def register_fetch_gui():
from chimera import fetch
fetch.registerIdType('EDS (2fo-fc)', 4, '1a0m', open_eds_2fofc_map,
'eds.bmc.uu.se/eds',
'http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=%s')
fetch.registerIdType('EDS (fo-fc)', 4, '1a0m', open_eds_fofc_map,
'eds.bmc.uu.se/eds',
'http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=%s')
def register_fetch_gui():
from chimera import fetch
fetch.registerIdType('PQS', 4, '2cwj', open_pqs, 'pqs.ebi.ac.uk',
'http://pqs.ebi.ac.uk/pqs-bin/pqs-hits?px=%s')
import chimera.extension
class ModBaseEMO(chimera.extension.EMO):
def name(self):
return "ModBase"
def description(self):
return "Fetch ModBase database entry"
def categories(self):
return ["Structure Analysis"]
def open(self, path):
# Comment out if cannot open new file type
return self.module("gui").processModBaseID(path)
emo = ModBaseEMO(__file__)
from chimera import fileInfo, FileInfo
fileInfo.register("ModBase", # name of file type
emo.open, # function to call
None, # extensions
['modbase', 'ModBase'], # prefixes
category=FileInfo.STRUCTURE) # category
from chimera import fetch, openModels
fetch.registerIdType("ModBase", # name of database
8, # identifier length
"P04848", # example
lambda id, om=openModels: om.open(id, type="ModBase"),
# callback
"modbase.compbio.ucsf.edu", # homepage
"http://modbase.compbio.ucsf.edu/modbase-cgi/display.cgi?displaymode=general") # info url
def openSmiles(self, smiles):
Smiles = self.module('Smiles')
return [Smiles.smiles2mol(smiles)]
def openPubChem(self, pcID):
PubChem = self.module('PubChem')
return [PubChem.pubChem2mol(pcID)]
emo = BuildStructureEMO(__file__)
chimera.extension.manager.registerExtension(emo)
chimera.fileInfo.register("SMILES",
emo.openSmiles,
None, ["smiles", "SMILES"],
category=chimera.FileInfo.STRUCTURE)
chimera.fileInfo.register("PubChem",
emo.openPubChem,
None, ["pubchem", "PubChem"],
category=chimera.FileInfo.STRUCTURE)
from chimera import fetch, openModels
fetch.registerIdType(
"PubChem", # name of database
6, # identifier length
"12123", # example
lambda id, om=openModels: om.open(id, type="PubChem"),
# callback
"pubchem.ncbi.nlm.nih.gov", # homepage
"http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=%s"
) # info url
site = 'viperdb.scripps.edu'
url_pattern = 'http://%s/cgi-bin/stream_vdb.cgi?VDB=%s'
url = url_pattern % (site, id)
name = 'VIPERdb %s' % id
minimum_file_size = 2048 # bytes
from chimera import fetch
path, headers = fetch.fetch_file(url, name, minimum_file_size,
'VIPERdb', id + '.vdb')
mlist = open_viper_model(path, model_name = id)
return mlist
# -----------------------------------------------------------------------------
# Register to open VIPERdb virus capsid models.
#
import chimera
fi = chimera.fileInfo
fi.register('VIPERdb', open_viper_model, ['.vdb'], ['viper'],
category = fi.STRUCTURE)
fi.register('VIPERID', open_viper_id, None, ['viperID'],
category = fi.STRUCTURE)
