Methods
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__init__
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__init__ (
self,
paper=None,
package=None,
)
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__iter__
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__iter__ ( self )
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add_atom_to
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add_atom_to (
self,
a1,
bond_to_use=None,
pos=None,
)
adds new atom bound to atom id with bond, the position of new atom can be specified in pos or is
decided calling find_place(), if x, y is specified and matches already existing atom it will be
used instead of creating new one
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add_edge
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add_edge (
self,
v1,
v2,
e=None,
)
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add_vertex
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add_vertex ( self, v=None )
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bbox
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bbox ( self )
returns the bounding box of the object as a list of [x1,y1,x2,y2]
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bond_between
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bond_between (
self,
a1,
a2,
)
returns id of bond between atoms a1 and a2
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check_fragments
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check_fragments ( self )
checks if all the fragments of this molecule are consistent and
removes and returns the ones that are not
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check_integrity
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check_integrity ( self )
after deleting atoms or bonds it is important to see if it's needed to divide molecule to fragments
and return them in form of list of new molecules
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children_generator
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children_generator ( self )
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create_edge
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create_edge ( self )
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create_fragment
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create_fragment (
self,
name,
edges,
vertices,
type="explicit",
strict=False,
)
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create_graph
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create_graph ( self )
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create_new_atom
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create_new_atom (
self,
x,
y,
name=None,
vertex_class=None,
)
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create_vertex
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create_vertex ( self, vertex_class=None )
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create_vertex_according_to_text
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create_vertex_according_to_text (
self,
old,
text,
interpret=1,
)
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delete
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delete ( self )
deletes the molecule from canvas by calling delete for its children
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delete_atom
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delete_atom ( self, item )
remove links to atom from molecule records
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delete_bond
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delete_bond ( self, item )
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delete_fragment
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delete_fragment ( self, f )
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delete_items
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delete_items (
self,
items,
redraw=1,
delete_single_atom=1,
)
deletes items and also makes cleaning of orphan bonds and atoms
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draw
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draw ( self, automatic="none" )
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eat_molecule
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eat_molecule ( self, mol )
transfers everything from mol to self, now only calls feed_data
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expand_groups
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expand_groups ( self, atoms=[] )
expands all group atoms; optional atoms selects atoms to expand - all used if not present
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find_least_crowded_place_around_atom
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find_least_crowded_place_around_atom (
self,
a,
range=10,
)
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find_place
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find_place (
self,
a,
distance,
added_order=1,
)
tries to find accurate place for next atom around atom id ,
returns x,y and list of ids of items found there for overlap, those atoms are not bound to id
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flush_graph_to_file
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flush_graph_to_file ( self, name="/home/beda/oasa/oasa/mol.graph" )
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gen_bonds_between
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gen_bonds_between (
self,
a1,
a2,
)
yields all bonds between atoms a1 and a2
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get_angle
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get_angle (
self,
a1,
a2,
)
what is the angle between horizontal line through i1 and i1-i2 line
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get_formula_dict
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get_formula_dict ( self )
returns a formula dict as defined in the periodic_table.py::formula_dict
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get_fragment_by_id
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get_fragment_by_id ( self, id )
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get_fragments_with_edge
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get_fragments_with_edge ( self, e )
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get_fragments_with_vertex
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get_fragments_with_vertex ( self, v )
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get_geometry
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get_geometry ( self )
returns a tuple of ((minx, miny, max, maxy), mean_bond_length)
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get_package
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get_package (
self,
doc,
items=None,
)
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handle_overlap
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handle_overlap ( self )
deletes one of overlaping atoms and updates the bonds
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insert_atom
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insert_atom ( self, at )
inserts atom to molecule without any connections
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is_empty
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is_empty ( self )
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lift
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lift ( self )
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mark_template_atom
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mark_template_atom ( self, v )
Exceptions
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ValueError, "submitted atom does not belong to this molecule"
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mark_template_bond
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mark_template_bond ( self, b )
Exceptions
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ValueError, "submitted bond does not belong to this molecule"
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move
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move (
self,
dx,
dy,
)
moves the whole molecule
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move_bonds_between_atoms
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move_bonds_between_atoms (
self,
a1,
a2,
)
transfers all bonds from one atom to the other; both atoms must be in self
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read_package
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read_package ( self, package )
reads the dom element package and sets internal state according to it
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redraw
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redraw ( self, reposition_double=0 )
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replace_vertices
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replace_vertices (
self,
old,
new,
)
replaces the vertex old with the vertex new
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transform
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transform ( self, tr )
applies given transformation to its children
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