def test_types_ffld(self):
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qprm = QPrm("oplsaa")
qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct)
print(list(qprm.torsions.keys()))
lj_A_i = (4 * 0.17 * ((3.25)**12))**0.5
lj_B_i = (4 * 0.17 * ((3.25)**6))**0.5
at = qprm.atom_types["nma.N"]
assert is_close(at.lj_A, lj_A_i)
assert is_close(at.lj_B, lj_B_i)
bond = qprm.bonds["ace.C ace.CH3"]
assert is_close(bond.fc / 2.0, 317.0)
assert is_close(bond.r0, 1.522)
ang = qprm.angles["ash.C ash.CA ash.CB"]
assert is_close(ang.fc / 2.0, 63.0)
assert is_close(ang.theta0, 111.1)
tors = qprm.torsions["ace.C ash.N ash.CA ash.C"]
assert is_close(tors.fcs[0] * 2.0, -2.365)
assert is_close(tors.fcs[1] * 2.0, 0.912)
assert is_close(tors.fcs[2] * 2.0, -0.850)
assert is_close(tors.multiplicities[0], 1.0)
assert is_close(tors.multiplicities[1], 2.0)
assert is_close(tors.multiplicities[2], 3.0)
assert is_close(tors.phases[0], 0.0)
assert is_close(tors.phases[1], 180.0)
assert is_close(tors.phases[2], 0.0)
def test_overwritten_prm(self):
qprm = QPrm("amber", ignore_errors=True) # duplicates
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
ow = qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# check overwritten parm
assert ow[0].prm_id == "C N CX CT"
assert ow[0].fcs == [0.0, 0.4, 2.0, 2.0]
def test_wrong_ff_fail(self):
qprm = QPrm("amber")
with pytest.raises(QPrmError):
qprm.read_ffld("data/ace_ash_nma.ffld11", None)
qprm = QPrm("oplsaa")
with pytest.raises(QPrmError):
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
with pytest.raises(QPrmError):
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
def test_read_ffld(self):
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qprm = QPrm("oplsaa")
qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct)
assert len(qprm.atom_types) == 25
assert len(qprm.bonds) == 24
assert len(qprm.angles) == 40
assert len(qprm.torsions) == 49
assert len(qprm.impropers) == 5
def test_read_amber_frcmod(self):
qprm = QPrm("amber", ignore_errors=True) # duplicates
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
assert len(qprm.atom_types) == 4
assert len(qprm.bonds) == 27
assert len(qprm.angles) == 92
assert len(qprm.generic_torsions) == 10
assert len(qprm.torsions) == 128
assert len(qprm.generic_impropers) == 1
assert len(qprm.impropers) == 2
def test_read_amber_parm(self):
qprm = QPrm("amber")
qprm.read_amber_parm("data/gaff.dat")
assert len(qprm.atom_types) == 71
assert len(qprm.bonds) == 832
assert len(qprm.angles) == 4618
assert len(qprm.generic_torsions) == 587
assert len(qprm.torsions) == 66
assert len(qprm.generic_impropers) == 8
assert len(qprm.impropers) == 27
def test_read_write_prm(self):
qp_str = open("data/qamber14.prm", "r").read()
qp_str = re.sub("(\*|\!|#).*", "", qp_str)
qp_str = re.sub("\s+$", "", qp_str, 0, re.MULTILINE)
qp_str = re.sub("^\n", "", qp_str, 0, re.MULTILINE)
qprm = QPrm("amber")
qprm.read_prm("data/qamber14.prm")
qp_str2 = qprm.get_string()
qp_str2 = re.sub("\s+$", "", qp_str2, 0, re.MULTILINE)
qp_str2 = re.sub("^\n", "", qp_str2, 0, re.MULTILINE)
assert qp_str == qp_str2
def test_read_write_prm2(self):
qp_str = open("data/ace_ash_nma.prm", "r").read()
qp_str = re.sub("(\*|\!|#).*", "", qp_str)
qp_str = re.sub("\s+$", "", qp_str, 0, re.MULTILINE)
qp_str = re.sub("^\n", "", qp_str, 0, re.MULTILINE)
qprm = QPrm("oplsaa")
qprm.read_prm("data/ace_ash_nma.prm")
qp_str2 = qprm.get_string()
qp_str2 = re.sub("(\*|\!|#).*", "", qp_str2)
qp_str2 = re.sub("\s+$", "", qp_str2, 0, re.MULTILINE)
qp_str2 = re.sub("^\n", "", qp_str2, 0, re.MULTILINE)
assert qp_str == qp_str2
def test_types(self):
qprm = QPrm("amber")
qprm.read_prm("data/qamber14.prm")
assert qprm.atom_types["CK"].lj_R == 1.908
assert qprm.atom_types["CK"].lj_eps == 0.086
assert qprm.atom_types["CK"].mass == 12.01
assert qprm.bonds["Br CA"].fc == 344.0
assert qprm.bonds["Br CA"].r0 == 1.89
assert qprm.angles["C4 C4 Nstar"].fc == 140.0
assert qprm.angles["C4 C4 Nstar"].theta0 == 121.2
assert qprm.torsions["Cstar CT CX N3"].fcs == [
0.079, 0.313, 0.234, 0.031
]
def test_amber_conversion(self):
qp_str = open("data/qamber14.prm", "r").read()
qp_str = re.sub("(\*|\!|#).*", "", qp_str)
qp_str = re.sub("\s+$", "", qp_str, 0, re.MULTILINE)
qp_str = re.sub("^\n", "", qp_str, 0, re.MULTILINE)
qprm = QPrm("amber", ignore_errors=True) # duplicates
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
ow = qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# add options section manually and compare with official lib
for line in """\
