reso = float(line[-2])
except:
reso = 'UNKNOWN'
elif 'EXPERIMENT TYPE' in line:
line = line.split()
exptyp = line[-1]
if line[-1] == 'DIFFRACTION' and line[-2] == 'X-RAY':
exptyp = 'X-RAY'
fp1.close()
#Get the metal ion which is the ion user want to process
metallist = []
for i in atids:
resname = mol.residues[mol.atoms[i].resid].resname
atname = mol.atoms[i].atname
if (resname, atname) in list(METAL_PDB.keys()):
if METAL_PDB[(resname, atname)][0] == ionname:
metallist.append(i)
#for each metal ion in the metal list, print the metal center
for i in metallist:
mccrds = [] #The crds of metal site
crdi = mol.atoms[i].crd
elmti = mol.atoms[i].element
residi = mol.atoms[i].resid
atnamei = mol.atoms[i].atname
resnamei = mol.residues[residi].resname
radiusi = CoRadiiDict[elmti]
mcresids = [] #MetalCenter residue IDs
def get_atominfo_fpdb(fname):
Atoms = {}
Residues = {}
atids = []
resids = []
resnamedict = {}
conterdict = {}
fp = open(fname, 'r')
for line in fp:
if (line[0:4] == "ATOM") or (line[0:6] == "HETATM"):
gtype = line[0:6].strip(" ")
atid = int(line[6:11])
atids.append(atid)
atname = line[12:16].strip(" ")
allocind = line[16:17]
resname = line[17:20].strip(" ")
chainid = line[21:22]
resid = int(line[22:26])
codeinsert = line[26:27]
crdx = float(line[30:38])
crdy = float(line[38:46])
crdz = float(line[46:54])
crd = (crdx, crdy, crdz)
occp = line[54:60]
tempfac = line[60:66]
atomtype = line[76:78].strip(" ")
charge = line[78:80]
if (resname, atname) in list(METAL_PDB.keys()):
element = METAL_PDB[(resname, atname)][0]
elif atname[0:2].upper() in ['CL', 'BR']:
element = atname[0].upper() + atname[1].lower()
else:
element = atname[0]
if atid not in list(Atoms.keys()):
Atoms[atid] = Atom(gtype, atid, atname, element, atomtype, crd,
charge, resid, resname)
else:
raise pymsmtError('There are more than one atom with atom id '
'%d in the PDB file : %s .' % (atid, fname))
if resid not in resids:
resids.append(resid)
if resid not in list(resnamedict.keys()):
resnamedict[resid] = resname
fp.close()
resids.sort()
for i in resids:
preconter = []
for j in atids:
if (Atoms[j].resid == i) and (j not in preconter):
preconter.append(j)
preconter.sort()
conterdict[i] = preconter
for i in resids:
resname = resnamedict[i]
resconter = conterdict[i]
Residues[i] = Residue(i, resname, resconter)
del resnamedict
del conterdict
mol = Molecule(Atoms, Residues)
return mol, atids, resids
def get_atominfo(fname):
#Detect the line numbers of each part information
fp = open(fname, 'r')
lnum = 1
for line in fp:
if ("@<TRIPOS>ATOM" in line):
atbgin = lnum + 1
elif ("@<TRIPOS>BOND" in line):
atend = lnum
lnum = lnum + 1
fp.close()
Atoms = {}
Residues = {}
atids = []
resids = []
resnamedict = {}
conterdict = {}
for i in range(atbgin, atend):
atid, atname, crdx, crdy, crdz, atomtype, resid, resname, charge = \
linecache.getline(fname, i).split()[:9]
#for atom part
gtype = "ATOM"
atid = int(atid)
atids.append(atid)
crd = (float(crdx),float(crdy),float(crdz))
charge = float(charge)
resid = int(resid)
if (resname, atname) in list(METAL_PDB.keys()):
element = METAL_PDB[(resname, atname)][0]
elif atname[0:2].upper() in ['CL', 'BR']:
element = atname[0].upper() + atname[1].lower()
else:
element = atname[0]
if atid not in list(Atoms.keys()):
Atoms[atid] = Atom(gtype, atid, atname, element, atomtype, crd, charge, resid, resname)
else:
raise pymsmtError('There are more than one atom with atom id '
'%d in the mol2 file : %s .' %(atid, fname))
#for the residue part
if resid not in resids:
resids.append(resid)
if resid not in list(resnamedict.keys()):
resnamedict[resid] = resname
#clean the memory
linecache.clearcache()
resids.sort()
for i in resids:
preconter = []
for j in atids:
if (Atoms[j].resid == i) and (j not in preconter):
preconter.append(j)
preconter.sort()
conterdict[i] = preconter
for i in resids:
resname = resnamedict[i]
resconter = conterdict[i]
Residues[i] = Residue(i, resname, resconter)
del resnamedict
del conterdict
mol = Molecule(Atoms, Residues)
return mol, atids, resids
reso = float(line[-2])
except:
reso = 'UNKNOWN'
elif 'EXPERIMENT TYPE' in line:
line = line.split()
exptyp = line[-1]
if line[-1] == 'DIFFRACTION' and line[-2] == 'X-RAY':
exptyp = 'X-RAY'
fp1.close()
#Get the metal ion which is the ion user want to process
metallist = []
for i in atids:
resname = mol.residues[mol.atoms[i].resid].resname
atname = mol.atoms[i].atname
if (resname, atname) in list(METAL_PDB.keys()):
if METAL_PDB[(resname, atname)][0] == ionname:
metallist.append(i)
#for each metal ion in the metal list, print the metal center
for i in metallist:
mccrds = [] #The crds of metal site
crdi = mol.atoms[i].crd
elmti = mol.atoms[i].element
residi = mol.atoms[i].resid
atnamei = mol.atoms[i].atname
resnamei = mol.residues[residi].resname
radiusi = CoRadiiDict[elmti]
mcresids = [] #MetalCenter residue IDs