Index

A

a2nm() (pmx.atomselection.Atomselection method) AbsRestraints (class in pmx.alchemy) add_bp() (in module pmx.builder) add_entry() (pmx.ffparser.RTPParser method) Af (pmx.estimators.Crooks attribute) angle1 (pmx.alchemy.AbsRestraints attribute) angle2 (pmx.alchemy.AbsRestraints attribute) angles (pmx.forcefield.Topology attribute) apply() (pmx.geometry.Rotation method) apply_fit_R() (in module pmx.geometry) Ar (pmx.estimators.Crooks attribute) assign_dihedral_params() (pmx.ffparser.RTPParser method)

assign_params() (pmx.ffparser.BondedParser method) (pmx.ffparser.NBParser method) (pmx.ffparser.RTPParser method) Atom (class in pmx.atom) atomlistFromTop() (pmx.atomselection.Atomselection method) atoms (pmx.chain.Chain attribute) (pmx.forcefield.Topology attribute) (pmx.molecule.Molecule attribute) Atomselection (class in pmx.atomselection) ATPParser (class in pmx.ffparser) attach_aminoacid() (in module pmx.builder) attach_group() (in module pmx.builder)

B

BAR (class in pmx.estimators) bb_super() (in module pmx.geometry) bfac (pmx.atom.Atom attribute) BondedParser (class in pmx.ffparser)

bonds (pmx.forcefield.Topology attribute) box (pmx.model.Model attribute) build_chain() (in module pmx.builder) build_dna_strand() (in module pmx.builder) build_rna_strand() (in module pmx.builder)

C

calc_conv() (pmx.estimators.BAR static method) calc_conv_err_boot() (pmx.estimators.BAR static method) calc_dg() (pmx.alchemy.AbsRestraints method) (pmx.estimators.BAR static method) (pmx.estimators.Crooks static method) (pmx.estimators.Jarz static method) (pmx.estimators.JarzGauss static method) calc_err() (pmx.estimators.BAR static method) (pmx.estimators.JarzGauss static method) calc_err_blocks() (pmx.estimators.BAR static method) (pmx.estimators.Crooks static method) (pmx.estimators.Jarz static method) (pmx.estimators.JarzGauss static method) calc_err_boot() (pmx.estimators.BAR static method) (pmx.estimators.Jarz static method) (pmx.estimators.JarzGauss static method) calc_err_boot1() (pmx.estimators.Crooks static method) calc_err_boot2() (pmx.estimators.Crooks static method)

calc_fit_R() (in module pmx.geometry) center_vector() (in module pmx.geometry) Chain (class in pmx.chain) chain (pmx.molecule.Molecule attribute) chain_id (pmx.atom.Atom attribute) (pmx.molecule.Molecule attribute) chains (pmx.model.Model attribute) chdic (pmx.model.Model attribute) check_overlaps() (in module pmx.rotamer) close() (pmx.xdrfile.XDRFile method) cmap (pmx.forcefield.Topology attribute) com() (pmx.atomselection.Atomselection method) constrains (pmx.forcefield.Topology attribute) conv (pmx.estimators.BAR attribute) conv_err_boot (pmx.estimators.BAR attribute) coords() (pmx.atomselection.Atomselection method) create_folder() (in module pmx.utils) Crooks (class in pmx.estimators)

D

data2gauss() (in module pmx.utils) devf (pmx.estimators.Crooks attribute) devr (pmx.estimators.Crooks attribute) dg (pmx.alchemy.AbsRestraints attribute) (pmx.estimators.BAR attribute) (pmx.estimators.Crooks attribute) dg_for (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute) dg_mean (pmx.estimators.Jarz attribute)

dg_rev (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute) dic (pmx.ndx.IndexFile attribute) dihedral1 (pmx.alchemy.AbsRestraints attribute) dihedral2 (pmx.alchemy.AbsRestraints attribute) dihedral3 (pmx.alchemy.AbsRestraints attribute) dihedrals (pmx.forcefield.Topology attribute) dist (pmx.alchemy.AbsRestraints attribute) doLog() (in module pmx.utils)