name Q-Amber14SB
type AMBER
vdw_rule arithmetic
scale_14 0.8333
switch_atoms off
improper_potential periodic
improper_definition explicit\
""".splitlines():
lf = line.split()
qprm.options[lf[0]] = " ".join(lf[1:])
qp_str2 = qprm.get_string()
qp_str2 = re.sub("\s+$", "", qp_str2, 0, re.MULTILINE)
qp_str2 = re.sub("^\n", "", qp_str2, 0, re.MULTILINE)
assert qp_str == qp_str2
def test_types_opls(self):
qprm = QPrm("oplsaa")
qprm.read_prm("data/ace_ash_nma.prm")
assert qprm.atom_types["ace.C"].lj_A == 1802.2385
assert qprm.atom_types["ace.C"].lj_B == 34.1758
assert qprm.atom_types["ace.C"].mass == 12.011
assert qprm.bonds["ace.CH3 ace.HH31"].fc == 680.0
assert qprm.bonds["ace.CH3 ace.HH31"].r0 == 1.09
assert qprm.angles["ash.OD1 ash.CG ash.OD2"].fc == 160.0
assert qprm.angles["ash.OD1 ash.CG ash.OD2"].theta0 == 121.0
t = qprm.torsions["ash.CA ash.CB ash.CG ash.OD2"]
assert t.fcs == [0.5, 0.273, 0.225]
assert t.multiplicities == [1.0, 2.0, 3.0]
i = qprm.impropers["ash.CA ash.C ash.O nma.N"]
assert i.fc == 10.5
assert i.phi0 == 180.0
print("FATAL! At least one frcmod file is required.")
sys.exit()
for k, v in six.iteritems(vars(args)):
if k in ["mol2", "prepi", "parm", "frcmods"]:
for fn in v:
if not os.path.lexists(fn):
print("File '{}' doesn't exist.".format(fn))
sys.exit(1)
#
# create QLib, QPrm, QStruct and QTopology objects
#
qlib = QLib("amber", ignore_errors=args.ignore_errors)
qprm = QPrm("amber", ignore_errors=args.ignore_errors)
try:
qlib.read_mol2(args.mol2[0])
except QLibError as e:
print("FATAL! Problem with mol2: {}".format(str(e)))
sys.exit(1)
try:
qlib.read_prepin_impropers(args.prepi[0])
except QLibError as e:
print("FATAL! Problem with prepi: {}".format(str(e)))
sys.exit(1)
for parm in args.parms:
try:
qprm.read_amber_parm(parm)
except QPrmError as e:
def test_overwritten_prm_fail(self):
qprm = QPrm("amber") # no ignore_errors
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
with pytest.raises(QPrmError):
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
def test_read_amber_parm_fail(self):
qprm = QPrm("amber")
with pytest.raises(QPrmError):
qprm.read_amber_parm("data/ff-amber14/parm/frcmod.ff14SB")
def test_ff14sb_conversion():
# Amber14FF to Qamber14
#
# Convert Amber14 lib (+prepin for impropers) and parm+frcmod to Q lib/prm
# Load the structure 'all_amino_acids.pdb' and build the topology
# Check the total bonding energy contributions and number of bonding terms
# and compare the library and parameter set with official qamber14.
#
qal = QLib("amber")
qap = QPrm("amber", ignore_errors=True) # duplicates
qal.read_amber_lib("data/ff-amber14/amber12_mod.lib")
qal.read_amber_lib("data/ff-amber14/arn.lib")
qal.read_prepin_impropers("data/ff-amber14/prep/amino12.in")
qal.read_prepin_impropers("data/ff-amber14/arn.prepi")
qap.read_amber_parm("data/ff-amber14/parm/parm10.dat")
qap.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
# add options to parameters
for line in """\
name Q-Amber14SB
type AMBER
vdw_rule arithmetic !vdW combination rule (geometric or arithmetic)
scale_14 0.8333 ! electrostatic 1-4 scaling factor
switch_atoms off
improper_potential periodic
improper_definition explicit\
""".splitlines():
lf = line.split()
qap.options[lf[0]] = " ".join(lf[1:])
# remove head from ACE and tail from NME
cons = qal.residue_dict["ACE"].connections
cons = [con for con in cons if "head" not in con]
qal.residue_dict["ACE"].connections = cons
cons = qal.residue_dict["NME"].connections
cons = [con for con in cons if "tail" not in con]
qal.residue_dict["NME"].connections = cons
qas1 = QStruct("data/all_amino_acids.pdb", "pdb", ignore_errors=True)
qat = QTopology(qal, qap, qas1)
q_tors = sum([len(list(tor.prm.get_prms())) for tor in qat.torsions])
assert len(qat.bonds) == 464
assert len(qat.angles) == 829
assert len(qat.torsions) == 1221
assert q_tors == 1950
assert len(qat.impropers) == 102
be = sum([bond.calc()[0] for bond in qat.bonds])
ae = sum([ang.calc()[0] for ang in qat.angles])
te = sum([tor.calc()[0] for tor in qat.torsions])
ie = sum([imp.calc()[0] for imp in qat.impropers])
assert is_close(be, 181.2572830)
assert is_close(ae, 212.8539304)
assert is_close(te, 417.2919960)
assert is_close(ie, 22.8171235)
# compare with official lib
qa14_lib = open("data/qamber14.lib", "r").read()
qa14_prm = open("data/qamber14.prm", "r").read()
assert qal.get_string() in qa14_lib
assert qap.get_string() in qa14_prm
def make_fep(qmap_file,
pdb_file,
forcefield,
parm_files,
lib_files,
ignore_errors=False):
"""Generate a template FEP file for EVB simulations in Q.
