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# the smaller the sigmas the more weight the restraints have
# This pushes up the weight a bit (c.f. 1.0)
global cho_bond_sigma_scale
cho_bond_sigma_scale = 3.0
def get_glyco_model_dir():
import os
return os.path.join(pkgdatadir(), "data", "cho-models")
def get_glyco_tree_acedrg_pyranose_dictionaries_dir():
import os
return os.path.join(pkgdatadir(), "data", "cho-acedrg")
def remove_duplicates(ls):
return list(set(ls))
def read_acedrg_pyranose_dictionaries():
import os
cho_list = ["NAG", "MAN", "BMA", "SIA", "GLC", "FUC", "XYP"]
for comp_id in cho_list:
fn = os.path.join(get_glyco_tree_acedrg_pyranose_dictionaries_dir(),
comp_id + "-acedrg.cif")
if os.path.isfile(fn):
coot.read_cif_dictionary(fn)
def add_cho_restraints_for_residue(imol, residue_spec):
if isinstance(residue_spec, list):
id = glyco_tree_residue_id(imol, residue_spec)
# print "BL DEBUG:: --------------------- add_cho_restraints_for_residue: glyco_tree_residue_id:", id
# print "BL DEBUG:: --------------------- add_cho_restraints_for_residue: glyco_tree_residues:", coot.glyco_tree_residues_py(imol, residue_spec)
add_cho_restraints_for_residue_with_id(imol, residue_spec, id)
def add_cho_restraints_for_residue_with_id(imol, residue_spec, glyco_id):
# hacky?!
def pad_name(str):
l = len(str)
ret = " "
if (l > 3):
return str
else:
return " " + str.ljust(3)
# return list [atom_1, atom_2, d, esd]
# or False
def line2extra_bond_restraint_spec(parent_residue_spec, line):
global cho_bond_sigma_scale
parts = line.split()
if (len(parts) == 7):
at_name_1 = pad_name(parts[0])
at_name_2 = pad_name(parts[1])
mean_str = parts[2]
sd_str = parts[3]
n_str = parts[4]
d_str = parts[5]
mod_sarle_str = parts[6]
# could be done in one?!
mean = float(mean_str)
sd = float(sd_str)
n = float(n_str)
d = float(d_str)
mod_sarle = float(mod_sarle_str)
if not (n >= 20):
return False
else:
if not (d < 4.3):
return False
else:
return [[residue_spec_to_chain_id(residue_spec),
res_spec_utils.residue_spec_to_res_no(residue_spec),
coot_utils.residue_spec_to_ins_code(residue_spec),
at_name_1, ""],
[residue_spec_to_chain_id(parent_residue_spec),
res_spec_utils.residue_spec_to_res_no(parent_residue_spec),
coot_utils.residue_spec_to_ins_code(parent_residue_spec),
at_name_2, ""],
mean, cho_bond_sigma_scale]
def glyco_id2level_number(glyco_id):
return glyco_id[0]
def glyco_id2prime_arm_sym(glyco_id):
return glyco_id[1]
def glyco_id2residue_type(glyco_id):
return glyco_id[2]
def glyco_id2link_type(glyco_id):
return glyco_id[3]
def glyco_id2parent_residue_type(glyco_id):
return glyco_id[4]
def glyco_id2residue_spec(glyco_id):
return glyco_id[5]
# main line
#
if isinstance(glyco_id, list):
dir = get_glyco_model_dir()
level = glyco_id2level_number(glyco_id)
prime_arm_sym = glyco_id2prime_arm_sym(glyco_id)
res_name = glyco_id2residue_type(glyco_id)
link_type = glyco_id2link_type(glyco_id)
parent_res_name = glyco_id2parent_residue_type(glyco_id)
parent_res_spec = glyco_id2residue_spec(glyco_id)
fn_file = "model-level-" + str(level) + "-" + res_name + "-" + \
link_type + "-" + parent_res_name + ".tab"
model_fn = os.path.join(dir, fn_file)
if not os.path.isfile(model_fn):
print("model file does not exist", model_fn)
else:
try:
f = open(filename, 'r')
lines = f.readlines()
f.close()
except:
print("BL WARNING: couldnt open file ", filename)
return False # with something?
print("INFO:: read %s lines from file %s" %(lines, model_fn))
new_restraints = [line2extra_bond_restraint_spec(line) for line in lines]
# print "BL DEBUG:: ", new_restraints
coot.add_extra_bond_restraints_py(imol, new_restraints)
def test_get_cho_restraints(imol):
raw_carbo_tree_list = []
for chain_id in coot_utils.chain_ids(imol):
for res_serial in range(coot.chain_n_residues(chain_id, imol)):
res_no = coot.seqnum_from_serial_number(imol, chain_id, res_serial)
rn = coot.residue_name(imol, chain_id, res_no, "")
if isinstance(rn, str):
if (rn == "NAG"):
residue_spec = [chain_id, res_no, ""]
rl = coot.glyco_tree_residues_py(imol, residue_spec)
print("rl:", rl)
coot.print_glyco_tree(imol, chain_id, res_no, "")
if not isinstance(rl, list):
print("bad glyco-tree for residue", residue_spec)
else:
if (len(rl) > 3):
id = glyco_tree_residue_id(imol, residue_spec)
print("residue %s residue id %s" %(residue_spec, id))
add_cho_restraints_for_residue_with_id(imol,
residue_spec,
id)
else:
print("BL WARNING:: rl <=3", rl)
def correlation_coefficient_of_this_tree():
with coot_utils.UsingActiveAtom(True) as [aa_imol, aa_chain_id, aa_res_no,
aa_ins_code, aa_atom_name, aa_alt_conf,
aa_res_spec]:
residues = glyco_tree_residues(aa_imol, aa_res_spec)
cc = coot.map_to_model_correlation(aa_imol, residues, [], 0,
coot.imol_refinement_map())
txt = "residues %s\ncc: %5.3f" %(residues, cc)
print(txt)
coot.info_dialog(txt)
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