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Open Source Chemistry Library

There is a newer version: 2024.11.2





  Osiris Structure Editor
  




Chemical Editor Concepts
The structure editor is used to draw chemical molecules, substructure fragments,
reactions and simple drawing objects like text, boxes, etc. Its functionality changes
depending on the kind of object(s) being edited. Thus, the atom mapping tool is only available,
when a reaction is edited. Query feature dialogs only open, when a substructure is edited, etc.


Atom and Bond Hot-Keys
Hot-keys allow to quickly change atoms and bonds or to attach common groups to an atom.
When the mouse pointer is moving near to an atom or bond then the atom or bond is automatically highlighted,
indicating that a mouse click or typing hot-keys will affect the highlighted atom or bond.

 
  Hot-Key
  Type
  Name
  Explanation
 
 
  'Delete'
  Atoms
Bonds
Mapping
  Delete
  Deletes highlighted and selected atoms and bonds. When a reaction is edited and
the mapping tool is selected, then pressing the 'Delete' key removes all atom mapping from the reaction.
  
 
 
  '1','2','3', ...
  Atom
  Atom Chain
  Attaches a chain of 'n' carbon atoms to the highlighted atom provided that its valence maximum is not exceeded.
 
 
  '+', '-'
  Atom
  Charge Modifiers
  Increases or decreases the charge of the highlighted atom.
 
 
  '.'
  Atom
  Radical State Modifier
  Adds or removes a single electron to change the atom's radical state.
 
 
  ':'
  Atom
  Radical State Modifier
  Add or removes two electrons and toggles between singlet and triplet states.
 
 
  '?'
  Atom
  Connection Point
  Converts an atom into a connection point of a substituent or building block.
 
 
  'q'
  Atom,
Bond
  Query Feature Dialog
  If a substructure query is edited then this key opens a query feature dialog,
which allows to specify additional atom/bond conditions for the substructure search.
 
 
  '1','2','3','0'
  Bond
  Bond Order
  Changes the highlighted bond into a single, double, triple, or coordinate (0-order) bond.
 
 
  'u'
  Bond
  Up Bond
  Changes the highlighted bond into 'up' stereo bond, if at least one of the associated
atoms is a relative or absolute stereo center.
 
 
  'd'
  Bond
  Down Bond
  Changes the highlighted bond into 'down' stereo bond, if at least one of the associated
atoms is a relative or absolute stereo center.
 
 
  'c'
  Bond
  Cross Bond
  Changes the highlighted bond into a double bond with unknown configuration.
 
 
  'v','4','5','6','7'
  Bond
  Annelate Ring
  Annellates a new saturated n-membered ring the highlighted bond ('v' adds a 3-membered ring).
 
 
  'b'
  Bond
  Annelate Benzo
  Annellates a new benzene ring to the highlighted bond.
 




Atom labels & Substituents & Protecting Groups
While the mouse pointer is near an atom such that the atom is highlighted, you may type one or
multiple keys to change the atom label or to attach common substituent.
The sequence of typed keys is shown in the editor. If it is recognized to represent a valid atom label,
then the key string is shown in black. If it is recognized as a known substituent or protecting group name,
then it is shown in blue. The key string is shown in gray, if it can be extended by adding more keys to
a known group name. Finally, it is shown in red, if no valid completion to a known name is possible.
Once a black or blue color indicates that your key string is recognized, you may move the mouse away or type
Enter to actually convert the atom into the new type or to automatically attach the recognized
substituent.
For the sake of convenience atom labels or group names can be typed using lower case letters only.
Dashes in group names may also be omitted. E.g. typing 'n' followed by 'a' converts the atom to a sodium atom
and typing 'otolyl' attaches an ortho-Tolyl group.
Known group names are: Ac, Alloc, Allyl, Am, Benzoyl, Benzyl, Boc, BOM, Bn, Bs, Bt, Btm, Bu, Bz,
Bzh, Bzl, BzOM, Cbz, Cy, cyclobutyl, cycloheptyl, cyclooctyl, cyclopentyl, cyclopropyl, Dan, DEAE, DEIPS,
DMIPS, DMPM, DMPS, DMTr, DNP, DNS, DPIPS, DPTBS, DTBMS, Et, Fmoc, i-Am, i-Bu, i-Pr, Im, m-Tolyl, MDIPS,
MDPS, MEM, MMTr, MOM, MPM, MTM, Me, Mes, Ms, N3, n-Am, n-Bu, n-Pr, neo-Am, nitro, NO2, Np, o-Tolyl, p-Tolyl,
PMB, PMBM, PNB, PPi, Ph, Phenyl, Pht, Piv, Poc, Pr, Pv, s-Am, s-Bu, s-Butyl, SEM, SES, t-Am, t-Bu, t-Butyl,
TBDMS, TBDPS, TBMPS, TBS, TDS, TFA, THF, THP, TIPS, TMS, Tf, Thexyl, Tos, Troc, Trt, Ts, Xyl.
To be compatible with ChemDraw, 'l' is recognized as chlorine atom. If you are editing a sub-structure,
you may use 'x' to convert an atom into an atom list containing all halogene atoms.