Parses a QMAP file (see below), state 1 structure file (PDB) and
all states libraries and parameters, and determines the changes
in connectivity/charges/parameters that occur between the states.
QMAP is a text file that defines mappings of library ids (for each state)
to state 1 structure/topology ids, best explained on an example:
q 315.O OHH.O OHH.O
q 315.H1 OHH.H1 HIP.HE2
q 315.H2 OHH.H2 OHH.H2
q 155.NE2 HID.NE2 HIP.NE2
...
n 155.CA HID.CA HIP.CA
The first column defines the atom as being a 'Q' atom or a 'neighbouring'
atom. The latter will not be included in the 'Q-region' but will be
included in the 'change_bonds/change_angles...' sections in case there is a
change in bonding/parameters outside the Q region. Additionally, you can
define a 'q' atom with 'q_qcp', which will create an additional section for
isotopically clean masses used in QCP calculations.
The second column is the PDB ID, comprised of residue index and atom name,
separated by a dot.
The third column is the library ID of this atom in state 1, comprised of
residue name and atom name (should be the same as in the structure).
The fourth column is the library ID of this atom in state 2.
Additional columns can be added for other states.
The returned template string contains several missing parts, denoted with
<FIX>, which have to be manually replaced with appropriate values. These
include the softpair C parameters, Morse parameters, Hij parameters.
Args:
qmap_file (string): QMAP file path
pdb_file (string): state 1 PDB file path (the one built with qprep)
forcefield (string): forcefield type (see SUPPORTED_FF)
prms_files (list): Q parameter-file paths
libs_files (list): Q library-file paths
ignore_errors (boolean, optional): don't fail on certain non critical
errors
Returns:
fepstr (string): fepfile template
Raises:
QMakeFepError
"""
if forcefield not in SUPPORTED_FF:
raise QMakeFepError("Force field '{}' not supported. Use {}"
"".format(forcefield, " or ".join(SUPPORTED_FF)))
fep_types = {
"atoms": [],
"bonds": [],
"angles": [],
"torsions": [],
"impropers": []
}
fep_changes = {
"atoms": [],
"charges": [],
"bonds": ODict(),
"angles": ODict(),
"torsions": ODict(),
"impropers": ODict()
}
fep_qcp_atoms = []
fep_morse_prms = {}
fep_reacting_atoms = set()
num_evb_states = None
# parse the MAP file
# pdb_ids_map = [ ('q', [pdbid1_state1,]),
# ('q', [pdbid2_state1,]),
# ...
# ('n', [pdbid11_state1,]),
# ...
# ]
# lib_ids_map = [ [lib_id1_state1, lib_id2_state1...],
# [lib_id1_state2, lib_id2_state2...],
# ...
# ]
#
lib_ids_map = []
pdb_ids_map = []
with open(qmap_file, 'r') as qatom_map:
for i, line in enumerate(qatom_map.readlines()):
line = re.split("#|\*|\!", line, 1)[0].strip() # remove comments
if line == "":
continue
c = line.split()
atom_type = c[0].lower()
pdb_id = c[1]
lib_ids = c[2:]
if atom_type not in ["q", "n", "q_qcp"]:
raise QMakeFepError("Lines in the QMAP file should begin "
"with either 'q' (qatom) or 'n' "
"(neighboring atom) or 'q_qcp' "
"(QPI q atom)")
try:
resid, name = pdb_id.split(".")
if not name or not int(resid): raise ValueError
except ValueError:
raise QMakeFepError("Invalid PDB ID '{}'. Should be "
"RESID.ATOMNAME".format(pdb_id))
tmp = (atom_type, [
pdb_id,
])
if tmp in pdb_ids_map:
raise QMakeFepError("Duplicate PDB ID: '{}'".format(pdb_id))
pdb_ids_map.append(tmp)
if num_evb_states == None:
num_evb_states = len(lib_ids)
elif len(lib_ids) != num_evb_states:
raise QMakeFepError("Number of states in line '{}' not equal "
"to number of PDB files".format(line))
for state, lib_id in enumerate(lib_ids):
try:
resname, name = lib_id.split(".")
