mirror of
https://github.com/PDB-REDO/dssp.git
synced 2026-06-04 13:44:21 +08:00
83 lines
2.5 KiB
Python
83 lines
2.5 KiB
Python
import mkdssp
|
|
import os
|
|
import gzip
|
|
|
|
file_path = os.path.join("..", "test", "1cbs.cif.gz")
|
|
|
|
with gzip.open(file_path, "rt") as f:
|
|
file_content = f.read()
|
|
|
|
dssp = mkdssp.dssp(file_content)
|
|
|
|
print("residues: ", dssp.statistics.residues)
|
|
print("chains: ", dssp.statistics.chains)
|
|
print("SS_bridges: ", dssp.statistics.SS_bridges)
|
|
print("intra_chain_SS_bridges: ", dssp.statistics.intra_chain_SS_bridges)
|
|
print("H_bonds: ", dssp.statistics.H_bonds)
|
|
print("H_bonds_in_antiparallel_bridges: ", dssp.statistics.H_bonds_in_antiparallel_bridges)
|
|
print("H_bonds_in_parallel_bridges: ", dssp.statistics.H_bonds_in_parallel_bridges)
|
|
|
|
count = 0
|
|
for res in dssp:
|
|
count += 1
|
|
print(res.asym_id, res.seq_id, res.compound_id)
|
|
print("alt_id", res.alt_id)
|
|
print("compound_letter", res.compound_letter)
|
|
print("auth_asym_id", res.auth_asym_id)
|
|
print("auth_seq_id", res.auth_seq_id)
|
|
print("pdb_strand_id", res.pdb_strand_id)
|
|
print("pdb_seq_num", res.pdb_seq_num)
|
|
print("pdb_ins_code", res.pdb_ins_code)
|
|
print("alpha", res.alpha)
|
|
print("kappa", res.kappa)
|
|
print("phi", res.phi)
|
|
print("psi", res.psi)
|
|
print("tco", res.tco)
|
|
print("omega", res.omega)
|
|
print("is_pre_pro", res.is_pre_pro)
|
|
print("is_cis", res.is_cis)
|
|
print("chiral_volume", res.chiral_volume)
|
|
print("chi", res.chi)
|
|
print("ca_location", res.ca_location)
|
|
print("chain_break", res.chain_break)
|
|
print("nr", res.nr)
|
|
print("type", res.type)
|
|
print("ssBridgeNr", res.ssBridgeNr)
|
|
print("helix(_3_10)", res.helix(mkdssp.helix_type._3_10))
|
|
print("helix(alpha)", res.helix(mkdssp.helix_type.alpha))
|
|
print("helix(pi)", res.helix(mkdssp.helix_type.pi))
|
|
print("helix(pp)", res.helix(mkdssp.helix_type.pp))
|
|
print("is_alpha_helix_end_before_start", res.is_alpha_helix_end_before_start)
|
|
print("bend", res.bend)
|
|
print("sheet", res.sheet)
|
|
print("strand", res.strand)
|
|
|
|
for i in range(0, 1):
|
|
(ri, nr, dir) = res.bridge_partner(i)
|
|
if ri != None:
|
|
print("bridge partner ", i, ri.asym_id, ri.seq_id, ri.compound_id, nr, dir)
|
|
|
|
for i in range(0, 1):
|
|
(ri, e) = res.acceptor(i)
|
|
if ri != None:
|
|
print("acceptor ", i, ri.asym_id, ri.seq_id, ri.compound_id, e)
|
|
print("test bond: ", mkdssp.TestBond(res, ri))
|
|
|
|
for i in range(0, 1):
|
|
(ri, e) = res.donor(i)
|
|
if ri != None:
|
|
print("donor ", i, ri.asym_id, ri.seq_id, ri.compound_id, e)
|
|
print("test bond: ", mkdssp.TestBond(res, ri))
|
|
|
|
print("accessibility", res.accessibility)
|
|
|
|
|
|
print("count: ", count)
|
|
|
|
a = dssp.get('A', 137)
|
|
b = dssp.get('A', 6)
|
|
|
|
print ("a & b", a, b)
|
|
|
|
assert(mkdssp.TestBond(a, b))
|