Chemistry Add-in for Word User's Guide
Contents
1. If you hover over a selected atom the editor displays the popup shown in Figure 13 which enables you to modify the atom in various ways Hover over the icons to see the names of the commands Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 17 The Rotate and Flip commands are disabled because they apply only to groups of atoms a ae e e eo pe A E eet Figure 13 Editing popup To edit the selected atom s properties click the appropriate command which typically displays a popup from which you can select alternatives The remainder of this section discusses how to use the various commands to edit the properties of an atom Important The 2 D editor attempts to provide guidance on the available chemically valid alternatives but it does not enforce that guidance For example the Set Isotope popup lists likely isotope numbers for oxygen but you can still choose to set the isotope number to 42 Delete Selection Delete Selection removes the atom from the diagram and attempts to remove dependent atoms as well For example if you delete the highlighted O atom in Figure 13 the editor also deletes the associated H atom Deleting any atom will also break all the bonds to this atom The resultant unfilled valencies will be filled by adding the correct number of h2. NC2 C1C 0 N C 0 N2C C C1 CC C C C1 C 0 0 Na CN1C NC2 C1C 0 N C 0 N2C C C C 0 O C CC 0 0 C 0 0 0 CC C CC1 C O NC O NC1 0 CC C CC 0 OC1 CC CC C1C 0 O CNIC NC2 C1C O N C O N2C C CN1C2 C N C1NN CC CI CIN C O N C2 0 0 C CC C CC1 C O NC O NC1 0 CC C CC 0 NC1 CC C C C1 O CN1C NC2 C1C O N C 0 N2C C CCN CC CCOC1 NC2 C N1C C O N C 0 N20 C CCICCCC C1 OC2 NC3 C N2C C 0 N C 0 N3C C CC1 C 0 N2C C 0 N3CCCC3C201 CC4 CC CC C4 NC O C5CN C6CC7 CNCB CC CC C78 C5 C5 C CNIC NC2 C1C O N C O N20 C C CIC Cancel Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 11 Manage the Zones in the Chemistry Gallery You can customize the Chemistry Gallery for your particular project or group by adding new zones in either of two ways e Insert a zone from your document e Import a CML file to add zones that are not already included with the Chemistry Add in This option is discussed in How to Import Chemical Data later in this document To add a zone 1 Select the appropriate 2D chemistry zone 2 Click Save to Gallery 3 Specify a name for the zone and click OK to add the zone to the gallery It is only possible to add 2D zones to the gallery Each item in the Chemistry Gallery represents a particular chemical zone not necessarily a
3. Phenyl hydride lt name gt lt formula concise C 6 H 6 gt Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 27 lt atomArray gt lt atom id al elementType C x2 1 924 y2 5 774 gt lt atom id a2 elementType C x2 3 258 y2 6 544 gt lt atom id a3 elementType C x2 3 258 y2 8 085 gt lt atom id a4 elementType C x2 1 924 y2 8 855 gt lt atom lt atom lt atom lt atom lt atom lt atom id a5 elementType C x2 0 591 y2 8 085 gt id a6 elementType C x2 0 591 y2 6 544 gt id a7 elementType H x2 1 924 y2 4 234 gt id a8 elementType H x2 4 592 y2 5 774 gt id a9 elementType H x2 4 592 y2 8 855 gt jd al0 elementType H x2 1 924 y2 10 395 gt lt atom id a11 elementType H x2 0 742 y2 8 855 gt lt atom id al2 elementType H x2 0 742 y2 5 774 gt lt atomArray gt lt bondArray gt lt bond id b1 atomRefs2 al a2 order S gt lt bond id b2 atomRefs2 a2 a3 order D gt lt bond id b3 atomRefs2 a3 a4 order S gt lt bond lt bond lt bond lt bond lt bond id b4 atomRefs2 a4 a5 order D gt jid b5 atomRefs2 a5 a6 order S gt jid b6 atomRefs2 al a6 order D gt jid b7 atomRefs2 al a7 order S gt id b8 atomRefs2 a2
4. Using the Load From option in the ribbon you can look up existing molecular structures from the NCBI s PubChem http pubchem ncbi nlm nih gov or the Unilever Centre s OPSIN http opsin ch cam ac uk databases e Handle most molecules The Chemistry Add in can handle any molecule that has appropriate CML data The Chemistry Add in includes CML data for several hundred common molecules For additional molecules you simply create or obtain a CML file and import it into a document e Store and expose chemical information in a semantically rich manner The Chemistry Add in supports publishing and data mining scenarios for authors readers publishers and other vendors across the chemical information community This paper describes how to use the Chemistry Add in to include chemical information in a Word document Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 4 Getting Started This section describes how to get started with the Chemistry Add in Prerequisites You should have a basic understanding of e Microsoft Word e Chemical nomenclature and diagrams An understanding of CML is helpful but not required System Requirements Hardware Requirements Any computer that can run Office 2007 or Office 2010 Software Requirements Your computer must have the following s