if not resname or not name: raise ValueError
except ValueError:
raise QMakeFepError("Invalid library ID '{}'. Should be "
"RESNAME.ATOMNAME".format(lib_id))
try:
if lib_id in lib_ids_map[state]:
raise QMakeFepError("The library IDs in one EVB state "
"should be unique (double '{}'), "
"otherwise proper bonding can't "
"be determined.".format(lib_id))
except IndexError:
lib_ids_map.append([])
lib_ids_map[state].append(lib_id)
# load libraries
qlib = QLib(forcefield, ignore_errors=ignore_errors)
for lib in lib_files:
try:
qlib.read_lib(lib)
except QLibError as e:
raise QMakeFepError("Problem parsing lib ({}): {}"
"".format(lib, e))
# make dummy structures for other states
structures = [None for _ in range(num_evb_states)]
structures[0] = pdb_file
libid_pdbid_map = [{} for _ in range(num_evb_states)]
for state in range(1, num_evb_states):
state_structure = []
atom_index = 1
processed_residues = []
for i, (q_or_n, pdb_ids_all_states) in enumerate(pdb_ids_map):
lib_id = lib_ids_map[state][i]
resname, aname = lib_id.split(".")
# add all atoms of current residue to the dummy structure
# at the same time, storing the mapping lib_id:pdb_id
# in libid_pdbid_map for later
if resname not in processed_residues:
try:
residue_lib = qlib.residue_dict[resname]
except KeyError:
raise QMakeFepError("Residue '{}' not found in library."
"".format(resname))
processed_residues.append(resname)
res_index = len(processed_residues)
for atom in residue_lib.atoms:
lib_id2 = "{}.{}".format(resname, atom.name)
pdb_id2 = "{}.{}".format(res_index, atom.name)
state_structure.append("{:<6}{:5} {:4} {:3} {:5} "
"{:8.3f}{:8.3f}{:8.3f}"
"".format("ATOM", atom_index,
atom.name, resname,
res_index, 0, 0, 0))
atom_index += 1
# map the newly created dummy atom's pdb_id to lib_id
libid_pdbid_map[state][lib_id2] = pdb_id2
# add pdb_id of current atom in current (dummy structure)
# state to pdb_ids_map (using its lib_id)
try:
pdb_id_this_state = libid_pdbid_map[state][lib_id]
except KeyError:
raise QMakeFepError(
"Library ID '{}' not valid.".format(lib_id))
pdb_ids_all_states.append(pdb_id_this_state)
_, structures[state] = tempfile.mkstemp()
open(structures[state], "w").write("\n".join(state_structure))
# DEBUG
# print "Dummy PDB for st.{}: {}".format(state + 1, structures[state])
# load parameters
qprm = QPrm(forcefield, ignore_errors=ignore_errors)
for parm in parm_files:
try:
qprm.read_prm(parm)
except QPrmError as e:
raise QMakeFepError("Problem with parm ({}): {}"
"".format(parm, e))
# load structures and make topologies
topologies = []
for state in range(num_evb_states):
try:
qstruct = QStruct(structures[state],
"pdb",
ignore_errors=ignore_errors)
except QStructError as e:
raise QMakeFepError("Problem parsing PDB file ({}): {} "
"".format(structures[state], e))
try:
topologies.append(QTopology(qlib, qprm, qstruct))
except QTopologyError as e:
raise QMakeFepError("Problem building the topology: {}"
"".format(e))
# Make _TopoAtom (atoms in QTopology) maps out of qmap's lists
# and extract types, type changes and charge changes
#
# atom_map = [ [_TopoAtom1_state1, _TopoAtom1_state2, ... ],
# [_TopoAtom2_state1, _TopoAtom2_state2, ... ],
# [_TopoAtom3_state1, _TopoAtom3_state2, ... ],
# ...
# ]
atom_map = []
for i, (q_or_n, pdb_id_all_states) in enumerate(pdb_ids_map):
atom_all_states = []
for state, pdb_id in enumerate(pdb_id_all_states):
residue, aname = pdb_id.split(".")
try:
residue = topologies[state].residues[int(residue) - 1]
atom = [a for a in residue.atoms if a.name == aname][0]
except (KeyError, IndexError) as e:
raise QMakeFepError("Atom '{}' doesn't exist in PDB '{}'"
"".format(pdb_id, structures[state]))
atom_all_states.append(atom)
atom_map.append(atom_all_states)
# check for stupidity - lib_id in QMAP state 1
# not matching the structure/topology
lib_id_qmap = lib_ids_map[0][i]
lib_id = "{}.{}".format(atom_all_states[0].residue.name,
atom_all_states[0].name)
if lib_id != lib_id_qmap:
pdb_id = pdb_ids_map[i][1][0]
raise QMakeFepError("QMAP state 1 library ID ({}) of atom '{}' "
"doesn't match topology library ID ({})."
"".format(lib_id_qmap, pdb_id, lib_id))
# For Q atoms (and not the neighbor atoms):
# get FEP atom types, type changes and charge changes
if q_or_n in ["q", "q_qcp"]:
for atom in atom_all_states:
if atom.prm not in fep_types["atoms"]:
fep_types["atoms"].append(atom.prm)
fep_changes["charges"].append([a.charge for a in atom_all_states])
fep_changes["atoms"].append(atom_all_states)
if q_or_n == "q_qcp":
fep_qcp_atoms.append(atom_all_states)
charge_sums = []
for state in range(num_evb_states):
charge_sum = sum([c[state] for c in fep_changes["charges"]])
if abs(round(charge_sum) - charge_sum) > 1e-6:
raise_or_log("Net charge in state {} not integer: {}"
"".format(state + 1, charge_sum),
QMakeFepError,
logger,
ignore_errors=ignore_errors)
charge_sums.append(charge_sum)
if any([abs(c - charge_sums[0]) > 1e-6 for c in charge_sums]):
logger.warning("Net charge changes between states: {}"
"".format(" -> ".join([str(c) for c in charge_sums])))
# get all Bonds, Angles, Torsions and Impropers which include
# at least one atom defined in qmap
batis = {"bonds": [], "angles": [], "torsions": [], "impropers": []}
batis["bonds"] = [set() for _ in range(num_evb_states)]
batis["angles"] = [set() for _ in range(num_evb_states)]
batis["torsions"] = [set() for _ in range(num_evb_states)]
batis["impropers"] = [set() for _ in range(num_evb_states)]
for atom_all_states in atom_map:
for state, atom in enumerate(atom_all_states):
_ = [batis["bonds"][state].add(b) for b in atom.bonds]
_ = [batis["angles"][state].add(a) for a in atom.angles]
_ = [batis["torsions"][state].add(t) for t in atom.torsions]
_ = [batis["impropers"][state].add(i) for i in atom.impropers]
# map the bonds,angles,torsions,impropers (bati) in different states
# to same key (ordered list of state1 PDB_IDs)
#
# bati_map =
# { "bonds": {state1_bond1_key: [bond1_state1, bond1_state2,...],
# state1_bond2_key: [bond2_state1, bond2_state2,...], ...},
# "angles": {state1_angle1_key: [angle1_state1, angle1_state2,...],...}
# ... }
#
# also, include only batis which have all atoms defined in qmap
# also, detect inter-residue batis and raies QMakeFepError
bati_map = {"bonds": {}, "angles": {}, "torsions": {}, "impropers": {}}
for state in range(num_evb_states):
atoms_in_state = [a_all_st[state] for a_all_st in atom_map]
for bati_type in bati_map:
for bati in batis[bati_type][state]:
# find the corresponding atoms in state1
try:
atoms_st1 = [
atom_map[atoms_in_state.index(a)][0]
for a in bati.atoms
]
except ValueError:
# one of the Atoms is not defined in QMAP
continue
pdbid_index = []
for atom in atoms_st1:
pdbid_index.append(
(atom.index, "{}.{}".format(atom.residue.index,
atom.name)))
# order the pdbids to prevent double entries
if bati_type == "bonds":
pids = sorted(pdbid_index)
elif bati_type == "angles":
pids = min(pdbid_index, list(reversed(pdbid_index)))
elif bati_type == "torsions":
pids = min(pdbid_index, list(reversed(pdbid_index)))
elif bati_type == "impropers":
# topology order == library order == correct order
pids = pdbid_index
key = " ".join([p[1] for p in pids])
# check for bonds/angles/torsions/impropers that are
# shared between residues
residue_ids = set(atom.residue.index for atom in bati.atoms)
if len(residue_ids) > 1:
raise QMakeFepError("Inter-residue bond/angle/torsion '{}'"
" not supported. Combine the residues "
"into a single library entry if you "
"want to make changes over the "
"'head-tail' bond.".format(key))
# add bati to bati_map
try:
bati_map[bati_type][key][state] = bati
except KeyError:
bati_map[bati_type][key] = [
None for _ in range(num_evb_states)
]
bati_map[bati_type][key][state] = bati
# DEBUG
# for k,v in bati_map.iteritems():
# print k
# for k2, v2 in v.iteritems():
# print k2, v2[0], v2[1]
def _bati_sort(key, bati_all_states):
# to sort bonds/angles.. based on the key
# also, breaking and forming bonds have priority
try:
return (-1 * bati_all_states.index(None), key)
except:
return (1, key)
# find changes between states (add to fep_changes dict)
for bati_type, batis in bati_map.iteritems():
for bati_key, bati_all_states in sorted(batis.items(),
key=lambda (key, val): \
_bati_sort(key, val)):
# bond/angle/.. breaking or forming
if None in bati_all_states:
fep_changes[bati_type][bati_key] = bati_all_states
# add bond atoms to "reactive atoms" set
# and replace the bond parameter with a Morse type
if bati_type == "bonds":
