def read_pdb(path):
sec = time.time()
records = pdbmodule.read(path)
sec = time.time() - sec
## collect some statistics from the PDB records
stats = {}
stats["path"] = path
## adverages
Bnum_prot = 0
Badv_prot = 0.0
Unum_prot = 0
Uadv_prot = 0.0
Anum_prot = 0
Aadv_prot = 0.0
for rec in records:
rec_type = rec["RECORD"]
if rec_type == "ATOM " or rec_type == "HETATM":
if res_dict.has_key(rec.get("resName", "")):
try:
stats["atoms"] += 1
except KeyError:
stats["atoms"] = 1
try:
Badv_prot += rec["tempFactor"]
except KeyError:
pass
else:
Bnum_prot += 1
cid = rec.get("chainID")
if cid:
try:
pchains = stats["prot_chains"]
except KeyError:
stats["prot_chains"] = [cid]
else:
if cid not in pchains:
pchains.append(cid)
elif rec_type == "HETATM":
try:
stats["hetatoms"] += 1
except KeyError:
stats["hetatoms"] = 1
elif rec_type == "ANISOU":
try:
stats["anisou"] += 1
except KeyError:
stats["anisou"] = 1
if res_dict.has_key(rec.get("resName", "")):
Usum = rec["u[0][0]"]+rec["u[1][1]"]+rec["u[2][2]"]
Uadv_prot += float(Usum)/30000.0
Unum_prot += 1
try:
aniso = set_aniso_dict(rec, stats["aniso_dict"])
except KeyError:
stats["aniso_dict"] = mk_aniso_dict()
aniso = set_aniso_dict(rec, stats["aniso_dict"])
if aniso != None:
Anum_prot += 1
Aadv_prot += aniso
elif rec_type == "REMARK":
try:
text = rec["text"]
except KeyError:
continue
m = re_res.match(text)
if m != None:
try:
stats["res"] = float(m.group(1))
except ValueError:
pass
continue
m = re_program.match(text)
if m != None:
stats["program"] = m.group(1)
elif rec_type == "REVDAT":
if rec.get("modType") == 0:
stats["date"] = rec.get("modDate", "dd-mmm-yy")
elif rec_type == "EXPDTA":
stats["tech"] = rec["technique"]
elif rec_type == "HEADER":
stats["id"] = rec.get("idCode", "XXXX")
## finish calculating some adverages
try:
stats["Badv_prot"] = Badv_prot / Bnum_prot
except ZeroDivisionError:
pass
try:
stats["Uadv_prot"] = Uadv_prot / Unum_prot
except ZeroDivisionError:
pass
try:
stats["Aadv_prot"] = Aadv_prot / Anum_prot
except ZeroDivisionError:
pass
return stats
def read_pdb(path):
sec = time.time()
records = pdbmodule.read(path)
sec = time.time() - sec
Ueq = []
atom_obj = []
atom_dict = {}
listx = []
state = 0
overall = {}
n = 1
has_anisou = 0
for rec in records:
## Start with empty dict
atom_dict = {'u[1][1]': 0, 'chainID': '', 'name': '',
'resSeq': 0, 'u[0][1]': 0, 'u[0][0]': 0,
'u[0][2]': 0, 'u[1][2]': 0, 'element': '',
'RECORD': '', 'u[2][2]': 0, 'resName': '',
'serial': 0, 'has_anisou': 0,
'tempFactor': 0.0, 'x': 0.0, 'y': 0.0, 'z': 0.0,
'occupancy': 0.0}
rec_type = rec["RECORD"]
if rec_type == "REMARK":
try:
text = rec["text"]
except KeyError:
continue
## Capture the "OVERALL ANISOTROPIC B VALUE" fields
if state == 0:
m = re_overall_b.match(text)
if m != None:
state = 1
elif state == 1:
m = re_b11.match(text)
if m != None:
b11 = m.groups(1)
if b11[0] != "NULL":
overall[0] = float(b11[0])
m = re_b22.match(text)
if m != None:
b22 = m.groups(1)
if b22[0] != "NULL":
overall[1] = float(b22[0])
m = re_b33.match(text)
if m != None:
b33 = m.groups(1)
if b22[0] != "NULL":
overall[2] = float(b33[0])
m = re_b12.match(text)