5. benzene lt m t gt lt mir gt lt m oMath gt lt w sdtContent gt lt w sdt gt The zone s CML data is stored separately in the document s customXml folder The zone s id element links the zone to the associated CML data file Figure 5 shows a portion of the Chem4Word_Example s customXml folder The itemN xml files contain various types of custom XML data including the CML data The numbering scheme is not related to the contents of the file For this example the benzene CML data is in item8 xml Folders v Name Sie a 4 Chem4Word_Example zip 2 i rels di _rels item1 xml 1KB d customXml item2 xml 1 KB d docProps item3 xml 1KB di word item4 xml 5 KB d Specs item5 xml 1KB 4 2009 07 22 zip item6 xml 1 KB Li Chem4WordDocumentation zip item7 xml OKB a amp Papers item8 xml 3KB Figure 5 The customXnil folder The benzene chemistry zone was created with a smart tag so item8 xml contains the CML formatted data from benzene s CML file in the Smart Tag folder 241 cml lt cml xmIns http www xml cml org schema xmIns nameDict http ww xml cml org dictionary cm name xmIns cmIDict http ww xml cml org dictionary cm1 xmIns conventions http www xml cml org convention convention conventions molecular gt lt molecule id m1 formalCharge 0 spinMultiplicity L gt lt name dictRef nameDict iupac gt benzene lt name gt lt name dictRef nameDict trivial gt
6. d customXml Ji media File Folder d docProps di theme File Folder J word comments xml XML Document d Specs S documentxml XML Document Jh 20N9 n7 22 zin endnotes xml XML Document Figure 4 Word document structure The document is primarily a collection of XML files Figure 3 shows the Word folder which contains the document s primary files In particular document xml contains the body of the document in Office Open XML OOXML format For more information on OOXML see Ecma Office Open XML File Formats overview Chemistry zones are represented in document xml by a structured document element lt w sdt gt The Chemistry Add in identifies the associated XML block as a chemistry Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 26 zone by setting the alias element s val attribute to chemistry The following example shows the chemistry zone XML for benzene lt w sdt gt lt w sdtPr gt lt w alias w val chemistry gt lt w id w val 23589811 gt lt w placeholder gt lt w docPart w val DefaultPlaceholder_22675703 gt lt w placeholder gt lt w sdtPr gt lt w sdtContent gt lt m oMath gt lt m r gt lt m rPr gt lt m sty m val p gt lt m rPr gt lt w rPr gt lt w rFonts w ascii MS ChemSans w hAnsi MS ChemSans gt lt wirPr gt lt m t gt
7. gt lt atom id a2 elementType H x2 0 05500002861022946 y2 1 1549999713897705 gt lt atom id a3 elementType H x2 2 3650000286102295 y2 2 4886790932178062 gt lt atomArray gt lt bondArray gt lt bond id b1 atomRefs2 al a2 order 1 gt lt bond id b2 atomRefs2 al a3 order 1 gt lt bondArray gt lt molecule gt lt cm1 gt The data is typical for the Chemistry Add in molecules and includes e The IUPAC name e Several trivial and systematic names e 2 D structural data including atom positions and bonding details For asummary of the commonly used CML elements in the molecular convention see http www xml cml org convention For details on CML including the current schema and related tools see http www xml cml org and cml sourceforge net OpenSource Site for CML CML Data Storage The Chemistry Add in stores CML data in the following ways Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 25 e The Chemistry Add in Smart Tag folder contains CML data for several hundred common molecules To simplify chemistry zone creation many molecules are represented by smart tags as discussed in the next section The associated data for each molecule is in a cml file in the add in s Smart Tag folder which is typically c Program Files Chem4Wor
8. in UI Overview The Chemistry tab contains the primary user interface for the Chemistry Add in as shown in Figure 2 r w W 2 ogl Document 1 docx Microsoft Word Home Insert Page Layout References Mailings Review View Chemistry mna ce bal TT ka O View Edit View Chemisty Options Help z v CML Navigator T Import _ Chemistry Settings Figure 2 Chemistry tab The tab has three command groups Import Import and save chemical data e Chemistry Gallery displays a gallery of chemistry zones that can be inserted into a document e Save To Gallery saves a chemistry zone to the Chemistry Gallery for easy re use in later documents e Load From imports a CML data file and adds it to the document Chemistry Manage chemistry zones e Mark as Chemistry marks selected text as a chemistry zone e View enables you to select which representation of a molecule to display e Edit displays the Edit 2D and Edit Labels options in order to modify the 2 D structure or the text associated with a zone e Chemistry Navigator displays a panel that contains all the chemistry zones in the current document Settings Manage the chemistry related aspects of the document e Options enables you to configure the Chemistry Add in defaults e Help displays the Help and Check for updates commands Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Titl