for bati in bati_all_states:
if bati != None:
fep_reacting_atoms |= set(bati.atoms)
# the bond parameter is replaced with a Morse
# parameter (_FepPrmMorse)
prm_id = bati.prm.prm_id
try:
bati.prm = fep_morse_prms[prm_id]
except KeyError:
bati.prm = _FepPrmMorse(bati.prm)
fep_morse_prms[prm_id] = bati.prm
# the actual values of the parameters are not exactly the same
else:
tmp = [
bati_all_states[0].prm.strval == bati.prm.strval
for bati in bati_all_states
]
if not all(tmp):
fep_changes[bati_type][bati_key] = bati_all_states
# DEBUG
# for k,v in fep_changes.iteritems():
# print k
# try:
# for k2,(v1,v2) in v.iteritems():
# print k2,v1,v2
# except:
# for (v1,v2) in v:
# print v1,v2
# add parameters of changing batis to fep_types
for bati_type in bati_map:
for bati_all_states in fep_changes[bati_type].values():
prms = [bati.prm for bati in bati_all_states if bati != None]
for prm in prms:
if prm not in fep_types[bati_type]:
fep_types[bati_type].append(prm)
# DEBUG
# for k,v in fep_types.iteritems():
# print k
# for v2 in v:
# print v2
# add reactive atoms from states that have bond==None to fep_reacting_atoms
for atom_all_states in fep_changes["atoms"]:
for atom in atom_all_states:
if atom in fep_reacting_atoms:
fep_reacting_atoms |= set(atom_all_states)
########################
# Prepare the output
########################
fep_l = {
"atoms": [],
"atom_types": [],
"qcp_mass": [],
"change_atoms": [],
"change_charges": [],
"soft_pairs": [],
"off_diagonals": [],
"bond_types": [],
"change_bonds": [],
"angle_types": [],
"change_angles": [],
"torsion_types": [],
"change_torsions": [],
"improper_types": [],
"change_impropers": []
}
####################
# ATOMS
# CHANGE_ATOMS
# CHANGE_CHARGES
####################
format_atoms = "{:<15} {:<10} # {:<15} {:<15} {:>3}"
format_ch_atoms = "{:<10} " + " {:<12}" * num_evb_states + " # {:<}"
format_ch_crgs = "{:<10} " + " {:12}"*num_evb_states + " # {:<10}"\
+ " {:>12}"*(num_evb_states-1)
format_qcp = "{:<15} {:<10} # {:<10}"
fep_l["atoms"].append(
format_atoms.format("#Q index", "PDB index", "St.1 PDB_ID",
"St.1 LIB_ID", ""))
tmp = ["#Q index"]
tmp.extend(["Type st.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_ID")
fep_l["change_atoms"].append(format_ch_atoms.format(*tmp))
tmp = ["#Q index"]
tmp.extend(["Charge st.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_ID")
tmp.extend(
["dq({}->{})".format(n + 1, n + 2) for n in range(num_evb_states - 1)])
fep_l["change_charges"].append(format_ch_crgs.format(*tmp))
if fep_qcp_atoms:
fep_l["qcp_mass"].append("[qcp_mass]")
fep_l["qcp_mass"].append(
format_qcp.format("#Q index", "Mass", "St.1 PDB_ID"))
for i, atom_all_states in enumerate(fep_changes["atoms"]):
q_index = i + 1
a = atom_all_states[0]
pdb_id = "{}.{}".format(a.residue.index, a.name)
lib_id = "{}.{}".format(a.residue.name, a.name)
# atoms
reacting_flag = " !" * bool(
[atom for atom in atom_all_states if atom in fep_reacting_atoms])
fep_l["atoms"].append(
format_atoms.format(q_index, "$" + pdb_id + "$", pdb_id, lib_id,
reacting_flag))
# change_atoms
tmp = [q_index] + [a.prm.prm_id for a in atom_all_states] + [pdb_id]
fep_l["change_atoms"].append(format_ch_atoms.format(*tmp))
# charges
crgs = [float(a.charge) for a in atom_all_states]
tmp = [q_index] + crgs + [pdb_id] \
+ [crgs[n+1]-crgs[n] for n in range(num_evb_states-1)]
fep_l["change_charges"].append(format_ch_crgs.format(*tmp))
# qcp_atoms
if atom_all_states in fep_qcp_atoms:
fep_l["qcp_mass"].append(
format_qcp.format(q_index, "<FIX>", pdb_id))
###############
# ATOM_TYPES
###############
format_atypes = "{:<12} {:>10} {:>10} {:>10} {:>10} {:>10} {:>10} {:>10}"
if forcefield == "amber":
fep_l["atom_types"].append(
format_atypes.format("#Atom_type", "LJ_Rm", "LJ_eps", "SP_Ci",
"SP_ai", "LJ_Rm", "LJ_eps_14", "mass"))
else:
fep_l["atom_types"].append(
format_atypes.format("#Atom_type", "LJ_A", "LJ_B", "SP_Ci",
"SP_ai", "LJ_A_14", "LJ_B_14", "mass"))
fep_reacting_atoms_prms = [a.prm for a in fep_reacting_atoms]
for prm in fep_types["atoms"]:
sp_c = 1
sp_a = 2.5
if prm in fep_reacting_atoms_prms:
sp_c = "<FIX>"
if forcefield == "amber":
lj1, lj2 = prm.lj_R, prm.lj_eps
lj3, lj4 = lj1, round(lj2 / 1.2, 4)
else:
lj1, lj2 = prm.lj_A, prm.lj_B
lj3, lj4 = round(lj1 / (2**0.5), 4), round(lj2 / (2**0.5), 4)
fep_l["atom_types"].append(
format_atypes.format(prm.prm_id, lj1, lj2, sp_c, sp_a, lj3, lj4,
prm.mass))
