]},
{"type": "sugar-glyc-2", "atoms":["C3", "+C1", "+C2"]}
+ ],
+ "dihedrals":[
+ {"type": "sugar-glyc-d1-3", "atoms":["C2", "C3", "C4", "+C1"]},
+ {"type": "sugar-glyc-d2-a-34", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d2-b-34", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].B"},
+ {"type": "sugar-glyc-d3-a", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d3-b", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].B"}
]
},
"4XX":{
@@ -110,6 +117,13 @@
"angles":[
{"type": "sugar-glyc-1", "atoms":["C3", "C4", "+C1"]},
{"type": "sugar-glyc-2", "atoms":["C4", "+C1", "+C2"]}
+ ],
+ "dihedrals":[
+ {"type": "sugar-glyc-d1-4", "atoms":["C2", "C3", "C4", "+C1"]},
+ {"type": "sugar-glyc-d2-a-34", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d2-b-34", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].B"},
+ {"type": "sugar-glyc-d3-a", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d3-b", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].B"}
]
},
"6XX":{
@@ -119,6 +133,13 @@
"angles":[
{"type": "sugar-glyc-1-C6", "atoms":["C4", "C5", "+C1"]},
{"type": "sugar-glyc-2", "atoms":["C5", "+C1", "+C2"]}
+ ],
+ "dihedrals":[
+ {"type": "sugar-glyc-d1-6", "atoms":["C2", "C3", "C4", "+C1"]},
+ {"type": "sugar-glyc-d2-a-6", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d2-b-6", "atoms":["C3", "C4", "+C1", "+C2"], "ifnext": "[0-9].B"},
+ {"type": "sugar-glyc-d3-a", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].A"},
+ {"type": "sugar-glyc-d3-b", "atoms":["C4", "+C1", "+C2", "+C3"], "ifnext": "[0-9].B"}
]
}
}
diff --git a/data/schema.json b/data/schema.json
index 548af5810901c9d0615ffb4564f19b126065a468..f0381a3570d8c9de84d8716f419c8f5ca4c6cf39 100644
--- a/data/schema.json
+++ b/data/schema.json
@@ -113,7 +113,8 @@
"maxLength": 2,
"uniqueItems": true,
"items": {"type": "string"}
- }
+ },
+ "ifnext": {"type": "string"}
}
},
@@ -129,7 +130,8 @@
"maxLength": 3,
"uniqueItems": true,
"items": {"type": "string"}
- }
+ },
+ "ifnext": {"type": "string"}
}
},
@@ -145,7 +147,8 @@
"maxLength": 4,
"uniqueItems": true,
"items": {"type": "string"}
- }
+ },
+ "ifnext": {"type": "string"}
}
},
diff --git a/lib/moldatabase.py b/lib/moldatabase.py
index 9a74bf45af8d084042d58b1563135ee0eeb6d9fe..49b5a697760f99dadf92c79c770a7fbfa4b4bb80 100644
--- a/lib/moldatabase.py
+++ b/lib/moldatabase.py
@@ -76,7 +76,6 @@ class MolDatabase:
for mol in self.molecules.values():
used_templates = set()
while mol.templates:
- print(mol.templates)
template = mol.templates.pop()
if template not in used_templates:
mol.extend(self.molecules[template])