def ligandInPDBConnectMatrixLigand(PDB_ID, ligand):
"""load ligand in structure in PDB file
out : list atom in ligands with connect matrix calculated"""
l_lines = openPdbFile(PDB_ID)
l_atom = []
l_serial = []
for line in l_lines:
if search ("^HETATM", line):
atom = parsing.lineCoords(line)
if atom["resName"] == ligand and atom["element"] != "H":
if not atom["serial"] in l_serial :
l_atom.append(atom)
l_serial.append(atom["serial"])
checkOnlyOneLigand(l_atom) ####retrieve only first ligand
calcul.buildConnectMatrix(l_atom, PDB_ID)
return l_atom
def neighbors(rayon, atom_central, pdb, subs = "global", l_atom_lig = [] ): # change the name because in the same time function and variable
"""Search neighbors for all ligand
in : rayon where is atoms, central atom, pdb file
out : list atoms found"""
l_atom = []
linesPDB = loadFile.openPdbFile(pdb)
for line in linesPDB:
if search("^ATOM", line) or search("^HETATM", line):
atom = parsing.lineCoords(line)
if atom != {} and atom["element"] != "H":
distance = calcul.distanceTwoatoms(atom_central, atom)
if distance <= rayon and distance != 0.0:
if atom_central["resSeq"] != atom["resSeq"]: # check if variation
if tool.atomInList(l_atom, atom) == 0:
atom["distance"] = distance
atom["angleSubs"] = calcul.angleSubs(atom_central, atom, l_atom_lig, subs)
atom["classification"] = structure.classificationATOM(atom)
l_atom.append(atom)
return l_atom
def ExtractInfoPDBID(PDB_ID) :
# control PDB exist in the folder where the PDB is included
p_PDBfile = pathManage.pathDitrectoryPDB() + PDB_ID.lower() + ".pdb"
if not path.exists(p_PDBfile) :
print "ERROR load PDB ID -> ", PDB_ID
return {}
# initialisation of the output
d_out = {}
d_out["protein"] = []
d_out["RX"] = 100.0
d_out["RFree"] = 100.0
filin = open (p_PDBfile, "r")
l_linesPDB = filin.readlines ()
filin.close ()
d_out["Header"] = l_linesPDB[0][6:].lower().strip ()
for linePDB in l_linesPDB :
# Resolution
if search("^REMARK 2 RESOLUTION", linePDB):
lineRX = sub('[ ]{2,}', ' ', linePDB)
try : d_out["RX"] = float (lineRX.split(" ")[3].replace (" ", ""))
except : pass
# Rfree
elif search ("REMARK 3 R VALUE", linePDB) :
rfactor = linePDB.strip ().split (":")[-1].replace (" ", "")
if rfactor == "NULL" :
rfactor = 0.0
else :
rfactor = float (rfactor)
d_out["RFree"] = rfactor
# protein
elif search ("^ATOM", linePDB) :
atom_prot = parsing.lineCoords (linePDB, remove_H = 1)
if atom_prot != None :
d_out["protein"].append (atom_prot)
elif search ("^HETATM", linePDB) :
atom_HET = parsing.lineCoords (linePDB, remove_H = 1)
if atom_HET != None :
name_lig = atom_HET["resName"]
if not name_lig in d_out.keys () :
d_out[name_lig] = []
d_out[name_lig].append (atom_HET)
# kept only first model in the protein in case of RMN structure
elif search ("^ENDMDL", linePDB) :
break
# separate the ligand in double
for k in d_out.keys() :
if k != "protein" and k != "RX" and k != "RFree" and k != "Header" :
d_out[k] = parsing.separateByLigand (d_out[k], debug = 0)
for l_atom_lig in d_out[k] :
l_atom_lig = calcul.buildConnectMatrix(l_atom_lig)
return d_out