###############
# BOND_TYPES
###############
format_hbonds = "{:<8} {:>10} {:>10} # {}"
format_mbonds = "{:<8} {:^10} {:^10} {:>10} # {}"
fep_l["bond_types"].append("## Harmonic format")
fep_l["bond_types"].append(
format_hbonds.format("#Index", "Fc", "r0", "PRM_ID"))
fep_l["bond_types"].append("## Morse format")
fep_l["bond_types"].append(
format_mbonds.format("#Index", "D", "alpha", "r0", "PRM_ID"))
for i, bond_type in enumerate(fep_types["bonds"]):
b_index = i + 1
if isinstance(bond_type, _FepPrmMorse):
prm_id = "-".join(bond_type.harmonic_prm.prm_id.split())
tmp = format_mbonds.format(b_index, "<FIX_D>", "<FIX_a>",
"<FIX_r0>", prm_id)
fep_l["bond_types"].append(tmp)
else:
prm_id = "-".join(bond_type.prm_id.split())
tmp = format_hbonds.format(b_index, bond_type.fc, bond_type.r0,
prm_id)
fep_l["bond_types"].append(tmp)
###############
# CHANGE_BONDS
###############
format_bondch = "{:<10} {:<10} " + "{:^5} " * num_evb_states + " # {}"
tmp = ["#Atom1", "Atom2"]
tmp.extend(["St.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_IDs")
fep_l["change_bonds"].append(format_bondch.format(*tmp))
for bond_key, bond_all_states in fep_changes["bonds"].iteritems():
# bond_key == "PDB_ID1 PDB_ID2"
prm_indexes = []
for b in bond_all_states:
if b == None:
prm_indexes.append(0)
else:
btype_index = fep_types["bonds"].index(b.prm) + 1
prm_indexes.append(btype_index)
placeholders = ["${}$".format(a) for a in bond_key.split()]
pdb_id = "-".join(bond_key.split())
tmp = placeholders + prm_indexes + [pdb_id]
fep_l["change_bonds"].append(format_bondch.format(*tmp))
###############
# ANGLE_TYPES
###############
format_angles = "{:<8} {:>10} {:>10} # {}"
fep_l["angle_types"].append(
format_angles.format("#Index", "Fc", "theta0", "PRM_ID"))
for i, angle_type in enumerate(fep_types["angles"]):
an_index = i + 1
prm_id = "-".join(angle_type.prm_id.split())
tmp = format_angles.format(an_index, angle_type.fc, angle_type.theta0,
prm_id)
fep_l["angle_types"].append(tmp)
#################
# CHANGE_ANGLES
#################
format_angch = "{:<10} {:<10} {:<10} " + "{:^5} " * num_evb_states + " # {}"
tmp = ["#Atom1", "Atom2", "Atom3"]
tmp.extend(["St.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_IDs")
fep_l["change_angles"].append(format_angch.format(*tmp))
for angle_key, angle_all_states in fep_changes["angles"].iteritems():
# angle_key == "PDB_ID1 PDB_ID2 PDB_ID3"
prm_indexes = []
for ang in angle_all_states:
if ang == None:
prm_indexes.append(0)
else:
atype_index = fep_types["angles"].index(ang.prm) + 1
prm_indexes.append(atype_index)
placeholders = ["${}$".format(a) for a in angle_key.split()]
pdb_id = "-".join(angle_key.split())
tmp = placeholders + prm_indexes + [pdb_id]
fep_l["change_angles"].append(format_angch.format(*tmp))
#################
# TORSION_TYPES
#################
format_torsions = "{:<8} {:>10} {:>10} {:>10} # {}"
fep_l["torsion_types"].append(
format_torsions.format("#Index", "Fc", "mult", "psi0", "PRM_ID"))
tor_index = 1
tor_indexes = []
for i, torsion_type in enumerate(fep_types["torsions"]):
prm_id = "-".join(torsion_type.prm_id.split())
prm_indexes = []
for fc, per, psi0, npath in torsion_type.get_prms():
fc = fc / npath
tmp = format_torsions.format(tor_index, fc, per, psi0, prm_id)
fep_l["torsion_types"].append(tmp)
prm_indexes.append(tor_index)
tor_index += 1
tor_indexes.append(prm_indexes)
###################
# CHANGE_TORSIONS
###################
format_torch = "{:<10} {:<10} {:<10} {:<10} " \
+ "{:^5} "*num_evb_states + " # {}"
tmp = ["#Atom1", "Atom2", "Atom3", "Atom4"]
tmp.extend(["St.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_IDs")
fep_l["change_torsions"].append(format_torch.format(*tmp))
for torsion_key, torsion_all_states in fep_changes["torsions"].iteritems():
# torsion_key == "PDB_ID1 PDB_ID2 PDB_ID3 PDB_ID4"
for state, tor in enumerate(torsion_all_states):
if tor == None:
continue
for i in range(len(tor.prm.fcs)):
tprm_index = fep_types["torsions"].index(tor.prm)
ttype_index = tor_indexes[tprm_index][i]
prm_indexes = [0 for _ in range(len(torsion_all_states))]
prm_indexes[state] = ttype_index
placeholders = ["${}$".format(t) for t in torsion_key.split()]
pdb_id = "-".join(torsion_key.split())
tmp = placeholders + prm_indexes + [pdb_id]
fep_l["change_torsions"].append(format_torch.format(*tmp))
#################
# IMPROPER_TYPES
#################
format_impropers = "{:<8} {:>10} {:>10} # {}"