9. insonman R 17 Change Aton TYDE reserse e E EE EE 17 Set Label Remove Label ccccccccccecsssesscecccececsssencceceeeceessseneceeeeseeeseneneeeeeeseeeess 19 aY fal Ae ASE TOE AE AO OS T O R E Tea A SERA 19 Undo REO Aee E EE ENO EA OEN E E 19 SE Tee et AA AEE EE IEE E E AE EEE eas in E E E 19 a a ET E P E AE ee eee E 19 Set Isotope Remove ISOTOPE cceescccssscecseceeseecsseecesaecessseceseecsaseecaeeecaeeessneees 19 Change the Bonding cireni re levied iexdev cheeses eases Meade ee ees 19 Modify the Diagrams Structure ccccccseessssececececessesaeaececeessesseaaaeseeeessessesneaeeeeess 20 Fip tHE Diagrames e E E E EN 20 Move Atoms Or Groups sietini insisi s u sie EER 20 Rotate Atoms Or GOUDSE Oia EEE Ra 21 Delete Atoms OF GLOUDS ireas ee ea e e e e E E Weaades 22 RESOUILGCES porisssinens iiie a EEEE RER EEN EA R EN E AES 23 Appendix 1 CMU Basics vossevied oceecccksawSeivendedveceeveeds access teases E EE 24 CML Data Storag E soran ccc veces dees een ASicadevteeecdi ee E ee eects 24 Appemdix 2 How CML Data is Stored in a DOCUMENL cccccccesessestseeeeeesssessaaees 25 Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 3 Introduction The Chemistry Add in provides a simple and flexible way to include chemical information in a Word document With the Chemistry Add in y
10. it before doing any further work in the document 3 Edit the diagram as described in the following sections Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 14 G w Chemistry Add in for Word 2D Editor CigH2302 CigH2302 Zoom ax jo General Selection Mode Atom Bond Atom gt 0 0 HHE 7 ASU 4 Isotope FIR IIE al mem Figure 9 2 D editor When you click OK to close the editor the zone s CML data is updated and the new diagram is displayed in the zone as well as in any linked zones Important When you modify a molecule you will be prompted to delete and or modify the labels You may also use Edit Labels to assign new labels to the modified molecule The diagram shown in the document is a PNG image which is generated from the CML data and inserted into the document Others can thus read documents authored using the Chemistry Add in even with earlier versions of Word such as Word 2003 If you view a chemistry document with a version of Word that lacks the Chemistry Add in Word simply displays the image and ignores the embedded CML data The Controls of the 2 D Editor The 2 D editor includes two controls for manipulating a diagram a zoom slider and a pan control e Zoom slider Click and drag the slider to zoo
11. of Medicine o http opsin ch cam ac uk o OPSIN is a database maintained by the University of Cambridge whch converts IUPAC compound names to semantic chemical information including a connection table To insert a chemistry zone from the web 1 Place the cursor at the appropriate place in the document 2 Click Load From in the Import section of the ribbon 3 Select PubChem W PubChem lookup service arma caffeind 4 Type in you search term and click the magnifying glass icon P 5 Select the desired search result from the list and click Import W PubChem lookup service caffeind Name 1 3 7 trimethylpurine 2 6 dione sodium 1 3 7 trimethylpurine 2 6 dione benzoate 2 hydroxypropane 1 2 3 tricarboxylic acid 1 3 7 trimethylpurine 2 6 dione 2 acetyloxybenzoic acid 5 2 methylpropyl 5 prop 2 enyl 1 3 diazinane 2 4 6 trione 1 3 7 trimethylpurine 2 6 dione 8 2E 2 2 2 dichloroethylidene hydrazinyl 1 3 7 trimethylpurine 2 6 dione N 4 hydroxyphenyl acetamide 5 2 methylpropyl 5 prop 2 enyl 1 3 diazinane 2 4 6 trione 1 3 7 trimethylpurine 2 6 dione 8 2 diethylaminoethyloxy 1 3 7 trimethylpurine 2 6 dione 1 3 7 trimethy 8 3 methylcyclohexyl oxypurine 2 6 dione Formula C8H10N402 C15H15N4Na04 C14H18N409 C28H34N609 C10H12CI2N602 C27H35N707 C14H23N503 C15H22N403 C45H51N9012 SMILES CN1C NC2 C1C 0 N C 0 N2C C CN1C
12. unique molecule For example if you modify a benzene zone by adding a new label or changing the 2 D representation you can add that zone to the gallery as a separate item To move or delete a zone 1 Open the Chemistry Gallery and right click a zone to display the Chemistry Gallery popup 2 Click Organize and Delete to display the Building Blocks Organizer dialog box 3 Use the dialog box to modify the zone order or delete zones The Chemistry Gallery zones are in the Custom 5 gallery How to Manage Chemistry Zones with the Chemistry Navigator The Chemistry Navigator helps you manage a document s chemistry zones To open the manager click the Chemistry Navigator command which opens the Chemistry Navigator panel on the right side of the document The Chemistry Navigator panel shows every chemistry zone in the document in document order left to right top to bottom as shown in Figure 8 Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 12 neces Mailings Review View Chemistry a 30 L Options Help Settings 6117 1 g 1 9 1 10 i oO OOO vx a a Show Hide Images CisH2202 CeHs EL S C2H402 Figure 8 Chemistry Navigator panel The items are represented in the panel by the preferred navigator depiction followed by the 2 D representa
