def readKinemageSuites(lines, dimension):
"""Read a list of kinemage data lines to yield a suite."""
suites = []
for line in lines:
if len(line.strip()) == 0 or line[0] == "#": # blank or comment line
continue
# A meaningful line begins with an id string enclosed in braces
if line[0] == "{":
mark = line.find("}")
if mark > 0:
idString = line[1:mark]
ids = idString.split(":")
# there may be some miscellaneous markers after the id string
k = mark + 1
while k < len(line) and not line[k].isdigit():
k = k + 1
mark2 = k
# once we see a number, everything else is angles
angleText = line[mark2:]
angleStrings = angleText.split(" ")
angleStrings2 = angleText.split(",")
if len(angleStrings2) > len(angleStrings):
angleStrings = angleStrings2
angleList = [stringToFloat(s) for s in angleStrings]
if len(angleList) != dimension:
continue # wrong number of dimensions means probably not a data point
if dimension == 9:
angles = np.array(angleList)
else: # given only 7 angles,skipping the chi angles on the ends
angles = np.array([180.0] + angleList + [180.0])
for i in range(len(angles)):
if angles[i] < 0:
angles[i] += 360.0
suite = Suite(ids, ids[9][2], angles)
suites.append(suite)
return suites
def buildSuiteLast(r1):
suite = Suite((), "")
if len(r1.angle) > 6:
suite.chiMinus = r1.chi
suite.deltaMinus = r1.delta
suite.epsilon = r1.epsilon
suite.zeta = r1.zeta
suite.alpha = 999
suite.beta = 999
suite.gamma = 999
suite.delta = 999
suite.chi = 999
return suite
def buildSuiteFirst(r2):
suite = Suite(r2.pointIDs, r2.base)
suite.alpha = r2.alpha
suite.beta = r2.beta
suite.gamma = r2.gamma
suite.delta = r2.delta
if len(r2.angle) > 6:
suite.chi = r2.chi
suite.epsilon = 999
suite.zeta = 999
suite.chiMinus = 999
suite.deltaMinus = 999
return suite
def buildSuiteBetweenResidues(r1, r2):
suite = Suite(r2.pointIDs, r2.base)
if len(r1.angle) > 6:
suite.chiMinus = r1.chi
suite.deltaMinus = r1.delta
suite.epsilon = r1.epsilon
suite.zeta = r1.zeta
suite.alpha = r2.alpha
suite.beta = r2.beta
suite.gamma = r2.gamma
suite.delta = r2.delta
if len(r2.angle) > 6:
suite.chi = r2.chi
return suite