def from_lowest(self, prmtop_filename, lowest_filename, state_type):
"""
Creates a new RotamerState of appropriate type from a GMIN lowest file.
:param prmtop_filename: File name of the AMBER topology file
:param lowest_filename: File name of the GMIN lowest file
:param state_type: Type of rotamer state (i.e. what sort of dependence on neighbours, backbone dihedrals etc.)
"""
molecule = ra.parse_topology_file(prmtop_filename)
find_dihedrals.map_dihedrals(*(molecule.identify_residues()))
self.configs = read_lowest(lowest_filename)
find_dihedrals.phi_psi_dihedrals(molecule)
find_dihedrals.sidechain_dihedrals(molecule)
lowest0 = self.lowest_config_coords(0)
lowest25 = self.lowest_config_coords(25)
for res in sorted([res for res in molecule.residues.nodes() if res.name != "ACE" and res.name != "NME"],
key=lambda x: x.index):
print "---------------"
print res.name, res.index
print "---------------"
print "phi", res.dihedrals["phi"].measure_dihedral(lowest0) * 180.0 / np.pi
print "psi", res.dihedrals["psi"].measure_dihedral(lowest0) * 180.0 / np.pi
for dihedral, dihe_object in sorted([(k, v) for k, v in res.dihedrals.items() if 'chi' in k]):
print dihedral, dihe_object.measure_dihedral(lowest0) * 180.0 / np.pi
print ""
for res in sorted([res for res in molecule.residues.nodes() if res.name != "ACE" and res.name != "NME"],
key=lambda x: x.index):
print "---------------"
print res.name, res.index
print "---------------"
print "phi", res.dihedrals["phi"].measure_dihedral(lowest25) * 180.0 / np.pi
print "psi", res.dihedrals["psi"].measure_dihedral(lowest25) * 180.0 / np.pi
for dihedral, dihe_object in sorted([(k, v) for k, v in res.dihedrals.items() if 'chi' in k]):
print dihedral, dihe_object.measure_dihedral(lowest25) * 180.0 / np.pi
print ""
def lowest_to_dihedral_csv(prmtop_filename, lowest_filename, csv_filename):
"""
Reads a topology and lowest filename and writes dihedral information to a csv file.
The file has the following structure:
<res_1>,<res_2>,<res_3>,...,<res_n>
global minimum,<energy of global minimum>
<res_1>,phi,psi,[chi_1],...,[chi_n]
<res_2>,phi,psi,[chi_1],...,[chi_n]
.
.
.
<res_n>,phi,psi,[chi_1],...,[chi_n]
<norm_energy_0>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
<norm_energy_1>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
.
.
.
<norm_energy_N>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
N.B. energies are given relative to the global minimum and angles are given in degrees in the order specified at the
top of the file
:param prmtop_filename: Amber topology filename
:param lowest_filename: GMIN lowest filename
:return:
"""
import csv
molecule = ra.parse_topology_file(prmtop_filename)
find_dihedrals.map_dihedrals(*(molecule.identify_residues()))
find_dihedrals.phi_psi_dihedrals(molecule)
find_dihedrals.sidechain_dihedrals(molecule)
lowest_configs = read_lowest(lowest_filename)
res_no_termini = [res for res in sorted(molecule.residues.nodes(), key=lambda x: x.index)
if res.name != "ACE" and res.name != "NME"]
with open(csv_filename, "w") as csv_file:
dihe_writer = csv.writer(csv_file)
dihe_writer.writerow(res_no_termini)
global_min_energy = norm_lowest_configs(lowest_configs)
dihe_writer.writerow(["global minimum", global_min_energy])
ordered_dihe = []
for res in res_no_termini:
backbone = sorted([dihe for dihe in res.dihedrals if 'p' in dihe])
sidechain = sorted([dihe for dihe in res.dihedrals if 'p' not in dihe])
dihe_writer.writerow([res.name] + backbone + sidechain)
ordered_dihe += [res.dihedrals[x] for x in backbone]
ordered_dihe += [res.dihedrals[x] for x in sidechain]
last_energy = 0.0
for config in lowest_configs:
energy = config["energy"]
if (energy - last_energy) > 10.0:
break
angles = [x.measure_dihedral(config["coords"]) * 180.0 / np.pi for x in ordered_dihe]
dihe_writer.writerow(["{:.8f}".format(energy)] + ["{: 9.4f}".format(angle) for angle in angles])
last_energy = energy
def from_lowest(self, prmtop_filename, lowest_filename, state_type):
"""
Creates a new RotamerState of appropriate type from a GMIN lowest file.