13. which will display a drop down list of the possible display options supported by add in based on the molecule s CML data Figure 4 shows the dialog box for benzene 3 Select the preferred representation from the list Bek E TT 3 Edit View Chemistry st CML Navigator 2D F pr 2st Y benzene EE C_ 6 H_ 6 Other Figure 4 Select View drop down The 2D option displays a structural diagram as shown in Figure 5 Figure 5 Benzene s 2 D representation Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 8 Change a Zone s Labels A molecule s CML data can include any number of labels For example the CML data for benzene includes two labels but water includes seven You can modify a zone s labels with the Edit Labels command To modify a zone s labels 1 Select the zone 2 Click Edit and then Edit Labels Figure 6 shows the Edit Labels dialog box for water Label H_ 2 0 oxidane aqua Choose label type Inline formula dihydrogen monoxide Label molecule bond number Name IUPAC Name systematic Name abbreviation Name CAS Name trivial Name unknown water hydrogen hydroxide 9 9 9 gt 9 9 9 Adam s ale The concise formulae and 2D Depictions are not shown A
14. Chemistry Add in for Word User s Guide Version 1 0 January 28 2011 Abstract This document describes how to use the Chemistry Add in for Word an add in for Microsoft Word that provides a simple and flexible way to include chemical information in a Word document Note e Most resources discussed in this paper are provided with the Chemistry Add in package For a complete list of documents and software discussed see Resources at the end of this document e For Chemistry Add in updates and software availability news see http chem4word codeplex com or http research microsoft com chem4word e For general news and discussion about the Chemistry Add in for Word please join our FaceBook page at http www facebook com home php sk group 186300551397797 Disclaimer This document is provided as is Information and views expressed in this document including URL and other Internet Web site references may change without notice You bear the risk of using it This document does not provide you with any legal rights to any intellectual property in any Microsoft product You may copy and use this document for your internal reference purposes 2011 Outercurve Foundation All rights reserved Microsoft and Windows are trademarks of the Microsoft group of companies All other trademarks are property of their respective owners Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la sche
15. Set Label Remove Label These commands enable you to modify an atom s label by assigning an arbitrary string which is displayed to the lower left of the label Figure 16 shows the O atom from the previous examples with an added Test label Figure 16 Adding a label to an atom e e These two commands add or remove electrons from an atom and display the new state to the upper right of the atom s label Undo Redo These commands undo or redo your changes beginning with the most recent H H These commands add or remove a proton from the selected atom H H These commands add or remove a hydrogen atom from the selected atom Set Ilsotope Remove Isotope Use the Set Isotope dropdown menu to select an isotope number It is displayed at the upper left of an atom s label Change the Bonding You can add one or more bonds to an existing bond and change the bond group To change the bonding 1 Right click anywhere in the diagram and select Bond Mode 2 Select a bond in the diagram and the bond popup is displayed 3 Use the Select bond order dropdown to add one or more bonds to the selected bond 4 Use the Select bond group dropdown to select a bond group for the selected bond Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 20 5 Use the Select bond stereo d
16. a8 order S gt lt bond id b9 atomRefs2 a3 a9 order S gt lt bond id b10 atomRefs2 a4 al0 order S gt lt bond id b11 atomRefs2 a5 a11 order S gt lt bond id b12 atomRefs2 a6 a12 order S gt lt bondArray gt lt molecule gt lt cm1 gt This data set contains the following benzene related data The IUPAC name benzene A trivial name phenyl hydride The concise formula CgH Data that can be used to create a 2 D structural diagram Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved
17. d Smart Tag e The Chemistry Gallery is a Word gallery that contains a collection of chemistry zones The gallery typically enables users to quickly find and insert a zone into a document It usually contains a small collection of commonly used molecules and users can customize the collection as appropriate The Chemistry Gallery has its own backing data a set of cml files in the add in s c Program Files Chem4Word data folder e When a user inserts a chemistry zone into a document the associated CML data is stored in the document Some commands modify the embedded CML data in various ways such as adding trivial names or modifying the 2 D structure However these commands affect only the data that is stored in the document Appendix 2 How CML Data is Stored in a Document A Word document is basically a structured collection of files stored a ZIP compatible Open Package Convention OPC format The document has a docx extension but you can use Windows Explorer to examine the contents of a Word document by simply changing the extension to zip Tip Although you can see the contents of a zip file in Windows Explorer the contents are easier to work if you first extract them to a folder Figure 4 shows the contents of a a document named Chem4Word_Example which was Saved after creating a benzene chemistry zone Folders vy Name lype 4 4 Chem4Word_Example zip a db rels File Folder J rels d glossary File Folder
