/usr/lib/python2.7/dist-packages/pymol/headering.py is in pymol 1.7.2.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import re
import sys
import string
import struct
import pymol
import math
from xray import space_group_map
if sys.byteorder == "big":
MACH_ARCH_CODE_INT = 1
MACH_ARCH_CODE_FLT = 1
else:
MACH_ARCH_CODE_INT = 4
MACH_ARCH_CODE_FLT = 4
class baseHeader:
"""
A simple base class used to parse biological data headers
"""
def __init__(self,filename):
self.filename = filename
self.cols = []
self.byteorder_int = None
self.byteorder_flt = None
self.wordsize = None
def parseFile(self):
pass
def getColumns(self):
return self.cols
def getColumnsOfType(self,targetType):
pass
def checkFile(self):
return os.path.isfile(self.filename)
def guessCols(self,mapType):
fC = self.getColumnsOfType("F")
pC = self.getColumnsOfType("P")
looksLike, FCol, PCol = [None]*3
for prg in ("refmac", "phenix", "phenix_no_fill", "buster"):
#
# default (refmac,phenix,phenix_no_fill,buster) names are in the format:
# "2FoFc-amplitude 2FoFc-phase FoFc-ampl FoFc-phase"
#
defaultNames = pymol.cmd.get_setting_text("default_%s_names" % (prg))
if len(defaultNames):
defaultNames = string.split(defaultNames)
if len(defaultNames):
if mapType.lower() == "2fofc":
defaultF, defaultP = defaultNames[0], defaultNames[1]
elif mapType.lower() == "fofc":
defaultF, defaultP = defaultNames[2], defaultNames[3]
else:
print "Error: Please provide the setting 'default_%s_names' a comma separated string" % (prg)
print " with the values for 2FoFc and FoFc, amplitude and phase names, respectively."
return [None]*3
else:
print "Error: Please provide the setting 'default_%s_names' a comma separated string" % (prg)
print " with the values for 2FoFc and FoFc, amplitude and phase names, respectively."
return [None]*3
# defaultF =~ "FWT", "2FOFCFWT", "2FOFCWT_no_fill", "2FOFCWT", "DELFWT", "FOFCWT", ..
for curFCol in fC:
if curFCol.endswith(defaultF):
# found F, now look for matching P
pfx = string.rstrip(curFCol,defaultF)
curPCol = pfx+defaultP
## print "curFCol = %s" % curFCol
## print "curPCol = %s" % curPCol
if curPCol in pC:
# found perfectly matching columns
looksLike = prg
FCol = curFCol
PCol = curPCol
return (FCol, PCol, looksLike)
return [None]*3
class CNSHeader(baseHeader):
"""
CNS format
"""
def __init__(self,filename):
## print "CNSHeader cstr"
baseHeader.__init__(self,filename)
self.parseFile()
class CIFHeader(baseHeader):
"""
mmCIF
"""
def __init__(self,filename):
baseHeader.__init__(self,filename)
self.parseFile()
def parseFile(self):
if self.checkFile():
try:
inFile = open(self.filename,'rb')
data = inFile.readlines()
inFile.close()
in_loop = False
curLine = data.pop(0)
while curLine!=None:
if in_loop:
if curLine.startswith("_refln."):
self.cols.append(string.split(curLine,".",1)[1].strip())
else:
in_loop=False
else:
if curLine.startswith("loop_"):
in_loop=True
if len(data):
curLine = data.pop(0)
else:
curLine = None
except IOError, e:
print "Error-CIFReader: Couldn't read '%s' for input." % (self.filename)
class MTZHeader(baseHeader):
HEADER_KEYWORDS = {
"VERS" : "VERS",
"TITLE" : "TITLE",
"NCOL" : "NCOL",
"CELL" : "CELL",
"SORT" : "SORT",
"SYMINF" : "SYMINF",
"SYMM" : "SYMM",
"RESO" : "RESO",
"VALM" : "VALM",
"NDIF" : "NDIF",
"COL" : "COL",
"PROJECT" : "PROJECT",
"CRYSTAL" : "CRYSTAL",
