def get_chain_type(res_name):
if Library.library_is_amino_acid(res_name):
#chain_type = 0
return 0
elif Library.library_is_nucleic_acid(res_name):
return 1
else:
## Unknown residue type
print "# UNKOWN RESIDUE!"
return 9
def get_chain_type(res_name):
"""Assign an integer value for residue type, identified by the actual name
of the residue. Assigns "0" to amino acids, "1" to nucleic acids, and "9"
to everything else.
"""
if Library.library_is_amino_acid(res_name):
return 0
elif Library.library_is_nucleic_acid(res_name):
return 1
else:
## Unknown residue type
print "# UNKOWN RESIDUE!"
return 9
def get_chain_type(res_name):
"""Assign an integer value for residue type, identified by the actual name
of the residue. Assigns "0" to amino acids, "1" to nucleic acids, and "9"
to everything else.
"""
if Library.library_is_amino_acid(res_name):
return 0
elif Library.library_is_nucleic_acid(res_name):
return 1
else:
## Unknown residue type
print "# UNKOWN RESIDUE!"
return 9
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 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 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 ''