moorhen 0.7.1 → 0.7.3

package/baby-gru/CootWorker.js

@@ -1 +1 @@
-var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var a,r=1,t=arguments.length;r<t;r++)for(var o in a=arguments[r])Object.prototype.hasOwnProperty.call(a,o)&&(e[o]=a[o]);return e},__assign.apply(this,arguments)};importScripts("./wasm/moorhen.js"),importScripts("./wasm/web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(a){var r=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===a?r:3&r|8).toString(16)}))},print=function(e){console.log(e),postMessage({consoleMessage:JSON.stringify(e)})},instancedMeshToMeshData=function(e,a,r,t){void 0===r&&(r=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],l=[],_=[],u=[],d=[],m=e.geom,p=e.markup,h=m.size(),g=0;g<h;g++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],T=[],A=m.get(g);"spherical-atoms"===A.name&&(f=!0);for(var x=A.vertices,w=A.triangles,F=w.size(),I=0;I<F;I++){var k=w.get(I).point_id;a?(v.push(k[0]),v.push(k[2]),v.push(k[1])):(v.push(k[0]),v.push(k[1]),v.push(k[2]))}w.delete();for(var D=x.size(),J=0;J<D;J++){var C=x.get(J),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var E=C.normal;S.push(E[0]),S.push(E[1]),S.push(E[2])}x.delete();var P=A.instancing_data_A,R=P.size();if(R>0)for(var U=0;U<R;U++){var L=(V=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=V.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=V.size;b.push(B[0]),b.push(B[1]),b.push(B[2]),T.push.apply(T,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}P.delete();var j=A.instancing_data_B,H=j.size();if(H>0)for(U=0;U<H;U++){var V;if(!((B=(V=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=V.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=V.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var q=V.orientation;T.push(q[0][0]),T.push(q[0][1]),T.push(q[0][2]),T.push(q[0][3]),T.push(q[1][0]),T.push(q[1][1]),T.push(q[1][2]),T.push(q[1][3]),T.push(q[2][0]),T.push(q[2][1]),T.push(q[2][2]),T.push(q[2][3]),T.push(q[3][0]),T.push(q[3][1]),T.push(q[3][2]),T.push(q[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),l.push(z),_.push(T),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var G=simpleMeshToMeshData(p);return G.idx_tri.length>0&&G.idx_tri[0].length>0&&G.idx_tri[0][0].length>0?r?{prim_types:[d,G.prim_types[0]],idx_tri:[o,G.idx_tri[0]],vert_tri:[l,G.vert_tri[0]],norm_tri:[n,G.norm_tri[0]],col_tri:[c,G.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[l,null],instance_orientations:[_,null]}:{prim_types:[d,G.prim_types[0]],idx_tri:[o,G.idx_tri[0]],vert_tri:[s,G.vert_tri[0]],norm_tri:[n,G.norm_tri[0]],col_tri:[c,G.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[l,null],instance_orientations:[_,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[l],instance_orientations:[_]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1);var r=performance.now(),t=e.vertices,o=e.triangles,s=t.size(),n=o.size(),i=new Uint32Array(3*n),c=new Float32Array(3*s),l=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getPositionsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,l),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,i)):(cootModule.getNormalsFromSimpleMesh2(e,l),cootModule.getTriangleIndicesFromSimpleMesh2(e,i));var u=performance.now();console.log("DEBUG: SIMPLE MESH TO MESH DATA C++",u-r);var d=c,m=_,p=l,h=i,g=performance.now();return console.log("DEBUG: SIMPLE MESH TO MESH DATA",g-r),t.delete(),o.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[h]],vert_tri:[[d]],norm_tri:[[p]],col_tri:[[m]]}},SuperposeResultsToJSArray=function(e){for(var a=e.aligned_pairs,r=a.size(),t=[],o=0;o<r;o++){var s=a.get(o),n=s.first,i=n.residue_spec,c=s.second,l=c.residue_spec,_={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:l.chain_id,insCode:l.ins_code,seqNum:l.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(_)}return a.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}a.push(n),o.delete()}return e.delete(),a},floatArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},mapMoleculeCentreInfoToJSObject=function(e){var a=e.updated_centre,r={updated_centre:[a.x(),a.y(),a.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return a.delete(),r},fitLigandInfoArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(__assign({},o))}return e.delete(),a},intArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},symmetryToJSData=function(e){for(var a=[],r=e.first,t=e.second,o=r.cell,s=r.symm_trans,n=s.size(),i=0;i<n;i++){var c=s.get(i),l=c.first,_=c.second,u=t.get(i);a.push({x:l.x(),y:l.y(),z:l.z(),asString:l.symm_as_string,isym:l.