SMArt.md.gromacs.io package

Submodules

SMArt.md.gromacs.io.additional_classes module

class SMArt.md.gromacs.io.additional_classes.Define(split_line=None, line=None, flag_generate_line=True, **kwargs)

Bases: SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults

gromacs define class :var

id v - values s - string (line)

container2write = 'defines'

write_define(from_str=False, **kwargs)

class SMArt.md.gromacs.io.additional_classes.ParsedSegments(seg_kw=None, seg_name=None, curr_dir=None, curr_inc=None, curr_if=None, curr_seg_num=None, **kwargs)

Bases: SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults

each parsed segment is an instance of this class ensures that writing gets done properly :attr

seg_type (include or define) seg_name curr_dir - current directive (e.g. [ bonds ]) curr_inc - current include (included file) curr_if - current if statement curr_seg_num set_curr_stack

container2write = '_segments'

get_curr_stack()

property gm_ord

set_curr_stack(curr_stack)

SMArt.md.gromacs.io.ana module

SMArt.md.gromacs.io.ana.get_xvg_labels(f_path, comments='#', '@')

SMArt.md.gromacs.io.ana.read_bar_data(f_path, dl_max=0.3, comments='#', '@', skip_stride=None, **kwargs)

SMArt.md.gromacs.io.ana.read_xvg_data(f_path, comments='#', '@', skip_stride=None, **kwargs)

SMArt.md.gromacs.io.gm_io_defaults module

class SMArt.md.gromacs.io.gm_io_defaults.gm_FDs_Defaults

Bases: SMArt.incl.Defaults

class SMArt.md.gromacs.io.gm_io_defaults.gm_FF_Defaults(iterable=(), /)

Bases: list

add_defs(gm_defaults)

write_defs()

class SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults

Bases: SMArt.incl.Defaults

SMArt.md.gromacs.io.incl module

class SMArt.md.gromacs.io.incl.GromacsFile(f_path, write=False, bck_num=False, pre=False, suf=False, flag_bck=True, **kwargs)

Bases: SMArt.incl.FileStream, SMArt.md.gromacs.io.incl.GromacsStream

handler class for gromos files - reading / writing functions

class SMArt.md.gromacs.io.incl.GromacsParser

Bases: SMArt.incl.GeneralContainer, SMArt.incl.Defaults

Genearal parsing functions

interesting attrib

gm_curr_stack - defines stack of directives, defines, IFs, etc.

self.curr_dir, self.curr_inc, self.curr_if, self.curr_seg_num

_gm_curr_fnc _gm_curr_int_type undefined_directives

class Define(split_line=None, line=None, flag_generate_line=True, **kwargs)

Bases: SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults

gromacs define class :var

id v - values s - string (line)

container2write = 'defines'

write_define(from_str=False, **kwargs)

add_define(split_line=None, line=None, flag_generate_line=True, **kwargs)

Parameters

kwargs – split_line = None, line = None, flag_generate_line = True add2container kwargs

Returns

static exchange_defs(l_split, defs)

parse_gm(parse_from, parse_from_file=True, **kwargs)

parsing gromacs format :param parse_from: :param parse_from_file: :param kwargs:

gm_curr_stack defines - gromacs defines ignore_title_lines

Returns

class SMArt.md.gromacs.io.incl.GromacsStream

Bases: SMArt.md.gromacs.io.gm_io_defaults.gm_FDs_Defaults, SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults

static find_directive(l)

lines()

this is implemented in GromacsFile or GromacsString

next_line()

static read_define(temp, defines, line=None, temp_seg=None)

read_lines(defines=None, curr_stack=None)

static read_undef(temp, defines)

write(s2w)

write_lines(lines)

class SMArt.md.gromacs.io.incl.GromacsString(s=None)

Bases: SMArt.incl.StringStream, SMArt.md.gromacs.io.incl.GromacsStream

handler class for gromos string - reading / writing functions

class SMArt.md.gromacs.io.incl.GromacsWriter

Bases: SMArt.incl.GeneralContainer, SMArt.incl.Defaults

Genearal writing functions

write_gromacs_format(gs, directives=None, flag_include=False, flag_if=False, flag_defines=True, flag_title=1, **kwargs)

class SMArt.md.gromacs.io.incl.gmConfigurationIO

Bases: SMArt.md.gromacs.io.incl.GromacsParser, SMArt.md.gromacs.io.incl.GromacsWriter

parse_gro(f_path)

write_gro(f_path)

class SMArt.md.gromacs.io.incl.gmFFParser

Bases: SMArt.md.gromacs.io.incl.GromacsParser

class gm_FF_Defaults(iterable=(), /)

Bases: list

add_defs(gm_defaults)

write_defs()

parse_ff_gm(parse_from, parse_from_file=True, **kwargs)

class SMArt.md.gromacs.io.incl.gmFFWriter

Bases: SMArt.md.gromacs.io.incl.GromacsWriter

write_ff_itp(f_path=None, **kwargs)

Parameters

• f_path –

• kwargs – flag_split_non_bonded = False sep2include_files - customizable flag_close = True (close gromacs stream)

Returns

class SMArt.md.gromacs.io.incl.gmFragmentMoleculeIO

Bases: SMArt.md.gromacs.io.incl.GromacsParser, SMArt.md.gromacs.io.incl.GromacsWriter

write_itp(f_path, directives=None, **kwargs)

write_molecule_type(gs, directives=None, **kwargs)

Parameters

• gs –

• directives –

• kwargs – flag_segment_order = True flag_general_defines = False(from top e.g) - generates defines2write defines2write - container of defines

Returns

class SMArt.md.gromacs.io.incl.gmTopologyIO

Bases: SMArt.md.gromacs.io.incl.GromacsParser, SMArt.md.gromacs.io.incl.GromacsWriter

parse_top_gm(parse_from, parse_from_file=True, **kwargs)

write_top_gm(f_path=None, **kwargs)

Parameters

• f_path –

• kwargs –

  see write_ff_itp sep_ff2itp - separate ff into itp file(s) sep_mol2itp - separate molecules to itp files

  sep_mol2itp = {mol_id1:f_path1}

Returns

SMArt.md.gromacs.io.incl_md_only module

class SMArt.md.gromacs.io.incl_md_only.gmCMAPWriter

Bases: SMArt.md.gromacs.io.gm_io_defaults.gm_io_Defaults, SMArt.md.gromacs.io.incl_md_only.gmInteractionTypeWriter

class SMArt.md.gromacs.io.incl_md_only.gmInteractionTypeWriter

Bases: SMArt.incl.Defaults

gm_params2define(define_id=None, **kwargs)

Module contents