if m != None:
b12 = m.groups(1)
if b22[0] != "NULL":
overall[3] = float(b12[0])
m = re_b13.match(text)
if m != None:
b13 = m.groups(1)
if b22[0] != "NULL":
overall[4] = float(b13[0])
m = re_b23.match(text)
if m != None:
b23 = m.groups(1)
if b22[0] != "NULL":
overall[5] = float(b23[0])
state = 2
#if tls_desc.name != "":
# listx.append("TLS %s" % (tls_desc.name))
#else:
# listx.append("TLS")
## Capture the TLS "RANGE"s fields
m = re_tls_range.match(text)
if m != None:
(chain_id1, frag_id1, chain_id2, frag_id2) = m.groups()
sel = "ALL"
frag_id1 = convert_frag_id_save(frag_id1)
frag_id2 = convert_frag_id_save(frag_id2)
listx.append("#RANGE '%s%s' '%s%s' %s" % (
chain_id1, frag_id1.rjust(5),
chain_id2, frag_id2.rjust(5), sel))
## Capture the TLS "ORIGIN"s fields
m = re_tls_origin.match(text)
if m != None:
strx = m.group(1)
## this is nasty -- I wish I could trust the numbers
## to stay in fixed columns, but I can't
ox = [0.0, 0.0, 0.0]
for i in (0,1,2):
j = strx.find(".")
if j==-1:
break
x = strx[ max(0, j-4) : j+5]
strx = strx[j+5:]
ox[i] = float(x)
try:
listx.append("#ORIGIN %8.4f %8.4f %8.4f" % (
ox[0], ox[1], ox[2]))
except:
print "ERROR!"
pass
## Capture the actual TLS values/fields.
## NOTE: These can be provided via an external TLSIN/TLSOUT file.
#m = re_tls_T.match(text)
#if m != None:
#if tls_desc.T is not None:
# ## REFMAC ORDER: t11 t22 t33 t12 t13 t23
# listx.append("T %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# tls_desc.T[0,0], tls_desc.T[1,1], tls_desc.T[2,2],
# tls_desc.T[0,1], tls_desc.T[0,2], tls_desc.T[1,2]))
#
#m = re_tls_L.match(text)
#if m != None:
#if tls_desc.L is not None:
# ## REFMAC ORDER: l11 l22 l33 l12 l13 l23
# listx.append("L %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# tls_desc.L[0,0] * Constants.RAD2DEG2,
# tls_desc.L[1,1] * Constants.RAD2DEG2,
# tls_desc.L[2,2] * Constants.RAD2DEG2,
# tls_desc.L[0,1] * Constants.RAD2DEG2,
# tls_desc.L[0,2] * Constants.RAD2DEG2,
# tls_desc.L[1,2] * Constants.RAD2DEG2))
#
#m = re_tls_S.match(text)
#if m != None:
#if tls_desc.S is not None:
# ## REFMAC ORDER:
# ## <S22 - S11> <S11 - S33> <S12> <S13> <S23> <S21> <S31> <S32>
# listx.append(
# "S %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# (tls_desc.S[1,1] - tls_desc.S[0,0]) * Constants.RAD2DEG,
# (tls_desc.S[0,0] - tls_desc.S[2,2]) * Constants.RAD2DEG,
# tls_desc.S[0,1] * Constants.RAD2DEG,
# tls_desc.S[0,2] * Constants.RAD2DEG,
# tls_desc.S[1,2] * Constants.RAD2DEG,
# tls_desc.S[1,0] * Constants.RAD2DEG,
# tls_desc.S[2,0] * Constants.RAD2DEG,
# tls_desc.S[2,1] * Constants.RAD2DEG))
## Now, capture the ATOM and/or HETATM fields
elif rec_type == "ATOM " or rec_type == "HETATM":
if Library.library_is_standard_residue(rec["resName"]) and \
rec["name"].strip() in Constants.BACKBONE_ATOMS:
atom_dict["serial"] = rec["serial"]
atom_dict["name"] = rec["name"]
atom_dict["resName"] = rec["resName"]
atom_dict["chainID"] = rec["chainID"]
atom_dict["resSeq"] = rec["resSeq"]
atom_dict["x"] = rec["x"]
atom_dict["y"] = rec["y"]
atom_dict["z"] = rec["z"]
atom_dict["occupancy"] = rec["occupancy"]
atom_dict["tempFactor"] = rec["tempFactor"]