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:u}),l.delete()}return o.delete(),s.delete(),t.delete(),a},mmrrccStatsToJSArray=function(e){var a=function(e){for(var a=[],r=e.keys(),t=r.size(),o=0;o<t;o++){var s=r.get(o),n=e.get(s);a.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return r.delete(),a},r=e.first,t=e.second,o={"All atoms":a(r),"Side-chains":a(t)};return r.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({chain_id:o.chain_id,res_no:o.res_no,ins_code:o.ins_code,atom_name:o.atom_name,alt_conf:o.alt_conf,int_user_data:o.int_user_data,float_user_data:o.float_user_data,string_user_data:o.string_user_data,model_number:o.model_number})}return e.delete(),a},residueSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({resNum:o.res_no,insCode:o.ins_code,modelNumber:o.model_number,chainId:o.chain_id,intUserData:o.int_user_data})}return e.delete(),a},stringPairVectorToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({first:o.first,second:o.second})}return e.delete(),a},validationDataToJSArray=function(e,a){void 0===a&&(a=null);for(var r=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==a&&n.chain_id!==a);else{for(var i=n.rviv,c=i.size(),l=0;l<c;l++){var _=i.get(l),u=_.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:_.function_value})}i.delete()}}return t.delete(),e.delete(),r},linesBoxToJSArray=function(e){for(var a=[],r=e.line_segments,t=r.size(),o=0;o<t;o++){for(var s=[],n=r.get(o),i=n.size(),c=0;c<i;c++){var l=n.get(c),_=l.getStart(),u=l.getFinish(),d=l.amplitude(),m={x:_.x(),y:_.y(),z:_.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),_.delete(),u.delete(),l.delete()}n.delete(),a.push(s)}return r.delete(),a},vectorHBondToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({hb_hydrogen:o.hb_hydrogen,donor:o.donor,acceptor:o.acceptor,donor_neigh:o.donor_neigh,acceptor_neigh:o.acceptor_neigh,angle_1:o.angle_1,angle_2:o.angle_2,angle_3:o.angle_3,dist:o.dist,ligand_atom_is_donor:o.ligand_atom_is_donor,hydrogen_is_ligand_atom:o.hydrogen_is_ligand_atom,bond_has_hydrogen_flag:o.bond_has_hydrogen_flag})}return e.delete(),a},interestingPlaceDataToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.residue_spec;a.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),a},histogramInfoToJSData=function(e){var a=e.counts;return{counts:intArrayToJSArray(a),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,Rfree:o.Rfree,F_obs:o.F_obs,sigF_obs:o.sigF_obs,weights_used:o.weights_used})}return e.delete(),a},ramachandranDataToJSArray=function(e,a){for(var r=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===a&&r.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),r},vectorPairClipperCoordFloatToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),a.push({value:s,coord:i})}return e.delete(),a},simpleMeshToLineMeshData=function(e,a){performance.now();var r=e.vertices,t=e.triangles,o=t.size(),s=r.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),l=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,l),performance.now();var _=n,u=i,d=c,m=l;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_open_mtz=function(e){var a=guid(),r=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),r,!0,!0);var t="./".concat(a,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,a,r){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(a);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,r.F,r.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,a){var r=0,t=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0].label.split("/"),r=a[3].split("."),o=r[0],s=r[1];s=s||"";var n=new cootModule.moved_residue_t(a[2],parseInt(o),s);e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);n.add_atom(a),a.delete()})),t.push_back(n),n.delete()}})),r+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),r},read_mtz=function(e,a,r){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,r.F,r.PHI,"",!1,r.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,a,r,t,o){var s=new Uint8Array(a.data);cootModule.FS_createDataFile(".","".concat(a.fileName,".mtz"),s,!0,!0);var n="./".concat(a.fileName,".mtz"),i=[e,n,r,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,a,r){var t=guid(),o=new Uint8Array(e),s="";a.endsWith(".map.gz")?s="map.gz":a.