:param prmtop_filename: File name of the AMBER topology file
:param lowest_filename: File name of the GMIN lowest file
:param state_type: Type of rotamer state (i.e. what sort of dependence on neighbours, backbone dihedrals etc.)
"""
molecule = ra.parse_topology_file(prmtop_filename)
find_dihedrals.map_dihedrals(*(molecule.identify_residues()))
self.configs = read_lowest(lowest_filename)
find_dihedrals.phi_psi_dihedrals(molecule)
find_dihedrals.sidechain_dihedrals(molecule)
lowest0 = self.lowest_config_coords(0)
lowest25 = self.lowest_config_coords(25)
for res in sorted([
res for res in molecule.residues.nodes()
if res.name != "ACE" and res.name != "NME"
],
key=lambda x: x.index):
print "---------------"
print res.name, res.index
print "---------------"
print "phi", res.dihedrals["phi"].measure_dihedral(
lowest0) * 180.0 / np.pi
print "psi", res.dihedrals["psi"].measure_dihedral(
lowest0) * 180.0 / np.pi
for dihedral, dihe_object in sorted([
(k, v) for k, v in res.dihedrals.items() if 'chi' in k
]):
print dihedral, dihe_object.measure_dihedral(
lowest0) * 180.0 / np.pi
print ""
for res in sorted([
res for res in molecule.residues.nodes()
if res.name != "ACE" and res.name != "NME"
],
key=lambda x: x.index):
print "---------------"
print res.name, res.index
print "---------------"
print "phi", res.dihedrals["phi"].measure_dihedral(
lowest25) * 180.0 / np.pi
print "psi", res.dihedrals["psi"].measure_dihedral(
lowest25) * 180.0 / np.pi
for dihedral, dihe_object in sorted([
(k, v) for k, v in res.dihedrals.items() if 'chi' in k
]):
print dihedral, dihe_object.measure_dihedral(
lowest25) * 180.0 / np.pi
print ""
def lowest_to_dihedral_csv(prmtop_filename, lowest_filename, csv_filename):
"""
Reads a topology and lowest filename and writes dihedral information to a csv file.
The file has the following structure:
<res_1>,<res_2>,<res_3>,...,<res_n>
global minimum,<energy of global minimum>
<res_1>,phi,psi,[chi_1],...,[chi_n]
<res_2>,phi,psi,[chi_1],...,[chi_n]
.
.
.
<res_n>,phi,psi,[chi_1],...,[chi_n]
<norm_energy_0>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
<norm_energy_1>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
.
.
.
<norm_energy_N>,<res_1_phi>,<res_1_psi>,[<res_1_chi_1>],...,<res_2_phi>,...,<res_n_phi>,...,[<res_n_chi_n>]
N.B. energies are given relative to the global minimum and angles are given in degrees in the order specified at the
top of the file
:param prmtop_filename: Amber topology filename
:param lowest_filename: GMIN lowest filename
:return:
"""
import csv
molecule = ra.parse_topology_file(prmtop_filename)
find_dihedrals.map_dihedrals(*(molecule.identify_residues()))
find_dihedrals.phi_psi_dihedrals(molecule)
find_dihedrals.sidechain_dihedrals(molecule)
lowest_configs = read_lowest(lowest_filename)
res_no_termini = [
res for res in sorted(molecule.residues.nodes(), key=lambda x: x.index)
if res.name != "ACE" and res.name != "NME"
]
with open(csv_filename, "w") as csv_file:
dihe_writer = csv.writer(csv_file)
dihe_writer.writerow(res_no_termini)
global_min_energy = norm_lowest_configs(lowest_configs)
dihe_writer.writerow(["global minimum", global_min_energy])
ordered_dihe = []
for res in res_no_termini:
backbone = sorted([dihe for dihe in res.dihedrals if 'p' in dihe])
sidechain = sorted(
[dihe for dihe in res.dihedrals if 'p' not in dihe])
dihe_writer.writerow([res.name] + backbone + sidechain)
ordered_dihe += [res.dihedrals[x] for x in backbone]
ordered_dihe += [res.dihedrals[x] for x in sidechain]
last_energy = 0.0
for config in lowest_configs:
energy = config["energy"]
if (energy - last_energy) > 10.0:
break
angles = [
x.measure_dihedral(config["coords"]) * 180.0 / np.pi
for x in ordered_dihe
]
dihe_writer.writerow(
["{:.8f}".format(energy)] +
["{: 9.4f}".format(angle) for angle in angles])
last_energy = energy
def parse_prmtop(self, prmtop_filename):
self.molecule = prmtop.parse_topology_file(prmtop_filename)
def parse_prmtop(self, prmtop_filename):
self.molecule = prmtop.parse_topology_file(prmtop_filename)