"DATASET" : "DATASET",
"DCELL" : "DCELL",
"DWAVEL" : "DWAVEL",
"BATCH" : "BATCH",
}
"""
MTZ/CCP4
"""
def __init__(self,filename):
baseHeader.__init__(self,filename)
self.version = None
self.title = None
self.ncol = None
self.nrefl = None
self.nbatches = None
self.cell = None
self.sort = None
self.syminf = None
self.symm = []
self.reso_min = None
self.reso_max = None
self.valm = None
self.ndif = None
self.col = None
self.project = None
self.crystal = None
self.dataset = None
self.dcell = None
self.dwavel = None
self.batch = None
self.datasets = {}
self.parseFile()
self.format_cols()
def format_cols(self,colType=None):
"""
updates self.cols to a list of cols of a
given MTZ type
"""
self.cols = []
# UNIQUE:
# crystal_name/dataset_name/col_label"
s = "/"
c = []
for key in self.datasets:
c=[]
## print "KEY = %s" % key
# user wants all columns
if colType==None:
c = self.datasets[key]["cols"].keys()
else:
# user wants a specfic column
for tmpCol in self.datasets[key]["cols"].keys():
if self.datasets[key]["cols"][tmpCol]["type"]==colType:
c.append(tmpCol)
## print "Columns of type %s are: " % colType
## print c
## print "Now formatting...."
if "crystal" in self.datasets[key]:
curCryst = [ self.datasets[key]["crystal"] ] * len(c)
else:
curCryst = "nameless_crystal" * len(c)
## print "CurCrystal is: %s." % curCryst
datName = [ self.datasets[key]["name"] ] * len(c)
self.cols.extend(
map(lambda x: "/".join(x),
zip(curCryst,datName,c)))
def getColumns(self):
self.format_cols()
return baseHeader.getColumns(self)
def getColumnsOfType(self,colType):
self.format_cols(colType)
return baseHeader.getColumns(self)
def get_byteorder(self):
f = open(self.filename, 'rb')
f.seek(8)
d = struct.unpack("BBBB",f.read(4))
f.close()
return (d[1]>>4) & 0x0f, (d[0]>>4) & 0x0f
def authorStamp(self,f):
# seek the machine stamp
f.seek(8,0)
# read machine stamp
(B0,B1,B2,B3) = struct.unpack("BBBB", f.read(4))
# determines big or little endian:
# double, float, int, char
d = (B0 & 0xF0) >> 4
f = (B0 & 0x0F)
i = (B1 & 0xF0) >> 4
c = (B1 & 0x0F)
if d==1:
# big endian
self.byteorder_flt = ">"
elif d==4:
# little endian
self.byteorder_flt = "<"
if i==1:
# big
self.byteorder_int = ">"
self.wordsize = 1
elif i==4:
self.byteorder_int = "<"
self.wordsize = 4
def parseFile(self):
if self.checkFile():
f = open(self.filename,'rb')
# sets authoring machine's details
self.authorStamp(f)
# get file size
f.seek(0,2)
file_len = f.tell()
# get header offset
f.seek(4)
if self.wordsize!=None:
(header_start,) = struct.unpack(self.byteorder_int+"i", f.read(4))
else:
print "Warning: Byte order of file unknown. Guessing header location."
(header_start,) = struct.unpack("i", f.read(4))
# bAdjust is the byte adjustment to compensate for
# older machines with smaller atomic sizes
host_word_size = len(struct.pack('i',0))
author_word_size = self.wordsize
if host_word_size<author_word_size:
bAdjust = author_word_size / host_word_size
elif host_word_size>author_word_size:
bAdjust = author_word_size * host_word_size
else:
bAdjust = host_word_size
header_start = (header_start-1) * (bAdjust)
if file_len<header_start:
print "Error: File '%s' cannot be parsed because PyMOL cannot find the header. If you think"
print " PyMOL should be able to read this, plese send the file and this mesage to "
print " help@schrodinger.com. Thanks!"
