Exemplos de write_sequences em Python

Exemplo n.º 1

Arquivo: go_builder_sc.py Projeto: apb210/GO_Builder

else:
    off = 0
    nres_tot = 0
    for c in chains:
        seqs[c] = map(lambda x: "G%s" % (x),
                      range(1 + off,
                            len(xyz[c]) + 1 + off))
        off += len(xyz[c])
        nres_tot += len(xyz[c])

if water == 0:
    nsolv = 0
else:
    nsolv = len(xyz["SOLV"])

go_lib.write_sequences(outp_base + "_seq.inp", seqs, "", key, nsolv)

# write out topology
# ======================================================================
if symm:
    chain = chains[0]
    nres = len(xyz[chain])
    residues = []
    for i in range(1, nres + 1):
        name = meta_crd[chain][i]["name"]
        #mass = go_lib.massmap[name]
        residues.append(("G%i" % (i), name))
else:
    residues = []
    idx = 0
    for c in chains:

Exemplo n.º 2

Arquivo: headgordon.py Projeto: apb210/GO_Builder

		seqs[c] = map(lambda x: "G%s"%(x), range(1,len(xyz[c])+1))
	nres_tot = len(xyz[chains[0]])
else:
	off = 0
	nres_tot = 0
	for c in chains:
		seqs[c] = map(lambda x: "G%s"%(x), range(1+off,len(xyz[c])+1+off))
		off += len(xyz[c])
		nres_tot += len(xyz[c])

if water == 0:
	nsolv = 0
else:
	nsolv = len(xyz["SOLV"])

go_lib.write_sequences(outp_base+"_seq.inp", seqs, disulf_str, key, nsolv)

# write out topology
# ======================================================================
if symm:
	chain = chains[0]
	nres = len(xyz[chain])
	residues = []
	for i in range(1,nres+1):
		name = meta_crd[chain][i]["name"]
		residues.append(("G%i"%(i),name))
else:
	residues = []
	idx = 0
	for c in chains:
		nres = len(xyz[c])

Exemplo n.º 3

Arquivo: go_builder.py Projeto: lafita/tadoss

    off = 0
    nres_tot = 0
    for c in chains:
        seqs[c] = map(lambda x: "G%s" % (x),
                      range(1 + off,
                            len(xyz[c]) + 1 + off))
        off += len(xyz[c])
        nres_tot += len(xyz[c])

if water == 0:
    nsolv = 0
else:
    nsolv = len(xyz["SOLV"])

if charmm:
    go_lib.write_sequences(outp_base + "_seq.inp", seqs, disulf_str, key, \
                              nsolv, ncrowd, n_repeat)
    if ncrowd > 0:
        if len(crowdprot) == 0:
            go_lib.write_sequences(outp_base + "_crowd_seq.inp", \
                                            seqs, disulf_str, key, nsolv, ncrowd)
        else:
            for i in range(ncrowd):
                seqs["C%i"%(i)]= map(lambda x: "G%s"%(x), \
                 range(1+off,len(xyz_crowd[crowd_chain])+1+off))
                off += len(xyz_crowd[crowd_chain])
                nres_tot += len(xyz_crowd[crowd_chain])
            go_lib.write_sequences(outp_base + "_crowd_seq.inp", \
                                            seqs, disulf_str, key, nsolv)

# ======================================================================
# WRITE OUT TOPOLOGY

Exemplo n.º 4

Arquivo: go_build_dimer.py Projeto: apb210/GO_Builder

seqs = {}
if symm:
    for c in chains:
        seqs[c] = map(lambda x: "G%s" % (x), range(1, len(xyz[c]) + 1))
    nres_tot = len(xyz[chains[0]])
else:
    off = 0
    nres_tot = 0
    for c in chains:
        seqs[c] = map(lambda x: "G%s" % (x),
                      range(1 + off,
                            len(xyz[c]) + 1 + off))
        off += len(xyz[c])
        nres_tot += len(xyz[c])

go_lib.write_sequences(outp_base + "_seq.inp", seqs, key)

# write out topology
# ======================================================================

if symm:
    chain = chains[0]
    nres = len(xyz[chain])
    residues = []
    for i in range(1, nres + 1):
        name = meta_crd[chain][i]["name"]
        mass = go_lib.massmap[name]
        residues.append(("G%i" % (i), mass))
else:
    residues = []
    idx = 0