vermouth.gmx.itp_read module

Read GROMACS .itp files.

class vermouth.gmx.itp_read.ITPDirector(force_field)[source]

Bases: SectionLineParser

class for reading itp files.

COMMENT_CHAR = ';'
METH_DICT = {('macros',): (<function SectionLineParser._macros>, {}), ('moleculetype',): (<function ITPDirector._block>, {}), ('moleculetype', 'angle_restraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'angle_restraints_z'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'angles'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'atoms'): (<function ITPDirector._block_atoms>, {}), ('moleculetype', 'bonds'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'constraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'dihedral_restraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'dihedrals'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'distance_restraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'exclusions'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'impropers'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'orientation_restraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'pairs'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'pairs_nb'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'position_restraints'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'settles'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'virtual_sites1'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'virtual_sites2'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'virtual_sites3'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'virtual_sites4'): (<function ITPDirector._interactions>, {}), ('moleculetype', 'virtual_sitesn'): (<function ITPDirector._interactions>, {})}

A dict of all known parser methods, mapping section names to the function to be called and the associated keyword arguments.

atom_idxs = {'angle_restraints': [slice(0, 4, None)], 'angle_restraints_z': [0, 1], 'angles': [0, 1, 2], 'bonds': [0, 1], 'constraints': [0, 1], 'dihedral_restraints': [slice(0, 4, None)], 'dihedrals': [0, 1, 2, 3], 'distance_restraints': [0, 1], 'exclusions': [slice(None, None, None)], 'orientation_restraints': [0, 1], 'pairs': [0, 1], 'pairs_nb': [0, 1], 'position_restraints': [0], 'settles': [0], 'virtual_sites1': [0], 'virtual_sites2': [0, 1, 2], 'virtual_sites3': [0, 1, 2, 3], 'virtual_sites4': [slice(0, 5, None)], 'virtual_sitesn': [0, slice(2, None, None)]}
dispatch(line)[source]

Looks at line to see what kind of line it is, and returns either parse_header() if line is a section header or vermouth.parser_utils.SectionLineParser.parse_section() otherwise. Calls vermouth.parser_utils.SectionLineParser.is_section_header() to see whether line is a section header or not.

Parameters:

line (str) –

Returns:

The method that should be used to parse line.

Return type:

collections.abc.Callable

finalize(lineno=0)[source]

Called at the end of the file and checks that all pragmas are closed before calling the parent method.

finalize_section(previous_section, ended_section)[source]

Called once a section is finished. It appends the current_links list to the links and update the block dictionary with current_block. Thereby it finishes reading a given section.

Parameters:

  • previous_section (list[str]) – The last parsed section.

  • ended_section (list[str]) – The sections that have been ended.

static is_pragma(line)[source]
Parameters:

line (str) – A line of text.

Returns:

True iff line is a def statement.

Return type:

bool

parse_header(line, lineno=0)[source]

Parses a section header with line number lineno. Sets vermouth.parser_utils.SectionLineParser.section when applicable. Does not check whether line is a valid section header.

Parameters:

  • line (str) –

  • lineno (str) –

Returns:

The result of calling finalize_section(), which is called if a section ends.

Return type:

object

Raises:

KeyError – If the section header is unknown.

parse_pragma(line, lineno=0)[source]

Parses the beginning and end of define sections with line number lineno. Sets attr current_meta when applicable. Does check if ifdefs overlap.

Parameters:

  • line (str) –

  • lineno (str) –

Returns:

The result of calling finalize_section(), which is called if a section ends.

Return type:

object

Raises:

IOError – If the def sections are missformatted

vermouth.gmx.itp_read.read_itp(lines, force_field)[source]

Parses lines of itp format and adds the molecule as a block to force_field.

Parameters: