Index

A

Acrylamide (class in mbuild_polybuild.aa_monomers.acrylamide) add() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) add_bond() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) all_ports() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

Amide (class in mbuild_polybuild.aa_functional_groups.amide) Ammonium (class in mbuild_polybuild.aa_functional_groups.ammonium) ancestors() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) apply_nbfix() (in module mbuild_polybuild.toolbox) atom2port() (in module mbuild_polybuild.toolbox) available_ports() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

B

Bead (class in mbuild_polybuild.cg_monomers.bead) Betaine (class in mbuild_polybuild.cg_monomers.betaine) bonds() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

box (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)

C

C (class in mbuild_polybuild.aa_fragments.c_quaternary) Cbma (class in mbuild_polybuild.aa_monomers.cbma) center (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) charge (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)

check_for_overlap() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) condense() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

D

direct_bonds() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

E

element (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) energy_minimize() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

Ester (class in mbuild_polybuild.aa_functional_groups.ester) Ethylene (class in mbuild_polybuild.aa_monomers.ethylene)

F

flatten() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) freud_generate_bonds() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) from_gmso() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

from_parmed() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) from_pybel() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) from_trajectory() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

G

generate_bonds() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) get_boundingbox() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

get_smiles() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

I

is_independent() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

M

mass (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) maxs (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) mbuild_polybuild.aa_fragments module mbuild_polybuild.aa_fragments.c_quaternary module mbuild_polybuild.aa_functional_groups module mbuild_polybuild.aa_functional_groups.amide module mbuild_polybuild.aa_functional_groups.ammonium module mbuild_polybuild.aa_functional_groups.ester module mbuild_polybuild.aa_functional_groups.mea module mbuild_polybuild.aa_functional_groups.mhta module mbuild_polybuild.aa_functional_groups.mptb module mbuild_polybuild.aa_functional_groups.phenyl module mbuild_polybuild.aa_functional_groups.ptp module mbuild_polybuild.aa_functional_groups.sulfonate module mbuild_polybuild.aa_functional_groups.tftb module mbuild_polybuild.aa_functional_groups.tftp module mbuild_polybuild.aa_functional_groups.tmstb module mbuild_polybuild.aa_molecules module mbuild_polybuild.aa_molecules.ion module mbuild_polybuild.aa_monomers module mbuild_polybuild.aa_monomers.acrylamide module mbuild_polybuild.aa_monomers.cbma module mbuild_polybuild.aa_monomers.ethylene module mbuild_polybuild.aa_monomers.methacrylate module mbuild_polybuild.aa_monomers.sbaa module

mbuild_polybuild.aa_monomers.sbma module mbuild_polybuild.cg_monomers module mbuild_polybuild.cg_monomers.bead module mbuild_polybuild.cg_monomers.betaine module mbuild_polybuild.toolbox module MEA (class in mbuild_polybuild.aa_functional_groups.mea) Methacrylate (class in mbuild_polybuild.aa_monomers.methacrylate) MHTA (class in mbuild_polybuild.aa_functional_groups.mhta) min_periodic_distance() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) mins (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) module mbuild_polybuild.aa_fragments mbuild_polybuild.aa_fragments.c_quaternary mbuild_polybuild.aa_functional_groups mbuild_polybuild.aa_functional_groups.amide mbuild_polybuild.aa_functional_groups.ammonium mbuild_polybuild.aa_functional_groups.ester mbuild_polybuild.aa_functional_groups.mea mbuild_polybuild.aa_functional_groups.mhta mbuild_polybuild.aa_functional_groups.mptb mbuild_polybuild.aa_functional_groups.phenyl mbuild_polybuild.aa_functional_groups.ptp mbuild_polybuild.aa_functional_groups.sulfonate mbuild_polybuild.aa_functional_groups.tftb mbuild_polybuild.aa_functional_groups.tftp mbuild_polybuild.aa_functional_groups.tmstb mbuild_polybuild.aa_molecules mbuild_polybuild.aa_molecules.ion mbuild_polybuild.aa_monomers mbuild_polybuild.aa_monomers.acrylamide mbuild_polybuild.aa_monomers.cbma mbuild_polybuild.aa_monomers.ethylene mbuild_polybuild.aa_monomers.methacrylate mbuild_polybuild.aa_monomers.sbaa mbuild_polybuild.aa_monomers.sbma mbuild_polybuild.cg_monomers mbuild_polybuild.cg_monomers.bead mbuild_polybuild.cg_monomers.betaine mbuild_polybuild.toolbox MonatomicIon (class in mbuild_polybuild.aa_molecules.ion) MPTB (class in mbuild_polybuild.aa_functional_groups.mptb)

