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theresearchsoftwarecompany
theresearchsoftwarecompany / dplus-api python
Repository URL to install this package:
|
Version:
5.3.2.2 ▾
|
dplus-api
/
metadata.py
|
|---|
_models_with_files_index_dict = {
"PDB": 999,
"EPDB": 1999,
"AMP": 1000,
"Scripted Geometry": 1001,
"Scripted Model": 1002,
"Scripted Symmetry": 1003,
}
def _type_to_int(type_str):
# handle the specific cases of pdb etc
if type_str in _models_with_files_index_dict:
return _models_with_files_index_dict[type_str]
# handle the ones loaded from that thing in the dumb fashion
test = type_str.split(",")
if test[0] != "":
raise ValueError("Dll should be default (empty string) dll")
try:
type_int = int(test[1])
except:
raise ValueError("Model index not an integer number")
return type_int
def _int_to_type(type_int):
for key, value in _models_with_files_index_dict.items():
if type_int == value:
return key
return "," + str(type_int)
def extra_param_creator(name, defaultValue=0.0, canBeInfinite=False, isAbsolute=False, brange=False, minval=0.0,
maxval=0.0, isIntegral=False, decimalPoints=6):
return {
"name": name,
"defaultValue": defaultValue,
"canBeInfinite": canBeInfinite,
"isAbsolute": isAbsolute,
# bool bRange=False
"range": {"min": minval, "max": maxval},
"isIntegral": isIntegral,
"decimalPoints": decimalPoints,
}
'''
ModelInformation(const char *modelname = "Abstract Model - DO NOT USE",
int cat = -1, int ind = -1, bool layerbased = True,
int layerparams = 2, int minlayer = 1, int maxlayer = 2,
int exparams = 2, int disps = 0, bool gpu = False,
bool slow = False, bool calcff = False, bool datarequired = False) :
category(cat), modelIndex(ind),
isLayerBased(layerbased), nlp(layerparams), minLayers(minlayer),
maxLayers(maxlayer), nExtraParams(exparams), nDispParams(disps),
isGPUCompatible(gpu), isSlow(slow), ffImplemented(calcff)
'''
# (tName, -1, -1, False, 0, 0, 0, 8, 0, False /*TODO::GPU*/, True, True, True/*even though this is never used*/);
def create_hard_model(modelname,
cat=-1, ind=-1, layerbased=True,
numlayerparams=2, minlayer=1, maxlayer=2,
exparams=2, disps=0, gpu=False,
slow=False, calcff=False, datarequired=False):
return {
"index": ind,
"name": modelname,
"category": cat,
"gpuCompatible": gpu,
"slow": slow,
"ffImplemented": calcff,
"isLayerBased": layerbased,
"layers": {
"min": minlayer,
"max": maxlayer,
"layerInfo": [],
"params": []
},
"extraParams": []
}
def pdbmodel():
# TODO:
# extraParamOptions[7].resize(RAD_SIZE);
# extraParamOptions[7][0] = "No Solvent";
# extraParamOptions[7][1] = "Van der Waals";
# extraParamOptions[7][2] = "Empirical";
# extraParamOptions[7][3] = "Calculated";
# extraParamOptions[7][4] = "Dummy Atoms";
pdbmod = create_hard_model("PDB", -1, 999, False, 0, 0, 0, 8, 0, False, True, True, True)
pdbmod["extraParams"] = [
extra_param_creator("Scale", 1.0, False, False, False, 0.0, 0.0, False, 12),
extra_param_creator("Solvent ED", 334.0),
extra_param_creator("C1", 1.0, False, True, True, 0.95, 1.05),
extra_param_creator("Solvent Voxel Size", 0.2),
extra_param_creator("Solvent Probe Radius", 0.14),
extra_param_creator("Solvation Thickness", 0.28, False, True, True, 0.0),
extra_param_creator("Outer Solvent ED"),
extra_param_creator("Fill Holes", 0.0, False, False, True, 0.0, 1.0, True),
extra_param_creator("Solvent Only", 0.0, False, False, True, 0.0, 1.0, True),
extra_param_creator("Solvent method", 4.0, False, False, True, 0.0, 4.0, True)
]
return pdbmod
def epdbmodel():
# TODO:
# extraParamOptions[7].resize(RAD_SIZE);
# extraParamOptions[7][0] = "No Solvent";
# extraParamOptions[7][1] = "Van der Waals";
# extraParamOptions[7][2] = "Empirical";
# extraParamOptions[7][3] = "Calculated";
# extraParamOptions[7][4] = "Dummy Atoms";
epdbmod = create_hard_model("EPDB", -1, 1999, False, 0, 0, 0, 8, 0, False, True, True, True)
epdbmod["extraParams"] = [
extra_param_creator("Scale", 1.0, False, False, False, 0.0, 0.0, False, 12),
extra_param_creator("Solvent ED", 334.0),
extra_param_creator("C1", 1.0, False, True, True, 0.95, 1.05),
extra_param_creator("Solvent Voxel Size", 0.2),
extra_param_creator("Solvent Probe Radius", 0.14),
extra_param_creator("Solvation Thickness", 0.28, False, True, True, 0.0),