18. d or even overlapping diagram To modify the structure select the atom or group of atoms that you want to move and drag it to the new location The editor will adjust the bonds accordingly The left side of figure 19 shows the diagram after adding a COCI group Figure 19 Moving atoms or groups When you make this change the oxygen atom ends up directly on top of a hydrogen atom One way to make the diagram more readable is to move COCI group The situation is complicated somewhat by the overlapping O and H atoms which makes it difficult to select just the COCI group The following procedure shows one way to address the problem and the resulting diagram is on the right side of Figure 19 To move Cl and O 1 Select the COCI group by gesturing along the bond connecting the group to the ring Using a gesture enables you to select the COCI group without including the H atom 2 Drag the COCI group to a better location Rotate Atoms or Groups Moving atoms or groups as shown in the previous section simply translates the atoms This can sometimes leave you with an awkward looking diagram Another way to improve readability is to rotate the group perhaps combined with translation To rotate a group 1 Select the group 2 Click Rotate on the popup 3 Drag the green button to rotate the group to a suitable orientation The right side of Figure 20 shows the same initial diagram as Figure 19 after selecting the COCI g
19. da Home 2 Contents INGPODUCUION ereinen aaa aaa a A ensue cesaatandeess S EE 3 Getting Started iniae e die Rae ee ee E ee ees 4 PFEPeQuISITES iscccwescieetilisi ais win wsstils wat ecdeecsiiaei ass cee eesiid E vaio edd EE 4 System REQUIFEMENTS eiiieaenii aiai aaea i aa EaR aiT ia 4 Instalati ON scsi iccce A cccesees Sicsece cweeleezc Sakateeiacbesdeiihibeveweedeestioceestietesdsi thant isteass beds eeed 4 Ul OVEIVIEW 22ccicnaia dil Aine Ae ae a O aE 5 How to Create and Manage Chemistry ZONES ccssccccccecessessssececeeseessessaeeeeeesseeseaaees 6 Specify a Chemistry Zone s Representation ccccccccccssssssssseeececessssesnsaeeeeeeesseseaees 7 Change a Zone s Labels iio secs cecicivseshacetecsients es aussi aa a a a Ra 8 Insert a Zone from the Chemistry Gallery cccccssssccececeesesesnececeeecessesseseeeeeeseesees 9 Insert a Chemistry Zone from the Web c cccccccscssssssssecececesessesneaeeeeeesseesesseaeeeeees 10 Manage the Zones in the Chemistry Gallery cccccssccccccssessesssaeeeeeeseessessaeeeeess 11 How to Manage Chemistry Zones with the Chemistry Navigator c ccscccccceeeeees 11 How to Edit 2 D Structures ccvesccccesssccccevasicecevasccecessccccesesccecenscce covsccecesnsteecensuncaceesbics 13 The Controls of the 2 D Eqitor ensnonssenoncneninancnenenonenaniiinnis 14 Select Atoms for Editing aeriene eei ea EE e EEN 15 Edit Individual ATOMS sesser N 16 Delete Selection
20. e al testo da visualizzare in questo punto utilizzare la scheda Home 6 How to Create and Manage Chemistry Zones A chemistry zone displays data for a particular molecule based on the molecule s CML data There are two kinds of chemistry zones textual and 2D Textual chemistry zones are based on equation zones and have a similar UI The 2D zones use a picture content control This section shows how to use the commands from the Chemistry group to create and manage chemistry zones At its most basic level a chemistry zone is simply a control that contains a selected block of text To create a chemistry zone from text 1 Select the word or phrase that you want to include in the zone and right click it 2 Click the Mark as Chemistry button and the corresponding text on the fly out menu to create a chemistry zone for the selected text as shown in Figure 3 Calibri E 11 A E i X B 7 UZY A J benzene amp Cut Ga Copy Paste Options Bj A Font E Paragraph Bullets gt Z Numbering gt Styles gt Hyperlink Look Up Synonyms gt GS Translate Additional Actions gt Ontology Mark up Selection gt Markas Chemistry benzene Figure 3 Creating a chemistry zone If you hover over a chemistry zone Word highlights it If you click the highlighted text Word displays the zone UI with a Chemistry label to identify it as a chemistry zone Unlike Math equation zones the chemi
21. ects all the atoms within a rectangle This step defines one corner of the rectangle Click and hold the left button and drag the cursor so that the rectangle includes the atoms that belong in the group Marquee select is based on the positions of the atoms themselves not the associated labels Release the left button The atoms in the group are indicated by closed blue circles as shown in Figure 11 Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 16 Figure 11 Marquee select Gesture selects multiple atoms downstream from a particular bond To use gesture to select a group of atoms 1 Position the cursor on the bond 2 Click and hold the left button 3 Move the cursor in the direction which you wish the selection to be Release the mouse to select all the downstream atoms in this direction Tip A green arrow appears to show which way you are going to be selecting Moving back to the center of the bond will make the arrow disappear and nothing will be selected on release The hydroxyl group in Figure 12 was selected by gesturing along the carbon oxygen bond Figure 12 Gesture selection Tip It is sometimes convenient to move the molecule to a different location in the editor To do so select the entire molecule and drag it to the new location Edit Individual Atoms
