schrodinger.application.desmond.ffiostructure module¶

The central interface for reading and editing Maestro format chemical sructures with force field data.

FFIOStructure is a pythonic, object oriented wrapper for the mmffio library that provides access to sites, bonds, angles, dihedrals, exclusions, pairs, vdwtypes, restraints, virtuals, drudes, pseudos, constraints and their properties. It inherits from Structure and hence provides access to atoms, bonds and their properties.

The default error handler for the ffiostructure module is set to mm.error_handler. If no error handler is specified for error_handler arguments, its value is what will be used.

schrodinger.application.desmond.ffiostructure.make_property(getter, setter, doc)¶

schrodinger.application.desmond.ffiostructure.get_ffio_sub_block_std_prop_short_name(block_type, prop_name)¶: Function to get short names of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

schrodinger.application.desmond.ffiostructure.get_ffio_sub_block_std_prop_getter(block_type, prop_name)¶: Function to get mmffio getter method of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

schrodinger.application.desmond.ffiostructure.get_ffio_sub_block_std_prop_setter(block_type, prop_name)¶: Function to get mmffio setter method of properties. It is picked from the ffio_sub_block_prop_links dict if avaiable, else deduced from property name

schrodinger.application.desmond.ffiostructure.make_property_fepio(getter, setter, doc)¶

schrodinger.application.desmond.ffiostructure.get_fepio_sub_block_std_prop_short_name(block_type, prop_name)¶: Function to get short names of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

schrodinger.application.desmond.ffiostructure.get_fepio_sub_block_std_prop_getter(block_type, prop_name)¶: Function to get mmfepio getter method of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

schrodinger.application.desmond.ffiostructure.get_fepio_sub_block_std_prop_setter(block_type, prop_name)¶: Function to get mmfepio setter method of properties. It is picked from the fepio_sub_block_prop_links dict if avaiable, else deduced from property name

class schrodinger.application.desmond.ffiostructure.FFIOStructure(handle, error_handler=- 1)¶

Bases: schrodinger.structure._structure.Structure

Class to create python interface to force field data. This is just a wrapper around the mmffio/mmfepio functionality. I/O happens through the underlying libraries. mmffio/mmfepio handles are created on demand when ffio/fepio blocks are accesssed.

__init__(handle, error_handler=- 1)¶: Parent class would take care of basic CT data.

ffio¶

fepio¶

hasFfio()¶

hasFepio()¶

copy()¶: Returns a copy of the structure.

write(filename, format=None)¶: Write the cms structure to a file, overwriting any previous content. Format is determined from the file suffix if None is specified. otherwise an explicit value of maestro, sd, pdb, or smiles can be used. Only cms format is supported as of know, if other types are choosen, basic CT information would be written, which is taken care by the parent class.

append(filename, format=None)¶: Append the structure to the file. Format is determined from the file suffix if None is specified, otherwise an explicit value of maestro, sd, pdb, or smiles can be used. Only cms format is supported as of know, if other types are choosen, basic CT information would be written, which is taken care by the parent class.

class schrodinger.application.desmond.ffiostructure.CMSReader(filename, index=1, error_handler=None, input_string=None)¶

Bases: schrodinger.structure._io.MaestroReader

A class for reading structures from a CMS format file.

schrodinger.application.desmond.ffiostructure.write_cms(ct, filename, mode=2)¶: Write a CT to a Maestro format file.

schrodinger.application.desmond.ffiostructure.write_cms_to_string(ct)¶: Write a CT to a string.

schrodinger.application.desmond.ffiostructure.merge_ct(ct0, ct1)¶: Returns a new ct which is the result of merging ct0 and ct1.

schrodinger.application.desmond.ffiostructure.convert_ffioff_to_dummy(ffio_ct: schrodinger.application.desmond.ffiostructure.FFIOStructure)¶: Remove all terms from ffio_ff block, and rename FF name to ‘NONE’