Buttons and Tools
Chemical structures are drawn by selecting an appropriate tool and applying it
while moving, clicking and dragging the mouse pointer over the drawing area. While the
selection of a tool has no immidiate effect on the drawn structure, pressing a button
does. Currently available buttons allow to clean up atom coordinates or to revert the
most recent structure change.

 
  Button or Tool
  Name
  Explanation
 
 
  
  Atom Tools
  The Atom Tools cover atoms frequently used in organic chemistry. After
selecting one of these tools, you may place new atoms by clicking into the
empty space or change existing atom by clicking onto them.
 
 
  
  Atom Detail Tool
  When this tool is selected and an atom is clicked with the left mouse button
while pressing the 'Ctrl'-key, then a dialog window open that allows to
specify an unusual/custom atom label, a specific isotop, an abnormal valence
and/or a radical state. When closing the dialog the clicked atom is changed
accordingly. The dialog settings are remembered and applied to any other clicked atom,
as long as the tool is selected.
 
 
  
  Charge Tools
  These tools let you assign charges to atoms. Multiple clicks on the
same atom will increase or decrease the charge by 1. The Osiris Structure
Editor assumes the presence of implicit hydrogens at any charged or non
charged atoms to meet the atom's default valence. However, implicit hydrogens
are only shown on hetero atoms.
 
 
  
  Ring Tools
  After selecting one of the predefined rings, one may create a new ring
or attach a ring to an existing bond or atom to create annelated ring systems
or a spiro compound, respectively.
 
 
  
  Bond Tools
  Bond Tools allow you to create new bonds and to change existing bonds
concerning their order or stereo-orientation. By clicking into the open
space you create a new bond of the selected type including two carbon atoms.
Clicking onto an existing atom will attach a new carbon. Dragging the mouse from
one atom to another one will just connect these atoms or increment the bond order
between them, if they were already connected. If the plain single bond tool is
selected, bonds may be multiply clicked to cycle through the possible bond orders.
Where reasonable, it also toggles between double bonds with known or unknown
configuration, the so-called cross bond.
When using stereo bonds please consider that the pointed tip of the bond should
always point to the stereo center.
 
 
  
  Chain Tool
  The Chain Tool provides the fastest way to draw aliphatic carbon chains in
zig-zag orientation. With the selected Chain Tool click into the empty space or at
an existing atom and drag the mouse to create a new zig-zag chain and flip its
orientation.
 
 
  
  ESR Tools
  The editor supports the enhanced stereo recognition (ESR) introduced by
Molecular Design Ltd. with IsisDraw V2.5. The ESR Tools allow to define for every
stereo center, whether it is an absolute one or if it belongs to a group of stereo
centers that have the drawn, but relative configuration. For any group of relative
stereo centers one may define that the drawn and the inverse configurations are present,
i.e. that we have a racemic situation concerning the group members. This is indicated by
green stereo bonds and an ampersand '&' at the stereo centers. Likewise one may
define groups of relative stereo centers that contain either the drawn configuration or
the opposite one. Stereo centers of such a group are indicated by blue stereo bonds and
the word 'or' at the stereo centers. In addition to the '&' or 'or'
indicators group numbers show which stereo centers belong to the same group.
 
 
  
   Unknown Configuration Tool
   This symbol is used to denote an unknown stereo configuration at a chiral center.
 
 
  
  Cleanup Button
  A cleanup will generate new coordinates of an existing molecule. It
rearranges bond and atom positions in order to have a proper 2D structure.
If a part of the molecule or reaction is selected, the cleanup will retain
the relative orientation of the non-selected atoms.
 