22. ernative way to add chemistry zones to a document is the Chemistry Gallery which contains a collection of zones that can be inserted directly into a document Figure 7 shows the first few items in the Chemistry Gallery that is included with the the Chemistry Add in package Home Insert Page Layout References Mailings Review View Chemistry H enemman E ok chemistry Akai tions izi Settings 1 6 1 7 on jose 3 1 10 Citric acid Ethanol Hydrogen cyanide Ps Figure 7 Chemistry Gallery To insert a chemistry zone into a document from the Chemistry Gallery 1 Place the cursor at the appropriate place in the document 2 Click Chemistry Gallery to display the gallery 3 Click the appropriate molecule to insert the associated chemistry zone into the document 4 Change the zone s representation to the appropriate representation Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 10 Insert a Chemistry Zone from the Web Although the add in ships with several hundred CML files you can also search the following online databases and import chemical structures directly e PubChem o http pubchem ncbi nlm nih gov o PubChem is a chemical structures database provided by the National Center for Biotechnology Information NCBI part of the U S National Library
23. lso non valid labels will not be updated Figure 6 Edit Labels dialog box The Chemistry Add in enables you to add or remove labels if they are not being used in the document or modify their properties To add a label 1 Click New Label which displays an empty label field below the last label on the current list 2 Type the new label s name in the empty box 3 Select the label type from the Choose label type dropdown to the right of the name A label can have one of the types shown in Figure 6 4 Click OK to add the new label to the zone s CML You can remove labels or modify their properties e To remove a label click the X at the label s right edge e To modify a label s text click the text box and edit the text Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 9 e To change the label type select a new type from the dropdown When you are finished click OK to accept the changes The changes apply only to the selected zone s CML data which is stored in the document and to any linked zones It does not change the CML file used to create the zone If you use the procedure in the preceding section to create a new water zone it will have a default set of labels Linked zones are discussed later in this paper Insert a Zone from the Chemistry Gallery An alt
24. m in and out of the diagram e Pan control Click one of the four points of the pan control to pan the diagram in that direction Click and drag the center of the pan control to pan the diagram in that direction Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 15 Select Atoms for Editing Before you start editing you must first select the atom or group of atoms that you want to work with To select single atoms 1 Position the cursor over the appropriate atom The editor displays an orange circle when the cursor is properly positioned Clickthe orange circle to select the atom The orange circle will change to a filled orange circle and then to a filled blue circle when you move the cursor away To select multiple atoms hold the CTRL key down and repeat steps 1 and 2 If you do not hold the CTRL key down repeating steps one and two selects a different atom CTRL Click on an atom which is already selected will deselect it Figure 10 shows testosterone with two atoms selected Figure 10 Selecting individual atoms The editor supports two approaches to selecting multiple atoms in one operation marquee select and gesture To use marquee select 1 3 Position the cursor just outside the corner of the group of atoms that you want to select This approach sel
25. oftware e Any version of Windows that can run Office 2007 or Office 2010 which includes Windows XP SP3 and later versions of Windows e Word 2007 or Word 2010 For details on Office requirements see the Resources section at the end of this document Installation The Chemistry Add in is packaged in a file named ChemistryAddinforWordv1 zip that contains the following files e Setup exe e Chem4Word Setup msi To Install the Chemistry Add in 1 Close all Word documents Copy the Chemistry Add in zip file to your hard drive Extract the contents of the zip file to a folder Pp wy Navigate to that folder and run Setup exe which runs the standard MSI installation wizard 5 Use the installation wizard to install the Chemistry Add in To verify the installation launch Word The ribbon should now include a Chemistry tab as shown in Figure 1 Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 5 a w HI y amp lz Document 1 docx Microsoft Word Home Insert Page Layout References Mailings Review View Chemistry zoo GA View Edit View Chemistry Options Help emis z CML Navigator v Import Chemistry Settings Figure 1 Word ribbon with Chemistry tab Tip The rest of the document will be easier to follow if you first install the Chemistry Add