E

editconf() (in module pmx.gmx) err (pmx.estimators.BAR attribute) err_blocks (pmx.estimators.BAR attribute) (pmx.estimators.Crooks attribute) err_blocks_for (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute) err_blocks_rev (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute) err_boot (pmx.estimators.BAR attribute) err_boot1 (pmx.estimators.Crooks attribute) err_boot2 (pmx.estimators.Crooks attribute) err_boot_for (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute) err_boot_rev (pmx.estimators.Jarz attribute) (pmx.estimators.JarzGauss attribute)

err_for (pmx.estimators.JarzGauss attribute) err_rev (pmx.estimators.JarzGauss attribute) exdr3DX (pmx.xdrfile.XDRFile attribute) exdrCLOSE (pmx.xdrfile.XDRFile attribute) exdrDOUBLE (pmx.xdrfile.XDRFile attribute) exdrENDOFFILE (pmx.xdrfile.XDRFile attribute) exdrFLOAT (pmx.xdrfile.XDRFile attribute) exdrHEADER (pmx.xdrfile.XDRFile attribute) exdrINT (pmx.xdrfile.XDRFile attribute) exdrMAGIC (pmx.xdrfile.XDRFile attribute) exdrNOMEM (pmx.xdrfile.XDRFile attribute) exdrNR (pmx.xdrfile.XDRFile attribute) exdrOK (pmx.xdrfile.XDRFile attribute) exdrSTRING (pmx.xdrfile.XDRFile attribute) exdrUINT (pmx.xdrfile.XDRFile attribute)

F

fetch_atoms() (pmx.atomselection.Atomselection method) ff_selection() (in module pmx.utils) ffopen() (in module pmx.utils) filename (pmx.forcefield.Topology attribute) (pmx.model.Model attribute)

fit() (in module pmx.geometry) fit_atoms() (in module pmx.geometry) fit_by_ndx() (in module pmx.geometry) forcefield (pmx.forcefield.Topology attribute) Frame (class in pmx.xdrfile)

G

gauss_func() (in module pmx.utils) gen_hybrid_top() (in module pmx.alchemy) genion() (in module pmx.gmx) get_angle_param() (pmx.ffparser.BondedParser method) get_b13() (pmx.atomselection.Atomselection method) get_b14() (pmx.atomselection.Atomselection method) get_bond_param() (pmx.ffparser.BondedParser method) get_box() (pmx.xdrfile.Frame method) get_by_id() (pmx.atomselection.Atomselection method) get_dihedral_param() (pmx.ffparser.BondedParser method) get_ff_path() (in module pmx.utils) get_fragments() (in module pmx.builder)

get_gmx() (in module pmx.gmx) get_long_name() (pmx.atomselection.Atomselection method) get_mtp_file() (in module pmx.utils) get_natoms() (pmx.xdrfile.Frame method) get_order() (pmx.atomselection.Atomselection method) get_pmxdata() (in module pmx.utils) get_prec() (pmx.xdrfile.Frame method) get_rotamers() (in module pmx.rotamer) get_step() (pmx.xdrfile.Frame method) get_symbol() (pmx.atomselection.Atomselection method) get_time() (pmx.xdrfile.Frame method) grompp() (in module pmx.gmx) groups (pmx.ndx.IndexFile attribute)

H

has_posre (pmx.forcefield.Topology attribute) has_vsites2 (pmx.forcefield.Topology attribute)

has_vsites3 (pmx.forcefield.Topology attribute) has_vsites4 (pmx.forcefield.Topology attribute) have_constraints (pmx.forcefield.Topology attribute)

I

id (pmx.atom.Atom attribute) (pmx.chain.Chain attribute) (pmx.molecule.Molecule attribute) ids (pmx.ndx.IndexGroup attribute) importError include_itps (pmx.forcefield.Topology attribute)

IndexFile (class in pmx.ndx) IndexGroup (class in pmx.ndx) initialise_logger() (in module pmx.utils) integrate_dgdl() (in module pmx.analysis) inters_bool (pmx.estimators.Crooks attribute) is_itp (pmx.forcefield.Topology attribute)

J

Jarz (class in pmx.estimators)

JarzGauss (class in pmx.estimators)

K

kickOutComments() (in module pmx.parser)

killBackups() (in module pmx.utils) ks_norm_test() (in module pmx.analysis)

L

lig_atoms (pmx.alchemy.AbsRestraints attribute) list2file() (in module pmx.utils)

listDirs() (in module pmx.utils) listFiles() (in module pmx.utils) load_bbdep() (in module pmx.rotamer)

M

make_3ter() (in module pmx.builder) make_5ter() (in module pmx.builder) make_bbdep() (in module pmx.rotamer) make_ii() (pmx.alchemy.AbsRestraints method) make_mol2_bondlist() (pmx.atomselection.Atomselection method) make_residue() (in module pmx.builder) make_stereoisomer_residue() (in module pmx.builder) max_crd() (pmx.atomselection.Atomselection method) mdrun() (in module pmx.gmx) mf (pmx.estimators.Crooks attribute) mini_nb() (in module pmx.rotamer) MissingTopolParamError Model (class in pmx.model) module pmx.alchemy pmx.analysis pmx.atomselection pmx.builder pmx.estimators pmx.ffparser pmx.geometry pmx.gmx pmx.library pmx.mutdb pmx.parser pmx.rotamer pmx.utils pmx.xdrfile