N

n_bonds (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) n_direct_bonds (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)

n_particles (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)

P

particles() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) particles_by_element() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) particles_by_name() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) particles_in_range() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

periodicity (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) Phenyl (class in mbuild_polybuild.aa_functional_groups.phenyl) pos (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) print_hierarchy() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) PTP (class in mbuild_polybuild.aa_functional_groups.ptp)

R

random_sequence() (in module mbuild_polybuild.toolbox) referenced_ports() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) remove() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) remove_bond() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) reset_labels() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

root (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property) rotate() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) rotate_dihedral() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

S

save() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) Sbaa (class in mbuild_polybuild.aa_monomers.sbaa) Sbma (class in mbuild_polybuild.aa_monomers.sbma) spin() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

successors() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) Sulfonate (class in mbuild_polybuild.aa_functional_groups.sulfonate)

T

TFTB (class in mbuild_polybuild.aa_functional_groups.tftb) TFTP (class in mbuild_polybuild.aa_functional_groups.tftp) TMSTB (class in mbuild_polybuild.aa_functional_groups.tmstb) to_freud() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_gmso() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_hoomdsnapshot() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_intermol() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_networkx() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_parmed() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

to_pybel() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_rdkit() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_smiles() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) to_trajectory() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) translate() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method) translate_to() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

U

update_coordinates() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

V

visualize() (mbuild_polybuild.aa_fragments.c_quaternary.C method) (mbuild_polybuild.aa_functional_groups.amide.Amide method) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium method) (mbuild_polybuild.aa_functional_groups.ester.Ester method) (mbuild_polybuild.aa_functional_groups.mea.MEA method) (mbuild_polybuild.aa_functional_groups.mhta.MHTA method) (mbuild_polybuild.aa_functional_groups.mptb.MPTB method) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl method) (mbuild_polybuild.aa_functional_groups.ptp.PTP method) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate method) (mbuild_polybuild.aa_functional_groups.tftb.TFTB method) (mbuild_polybuild.aa_functional_groups.tftp.TFTP method) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB method) (mbuild_polybuild.aa_molecules.ion.MonatomicIon method) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide method) (mbuild_polybuild.aa_monomers.cbma.Cbma method) (mbuild_polybuild.aa_monomers.ethylene.Ethylene method) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate method) (mbuild_polybuild.aa_monomers.sbaa.Sbaa method) (mbuild_polybuild.aa_monomers.sbma.Sbma method) (mbuild_polybuild.cg_monomers.bead.Bead method) (mbuild_polybuild.cg_monomers.betaine.Betaine method)

X

xyz (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)

xyz_with_ports (mbuild_polybuild.aa_fragments.c_quaternary.C property) (mbuild_polybuild.aa_functional_groups.amide.Amide property) (mbuild_polybuild.aa_functional_groups.ammonium.Ammonium property) (mbuild_polybuild.aa_functional_groups.ester.Ester property) (mbuild_polybuild.aa_functional_groups.mea.MEA property) (mbuild_polybuild.aa_functional_groups.mhta.MHTA property) (mbuild_polybuild.aa_functional_groups.mptb.MPTB property) (mbuild_polybuild.aa_functional_groups.phenyl.Phenyl property) (mbuild_polybuild.aa_functional_groups.ptp.PTP property) (mbuild_polybuild.aa_functional_groups.sulfonate.Sulfonate property) (mbuild_polybuild.aa_functional_groups.tftb.TFTB property) (mbuild_polybuild.aa_functional_groups.tftp.TFTP property) (mbuild_polybuild.aa_functional_groups.tmstb.TMSTB property) (mbuild_polybuild.aa_molecules.ion.MonatomicIon property) (mbuild_polybuild.aa_monomers.acrylamide.Acrylamide property) (mbuild_polybuild.aa_monomers.cbma.Cbma property) (mbuild_polybuild.aa_monomers.ethylene.Ethylene property) (mbuild_polybuild.aa_monomers.methacrylate.Methacrylate property) (mbuild_polybuild.aa_monomers.sbaa.Sbaa property) (mbuild_polybuild.aa_monomers.sbma.Sbma property) (mbuild_polybuild.cg_monomers.bead.Bead property) (mbuild_polybuild.cg_monomers.betaine.Betaine property)