def InitWalls(pdbid: str) -> TunnelWalls:
"""Initiate walls for a particular structure. This consumes a dataframe given that a choice of tunnel is present"""
def get_tunnels_dataframe(csvpath: str) -> pd.DataFrame:
tunnel_instance = pd.read_csv(csvpath)
xyzr = tunnel_instance[['Distance', 'FreeRadius', 'X', 'Y', 'Z']]
return xyzr
TUNNELS = os.getenv("TUNNELS")
log = Log(os.getenv('TUNNEL_LOG'))
struct = log.get_struct(pdbid)
taxid = str(int(struct['taxid'].values[0]))
choice = int(struct['moletunnel'].values[0])
tunnelfile = "tunnel_{}.csv".format(choice)
if choice < 1:
"""See docs for disambiguation. Either mole hasn't succeeded or there is something blockign the tunnel."""
print("Choice under 1.")
return
tunnelcsv = get_tunnels_dataframe(
os.path.join(TUNNELS, taxid, pdbid, 'csv', tunnelfile))
tw = TunnelWalls(pdbid, fetchStructure(pdbid), tunnelcsv)
tw.consumeMoleDataframe(10)
return tw
def root_self(rootname: str = '') -> str:
"""Returns the rootpath for the project if it's unique in the current folder tree."""
root = os.path.abspath(
__file__)[:os.path.abspath(__file__).find(rootname) + len(rootname)]
sys.path.append(root)
load_dotenv(os.path.join(root, '.env'))
if __name__ == "__main__":
root_self('ribxz')
from ciftools.Structure import fetchStructure
from ciftools.TunnelScripts.TunnelLog import (Log)
from ciftools.Neoget import _neoget
log = Log(os.getenv("TUNNEL_LOG"))
def getConstrictedProteins(pdbid: str) -> List[str]:
cypher = """
match (n:RibosomeStructure{{rcsb_id:"{pdbid}"}})-[]-(rp:RibosomalProtein)
where "uL4" in rp.nomenclature or "uL22" in rp.nomenclature
return rp.entity_poly_strand_id,rp.nomenclature, n.rcsb_id
""".format_map({"pdbid": pdbid.upper()})
response = _neoget(cypher)
resplist = [
*map(
lambda x:
(x['rp.nomenclature'][0], x['rp.entity_poly_strand_id']), response)
]
load_dotenv(os.path.join(ROOT, '.env'))
if __name__ == "__main__":
root_self('ribxz')
from ciftools.Structure import fetchStructure
from ciftools.TunnelScripts.TunnelLog import (Log)
from ciftools.TunnelScripts.ptc_site import (residues_average,
get_ptc_residues)
from ciftools.TunnelScripts.WallsReportGeneration import InitWalls
from ciftools.TunnelScripts.WallsReportGeneration import add_nomenclature_map_to_report
TUNNELS = os.getenv("TUNNELS")
STATIC_ROOT = os.getenv("STATIC_ROOT")
log = Log(os.getenv('TUNNEL_LOG'))
# for struct in log.all_structs():
# pdbid='3J7Z'
# REPORT_PATH=os.path.join(STATIC_ROOT,pdbid,"{}_TUNNEL_REPORT.json".format(pdbid))
# ## Generating report
# walls =InitWalls(pdbid)
# walls.consumeMoleDataframe(10)
# walls.generateReport(REPORT_PATH)
# add_nomenclature_map_to_report(pdbid,REPORT_PATH)
## Adding ptc
# for struct in log.all_structs():
# log.update_struct(struct,
# dowrite=True,
# **{"PTC_average":
from ciftools.Structure import fetchStructure
from ciftools.scripts.splitStruct import fetchChain
from typing import List
from Bio.PDB.Residue import Residue
from pymol import cmd
from ciftools.TunnelScripts.TunnelLog import Log
RADIUS = os.getenv('SCOOP_RADIUS')
TUNNELS = os.getenv('TUNNELS')
STATIC_ROOT = os.getenv('STATIC_ROOT')
pdbid = sys.argv[1].upper()
log = Log(os.getenv('TUNNEL_LOG'))
struct = fetchStructure(pdbid)
record = log.get_struct(pdbid)
species = str( int( record.taxid.values[0] ) )
structpath = os.path.join(STATIC_ROOT,pdbid,"{}.cif".format(pdbid))
scoopsavepath = os.path.join(TUNNELS,species,pdbid,'{}_{}Ascoop.pdb'.format(pdbid,RADIUS))
if not os.path.exists(os.path.dirname( scoopsavepath )):
os.makedirs(os.path.dirname( scoopsavepath ))
cmd.load(structpath)
x = cmd.select(f'resi 2504')
cmd.select(f'br. {pdbid} w. {RADIUS} of \'sele\'')
cmd.save( scoopsavepath, 'sele' )
print("Saved to {}".format(scoopsavepath))
PDBID = sys.argv[1].upper()
STATIC_ROOT = os.getenv("STATIC_ROOT")
STRUCT_REPORT_PATH = os.path.join(STATIC_ROOT,PDBID,f'{PDBID}_TUNNEL_REPORT.json')
if not os.path.exists(STRUCT_REPORT_PATH):
try:
## Generating report
walls = InitWalls(PDBID)
walls.consumeMoleDataframe(10)
walls.generateReport(STRUCT_REPORT_PATH)
add_nomenclature_map_to_report(PDBID,STRUCT_REPORT_PATH)
except error:
print(error)
exit("Failed to generate report for {}. Does the tunnel csv exist?".format(PDBID))
log = Log(os.getenv('TUNNEL_LOG'))
ProteinsColorgenerator = iter( ['purple','cyan','orange',"gray",'yellow','magenta','brown','turqoise','pink'] )
with open(STRUCT_REPORT_PATH, 'rb') as infile:
report = json.load(infile)
walls = InitWalls(PDBID)
tunneldf = walls.mole_dataframe
def locate_res_in_df(rescoords:List[float],tunnel_df:pd.DataFrame):
respos = np.array(rescoords)
rowid = -1
currdist = 10000000
for index,row in tunnel_df.iterrows():
moleparser = makeparser()
load_dotenv(dotenv_path='/home/rxz/dev/ribxz/.env')
MOLE_EXE = os.getenv('MOLE_EXECUTABLE')
TUNNELS = os.getenv("TUNNELS")
SCOOP_RADIUS = os.getenv("SCOOP_RADIUS")
args = moleparser.parse_args()
args = filter((lambda kvpair: None not in kvpair), vars(args).items())
args = dict(args)
pdbid = args['PDBID'].upper()
load_dotenv('/home/rxz/dev/ribxz/.env')
log = Log(os.getenv("TUNNEL_LOG"))
record = log.get_struct(pdbid)
species = str( int( record.taxid.values[0] ) )
constriction = record.constriction_coord.values[0]
inputconfigpath = os.path.join(TUNNELS, species, pdbid, '{}_moleinput.xml'.format(pdbid) )
inputstructpath = os.path.join(TUNNELS, species, pdbid, '{}_{}Ascoop.pdb'.format(pdbid, SCOOP_RADIUS))
outpath = os.path.join(TUNNELS, species, pdbid)
args['Input'] = inputstructpath
args['Output'] = outpath
args['ConfigPath'] = inputconfigpath
# pymol.cmd.load(inputstructpath)
# pymol.cmd.select('PTC', 'resi 2506')