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
def check_upload(job_id, file):
"""Runs sanity checks on uploaded file
"""
## Checks if PDB contains valids aa/na residues
## PDB must have at least 30 ATOMs
## PDB can not have lowercase alt. res. numbers
## Check Standard deviation of temp. factors
## Check that not all occupancies are 0.00
atom_num = []
res_type = []
res_num = []
chain = []
temp_factors = []
bad_std = -1
num_total = 0
num_good = 0
occupancy = 0.0
ignore = 0
line_num = 0
for line in file:
line_num += 1
if line.startswith('HEADER'):
header_id = re.sub(r"^HEADER.{56}(....)", '\\1', line).strip()
elif line.startswith('EXPDTA NMR'):
return "NMR structure! Skipping: %s [%s]" % (job_id, header_id)
elif re.match(r'^REMARK 2 RESOLUTION\. ([0-9\.]{1,}) ANGSTROMS.*',
line):
resolution = re.sub(
r'^REMARK 2 RESOLUTION\. ([0-9\.]{1,}) ANGSTROMS.*', '\\1',
line).strip()
elif re.match('^ATOM.....................[0-9][a-z]', line):
## E.g., Don't allow "100b". Force it to be "100B"
return "Lowercase alternate residue names: %s [%s]" % (job_id,
header_id)
elif line.startswith('ATOM') and (Library.library_is_standard_residue(
line[17:20].strip())):
num_total += 1
if float(line[56:60].strip()) < 1.00:
## ignore occupancies < 1.00
ignore += 1
continue
else:
num_good += 1
atom_num.append(int(line[7:11].strip()))
res_type.append(line[17:20].strip())
res_num.append(int(line[23:26].strip()))
chain.append(line[21:22])
occupancy += float(line[56:60].strip())
temp_factors.append(float(line[60:65].strip()))
else:
continue
if (len(atom_num) < 30):
return "Not a PDB structure or has unrecognized residue names: %s [%s]" % (
job_id, header_id)
if (occupancy / num_good == 0.0):
return "All occupancies are 0.0. TLSMD won't run on this structure: %s [%s]" % (
job_id, header_id)
bad_std, tmpfile = running_stddev(atom_num, res_type, res_num, chain,
temp_factors)
if bad_std > 0:
## If there are a string of "bad" B-factors, return a plot showing the
## "bad" regions and do not proceed any further in the analysis.
return_string = "STDDEV %s > Bfact < %s for job_id: %s [%s]" % (
conf.MAX_STDDEV_BFACT, conf.MIN_STDDEV_BFACT, job_id, header_id)
return return_string
return ''
def check_upload(job_id, file):
"""Runs sanity checks on uploaded file
"""
## Checks if PDB contains valids aa/na residues
## PDB must have at least 30 ATOMs
## PDB can not have lowercase alt. res. numbers
## Check Standard deviation of temp. factors
## Check that not all occupancies are 0.00
atom_num = []
res_type = []
res_num = []
chain = []
temp_factors = []
bad_std = -1
num_total = 0
num_good = 0
occupancy = 0.0
ignore = 0
line_num = 0
for line in file:
line_num += 1
if line.startswith('HEADER'):
header_id = re.sub(r"^HEADER.{56}(....)", '\\1', line).strip()
elif line.startswith('EXPDTA NMR'):
return "NMR structure! Skipping: %s [%s]" % (job_id, header_id)
elif re.match(r'^REMARK 2 RESOLUTION\. ([0-9\.]{1,}) ANGSTROMS.*', line):
resolution = re.sub(r'^REMARK 2 RESOLUTION\. ([0-9\.]{1,}) ANGSTROMS.*', '\\1', line).strip()
elif re.match('^ATOM.....................[0-9][a-z]', line):
## E.g., Don't allow "100b". Force it to be "100B"
return "Lowercase alternate residue names: %s [%s]" % (job_id, header_id)
elif line.startswith('ATOM') and (
Library.library_is_standard_residue(line[17:20].strip())):
num_total += 1
if float(line[56:60].strip()) < 1.00:
## ignore occupancies < 1.00
ignore += 1
continue
else:
num_good += 1
atom_num.append(int(line[7:11].strip()))
res_type.append(line[17:20].strip())
res_num.append(int(line[23:26].strip()))
chain.append(line[21:22])
occupancy += float(line[56:60].strip())
temp_factors.append(float(line[60:65].strip()))
else:
continue
if(len(atom_num) < 30):
return "Not a PDB structure or has unrecognized residue names: %s [%s]" % (
job_id, header_id)
if(occupancy / num_good == 0.0):
return "All occupancies are 0.0. TLSMD won't run on this structure: %s [%s]" % (
job_id, header_id)
bad_std, tmpfile = running_stddev(atom_num, res_type, res_num, chain, temp_factors)
if bad_std > 0:
## If there are a string of "bad" B-factors, return a plot showing the
## "bad" regions and do not proceed any further in the analysis.
return_string = "STDDEV %s > Bfact < %s for job_id: %s [%s]" % (
conf.MAX_STDDEV_BFACT, conf.MIN_STDDEV_BFACT, job_id, header_id)
return return_string
return ''
