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Working moe import lb and other changes #26

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Jan 18, 2024
Merged

Working moe import lb and other changes #26

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45c7058
Remove get_include_lib and replace with load_tk_module helper
themoenen Jan 17, 2024
fe17960
Cleaned up mol viewer + replaces new_molecule everywhere
themoenen Jan 18, 2024
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86 changes: 86 additions & 0 deletions openad/flask_apps/molviewer/index copy.html
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@@ -0,0 +1,86 @@
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Document</title>
<link rel="stylesheet" href="css/carbon.css" />
<link rel="stylesheet" href="css/main.css" />
<link rel="stylesheet" href="app/molviewer-main.css" />
<script src="app/3dmol/3Dmol-min.js"></script>
<script src="app/jsmol/JSmol.min.js"></script>
</head>
<body>
<div id="mol-render">
<div class="mol-2d">{{mol_svg | safe}}</div>
<div class="mol-3d"></div>
</div>

<div id="grid">
<!-- <div class="grid grid-1"></div>
<div class="grid grid-2"></div>
<div class="grid grid-3"></div>
<div class="grid grid-4"></div>
<div class="grid grid-5"></div>
<div class="grid grid-6"></div>
<div class="grid grid-7"></div>
<div class="grid grid-8"></div>
<div class="grid grid-9"></div>
<div class="grid grid-10"></div>
<div class="grid grid-11"></div>
<div class="grid grid-12"></div> -->

<!-- Left -->
<div class="col-left">
<!-- <div id="breadcrumbs">Molecules &nbsp;&rsaquo;&nbsp; Ibuprofen.json</div> -->
<div id="title-wrap">
<div class="icn-mol"></div>
<h1 id="data-name" data-val="{{mol.name}}" class="loading">{% if mol.name %}{{mol.name}}{% else %}Unnamed Molecule{% endif %}</h1>
<!-- <div id="btn-bookmark" class="icn-star"></div> -->
</div>
<div id="identification">
<div><b>InChI:</b> <span id="data-inchi">{{mol['properties']['inchi']}}</span></div>
<div><b>InChIKey:</b> <span id="data-inchikey">{{mol['properties']['inchikey']}}</span></div>
<div><b>Canonical SMILES:</b> <span id="data-canonical-smiles">{{mol['properties']['canonical_smiles']}}</span></div>
<div><b>Isomeric SMILES:</b> <span id="data-isomeric-smiles">{{mol['properties']['isomeric_smiles']}}</span></div>
<div>
<b>PubChem CID:</b> {% if mol['properties']['cid'] %}<a id="data-cid" href="https://pubchem.ncbi.nlm.nih.gov/compound/{{mol['properties']['cid']}}" target="_blank">{{mol['properties']['cid']}}</a>{% else %}<span
id="fetching-pubchem"
data-text="Fetching"
>Fetching</span
>{% endif %}
</div>
</div>

<br />
<hr />
<br />

<div id="parameters">
<h2>Parameters</h2>
<div class="param-wrap">
{% for prop in mol['properties'] %}
{% if prop != 'record' %}
<div{% if mol['property_sources'][prop] %} title="{{mol['property_sources'][prop]}}"{% endif %}><b>{{prop}}:</b> {% if mol['properties'][prop] %}{{mol['properties'][prop]}}{% else %}<span class="non-val"></span>{% endif %}</div>
{% endif %}
{% endfor %}
</div>
</div>

<br />
<a class="toggle-expand" id="show-json" href="#">JSON</a>
<pre style="tab-size: 30px">{{mol_json}}</pre>
<br /><br />

<a class="toggle-expand" id="show-json-pubchem" href="#">PubChem Record</a>
<pre style="tab-size: 30px">{{pubchem_json}}</pre>
</div>

<!-- Right -->
<div class="col-right"></div>
</div>
<div id="mol-data" data-sdf="{{mol_sdf}}" data-json="{{mol_json}}"></div>