26. ou can e Create inline chemistry zones to represent chemical data Chemistry zones are controls that contain information about a molecule and display the information in a variety of ways The underlying data is stored as Chemical Markup Language CML a widely used XML schema for representing chemical data The data typically includes trivial and International Union of Pure and Applied Chemistry IUPAC names the concise formula and data for a 2 D structure e Display chemical information in a variety of ways A chemistry zone can display any representation that is supported by the underlying CML data With a few clicks you can switch from the molecule s trivial name to its concise formula to its 2 D representation e Display print quality 2 D chemical structures Chemistry zones can represent molecules by displaying a 2 D structure diagram The Chemistry Add in also includes an editor that enables you to modify the structure The diagram is inserted into the document as a PNG image so that others can view it whether or not they have installed the Chemistry Add in on their system You can also publish a document authored using the Chemistry Add in as a PDF file e Accept chemical data in a variety of formats You can create a chemistry zone by typing a simple common name such as water and then using the Chemistry Add in to convert it to your preferred representation e Import CML files from online web services
27. ppropriate place in the document 2 Click the unlinked icon right to insert the zone 3 Specify the preferred representation in the document from the drop down The new unlinked zone appears in the Chemistry Navigator in the appropriate document position How to Edit 2 D Structures The CML files can contain structural information such as the x y position of the atoms When you specify the 2 D representation to be used in the document the Chemistry Add in uses this data to generate and display a 2 D diagram The Chemistry Add in also enables you to modify a zone s 2 D representation typically for one of the following reasons e To modify the positions of the atoms to make the diagram easier to read e To modify the composition of the molecule by replacing one or more atoms or by modifying bonds e To add labels to atoms Note The current 2D editor can modify the geometry or composition of existing structures However its ability to add to the structure is limited and you cannot create a structure from scratch To edit a zone s 2 D structure 1 Select a chemistry zone 2 Click Edit 2D available on the lower portion of the Edit command on the ribbon which opens the 2 D editor in a separate window The 2 D editor is only available as an option when the zone depicted in the document has an associated 2D structure Figure 9 shows the 2 D editor with a testosterone molecule The window is modal so you must close
28. ropdown to specify the stereo chemistry about an atom Figure 17 shows the upper right part of the testosterone molecule after a double bond has been added into the right most ring Notice that the editor removed two hydrogen atoms to compensate Figure 17 Add a bond Modify the Diagram s Structure You can modify the diagram s geometry in several ways typically to improve readability Flip the Diagram You can use the Flip commanadsto flip the diagram e FlipVertical rotates the diagram about a vertical axis e Flip Horizontal rotates the diagram about a horizontal axis e Flip About Bond rotates the selected atoms about the vector of the selected external bond To flip the diagram select any atom and click the appropriate button Figure 18 shows the default testosterone diagram followed by how it is changed by Flip Vertical and Flip Horizontal BA Default Flip Vertical Flip Horizontal Figure 18 Flipping the diagram Move Atoms or Groups The layout of the default diagram is sufficient for most purposes However it is sometimes useful to modify the layout typically to improve readability by moving Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 21 atoms or groups of atoms For example when you replace an atom with a group of atoms you can end up with a crowde
29. roup and clicking Rotate The right side shows the diagram after the COCI group has been rotated clockwise and translated slightly Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 22 Figure 20 Rotating groups Delete Atoms or Groups In addition to the Delete command on the popup the editor also includes a Delete button on the left side of the window You can use this button to quickly delete atoms or groups of atoms Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 23 Resources This section provides links to additional information about the Chemistry Add in 2007 Microsoft Office system requirements http office microsoft com en us products HA101668651033 aspx 2010 Microsoft Office system requirements http technet microsoft com en us library ee624351 office 14 aspx cml sourceforge net OpenSource Site for CML http cml sourceforge net Ecma Office Open XML File Formats overview http office microsoft com en us products HA102058151033 aspx ISO Standard http www iso org iso iso_catalogue htm Open XML Formats http www openxmideveloper or JUMBO FAQ http www ch ic ac uk omf cml doc jumbo faq html Office Development with Visual St