#atom_dict["u[1][1]"] = 0.0
# Initialize ANISOU values to isotropic = I3x3 * B/8*pi^2
# in case this atom has no ANISOU record, e.g.
# if it is next to but not in a TLS group
Uiso = rec["tempFactor"] * B2UE4
atom_dict["u[0][0]"] = Uiso
atom_dict["u[1][1]"] = Uiso
atom_dict["u[2][2]"] = Uiso
atom_dict["u[0][1]"] = 0.0
atom_dict["u[0][2]"] = 0.0
atom_dict["u[1][2]"] = 0.0
atom_dict["has_anisou"] = 0
atom_obj.append(atom_dict)
## Capture the ANISOU fields, if they are present
elif rec_type == "ANISOU":
#print rec["serial"], rec["resName"]
#print rec["u[0][0]"], rec["u[1][1]"], rec["u[2][2]"]
try:
Usum = rec["u[0][0]"] + rec["u[1][1]"] + rec["u[2][2]"]
except KeyError:
print "# STRANGE Uij VALUE(S) FOR ATOM=%s; RESIDUE=%s:%s:%s" % (
rec["serial"], rec["chainID"], rec["resName"], rec["resSeq"])
continue
try:
#text = rec["text"]
foo = 1
except KeyError:
continue
if Library.library_is_standard_residue(rec["resName"]) and \
rec["name"].strip() in Constants.BACKBONE_ATOMS:
## We only keep the backbone atom's Uij values.
U11 = rec["u[0][0]"]
U22 = rec["u[1][1]"]
U33 = rec["u[2][2]"]
U12 = U21 = rec["u[0][1]"]
U13 = U31 = rec["u[0][2]"]
U23 = U32 = rec["u[1][2]"]
ADD_B_OVERALL = False # (default: False)
if ADD_B_OVERALL:
atom_obj[-1]["u[0][0]"] = rec["u[0][0]"] + overall[0]
atom_obj[-1]["u[1][1]"] = rec["u[1][1]"] + overall[1]
atom_obj[-1]["u[2][2]"] = rec["u[2][2]"] + overall[2]
atom_obj[-1]["u[0][1]"] = rec["u[0][1]"] + overall[3]
atom_obj[-1]["u[0][2]"] = rec["u[0][2]"] + overall[4]
atom_obj[-1]["u[1][2]"] = rec["u[1][2]"] + overall[5]
else:
atom_obj[-1]["u[0][0]"] = rec["u[0][0]"]
atom_obj[-1]["u[1][1]"] = rec["u[1][1]"]
atom_obj[-1]["u[2][2]"] = rec["u[2][2]"]
atom_obj[-1]["u[0][1]"] = rec["u[0][1]"]
atom_obj[-1]["u[0][2]"] = rec["u[0][2]"]
atom_obj[-1]["u[1][2]"] = rec["u[1][2]"]
atom_obj[-1]["has_anisou"] = 1
has_anisou = 1
return "\n".join(listx), overall, atom_obj
def read_pdb(path):
sec = time.time()
records = pdbmodule.read(path)
sec = time.time() - sec
Ueq = []
atom_obj = []
atom_dict = {}
listx = []
state = 0
overall = {}
n = 1
has_anisou = 0
for rec in records:
## Start with empty dict
atom_dict = {'u[1][1]': 0, 'chainID': '', 'name': '',
'resSeq': 0, 'u[0][1]': 0, 'u[0][0]': 0,
'u[0][2]': 0, 'u[1][2]': 0, 'element': '',
'RECORD': '', 'u[2][2]': 0, 'resName': '',
'serial': 0, 'has_anisou': 0,
'tempFactor': 0.0, 'x': 0.0, 'y': 0.0, 'z': 0.0,
'occupancy': 0.0}
rec_type = rec["RECORD"]
if rec_type == "REMARK":
try:
text = rec["text"]
except KeyError:
continue
if state == 0:
m = re_overall_b.match(text)
if m != None:
state = 1
elif state == 1:
m = re_b11.match(text)
if m != None:
b11 = m.groups(1)
if b11[0] != "NULL":
overall[0] = float(b11[0])