<script src="app/molviewer-main.js"></script>
</body>
</html>
41 changes: 30 additions & 11 deletions openad/flask_apps/molviewer/index.html
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Expand Up @@ -39,39 +39,58 @@ <h1 id="data-name" data-val="{{mol.name}}" class="loading">{% if mol.name %}{{mo
<!-- <div id="btn-bookmark" class="icn-star"></div> -->
</div>
<div id="identification">
<div><b>InChI:</b> <span id="data-inchi">{{mol['properties']['inchi']}}</span></div>
<div><b>InChIKey:</b> <span id="data-inchikey">{{mol['properties']['inchikey']}}</span></div>
<div><b>Canonical SMILES:</b> <span id="data-canonical-smiles">{{mol['properties']['canonical_smiles']}}</span></div>
<div><b>Isomeric SMILES:</b> <span id="data-isomeric-smiles">{{mol['properties']['isomeric_smiles']}}</span></div>
<div><b>InChI:</b> <span id="data-inchi">{{mol['identifiers']['inchi']}}</span></div>
<div><b>InChIKey:</b> <span id="data-inchikey">{{mol['identifiers']['inchikey']}}</span></div>
<div><b>Canonical SMILES:</b> <span id="data-canonical-smiles">{{mol['identifiers']['canonical_smiles']}}</span></div>
<div><b>Isomeric SMILES:</b> <span id="data-isomeric-smiles">{{mol['identifiers']['isomeric_smiles']}}</span></div>
<div><b>Formula:</b> <span id="data-isomeric-smiles">{{mol['identifiers']['formula']}}</span></div>
<div>
<b>PubChem CID:</b> {% if mol['properties']['cid'] %}<a id="data-cid" href="https://pubchem.ncbi.nlm.nih.gov/compound/{{mol['properties']['cid']}}" target="_blank">{{mol['properties']['cid']}}</a>{% else %}<span
<b>PubChem CID:</b> {% if mol['identifiers']['cid'] %}<a id="data-cid" href="https://pubchem.ncbi.nlm.nih.gov/compound/{{mol['identifiers']['cid']}}" target="_blank">{{mol['identifiers']['cid']}}</a>{% else %}<span
id="fetching-pubchem"
data-text="Fetching"
>Fetching</span
>{% endif %}
</div>
</div>

<br />
<hr />
<br />

<div id="synonyms">
<h2>Synonyms</h2>
<div class="synonyms-wrap">
{% for synonym in mol['synonyms'] %}
{{synonym}}<br/>
{% endfor %}
</div>
</div>

<br />
<hr />
<br />

<div id="parameters">
<h2>Parameters</h2>
<div class="param-wrap">
{% for prop in mol['properties'] %}
{% if prop != 'record' %}
<div{% if mol['property_sources'][prop] %} title="{{mol['property_sources'][prop]}}"{% endif %}><b>{{prop}}:</b> {% if mol['properties'][prop] %}{{mol['properties'][prop]}}{% else %}<span class="non-val"></span>{% endif %}</div>
{% endif %}
{% endfor %}
</div>
</div>

<br />
<hr />
<br />

<div id="analysis">
<h2>Analysis</h2>
Comin soon...
</div>

<br />
<a class="toggle-expand" id="show-json" href="#">JSON</a>
<pre style="tab-size: 30px">{{mol_json}}</pre>
<br /><br />

<a class="toggle-expand" id="show-json-pubchem" href="#">PubChem Record</a>
<pre style="tab-size: 30px">{{pubchem_json}}</pre>
</div>

<!-- Right -->
Expand Down
13 changes: 12 additions & 1 deletion openad/flask_apps/molviewer/molviewer-main.css
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Expand Up @@ -183,8 +183,19 @@ body {
* TEMP
*/

#parameters div {
#parameters .param-wrap {
display: flex;
flex-wrap: wrap;
}

#parameters .param-wrap div {
margin-bottom: 4px;
padding-right: 20px;
width: 25%;
box-sizing: border-box;
}
#synonyms .synonyms-wrap {
column-count: 4;
}

pre {
Expand Down
6 changes: 4 additions & 2 deletions openad/flask_apps/molviewer/routes.py
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Expand Up @@ -4,14 +4,16 @@


def fetchRoutesMolViewer(cmd_pointer, mol, mol_sdf, mol_svg):
from openad.molecules.mol_functions import organize_properties