30. stry zone UI does not display a dropdown menu It simply indicates the zone s type and extent Each chemistry zone is based on CML data that is included in the document Marking text as a chemistry zone automatically creates a CML data file which only contains the selected text as a chemical name of unknown type Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 7 Specify a Chemistry Zone s Representation When you click Mark as Chemistry the add in adds the molecule s CML data to the document which includes e One or more text labels a molecule s CML data usually includes the IUPAC name and usually one or more trivial names e The concise formula e g CgHe e 2 D structural data The benzene CML data contains two labels the IUPAC name benzene and a trivial name phenyl hydride the concise formula and a set of 2 D data The CML infrastructure recognizes all of benzene s names and its concise formula so you can use any of them to enter benzene into your document and convert it to a chemistry zone After you have converted an instance of benzene or one of its equivalents into a chemistry zone you can easily change the representation To change a chemistry zone s representation 1 Click the zone to select it 2 Click the Chemistry group s View command
31. tion where possible There are two zone types e Unlinked zones independent entities that have their own CML data You can change an unlinked zone s representation or modify its labels or 2 D structure without affecting any other zone even those that represent the same molecule e Linked zones a collection of zones that are based on the same stored CML data If for example you change a particular linked zone s representation or modify its 2 D structure you also change every other zone in the collection You can use Chemistry Navigator to insert linked or unlinked zones by using the buttons to the right of the appropriate concise formula as shown in the second instance of C6H6 in Figure 8 To insert a linked zone 1 Place the cursor at the appropriate place in the document 2 Click the link icon left to insert the zone 3 Specify the preferred representation in the document from the drop down The new linked zone appears in the Chemistry Navigator in the appropriate document position Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 13 Note You must create the first instance of a linked zone by using the techniques discussed earlier in this paper Then you can use Chemistry Navigator to insert additional instances To insert an unlinked zone 1 Place the cursor at the a
32. udio Developer Center http msdn microsoft com en us vsto default aspx PubChem http pubchem ncbi nim nih gov Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 24 Appendix 1 CML Basics CML is an XML based format for representing a wide range of chemical data The Chemistry Add in uses a subset of CML the molecular convention which includes support for e IUPAC and other names e Chemical structure e Formulae The following example shows the CML data for water lt xml version 1 0 gt lt cm convention conventions molecular xmIns http www xml cml org schema xmIns conventions http ww xml cml org convention xmIns nameDict http www xml cml org dictionary cm name gt lt molecule id m1 gt lt name dictRef nameDict trivial gt H_ 2 0 lt name gt lt name dictRef nameDict iupac gt oxidane lt name gt lt name dictRef nameDict trivial gt aqua lt name gt lt name dictRef nameDict trivial gt water lt name gt lt name dictRef nameDict systematic gt dihydrogen monoxide lt name gt lt name dictRef nameDict systematic gt hydrogen hydroxide lt name gt lt name dictRef nameDict trivial gt Adam s ale lt name gt lt formula concise H 2 0 1 gt lt atomArray gt lt atom id al elementType 0 x2 1 5950000286102295 y2 1 1549999713897705
33. ydrogen atoms except where this would cause H to be created Change Atom Type This command changes the atom assigned to the selected location in the diagram When you click Change Atom Type the editor displays a dropdown list that enables you to select an alternative atom or group Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 18 amp Chemistry Add in for Word 2D Editor 5 De n tor C19H2302 C19H2302 ax ele General Selection Mode Atom Bond Change Atom Type Isotope Figure 14 Change Atom Type drop down menu The first part of the list shows individual atom substitutions and the second a selected set of groups that can replace oxygen in the current chemical environment ina chemically sensible way The editor adds or removes attached H atoms as required However you can insert any atom by clicking More This item displays a periodic table shown in Figure 15 from which you can select any atom by clicking it w Choose an element AEJ r ou Tn Pa u Np Pu Am Cm Bk ce Es Fm ma No Lr Figure 15 Periodic Table Version 1 0 January 28 2011 2011 Outercurve Foundation All rights reserved Errore Per applicare Title al testo da visualizzare in questo punto utilizzare la scheda Home 19
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