extra_param_creator("Outer Solvent ED"),
extra_param_creator("Fill Holes", 0.0, False, False, True, 0.0, 1.0, True),
extra_param_creator("Solvent Only", 0.0, False, False, True, 0.0, 1.0, True),
extra_param_creator("Solvent method", 4.0, False, False, True, 0.0, 4.0, True)
]
return epdbmod
def ampmodel():
amp = create_hard_model("AMP", -1, 1000, False, 0, 0, 0, 1, 0, False, False, False, True)
amp["extraParams"] = [
extra_param_creator("Scale", 1.0, False, False, False, 0.0, 0.0, False, 12)
]
return amp
def scriptedsymm():
s_symm = create_hard_model("Scripted Symmetry", 9, 1003)
return s_symm
def scriptedmodel():
raise NotImplemented
def scriptedgeometry():
raise NotImplemented
hardcode_models = [
pdbmodel(),
epdbmodel(),
ampmodel(),
# scriptedsymm()
]
program_metadata = [
{
"containerName": "xplusmodels",
"models": [
{
"index": 0,
"name": "Uniform Hollow Cylinder",
"category": 0,
"gpuCompatible": False,
"slow": False,
"ffImplemented": True,
"isLayerBased": True,
"layers": {
"min": 2,
"max": -1,
"layerInfo": [
{
"index": 0,
"name": "Solvent",
"applicability": [
0,
1
],
"defaultValues": [
0.0,
333.0
]
},
{
"index": 1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
},
{
"index": -1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
}
],
"params": [
"Radius",
"ED"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Background",
"defaultValue": 0.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Height",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
}
]
},
{
"index": 2,
"name": "Sphere",
"category": 1,
"gpuCompatible": False,
"slow": False,
"ffImplemented": True,
"isLayerBased": True,
"layers": {
"min": 2,
"max": -1,
"layerInfo": [
{
"index": 0,
"name": "Solvent",
"applicability": [
0,
1
],
"defaultValues": [
0.0,
333.0
]
},
{
"index": 1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
},
{
"index": -1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
}
],
"params": [
"Radius",
"ED"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Background",
"defaultValue": 0.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
}
]
},
{
"index": 4,
"name": "Symmetric Layered Slabs",
"category": 2,
"gpuCompatible": False,
"slow": False,
"ffImplemented": True,
"isLayerBased": True,
"layers": {
"min": 2,
"max": -1,
"layerInfo": [
{
"index": 0,
"name": "Solvent",
"applicability": [
0,
1
],
"defaultValues": [
0.0,
333.0
]
},
{
"index": 1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
280.0
]
},
{
"index": -1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
}
],
"params": [
"Width",
"ED"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Background",
"defaultValue": 0.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "X Domain Size",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
},
{
"name": "Y Domain Size",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
}
]
},
{
"index": 5,
"name": "Asymmetric Layered Slabs",
"category": 2,
"gpuCompatible": False,
"slow": False,
"ffImplemented": True,
"isLayerBased": True,
"layers": {
"min": 2,
"max": -1,
"layerInfo": [
{
"index": 0,
"name": "Solvent",
"applicability": [
0,
1
],
"defaultValues": [
0.0,
333.0
]
},
{
"index": 1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
280.0
]
},
{
"index": -1,
"name": "Layer %d",
"applicability": [
1,
1
],
"defaultValues": [
1.0,
400.0
]
}
],
"params": [
"Width",
"ED"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Background",
"defaultValue": 0.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "X Domain Size",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
},
{
"name": "Y Domain Size",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
}
]
},
{
"index": 6,
"name": "Helix",
"category": 3,
"gpuCompatible": False,
"slow": False,
"ffImplemented": True,
"isLayerBased": True,
"layers": {
"min": 2,
"max": 2,
"layerInfo": [
{
"index": 0,
"name": "Solvent",
"applicability": [
0,
1,
0
],
"defaultValues": [
0.0,
333.0,
0.0
]
},
{
"index": 1,
"name": "Helix %d",
"applicability": [
0,
1,
1
],
"defaultValues": [
0.0,
400.0,
3.0
]
},
{
"index": -1,
"name": "Helix %d",
"applicability": [
1,
1,
1
],
"defaultValues": [
1.0,
400.0,
3.0
]
}
],
"params": [
"Phase",
"ED",
"Cross Section"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Background",