m = re_b22.match(text)
if m != None:
b22 = m.groups(1)
if b22[0] != "NULL":
overall[1] = float(b22[0])
m = re_b33.match(text)
if m != None:
b33 = m.groups(1)
if b22[0] != "NULL":
overall[2] = float(b33[0])
m = re_b12.match(text)
if m != None:
b12 = m.groups(1)
if b22[0] != "NULL":
overall[3] = float(b12[0])
m = re_b13.match(text)
if m != None:
b13 = m.groups(1)
if b22[0] != "NULL":
overall[4] = float(b13[0])
m = re_b23.match(text)
if m != None:
b23 = m.groups(1)
if b22[0] != "NULL":
overall[5] = float(b23[0])
state = 2
#if tls_desc.name != "":
# listx.append("TLS %s" % (tls_desc.name))
#else:
# listx.append("TLS")
m = re_tls_range.match(text)
if m != None:
(chain_id1, frag_id1, chain_id2, frag_id2) = m.groups()
sel = "ALL"
frag_id1 = convert_frag_id_save(frag_id1)
frag_id2 = convert_frag_id_save(frag_id2)
listx.append("#RANGE '%s%s' '%s%s' %s" % (
chain_id1, frag_id1.rjust(5),
chain_id2, frag_id2.rjust(5), sel))
m = re_tls_origin.match(text)
#if tls_desc.origin is not None:
# listx.append("ORIGIN %8.4f %8.4f %8.4f" % (
# tls_desc.origin[0], tls_desc.origin[1], tls_desc.origin[2]))
#elif re_key == "origin":
if m != None:
strx = m.group(1)
## this is nasty -- I wish I could trust the numbers
## to stay in fixed columns, but I can't
ox = [0.0, 0.0, 0.0]
for i in (0,1,2):
j = strx.find(".")
if j==-1:
break
x = strx[ max(0, j-4) : j+5]
strx = strx[j+5:]
ox[i] = float(x)
try:
#self.tls_desc.set_origin(ox[0], ox[1], ox[2])
#origin = numpy.array((ox[0], ox[1], ox[2]), float)
#listx.append("ORIGIN %8.4f %8.4f %8.4f" % (
# origin[0], origin[1], origin[2]))
listx.append("#ORIGIN %8.4f %8.4f %8.4f" % (
ox[0], ox[1], ox[2]))
except:
print "ERROR!"
pass
#m = re_tls_T.match(text)
#if m != None:
#if tls_desc.T is not None:
# ## REFMAC ORDER: t11 t22 t33 t12 t13 t23
# listx.append("T %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# tls_desc.T[0,0], tls_desc.T[1,1], tls_desc.T[2,2],
# tls_desc.T[0,1], tls_desc.T[0,2], tls_desc.T[1,2]))
#
#m = re_tls_L.match(text)
#if m != None:
#if tls_desc.L is not None:
# ## REFMAC ORDER: l11 l22 l33 l12 l13 l23
# listx.append("L %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# tls_desc.L[0,0] * Constants.RAD2DEG2,
# tls_desc.L[1,1] * Constants.RAD2DEG2,
# tls_desc.L[2,2] * Constants.RAD2DEG2,
# tls_desc.L[0,1] * Constants.RAD2DEG2,
# tls_desc.L[0,2] * Constants.RAD2DEG2,
# tls_desc.L[1,2] * Constants.RAD2DEG2))
#
#m = re_tls_S.match(text)
#if m != None:
#if tls_desc.S is not None:
