diff --git "a/output_helpers.py" "b/output_helpers.py" new file mode 100644--- /dev/null +++ "b/output_helpers.py" @@ -0,0 +1,1566 @@ + +import json +import os + +local_url = "http://localhost:8888/frontend/" +remote_url = "https://cdn.jsdelivr.net/gh/duerrsimon/vue_3dmol_gradio@latest/" + + +if os.environ.get("GRADIO_LOCAL") is not None: + url = local_url +else: + url = remote_url + +def viewer_html(path_to_file, name="input", selectionStyle={"color": "greenCarbon", + "representation": "cartoon", + "multiple": True}, representations={}): + + ext = path_to_file.split(".")[-1] + with open(path_to_file, "r") as f: + data = f.read() + moldata = {"moldata": [{"data": data, "name": name, "selectionStyle": selectionStyle,"format": ext, + "selectable": True, + "asFrames":False, + "clickable": False}] + } + # dict to json + moldata = json.dumps(moldata) + representations = json.dumps(representations) + + return """ + + + + + + + + + + Molecule View + + + + + +
+
+ Resampling the whole PDB file, select + residues in the + sequence view to resample only parts + of the structure + Resampling the selected + residues + +
+
+ + + +
+ +
+
+
+ + +
+ + + + + + +
+ + +
+
+
+  Very high ({{confidenceLabel}} > 90) +
+
+  Confident (90 > {{confidenceLabel}} > 70) +
+
+  Low (70 > {{confidenceLabel}} > 50) +
+
+  Very low ({{confidenceLabel}} < 50) +
+
+
+ + + +
+ + + + + +
+ +
+
+
+
+ + +
+ {{aa.resn}} +
+ + + +
+
+
+
+ + + + +
+ +
+ +
+ + + +
+
+
+ Settings +
+ +
+ +
+
+ + + + + + + + + + + + +
+ + {{config[setting]}} +
+ + + + +
+
+ +
+
+ + +
+
+
+ + + +
+
+
+ Representations +
+ +
+ + +
+ +
+
+ + + +
+ +
+
+ + +
+
+ + +
+
+ + +
+
+
Expand selection
+ + +
Å
+
+ +
+
+ Full residue + +
+
+ Only sidechain + +
+
+ +
+
+
+ + + + +
+
+ + + + + + + + + +
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+ + +
+ + + + + + +
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+ + + +""" +import os +import subprocess +import shlex + +def get_color(i): + colors= ["orange", "cyan", "blue", "yellow", "magenta"] + return colors[i % len(colors)]+"Carbon" + + +def output_html(path_to_file,path_to_designs,metrics, resample_idx="",mode="unconditional", selectionStyle={"color": "greenCarbon", + "representation": "cartoon", + "multiple": True}): + + if mode=="conditional": + ext = path_to_file.split(".")[-1] + with open(path_to_file, "r") as f: + data = f.read() + moldata = [{"data": data, "name": os.path.basename(path_to_file), + "selectionStyle": selectionStyle, + "format": ext, + "selectable": True, + "asFrames":False, + "clickable": False}] + representations = [{ + "model": 0, + "chain": "", + "resname": "", + "style": "cartoon", + "color": "whiteCarbon", + "residue_range": "", + "around": 0, + "byres": False, + "visible": False, + }] + if resample_idx!="": + representations.append({ + "model": 0, + "chain": "", + "resname": "", + "style": "cartoon", + "color": "greenCarbon", + "residue_range": resample_idx[1:-1], #remove leading and trailing quotes + "around": 0, + "byres": False, + "visible": False, + }) + # move file from temp to save dir + subprocess.run(shlex.split(f"cp {path_to_file} {os.path.dirname(path_to_designs[0])}/template.pdb")) + path_to_file = f"{os.path.dirname(path_to_designs[0])}/template.pdb" + designs = [{ + "model":0, + "name":"template.pdb", + "fullpath": path_to_file, + "len":76, + "metric":{ + "resample idx": resample_idx[1:-1], + }, + "visible":True, + "color":"gray" + }] + add_index = 1 + else: + designs = [] + moldata = [] + representations = [] + add_index = 0 + + for i,d in enumerate(path_to_designs): + ext = d.split(".")[-1] + with open(d, "r") as f: + data = f.read() + moldata.append({"data": data, "name": os.path.basename(d), + "selectionStyle": selectionStyle, + "format": ext, + "selectable": True, + "asFrames":False, + "clickable": False}) + representations.append({ + "model": i+add_index, + "chain": "", + "resname": "", + "style": "cartoon", + "color": get_color(i), + "residue_range": "", + "around": 0, + "byres": False, + "visible": False, + }) + designs.append({ + "model":i+add_index, + "fullpath": d, + "name":os.path.basename(d), + "metric":metrics[i], + "visible":True, + "color":"" + }) + # dict to json + moldata = json.dumps(moldata) + representations = json.dumps(representations) + designs = json.dumps(designs) + return """ + + + + + + + + Molecule View + + + + +
+
+
+
+
+
+ + +
+ + + + + + +
+ + +
+
+
+  Very high ({{confidenceLabel}} > 90) +
+
+  Confident (90 > {{confidenceLabel}} > 70) +
+
+  Low (70 > {{confidenceLabel}} > 50) +
+
+  Very low ({{confidenceLabel}} < 50) +
+
+
+ + + +
+ + + + + +
+ +
+
+
+
+ + +
+ {{aa.resn}} +
+ + + +
+
+
+
+ + + + +
+ +
+ +
+ + + +
+
+
+ Settings +
+ +
+ +
+
+ + + + + + + + + + + + +
+ + {{config[setting]}} +
+ + + + +
+
+ +
+
+ + +
+
+
+ + + +
+
+
+ Representations +
+ +
+ + +
+ +
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+ + + +
+ +
+
+ + +
+
+ + +
+
+ + +
+
+
Expand selection
+ + +
Å
+
+ +
+
+ Full residue + +
+
+ Only sidechain + +
+
+ +
+
+
+ + + + +
+
+ + + + + + + + + +
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+
{{d.model}}{{d.name}} {{k}}: {{v}}
+ +
+ +
+ +
+
+
+
+
+ + + + + + +""" + +load_js = """ + +async () => { + // create empty textarea with id selectedAtoms that is hidden + // and append it to the body + var selectedAtoms = document.createElement("textarea"); + selectedAtoms.id = "selectedAtoms"; + selectedAtoms.style.display = "none"; + document.body.appendChild(selectedAtoms); + +window.onmessage = function(e) { +selectedAtoms.value = JSON.stringify(e.data); +}; +} +""" + +get_js = """ +async (resample_idxs) => { + + var selectedAtoms = document.getElementById("selectedAtoms"); + var selectedAtomsValue = selectedAtoms.value; + + var hasNumber = /\d/; + + + if (hasNumber.test(selectedAtomsValue)==false) { + selectedAtomsValue = resample_idxs.replace(/.$/,' "') + + } + return selectedAtomsValue; + +} +"""