Molecule (class in pmx.molecule) molecules (pmx.forcefield.Topology attribute) moltype (pmx.model.Model attribute) (pmx.molecule.Molecule attribute) mr (pmx.estimators.Crooks attribute) mtpError multiple_replace() (in module pmx.utils) mutate() (in module pmx.alchemy) (in module pmx.rotamer)

N

name (pmx.atom.Atom attribute) (pmx.ndx.IndexGroup attribute) names (pmx.ndx.IndexFile attribute) natoms (pmx.chain.Chain attribute) (pmx.molecule.Molecule attribute) natural_sort() (in module pmx.utils)

NBParser (class in pmx.ffparser) next() (pmx.ffparser.RTPParser method) nm2a() (pmx.atomselection.Atomselection method) nres (pmx.chain.Chain attribute) nrexcl (pmx.forcefield.Topology attribute) nuc_super() (in module pmx.geometry)

O

occ (pmx.atom.Atom attribute)

P

pairs (pmx.forcefield.Topology attribute) parse() (pmx.ffparser.ATPParser method) (pmx.ffparser.BondedParser method) (pmx.ffparser.NBParser method) (pmx.ffparser.RTPParser method) parseList() (in module pmx.parser) ParserError pdb2gmx() (in module pmx.gmx) planarity() (in module pmx.geometry) plot_work_dist() (in module pmx.analysis) pmx.alchemy module pmx.analysis module pmx.atomselection module pmx.builder module pmx.estimators module

pmx.ffparser module pmx.geometry module pmx.gmx module pmx.library module pmx.mutdb module pmx.parser module pmx.rotamer module pmx.utils module pmx.xdrfile module pmx_data_file() (in module pmx.library) posre (pmx.forcefield.Topology attribute) pro_atoms (pmx.alchemy.AbsRestraints attribute)

Q

qA (pmx.forcefield.Topology attribute)

qB (pmx.forcefield.Topology attribute)

R

random_rotation() (pmx.atomselection.Atomselection method) read_and_format() (in module pmx.parser) read_dgdl_files() (in module pmx.analysis) read_fasta() (in module pmx.parser) read_mtp() (in module pmx.mutdb) read_mtp_entry() (in module pmx.mutdb) read_mutpdb() (in module pmx.mutdb) read_new_mtp_entry() (in module pmx.mutdb) read_pdb_with_connect() (in module pmx.builder) read_xvg() (in module pmx.parser) readSection() (in module pmx.parser)

real_resname() (in module pmx.rotamer) remove_netmount() (in module pmx.utils) removeBackups() (in module pmx.utils) rename_atoms_to_gmx() (pmx.atomselection.Atomselection method) renumber_atoms() (pmx.atomselection.Atomselection method) residues (pmx.chain.Chain attribute) (pmx.forcefield.Topology attribute) (pmx.model.Model attribute) resname (pmx.atom.Atom attribute) (pmx.molecule.Molecule attribute) Rotation (class in pmx.geometry) RTPParser (class in pmx.ffparser)

S

search_neighbors() (pmx.atomselection.Atomselection method) select_best_rotamer() (in module pmx.rotamer) select_restraints() (pmx.alchemy.AbsRestraints method) set_gmxlib() (in module pmx.gmx) set_omega() (in module pmx.builder)

set_phi() (in module pmx.builder) set_psi() (in module pmx.builder) show_ff() (in module pmx.utils) solvate() (in module pmx.gmx) symbol (pmx.atom.Atom attribute) system (pmx.forcefield.Topology attribute)

T

title (pmx.model.Model attribute) Topology (class in pmx.forcefield) Trajectory (class in pmx.xtc)

translate() (pmx.atomselection.Atomselection method) translate_by_ndx() (in module pmx.geometry) trjconv() (in module pmx.gmx)

U

unity (pmx.atom.Atom attribute) (pmx.model.Model attribute) UnknownResidueError

update() (pmx.xdrfile.Frame method) update_atoms() (pmx.xdrfile.Frame method) update_box() (pmx.xdrfile.Frame method)

V

vec_ang() (in module pmx.geometry) virtual_sites2 (pmx.forcefield.Topology attribute)

virtual_sites3 (pmx.forcefield.Topology attribute) virtual_sites4 (pmx.forcefield.Topology attribute)

W

which() (in module pmx.utils) write() (pmx.atomselection.Atomselection method) (pmx.ffparser.RTPParser method) write_mdp() (in module pmx.gmx) write_pdb_with_connect() (in module pmx.builder)

write_split_top() (in module pmx.alchemy) write_summary() (pmx.alchemy.AbsRestraints method) write_xtc_frame() (pmx.xdrfile.XDRFile method) writeGRO() (pmx.atomselection.Atomselection method) writePDB() (pmx.atomselection.Atomselection method)

X

x (pmx.atom.Atom attribute)

XDRFile (class in pmx.xdrfile)