mol_json = json.dumps(mol, indent="\t")
pubchem_json = {}

def main():
_stringify_prop_sources(mol)
return render_template(
"/molviewer/index.html",
mol=mol,
mol=organize_properties(mol),
mol_json=mol_json,
pubchem_json=pubchem_json,
mol_sdf=mol_sdf,
Expand All @@ -28,7 +30,7 @@ def enrich():
_stringify_prop_sources(mol)
html = render_template(
"/molviewer/index.html",
mol=mol,
mol=organize_properties(mol),
mol_json=mol_json,
pubchem_json=pubchem_json,
mol_sdf=mol_sdf,
Expand Down
14 changes: 14 additions & 0 deletions openad/helpers/general.py
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Expand Up @@ -321,6 +321,20 @@ def print_separator(style=None, width=None, return_val=False):
return output_text(f"{'-' * width}", nowrap=True, return_val=return_val)


# Load a module or a module's function from a toolkit folder.
def load_tk_module(cmd_pointer, toolkit_name, lib_name, func_name=None):
import importlib.util as ilu

folder = cmd_pointer.toolkit_dir + f"/{toolkit_name}/{lib_name}.py"
spec = ilu.spec_from_file_location(lib_name, folder)
module = ilu.module_from_spec(spec)
spec.loader.exec_module(module)
if func_name:
return getattr(module, func_name)
else:
return module


#
#
#
Expand Down
14 changes: 4 additions & 10 deletions openad/molecules/mol_api.py
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Expand Up @@ -4,22 +4,16 @@ def get_molecule_data(cmd_pointer, molecule_identifier):
Used to enrich the molecule data from the molecule viewer Flask app.
"""

from openad.molecules.mol_commands import retrieve_mol_from_list, retrieve_mol, get_identifiers, get_properties

return_dict = {}
from openad.molecules.mol_commands import retrieve_mol_from_list, retrieve_mol

mol = retrieve_mol_from_list(cmd_pointer, molecule_identifier)

if mol is None:
mol = retrieve_mol(molecule_identifier)
if mol is not None:
cmd_pointer.last_external_molecule = mol.copy()
return mol
# # cmd_pointer.last_external_molecule = mol.copy()
# return_dict["smiles"] = get_identifiers(mol)["canonical_smiles"]
# return_dict["identifiers"] = get_identifiers(mol)
# return_dict["properties"] = get_properties(mol)
# return_dict["synonyms"] = mol["synonyms"]["Synonym"]
# return_dict["analysis"] = mol["analysis"]
# return return_dict
# return organize_properties(mol)

else:
return None
10 changes: 5 additions & 5 deletions openad/molecules/mol_batch_files.py
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Expand Up @@ -5,7 +5,7 @@
from openad.molecules.mol_functions import (
merge_molecule_properties,
valid_smiles,
new_molecule_TRASH,
new_molecule,
canonical_smiles,
)
from openad.molecules.mol_commands import retrieve_mol_from_list, add_molecule
Expand All @@ -29,7 +29,7 @@ def load_batch_molecules(cmd_pointer, inp):
if "pubchem_merge" in inp.as_dict():
batch_pubchem(cmd_pointer, mol_dataframe)
if mol_dataframe is not None:
shred_merge_add_Dataframe_mols(mol_dataframe, cmd_pointer)
shred_merge_add_df_mols(mol_dataframe, cmd_pointer)
return True


Expand Down Expand Up @@ -87,8 +87,8 @@ def __init__(self):
batch_spinner.stop()


def shred_merge_add_Dataframe_mols(dataframe, cmd_pointer):
"""shreds the molecule relevent propoerties from data frame and loads into molecules"""
def shred_merge_add_df_mols(dataframe, cmd_pointer):
"""shreds the molecule relevent properties from dataframe and loads into molecules"""
dict_list = dataframe.to_dict("records")
for a_mol in dict_list:
Name_Flag = False
Expand Down Expand Up @@ -121,7 +121,7 @@ def shred_merge_add_Dataframe_mols(dataframe, cmd_pointer):
if merge_mol is None:
if name is None:
name = a_mol["SMILES"]
merge_mol = new_molecule_TRASH(name, a_mol["SMILES"])
merge_mol = new_molecule(a_mol["SMILES"], name)
if merge_mol is not None:
merge_mol = merge_molecule_properties(a_mol, merge_mol)
else:
Expand Down
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