fep_l["improper_types"].append(
format_impropers.format("#Index", "Fc", "phi0", "PRM_ID"))
for i, improper_type in enumerate(fep_types["impropers"]):
imp_index = i + 1
prm_id = "-".join(improper_type.prm_id.split())
tmp = format_impropers.format(imp_index, improper_type.fc,
improper_type.phi0, prm_id)
fep_l["improper_types"].append(tmp)
###################
# CHANGE_IMPROPERS
###################
format_impch = "{:<10} {:<10} {:<10} {:<10} " \
+ "{:^5} "*num_evb_states + " # {}"
tmp = ["#Atom1", "Atom2", "Atom3", "Atom4"]
tmp.extend(["St.{}".format(n + 1) for n in range(num_evb_states)])
tmp.append("St.1 PDB_IDs")
fep_l["change_impropers"].append(format_impch.format(*tmp))
for improper_key, improper_all_states in fep_changes[
"impropers"].iteritems():
# improper_key == "PDB_ID1 PDB_ID2 PDB_ID3 PDB_ID4"
prm_indexes = []
for imp in improper_all_states:
if imp == None:
prm_indexes.append(0)
else:
itype_index = fep_types["impropers"].index(imp.prm) + 1
prm_indexes.append(itype_index)
placeholders = ["${}$".format(i) for i in improper_key.split()]
pdb_id = "-".join(improper_key.split())
tmp = placeholders + prm_indexes + [pdb_id]
fep_l["change_impropers"].append(format_impch.format(*tmp))
##############
# SOFT_PAIRS
##############
for bond_key, bond_all_states in fep_changes["bonds"].iteritems():
if None in bond_all_states:
for state, bond in enumerate(bond_all_states):
if bond == None:
continue
atoms_in_state = [atom_all_states[state] for atom_all_states \
in fep_changes["atoms"]]
a1_qindex = atoms_in_state.index(bond.atoms[0]) + 1
a2_qindex = atoms_in_state.index(bond.atoms[1]) + 1
fep_l["soft_pairs"].append("{:10} {:10}".format(
a1_qindex, a2_qindex))
for k in fep_l.keys():
fep_l[k] = "\n".join(fep_l[k])
fepstr = """\
# Generated with Qtools, version {version}
# Date: {date}
# CWD: {cwd}
# CMDline: {cmd}
#
[FEP]
states {states}
[atoms]
{atoms}
[atom_types]
{atom_types}
[change_atoms]
{change_atoms}
[change_charges]
{change_charges}
[soft_pairs]
{soft_pairs}
[off_diagonals]
# State_i State_j Atom1 Atom2 A_ij mu_ij
#
## Example1, Hij=H12=0 (not known in advance)
## 1 2 13 14 0 0
## Example2, Hij=H12=C*exp(-mu * r_13_14) (C=20.0, mu=0.45)
## 1 2 13 14 20.0 0.45
#
<FIX>
[bond_types]
{bond_types}
[change_bonds]
{change_bonds}
[angle_types]
{angle_types}
[change_angles]
{change_angles}
[torsion_types]
{torsion_types}
[change_torsions]
{change_torsions}
[improper_types]
{improper_types}
[change_impropers]
{change_impropers}
{qcp_mass}
""".format(states=num_evb_states,
date=time.ctime(),
cmd=" ".join(sys.argv),
cwd=os.getcwd(),
version=__version__,
**fep_l)
return fepstr
sys.exit(1)
args = parser.parse_args()
for k, v in vars(args).iteritems():
if k in ['ffld_output', 'pdb'] and not os.path.lexists(v):
print "FATAL! File '{}' doesn't exist.".format(v)
sys.exit(1)
#
# create QLib, QPrm, QStruct and QTopology objects
#
qlib = QLib("oplsaa", ignore_errors=args.ignore_errors)
qprm = QPrm("oplsaa", ignore_errors=args.ignore_errors)
try:
qstruct = QStruct(args.pdb, "pdb", ignore_errors=args.ignore_errors)
except QStructError as err:
print "FATAL! Problem with pdb: {}".format(err)
sys.exit(1)
try:
qprm.read_ffld(args.ffld_output, qstruct)
except QPrmError as err:
print "FATAL! Problem with ffld file: {}".format(err)
sys.exit(1)
try:
def log_dups(dups):
for dup in dups:
logger.info("Overwritten: {}".format(dup))
#
# Amber14FF to Qamber14
#
# Convert Amber14 lib (+prepin for impropers) and parm+frcmod to Q lib/prm
# Load all_amino_acids.pdb and all_amino_acids.mol2 and build topology
# separately.
#
# ignore_errors=True is needed because frcmod.ff14SB overwrites some parameters
#
qal = QLib("amber")
qap = QPrm("amber", ignore_errors=True)
qal.read_amber_lib("../Amber/ff-amber14/amber12_mod.lib")
qal.read_amber_lib("../Amber/ff-amber14/arn.lib")
qal.read_prepin_impropers("../Amber/ff-amber14/prep/amino12.in")
qal.read_prepin_impropers("../Amber/ff-amber14/arn.prepi")
log_dups(qap.read_amber_parm("../Amber/ff-amber14/parm/parm10.dat"))
log_dups(qap.read_amber_parm("../Amber/ff-amber14/parm/parm10.dat"))
log_dups(qap.read_amber_frcmod("../Amber/ff-amber14/parm/frcmod.ff14SB"))
# add options to parameters
for line in """name Q-Amber14SB
type AMBER
vdw_rule arithmetic !vdW combination rule (geometric or arithmetic)
scale_14 0.8333 ! electrostatic 1-4 scaling factor
switch_atoms off
improper_potential periodic