# -----------------------------------------------------------------------------
# Register to fetch models from VIPERdb web site.
#
from chimera import fetch
fetch.registerIdType('VIPERdb', 4, '1ej6', open_viper_id, 'viperdb.scripps.edu',
'http://viperdb.scripps.edu/info_page.php?VDB=%s')
def description(self):
return "Fetch CASTp database entry"
def categories(self):
return ["Structure Analysis"]
def openID(self, id):
return self.module("gui").processCastpID(id)
def openPath(self, path):
return self.module("gui").openCastp(path)
emo = CastpEMO(__file__)
from chimera import fileInfo, FileInfo
fileInfo.register("CASTp ID", # name of file type
emo.openID, # function to call
None, # extensions
['castp', 'CASTp'], # prefixes
category=FileInfo.STRUCTURE) # category
fileInfo.register("CASTp", # name of file type
emo.openPath, # function to call
[".poc"], # extensions
[], # prefixes
category=FileInfo.STRUCTURE) # category
from chimera import fetch, openModels
fetch.registerIdType("CASTp", # name of database
6, # identifier length
"1www", # example
lambda id, om=openModels: om.open(id, type="CASTp ID"),
# callback
"sts-fw.bioengr.uic.edu/castp/", # homepage
"http://sts-fw.bioengr.uic.edu/castp/query.php?pdbid=%s&visual=jmol&submitid=Search") # info url
def openPath(self, path):
return self.module("gui").openCastp(path)
emo = CastpEMO(__file__)
from chimera import fileInfo, FileInfo
fileInfo.register(
"CASTp ID", # name of file type
emo.openID, # function to call
None, # extensions
['castp', 'CASTp'], # prefixes
category=FileInfo.STRUCTURE) # category
fileInfo.register(
"CASTp", # name of file type
emo.openPath, # function to call
[".poc"], # extensions
[], # prefixes
category=FileInfo.STRUCTURE) # category
from chimera import fetch, openModels
fetch.registerIdType(
"CASTp", # name of database
6, # identifier length
"1www", # example
lambda id, om=openModels: om.open(id, type="CASTp ID"),
# callback
"sts-fw.bioengr.uic.edu/castp/", # homepage
"http://sts-fw.bioengr.uic.edu/castp/query.php?pdbid=%s&visual=jmol&submitid=Search"
) # info url
def categories(self):
return ['Structure Editing']
def activate(self):
from chimera import dialogs
gui = self.module('gui')
dlg = dialogs.display(gui.BuildStructureDialog.name)
dlg.notebook.selectpage(gui.ADD_ATOMS)
return None
def openSmiles(self, smiles):
Smiles = self.module('Smiles')
return [Smiles.smiles2mol(smiles)]
def openPubChem(self, pcID):
PubChem = self.module('PubChem')
return [PubChem.pubChem2mol(pcID)]
emo = BuildStructureEMO(__file__)
chimera.extension.manager.registerExtension(emo)
chimera.fileInfo.register("SMILES", emo.openSmiles, None,
["smiles", "SMILES"], category=chimera.FileInfo.STRUCTURE)
chimera.fileInfo.register("PubChem", emo.openPubChem, None,
["pubchem", "PubChem"], category=chimera.FileInfo.STRUCTURE)
from chimera import fetch, openModels
fetch.registerIdType("PubChem", # name of database
6, # identifier length
"12123", # example
lambda id, om=openModels: om.open(id, type="PubChem"),
# callback
"pubchem.ncbi.nlm.nih.gov", # homepage
"http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=%s") # info url
url_pattern = 'http://%s/cgi-bin/stream_vdb.cgi?VDB=%s'
url = url_pattern % (site, id)
name = 'VIPERdb %s' % id
minimum_file_size = 2048 # bytes
from chimera import fetch
path, headers = fetch.fetch_file(url, name, minimum_file_size, 'VIPERdb',
id + '.vdb')
mlist = open_viper_model(path, model_name=id)
return mlist
# -----------------------------------------------------------------------------
# Register to open VIPERdb virus capsid models.
#
import chimera
fi = chimera.fileInfo
fi.register('VIPERdb',
open_viper_model, ['.vdb'], ['viper'],
category=fi.STRUCTURE)
fi.register('VIPERID', open_viper_id, None, ['viperID'], category=fi.STRUCTURE)
# -----------------------------------------------------------------------------
# Register to fetch models from VIPERdb web site.
#
from chimera import fetch
fetch.registerIdType('VIPERdb', 4, '1ej6', open_viper_id,
'viperdb.scripps.edu',
'http://viperdb.scripps.edu/info_page.php?VDB=%s')