SMArt.md.gromos.io package

Submodules

SMArt.md.gromos.io.ana module

SMArt.md.gromos.io.ana.get_sim_l_from_fpath(f_path)[source]
SMArt.md.gromos.io.ana.read_bar_dhdl(f_path, dl_max=0.3, comments='#', skip_stride=None, N_comm_lines=2, **kwargs)[source]

parse bar / dhdl data from GROMOS (output of ext_ti_ana)

Parameters

  • f_path – path to file

  • dl_max – max delta lam to read (e.g. if sim_lp == 0.1 and dl_max=0.3, read data for lam in range [0., 0.4])

  • comments – comment characters (skip these lines)

  • skip_stride – (int, int) - skipping lines

  • N_comm_lines – number of commented lines in the header (default 2)

  • kwargs –

    float_precision: number of digits used to write float in the output file - use if numbers are not separated with a space col_format: list of int (num of characters for each column) - use if numbers are not separated with a space.

    if only one number given, one can provide N_cols (if not, N_cols is determined from the header) if True given, col_format will be deduced from len(line)

    N_cols: number of columns

Returns

data as a pandas DataFrame simulated lambda (float)

SMArt.md.gromos.io.ana.read_exTI(f_path, sim_l=None, fnc2call=<function get_sim_l_from_fpath>)[source]

SMArt.md.gromos.io.incl module

class SMArt.md.gromos.io.incl.BBParsing[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

class SMArt.md.gromos.io.incl.BBWriting[source]

Bases: SMArt.md.gromos.io.incl.GromosWriter

class SMArt.md.gromos.io.incl.GeneralCnfWriter[source]

Bases: SMArt.md.gromos.io.incl.GromosWriter

class SMArt.md.gromos.io.incl.GromosFile(f_path, write=False, bck_num=False, pre=False, suf=False, flag_bck=True, **kwargs)[source]

Bases: SMArt.incl.FileStream, SMArt.md.gromos.io.incl.GromosStream

handler class for gromos files - reading / writing functions

class SMArt.md.gromos.io.incl.GromosParser[source]

Bases: SMArt.incl.GeneralContainer, SMArt.md.gromos.incl.GromosDefaults

contains basic functions that allow reading of different blocks

add_gr_title(title_lines, **kwargs)[source]
class SMArt.md.gromos.io.incl.GromosStream[source]

Bases: SMArt.incl.Defaults

block_lines()[source]

generator yielding line by line of a block (comments removed)

property block_names

reads the whole file and yields block names

property block_split_fnc

generator yielding elements of a block split by empty spaces (‘ ‘ or ‘ ‘ …)

end_block_split(bl_name='')[source]

reads the last END of the block - basically a workaround

next_block()[source]

goes to the next block - reads lines till the end of the block

property report_nl_block_split_fnc
write_block(bl_name, text2write)[source]

text2write: str or list of lines

class SMArt.md.gromos.io.incl.GromosString(s=None)[source]

Bases: SMArt.incl.StringStream, SMArt.md.gromos.io.incl.GromosStream

handler class for gromos string - reading / writing functions

class SMArt.md.gromos.io.incl.GromosWriter[source]

Bases: SMArt.incl.GeneralContainer, SMArt.md.gromos.incl.GromosDefaults

contains basic functions that allow writing of different blocks

write_gromos_format(gs, *blocks, **kwargs)[source]
class SMArt.md.gromos.io.incl.IFPBlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

contains functions that read of different IFP-related blocks

parse_ifp(parse_from, parse_from_file=True, **kwargs)[source]

parses an ifp file

class SMArt.md.gromos.io.incl.IFPBlocksWriter[source]

Bases: SMArt.md.gromos.io.incl.GromosWriter

write_ifp(f_path=None, **kwargs)[source]
class SMArt.md.gromos.io.incl.MTBBlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

parse_mtb(parse_from, parse_from_file=True, **kwargs)[source]

parses a mtb file and set appropriate parameters within the instance of MTB

class SMArt.md.gromos.io.incl.PTP_EDS_BlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

write_EDS(f_path, **kwargs)[source]
class SMArt.md.gromos.io.incl.TrjCnfBlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

parser for cnf trajectories

class SMArt.md.gromos.io.incl.TrjCnfBlocksWriter[source]

Bases: SMArt.md.gromos.io.incl.GeneralCnfWriter

write_trc(f_path=None, **kwargs)[source]
write_trc_npz(f_path)[source]
class SMArt.md.gromos.io.incl.cnfBlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

class SMArt.md.gromos.io.incl.cnfBlocksWriter[source]

Bases: SMArt.md.gromos.io.incl.GromosWriter

class SMArt.md.gromos.io.incl.grAtomWriting[source]

Bases: object

gr_id_format = '{:>5}'
n_atoms_format = '{:4d}'
new_line_format = '\n '
property write_gr_id
class SMArt.md.gromos.io.incl.grBBAtomWriting[source]

Bases: SMArt.md.gromos.io.incl.grAtomWriting

gr_id_format = '{:>5}'
n_atoms_format = '{:4d}'
new_line_format = '\n '
property write_gr_excl
property write_gr_prop
class SMArt.md.gromos.io.incl.grTOPAtomWriting[source]

Bases: SMArt.md.gromos.io.incl.grAtomWriting

gr_id_format = '{:>6}'
n_atoms_format = '{:6d}'
new_line_format = '\n '
write_gr_excl(e_l)[source]
write_gr_pairs(p_l)[source]
property write_gr_prop
property write_rev_prop
class SMArt.md.gromos.io.incl.topBlocksParser[source]

Bases: SMArt.md.gromos.io.incl.GromosParser

parse_dsr(parse_from, parse_from_file=True, **kwargs)[source]

parses a top file (GROMOS format)

parse_top_gr(parse_from, parse_from_file=True, **kwargs)[source]

parses a top file (GROMOS format)

class SMArt.md.gromos.io.incl.topBlocksWriter[source]

Bases: SMArt.md.gromos.io.incl.GromosWriter

write_ptp(f_path, **kwargs)[source]
write_rev_ptp_top_names(f_path, **kwargs)[source]
write_top_gr(f_path=None, **kwargs)[source]

Module contents