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_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_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_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_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
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: print("FATAL! Problem with parm: {}".format(str(e))) sys.exit(1) for frcmod in args.frcmods: try: qprm.read_amber_frcmod(frcmod) except QPrmError as e: print("FATAL! Problem with frcmod: {}".format(str(e))) sys.exit(1) try: qstruct = QStruct(args.mol2[0], "mol2") except QStructError as e: print("FATAL! Problem with mol2: {}".format(str(e)))
# # 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 improper_definition explicit""".splitlines(): lf = line.split() qap.options[lf[0]] = " ".join(lf[1:]) # remove head from ACE and tail from NME