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from flask import Blueprint | |
import converters # module containing the custom converter classes | |
def add_app_url_map_converter(self, func, name=None): | |
""" | |
Register a custom URL map converters, available application wide. | |
:param name: the optional name of the filter, otherwise the function name | |
will be used. | |
""" |
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import requests | |
# make sure the headers accept JSON | |
headers = {'accept': 'application/json'} | |
response = requests.get('http://marid.bioc.cam.ac.uk/credo/chemcomps/001', headers=headers) | |
response.status_code # returns 200 |
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COMPND INTERLEUKIN-2 | |
CRYST1 50.470 58.020 93.080 90.00 90.00 90.00 P 21 21 21 8 | |
HETATM 2060 C1 FRG A 301 0.168 6.479 -8.783 1.00 32.66 C | |
HETATM 2059 C2 FRG A 301 1.023 7.189 -7.948 1.00 29.42 C | |
HETATM 2058 C3 FRG A 301 1.016 8.567 -7.956 1.00 31.14 C | |
HETATM 2055 C4 FRG A 301 0.160 9.195 -8.824 1.00 28.64 C | |
HETATM 2056 C5 FRG A 301 -0.699 8.509 -9.669 1.00 33.72 C | |
HETATM 2057 C6 FRG A 301 -0.693 7.128 -9.658 1.00 31.32 C | |
HETATM 2054 C7 FRG A 301 0.114 10.638 -8.862 1.00 25.03 C | |
HETATM 2053 C8 FRG A 301 0.045 11.930 -8.932 1.00 26.20 C |
We can make this file beautiful and searchable if this error is corrected: No commas found in this CSV file in line 0.
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DB03304;NCc1cnc2N=C(N)NC(=O)c12 | |
DB02543;[O-]C(=O)c1cccn1 | |
DB03254;c1ncc(n1)C1=CC=CC=C1 | |
DB01653;C[C@@H](O)[C@@H](N)C1=N\C(=C/c2cnc3ccccc23)C(=O)N1CCO | |
DB02931;CC(C)(CO[P@](O)(=O)O[P@@](O)(=O)OC[C@@H]1O[C@H]([C@H](O)[C@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)[C@@H](O)C(=O)NCCC(=O)NCCSCC(=O)NCCc1cnc2ccccc12 | |
DB01876;NC(=N)c1ccc2nc(nc2c1)C(=O)c1nc2ccc(cc2n1)C(N)=N | |
DB04534;[O-][N+](=O)c1ccc2nncc2c1 | |
DB01912;c1ccn2[Pt]3n4ccccc4-c4cccc(-c2c1)n34 | |
DB03164;C[n+]1cnc2ncnc2c1N | |
DB02557;CC(C)C[C@@H](N[P@](O)(=O)O[C@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@@H]1O)C(=O)N[C@H](Cc1cnc2ccccc12)C(O)=O |
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for res in db.structures.find({"entry.id": "2P33"}, {'pdbx_entity_nonpoly.comp_id': 1}): | |
print res | |
{u'pdbx_entity_nonpoly': [{u'comp_id': u'J07'}, {u'comp_id': u'HOH'}], u'_id': u'2P33'} |
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CREATE OR REPLACE FUNCTION tanimoto_sim_query(smiles TEXT) | |
RETURNS TABLE (molregno INTEGER, similarity REAL) AS | |
$BODY$ | |
SELECT molregno, | |
-- Tanimoto similarity | |
fp % make_circular_fp($1) | |
FROM fps | |
-- Boolean operator returning true if the Tanimoto similarity | |
-- is above the user-defined limit | |
WHERE fp %? make_circular_fp($1) |
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# select molregno, tanimoto_sml(morganbv_fp('CC(C(=O)c1ccccc1)C[NH+]1CC[NH+](CC(c2ccc(F)cc2)[NH+]2CC[NH+](C)CC2)CC1',2), circular_fp) as tanimoto | |
from chembl.fps | |
where morganbv_fp('CC(C(=O)c1ccccc1)C[NH+]1CC[NH+](CC(c2ccc(F)cc2)[NH+]2CC[NH+](C)CC2)CC1',2) % circular_fp | |
order by 2 desc | |
limit 10; | |
molregno | tanimoto | |
----------+------------------- | |
10464 | 1 | |
10451 | 0.869565217391304 |
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sift = (func.sum(cast(subquery.c.credo_contacts_is_covalent, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_vdw_clash, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_vdw, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_proximal, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_hbond, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_weak_hbond, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_xbond, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_ionic, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_metal_complex, INTEGER)), | |
func.sum(cast(subquery.c.credo_contacts_is_aromatic, INTEGER)), |
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from credoscript.extensions import chembl | |
m = ma.fetch_by_molregno(410891) | |
# get all activity cliffs of this molecule | |
m.get_activity_cliffs(chembl.ActivityCliff.sali>10) | |
>>> [<ActivityCliff(455590, 2030543, 2030536)>, | |
<ActivityCliff(455592, 2030585, 2030582)>, | |
<ActivityCliff(455594, 2030630, 2030623)>, |
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from credoscript import * | |
# FETCH PDB ENTRY 3CS9 | |
s = StructureAdaptor().fetch_by_pdb('3cs9') | |
s.title | |
>>> 'Human ABL kinase in complex with nilotinib' | |
# 3CS9 CONTAINS 4 BIOLOGICAL ASSEMBLIES | |
s.Biomolecules | |
>>> {1: <Biomolecule(1)>, |