f.seek(header_start)
curLine = struct.unpack("80s", f.read(80))[0]
while not (curLine.startswith("END")):
# yank field identifier
(field, tokens) = string.split(curLine," ",1)
H = MTZHeader.HEADER_KEYWORDS
try:
if field.startswith(H["VERS"]):
self.version = tokens
elif field.startswith(H["TITLE"]):
self.title = tokens
elif field.startswith(H["NCOL"]):
(self.ncols, self.nrefl, self.nbatches) = string.split(tokens)
elif field.startswith(H["CELL"]):
tokens = string.split(tokens)
self.cell_dim = tokens[:3]
self.cell_angles = tokens[3:]
elif field.startswith(H["SORT"]):
self.sort = string.split(tokens)
elif field.startswith(H["SYMINF"]):
tokens = filter(None, pymol.parsing.split(tokens, " "))
self.nsymmop = tokens[0]
self.nprimop = tokens[1]
self.lattice = tokens[2]
self.groupnum = tokens[3]
# try official MTZ format
self.space_group = pymol.cmd.safe_eval(tokens[4])
self.pt_group = pymol.cmd.safe_eval(tokens[5])
# valid format for MTZ space group?
self.space_group = space_group_map.get(self.space_group, self.space_group)
elif field.startswith(H["SYMM"]):
tokens = string.split(tokens)
tokens = map(lambda x: string.strip(string.strip(x, ",")),tokens)
self.symm.append(tokens)
elif field.startswith(H["RESO"]):
self.reso_min, self.reso_max = string.split(tokens)
self.reso_min = math.sqrt(1./float(self.reso_min))
self.reso_max = math.sqrt(1./float(self.reso_max))
elif field.startswith(H["VALM"]):
self.missing_flag = tokens
elif field.startswith(H["COL"]):
if field == "COLSRC":
raise pymol.cmd.QuietException
(lab,typ,m,M,i) = string.split(tokens)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]["cols"] = {}
self.datasets[i]["cols"][lab] = {}
self.datasets[i]["cols"][lab]["type"] = typ
self.datasets[i]["cols"][lab]["min"] = m
self.datasets[i]["cols"][lab]["max"] = M
self.datasets[i]["cols"][lab]["id"] = i
elif field.startswith(H["NDIF"]):
self.ndif = int(tokens)
elif field.startswith(H["PROJECT"]):
(i,proj) = string.split(tokens,maxsplit=1)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]["project"] = string.strip(proj)
elif field.startswith(H["CRYSTAL"]):
# can have multiple crystals per dataset?
# if, so not supported (overwritten) here.
(i,cryst) = string.split(tokens,maxsplit=1)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]["crystal"] = string.strip(cryst)
elif field.startswith(H["DATASET"]):
(i,d) = string.split(tokens,maxsplit=1)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]["name"] = string.strip(d)
elif field.startswith(H["DCELL"]):
(i,x,y,z,a,b,g) = string.split(tokens)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]['x'] = x
self.datasets[i]['y'] = y
self.datasets[i]['z'] = z
self.datasets[i]['alpha'] = a
self.datasets[i]['beta'] = b
self.datasets[i]['gamma'] = g
elif field.startswith(H["DWAVEL"]):
(i,wl) = string.split(tokens)
if i not in self.datasets:
self.datasets[i] = {}
self.datasets[i]["wavelength"] = wl
elif field.startswith(H["BATCH"]):
self.batch = tokens
else:
print "Error Parsing MTZ Header: bad column name: '%s'" % field
except ValueError:
print "Error: Parsing MTZ Header poorly formatted MTZ file"
print " bad field: '%s'" % field
except pymol.cmd.QuietException:
pass
curLine = struct.unpack("80s", f.read(80))[0]
if __name__=="__main__":
c = CIFHeader("test.cif")
print c.getColumns()
m = MTZHeader("test.mtz")
print m.getColumns()
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