# ## REFMAC ORDER:
# ## <S22 - S11> <S11 - S33> <S12> <S13> <S23> <S21> <S31> <S32>
# listx.append(
# "S %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f" % (
# (tls_desc.S[1,1] - tls_desc.S[0,0]) * Constants.RAD2DEG,
# (tls_desc.S[0,0] - tls_desc.S[2,2]) * Constants.RAD2DEG,
# tls_desc.S[0,1] * Constants.RAD2DEG,
# tls_desc.S[0,2] * Constants.RAD2DEG,
# tls_desc.S[1,2] * Constants.RAD2DEG,
# tls_desc.S[1,0] * Constants.RAD2DEG,
# tls_desc.S[2,0] * Constants.RAD2DEG,
# tls_desc.S[2,1] * Constants.RAD2DEG))
#elif rec_type == "ATOM ":
elif rec_type == "ATOM " or rec_type == "HETATM":
if Library.library_is_standard_residue(rec["resName"]) and \
rec["name"].strip() in Constants.BACKBONE_ATOMS:
atom_dict["serial"] = rec["serial"]
atom_dict["name"] = rec["name"]
atom_dict["resName"] = rec["resName"]
atom_dict["chainID"] = rec["chainID"]
atom_dict["resSeq"] = rec["resSeq"]
atom_dict["x"] = rec["x"]
atom_dict["y"] = rec["y"]
atom_dict["z"] = rec["z"]
atom_dict["occupancy"] = rec["occupancy"]
atom_dict["tempFactor"] = rec["tempFactor"]
#atom_dict["u[1][1]"] = 0.0
# Initialize ANISOU values to isotropic = I3x3 * B/8*pi^2
# in case this atom has no ANISOU record, e.g.
# if it is next to but not in a TLS group
Uiso = rec["tempFactor"] * B2UE4
atom_dict["u[0][0]"] = Uiso
atom_dict["u[1][1]"] = Uiso
atom_dict["u[2][2]"] = Uiso
atom_dict["u[0][1]"] = 0.0
atom_dict["u[0][2]"] = 0.0
atom_dict["u[1][2]"] = 0.0
atom_dict["has_anisou"] = 0
atom_obj.append(atom_dict)
elif rec_type == "ANISOU":
#print rec["serial"], rec["resName"]
#print rec["u[0][0]"], rec["u[1][1]"], rec["u[2][2]"]
try:
Usum = rec["u[0][0]"] + rec["u[1][1]"] + rec["u[2][2]"]
except KeyError:
print "# STRANGE Uij VALUE(S) FOR ATOM=%s; RESIDUE=%s:%s:%s" % (
rec["serial"], rec["chainID"], rec["resName"], rec["resSeq"])
continue
try:
#text = rec["text"]
foo = 1
except KeyError:
continue
if Library.library_is_standard_residue(rec["resName"]) and \
rec["name"].strip() in Constants.BACKBONE_ATOMS:
U11 = rec["u[0][0]"]
U22 = rec["u[1][1]"]
U33 = rec["u[2][2]"]
U12 = U21 = rec["u[0][1]"]
U13 = U31 = rec["u[0][2]"]
U23 = U32 = rec["u[1][2]"]
ADD_B_OVERALL = False
if ADD_B_OVERALL:
atom_obj[-1]["u[0][0]"] = rec["u[0][0]"] + overall[0]
atom_obj[-1]["u[1][1]"] = rec["u[1][1]"] + overall[1]
atom_obj[-1]["u[2][2]"] = rec["u[2][2]"] + overall[2]
atom_obj[-1]["u[0][1]"] = rec["u[0][1]"] + overall[3]
atom_obj[-1]["u[0][2]"] = rec["u[0][2]"] + overall[4]
atom_obj[-1]["u[1][2]"] = rec["u[1][2]"] + overall[5]
else:
atom_obj[-1]["u[0][0]"] = rec["u[0][0]"]
atom_obj[-1]["u[1][1]"] = rec["u[1][1]"]
atom_obj[-1]["u[2][2]"] = rec["u[2][2]"]
atom_obj[-1]["u[0][1]"] = rec["u[0][1]"]
atom_obj[-1]["u[0][2]"] = rec["u[0][2]"]
atom_obj[-1]["u[1][2]"] = rec["u[1][2]"]
atom_obj[-1]["has_anisou"] = 1
has_anisou = 1
#U = tlsvld.array([[U11,U12,U13],[U21,U22,U23],[U31,U32,U33]])
#Ueq.append(U)
#return "\n".join(listx), overall, Ueq, atom_obj
return "\n".join(listx), overall, atom_obj
