def RunAnalTrj(TrjFile,
PrmtopFile,
OutputPath=None,
Prefix=None,
NSkip=0,
NRead=None,
NStride=1):
"Runs a mesostring analysis of a trajectory."
#make the coords object
CoordsObj = coords.TrjClass(TrjFile,
PrmtopFile,
NSkip=NSkip,
NRead=NRead,
NStride=NStride)
ConfMeso, MesoPop, MesoEntropy = RunAnal(CoordsObj, OutputPath, Prefix)
return ConfMeso, MesoPop, MesoEntropy
#get options
Align = "align" in Args["FLAGS"]
CompResInd = GetResList(Args.get("compres", None))
CalcResInd = GetResList(Args.get("calcres", None))
#check for a trajectory
if "traj" in Args["FLAGS"]:
PdbRef, TrjFile, PrmtopFile = Args["ARGS"][:3]
NAvg = int(Args.get("avg", 1))
Cut = float(Args.get("frac", 0.))
NSkip = int(Args.get("nskip", 0))
NRead = int(Args.get("nread", -1))
NStride = int(Args.get("nstride", 1))
Trj = coords.TrjClass(TrjFile,
PrmtopFile,
NSkip=NSkip,
NRead=NRead,
NStride=NStride)
pTrj = protein.ProteinClass()
pTrj.LinkTrj(Trj)
pRef = protein.ProteinClass(Pdb=PdbRef)
print "%-10s %-8s %-8s %-5s" % ("Frame", "BB_RMSD", "All_RMSD", "NRes")
i = 0
y1, y2 = [], []
z1, z2 = [], []
for Pos in Trj:
i += 1
x1, NRes = RMSDProteinClass(pRef,
pTrj,
Backbone=True,
AlignSeq=Align,
DihThresh = Args["dihthresh"]
SSThresh = Args["ssthresh"]
NSkip, NRead, NStride = Args["nskip"], Args["nread"], Args["nstride"]
WriteZam = "writezam" in Args["FLAGS"]
Verbose = not "quiet" in Args["FLAGS"]
ScaleDih = "scaledih" in Args["FLAGS"]
ScaleCont = "scalecont" in Args["FLAGS"]
DihFConst = Args["dihfconst"]
ContFConst = Args["contfconst"]
ZamInputs = "zaminputs" in Args["FLAGS"]
PhobicsOnly = "phobics" in Args["FLAGS"]
RunSS = "runss" in Args["FLAGS"]
#check the input files
Files = [x for x in Args["ARGS"][1:] if os.path.isfile(x)]
if all([".pdb" in x for x in Files]):
CObj = coords.PdbListClass(Files)
else:
CObj = coords.TrjClass(Files[0],
Files[1],
NSkip=NSkip,
NRead=NRead,
NStride=NStride)
#get common parameters from consensus
Seq, Contacts, ResSS, ResSSFrac, FixedDih = GetCommon(CObj,
RunSS,
Verbose=Verbose)
#write zam output
if ZamInputs:
WriteZamFiles(".", FixedDih, Contacts, DihFConst, ContFConst,
ScaleCont)
def SaveTrjDists(TrjFile,
PrmtopFile,
OutputPath,
PairAtoms,
PairLabels=None,
NSkip=0,
NRead=None,
NStride=1,
Prefix="",
Verbose=VerboseDflt):
"""Saves distances from a trajectory to a gzipped file.
* TrjFile: string, path of trajectory file
* PrmtopFile: string, path of prmtop file
* OutputPath: string, path to save distance file(s)
* PairAtoms: list of pairs of lists of atom numbers
* PairLabels: list of labels for each distance pair
* NSkip: number of configurations to skip
* NRead: maximum number of configurations to read (default is all)
* NStride: stride between configuration frames (default is 1)
* Prefix: string, prefix to add to the name of the distance file
* Verbose: boolean, display verbose messages?"""
#make sure any pairs are specified
if len(PairAtoms) == 0:
return
#convert to groups
GroupAtoms, PairGroups = MakeAtomGroups(PairAtoms)
NGroup = len(GroupAtoms)
#make trj object
Trj = coords.TrjClass(TrjFile,
PrmtopFile,
NSkip=NSkip,
NRead=NRead,
NStride=NStride)
#check labels
if PairLabels is None:
PairLabels = ["pair%d" % i for i in range(0, len(PairAtoms))]
#open the output file output the header
ColHead = ["index".ljust(BlockLen)
] + [s.ljust(BlockLen) for s in PairLabels]
fn = os.path.join(OutputPath, Prefix + "dist.txt.gz")
f = gzip.GzipFile(fn, "w")
f.write("".join(ColHead) + "\n")
#initialize variables
GroupPos = zeros((NGroup, 3), float)
#now parse the trajectory
for Pos in Trj:
#calculate the centroid of group coordinates
GroupPos.fill(0.)
for i in range(0, NGroup):
Group = GroupAtoms[i]
for AtomNum in Group:
GroupPos[i, :] += Pos[AtomNum, :]
GroupPos[i, :] /= float(len(Group))
#calculate the distances
DistList = []
for Group1, Group2 in PairGroups:
Dist = sqrt(sum((GroupPos[Group1, :] - GroupPos[Group2, :])**2))
DistList.append(Dist)
#output to file
s = ("%d" % Trj.Index).ljust(BlockLen - 1) + " "
s += " ".join([(DistFmt % d).ljust(BlockLen - 1) for d in DistList])
s += "\n"
f.write(s)
f.close()
Trj.Close()
MinDist=float(ARGS[input+1])
elif ARGS[input].startswith('-max'):
MaxDist=float(ARGS[input+1])
elif ARGS[input].startswith('-x'):
mdcrd=ARGS[input+1]
elif ARGS[input].startswith('-skip'):
nskip=int(ARGS[input+1])
elif ARGS[input].startswith('-int'):
nstride=int(ARGS[input+1])
elif ARGS[input].startswith('-'):
print str(ARGS[input]) + " flag is not recognized\n"
sys.exit()
#open the trajectory file
Trj = coords.TrjClass(str(Trjfn),str(Prmtopfn), NSkip=nskip, NStride=nstride)
NDigits = int(log(len(Trj) + 0.1) / log(10.) + 1.)
print "Found %d snapshots in trajectory file" % len(Trj)
#link a proteinclass object
p = protein.ProteinClass()
p.LinkTrj(Trj)
pdbfiles=[]
#check residues
if ResNum1 > len(p):
print "Error: first residue number exceeds protein length."
sys.exit()
if ResNum2 > len(p):
print "Error: second residue number exceeds protein length."
sys.exit()