def methodStructure (namePDB):
l_lines = loadFile.openPdbFile(namePDB)
for l in l_lines :
if search("^EXPDTA", l) and search("SOLUTION", l) :
return "SOLUTION"
return "XRAY"
def Quality(namePDB):
"""Retrieve by PDB file the Quality if X-ray header
in : name of pdb file
out : Quality -> format float, return 1000.00 if have not Quality in file"""
l_lines = loadFile.openPdbFile(namePDB)
nb_line = len (l_lines)
i = 0
while i < nb_line :
if "rfactor" in locals ().keys () and "resolution" in locals ().keys () :
return [resolution, rfactor]
if search("^REMARK 2 RESOLUTION", l_lines[i]):
line = sub('[ ]{2,}', ' ', l_lines[i])
try:
resolution = formatCharacter.formatFloat(line.split(" ")[3])
except:
resolution = 1000.0
elif search ("REMARK 3 R VALUE", l_lines[i]) :
rfactor = l_lines[i].strip ().split (":")[-1].replace (" ", "")
if rfactor == "NULL" :
rfactor = 0.0
else :
rfactor = float (rfactor)
i = i + 1
return [1000.0, 100.0]
def header(namePDB):
"""Retrieve for one PDB file the header
in : name PDB file
out : header -> format string lower"""
l_lines = loadFile.openPdbFile(namePDB)
return l_lines[0][6:].lower().strip ()
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