 
  
  Lasso Pointer Tool
  This tools allows you to select multiple atoms and bonds to rearrange,
rotate, resize, delete or duplicate at the same time. Just drag the mouse pointer
around the atoms of interest. Selected atoms and bonds are shown in red. By pressing
the control key you switch to the rectangular selection mode and the shift key lets
you add atoms to the current selection. By clicking onto an atom or bonds and dragging
the mouse one may more it or all selected atoms, if the clicked one is selected.
When pressing the shift key while dragging a selected fragment, an automatically created
copy of the selected fragment is dragged.
Where the editor needs to support multiple molecules, e.g. if a reaction is edited,
then every reactant and product is indicated by a large light gray indicator in
the background ('A', 'B', 'P1', etc.). Where independent fragments shall be treated
as one molecule, e.g. anion and kation of one salt, one must locate those fragments
close enough that there is only one indicator behind them.
If a reaction or molecule query is edited, then one may double click an atom or
a set of selected atoms to open a query feature dialog to specify additional conditions
for a fragment to match in a substructure search. The same applies to individual or
multiple selected bonds. If the edited object is not a query then double clicking of
an atom or bond will just select the entire fragment.
 
 
  
  Delete Tool
  It allows you to delete individual atoms or bonds or selected parts of the molecule.
Selected areas may also be removed by pressing the delete key from the keyboard.
 
 
  
  Zoom and Rotate Tool
  This tool allows to zoom or rotate the entire drawing or a selected subset.
Just click at the intended origin for the rotation or zooming and drag the mouse vertically
to zoom or horizontically to rotate.
 
 
  
  Mapping Tool
  This tool is only available when a reaction is edited. Use this tool to
map reactant atoms to the respective product atoms. This is done by clicking on
a reactant atom and dragging the mouse onto the corresponding product atom. The
editor will acknowledge the link by displaying a red mapping number at both atoms.
Afterwards it tries to map atoms in the vicinity automatically and displays green
numbers at automatically mapped atoms. Please assign manually as many reactant-product
pairs as are needed that the entire reaction is mapped completely and correctly.
Pressing the 'Delete' key while this tool is selected removes all mapping from the reaction.
 
 
  
  Text Tool
  The text tool may only be selected in certain situations. If it is selected
one may use it to place text elements directly into the drawing. These text elements
will be integral part of the drawing and, thus, move, resize and rotate with the molecules
or reaction.

Hot-Key	Type	Name	Explanation
'Delete'	Atoms Bonds Mapping	Delete	Deletes highlighted and selected atoms and bonds. When a reaction is edited and the mapping tool is selected, then pressing the 'Delete' key removes all atom mapping from the reaction.
'1','2','3', ...	Atom	Atom Chain	Attaches a chain of 'n' carbon atoms to the highlighted atom provided that its valence maximum is not exceeded.
'+', '-'	Atom	Charge Modifiers	Increases or decreases the charge of the highlighted atom.
'.'	Atom	Radical State Modifier	Adds or removes a single electron to change the atom's radical state.
':'	Atom	Radical State Modifier	Add or removes two electrons and toggles between singlet and triplet states.
'?'	Atom	Connection Point	Converts an atom into a connection point of a substituent or building block.
'q'	Atom, Bond	Query Feature Dialog	If a substructure query is edited then this key opens a query feature dialog, which allows to specify additional atom/bond conditions for the substructure search.
'1','2','3','0'	Bond	Bond Order	Changes the highlighted bond into a single, double, triple, or coordinate (0-order) bond.
'u'	Bond	Up Bond	Changes the highlighted bond into 'up' stereo bond, if at least one of the associated atoms is a relative or absolute stereo center.
'd'	Bond	Down Bond	Changes the highlighted bond into 'down' stereo bond, if at least one of the associated atoms is a relative or absolute stereo center.
'c'	Bond	Cross Bond	Changes the highlighted bond into a double bond with unknown configuration.
'v','4','5','6','7'	Bond	Annelate Ring	Annellates a new saturated n-membered ring the highlighted bond ('v' adds a 3-membered ring).
'b'	Bond	Annelate Benzo	Annellates a new benzene ring to the highlighted bond.

Button or Tool	Name	Explanation
	Atom Tools	The Atom Tools cover atoms frequently used in organic chemistry. After selecting one of these tools, you may place new atoms by clicking into the empty space or change existing atom by clicking onto them.
	Atom Detail Tool	When this tool is selected and an atom is clicked with the left mouse button while pressing the 'Ctrl'-key, then a dialog window open that allows to specify an unusual/custom atom label, a specific isotop, an abnormal valence and/or a radical state. When closing the dialog the clicked atom is changed accordingly. The dialog settings are remembered and applied to any other clicked atom, as long as the tool is selected.
	Charge Tools	These tools let you assign charges to atoms. Multiple clicks on the same atom will increase or decrease the charge by 1. The Osiris Structure Editor assumes the presence of implicit hydrogens at any charged or non charged atoms to meet the atom's default valence. However, implicit hydrogens are only shown on hetero atoms.
	Ring Tools	After selecting one of the predefined rings, one may create a new ring or attach a ring to an existing bond or atom to create annelated ring systems or a spiro compound, respectively.
	Bond Tools	Bond Tools allow you to create new bonds and to change existing bonds concerning their order or stereo-orientation. By clicking into the open space you create a new bond of the selected type including two carbon atoms. Clicking onto an existing atom will attach a new carbon. Dragging the mouse from one atom to another one will just connect these atoms or increment the bond order between them, if they were already connected. If the plain single bond tool is selected, bonds may be multiply clicked to cycle through the possible bond orders. Where reasonable, it also toggles between double bonds with known or unknown configuration, the so-called cross bond. When using stereo bonds please consider that the pointed tip of the bond should always point to the stereo center.
	Chain Tool	The Chain Tool provides the fastest way to draw aliphatic carbon chains in zig-zag orientation. With the selected Chain Tool click into the empty space or at an existing atom and drag the mouse to create a new zig-zag chain and flip its orientation.
	ESR Tools	The editor supports the enhanced stereo recognition (ESR) introduced by Molecular Design Ltd. with IsisDraw V2.5. The ESR Tools allow to define for every stereo center, whether it is an absolute one or if it belongs to a group of stereo centers that have the drawn, but relative configuration. For any group of relative stereo centers one may define that the drawn and the inverse configurations are present, i.e. that we have a racemic situation concerning the group members. This is indicated by green stereo bonds and an ampersand '&' at the stereo centers. Likewise one may define groups of relative stereo centers that contain either the drawn configuration or the opposite one. Stereo centers of such a group are indicated by blue stereo bonds and the word 'or' at the stereo centers. In addition to the '&' or 'or' indicators group numbers show which stereo centers belong to the same group.
	Unknown Configuration Tool	This symbol is used to denote an unknown stereo configuration at a chiral center.
	Cleanup Button	A cleanup will generate new coordinates of an existing molecule. It rearranges bond and atom positions in order to have a proper 2D structure. If a part of the molecule or reaction is selected, the cleanup will retain the relative orientation of the non-selected atoms.
	Lasso Pointer Tool	This tools allows you to select multiple atoms and bonds to rearrange, rotate, resize, delete or duplicate at the same time. Just drag the mouse pointer around the atoms of interest. Selected atoms and bonds are shown in red. By pressing the control key you switch to the rectangular selection mode and the shift key lets you add atoms to the current selection. By clicking onto an atom or bonds and dragging the mouse one may more it or all selected atoms, if the clicked one is selected. When pressing the shift key while dragging a selected fragment, an automatically created copy of the selected fragment is dragged. Where the editor needs to support multiple molecules, e.g. if a reaction is edited, then every reactant and product is indicated by a large light gray indicator in the background ('A', 'B', 'P1', etc.). Where independent fragments shall be treated as one molecule, e.g. anion and kation of one salt, one must locate those fragments close enough that there is only one indicator behind them. If a reaction or molecule query is edited, then one may double click an atom or a set of selected atoms to open a query feature dialog to specify additional conditions for a fragment to match in a substructure search. The same applies to individual or multiple selected bonds. If the edited object is not a query then double clicking of an atom or bond will just select the entire fragment.
	Delete Tool	It allows you to delete individual atoms or bonds or selected parts of the molecule. Selected areas may also be removed by pressing the delete key from the keyboard.
	Zoom and Rotate Tool	This tool allows to zoom or rotate the entire drawing or a selected subset. Just click at the intended origin for the rotation or zooming and drag the mouse vertically to zoom or horizontically to rotate.
	Mapping Tool	This tool is only available when a reaction is edited. Use this tool to map reactant atoms to the respective product atoms. This is done by clicking on a reactant atom and dragging the mouse onto the corresponding product atom. The editor will acknowledge the link by displaying a red mapping number at both atoms. Afterwards it tries to map atoms in the vicinity automatically and displays green numbers at automatically mapped atoms. Please assign manually as many reactant-product pairs as are needed that the entire reaction is mapped completely and correctly. Pressing the 'Delete' key while this tool is selected removes all mapping from the reaction.
	Text Tool	The text tool may only be selected in certain situations. If it is selected one may use it to place text elements directly into the drawing. These text elements will be integral part of the drawing and, thus, move, resize and rotate with the molecules or reaction.