"defaultValue": 0.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
},
{
"name": "Height",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": True
},
{
"name": "Helix Radius",
"defaultValue": 10.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": False
},
{
"name": "Pitch",
"defaultValue": 8.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": True,
"canBeInfinite": False
}
]
},
{
"index": 25,
"name": "Space-filling Symmetry",
"category": 9,
"gpuCompatible": False,
"slow": False,
"ffImplemented": False,
"isLayerBased": True,
"layers": {
"min": 3,
"max": 3,
"layerInfo": [
{
"index": 0,
"name": "Vector 1",
"applicability": [
1,
1,
1
],
"defaultValues": [
2.5,
90.0,
2.0
]
},
{
"index": 1,
"name": "Vector 2",
"applicability": [
1,
1,
1
],
"defaultValues": [
2.5,
90.0,
2.0
]
},
{
"index": 2,
"name": "Vector 3",
"applicability": [
1,
1,
1
],
"defaultValues": [
2.5,
90.0,
2.0
]
}
],
"params": [
"Distance",
"Angle",
"Repetitions"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
}
]
},
{
"index": 26,
"name": "Manual Symmetry",
"category": 9,
"gpuCompatible": False,
"slow": False,
"ffImplemented": False,
"isLayerBased": True,
"layers": {
"min": 0,
"max": -1,
"layerInfo": [
{
"index": -1,
"name": "Instance %d",
"applicability": [
1,
1,
1,
1,
1,
1
],
"defaultValues": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
]
}
],
"params": [
"X",
"Y",
"Z",
"Alpha",
"Beta",
"Gamma"
]
},
"extraParams": [
{
"name": "Scale",
"defaultValue": 1.0,
"isIntegral": False,
"decimalPoints": 12,
"isAbsolute": False,
"canBeInfinite": False
}
]
}
],
"modelCategories": [
{
"name": "Cylindrical Models",
"index": 0,
"type": 1,
"models": [
0,
11
]
},
{
"name": "Spherical Models",
"index": 1,
"type": 1,
"models": [
2
]
},
{
"name": "Slab Models",
"index": 2,
"type": 1,
"models": [
4,
5
]
},
{
"name": "Helical Models",
"index": 3,
"type": 1,
"models": [
6
]
},
{
"name": "Cylindroids",
"index": 4,
"type": 1,
"models": []
},
{
"name": "Microemulsions",
"index": 5,
"type": 1,
"models": []
},
{
"name": "Cuboids",
"index": 6,
"type": 1,
"models": []
},
{
"name": "Structure Factors",
"index": 7,
"type": 2,
"models": []
},
{
"name": "Backgrounds",
"index": 8,
"type": 4,
"models": []
},
{
"name": "Symmetries",
"index": 9,
"type": 8,
"models": [
25,
26
]
}
]
}
]
meta_models = program_metadata[0]["models"]
# NOTES:
# isIntegral(bInt), decimalPoints(decPoints), isRanged(bRange),
# rangeMin(minval), rangeMax(maxval), isAbsolute(bAbs),
# canBeInfinite(bInf), defaultVal(defval) {
# if(bInt)
# decimalPoints = 0;
'''
PDBModelUI::PDBModelUI(const char *tName) {
mi.nExtraParams = 8;
this->extraParamsInfo.resize(mi.nExtraParams);
extraParamsInfo[0] = ExtraParam("Scale", 1.0, False, False, False, 0.0, 0.0, False, 12);
extraParamsInfo[1] = ExtraParam("Solvent ED");
extraParamsInfo[2] = ExtraParam("Solvent Voxel Size", 0.05);
extraParamsInfo[3] = ExtraParam("Solvent Radius", 0.14);
extraParamsInfo[4] = ExtraParam("Outer Solvent ED");
extraParamsInfo[5] = ExtraParam("Fill Holes", 0.0, False, False, True, 0.0, 1.0, True);
extraParamsInfo[6] = ExtraParam("Solvent Only", 0.0, False, False, True, 0.0, 1.0, True);
extraParamsInfo[7] = ExtraParam("Solvent method", 0.0, False, False, True, 0.0, 4.0, True);
extraParamsTypes.resize(mi.nExtraParams, EPT_DOUBLE);
extraParamOptions.resize(mi.nExtraParams, std::vector<std::string>());
extraParamsTypes[5] = EPT_CHECKBOX;
extraParamsTypes[6] = EPT_CHECKBOX;
extraParamsTypes[7] = EPT_MULTIPLE_CHOICE;
extraParamOptions[7].resize(RAD_SIZE);
extraParamOptions[7][0] = "No Solvent";
extraParamOptions[7][1] = "Van der Waals";
extraParamOptions[7][2] = "Empirical";
extraParamOptions[7][3] = "Calculated";
extraParamOptions[7][4] = "Dummy Atoms";
mi = ModelInformation(tName, -1, -1, False, 0, 0, 0, 8, 0, False /*TODO::GPU*/, True, True, True/*even though this is never used*/);
}
mi.nExtraParams = 1;
this->extraParamsInfo.resize(mi.nExtraParams);
extraParamsInfo[0] = ExtraParam("Scale", 1.0, False, False, False, 0.0, 0.0, False, 12);
extraParamsTypes.resize(mi.nExtraParams, EPT_DOUBLE);
extraParamOptions.resize(mi.nExtraParams, std::vector<std::string>());
mi = ModelInformation(tName, -1, -1, False, 0, 0, 0, 1, 0, False /*TODO::GPU*/, False, False, True/*even though this is never used*/);
'''