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,r],c=molecules_container.read_ccp4_map.apply(molecules_container,i);return cootModule.FS_unlink(n),c},setUserDefinedBondColours=function(e,a,r){void 0===r&&(r=!1);var t=new cootModule.MapIntFloat3,o=new cootModule.VectorStringUInt_pair;a.forEach((function(e,a){t.set(a+51,e.rgb);var r={first:e.cid,second:a+51};o.push_back(r)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,r),o.delete(),t.delete()},doCootCommand=function(e){var a=e.returnType,r=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(r){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_open_mtz":i=auto_open_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;default:i=molecules_container[r].apply(molecules_container,t)}var c=void 0;switch(a){case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;default:c=i}return{messageId:o,messageSendTime:Date.now(),command:r,consoleMessage:"Completed ".concat(r," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return console.log(e),{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(r,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(a){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=a).molecules_container_js(!1)).set_show_timings(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){console.log(e),print(e)})),createCCP4Module({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){console.log(e),print(e)}));else if("get_mtz_data"===e.data.message){var a=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:a}})}else if("get_map"===e.data.message){var r=guid(),t="./".concat(r,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(a){return doCootCommand(__assign(__assign({},e.data),a))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};
+var cootModule,molecules_container,ccp4Module,__assign=this&&this.__assign||function(){return __assign=Object.assign||function(e){for(var a,r=1,t=arguments.length;r<t;r++)for(var o in a=arguments[r])Object.prototype.hasOwnProperty.call(a,o)&&(e[o]=a[o]);return e},__assign.apply(this,arguments)};importScripts("./wasm/moorhen.js"),importScripts("./wasm/web_example.js");var guid=function(){var e=Date.now();return"xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(/[xy]/g,(function(a){var r=(e+16*Math.random())%16|0;return e=Math.floor(e/16),("x"===a?r:3&r|8).toString(16)}))},print=function(e){console.log(e),postMessage({consoleMessage:JSON.stringify(e)})},instancedMeshToMeshData=function(e,a,r,t){void 0===r&&(r=!1),void 0===t&&(t=1e4);for(var o=[],s=[],n=[],i=[],c=[],l=[],_=[],u=[],d=[],m=e.geom,p=e.markup,h=m.size(),g=0;g<h;g++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],T=[],x=m.get(g);"spherical-atoms"===x.name&&(f=!0);for(var A=x.vertices,F=x.triangles,w=F.size(),I=0;I<w;I++){var k=F.get(I).point_id;a?(v.push(k[0]),v.push(k[2]),v.push(k[1])):(v.push(k[0]),v.push(k[1]),v.push(k[2]))}F.delete();for(var D=A.size(),J=0;J<D;J++){var C=A.get(J),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var E=C.normal;S.push(E[0]),S.push(E[1]),S.push(E[2])}A.delete();var R=x.instancing_data_A,P=R.size();if(P>0)for(var U=0;U<P;U++){var L=(V=R.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=V.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=V.size;b.push(B[0]),b.push(B[1]),b.push(B[2]),T.push.apply(T,[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1])}R.delete();var j=x.instancing_data_B,H=j.size();if(H>0)for(U=0;U<H;U++){var V;if(!((B=(V=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=V.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=V.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var q=V.orientation;T.push(q[0][0]),T.push(q[0][1]),T.push(q[0][2]),T.push(q[0][3]),T.push(q[1][0]),T.push(q[1][1]),T.push(q[1][2]),T.push(q[1][3]),T.push(q[2][0]),T.push(q[2][1]),T.push(q[2][2]),T.push(q[2][3]),T.push(q[3][0]),T.push(q[3][1]),T.push(q[3][2]),T.push(q[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),l.push(z),_.push(T),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var G=simpleMeshToMeshData(p);return G.idx_tri.length>0&&G.idx_tri[0].length>0&&G.idx_tri[0][0].length>0?r?{prim_types:[d,G.prim_types[0]],idx_tri:[o,G.idx_tri[0]],vert_tri:[l,G.vert_tri[0]],norm_tri:[n,G.norm_tri[0]],col_tri:[c,G.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[l,null],instance_orientations:[_,null]}:{prim_types:[d,G.prim_types[0]],idx_tri:[o,G.idx_tri[0]],vert_tri:[s,G.vert_tri[0]],norm_tri:[n,G.norm_tri[0]],col_tri:[c,G.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[l,null],instance_orientations:[_,null]}:{prim_types:[d],idx_tri:[o],vert_tri:[s],norm_tri:[n],col_tri:[c],instance_use_colors:[u],instance_sizes:[i],instance_origins:[l],instance_orientations:[_]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1);var r=performance.now(),t=e.vertices,o=e.triangles,s=t.size(),n=o.size(),i=new Uint32Array(3*n),c=new Float32Array(3*s),l=new Float32Array(3*s),_=new Float32Array(4*s);cootModule.getPositionsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,l),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,i)):(cootModule.getNormalsFromSimpleMesh2(e,l),cootModule.getTriangleIndicesFromSimpleMesh2(e,i));var u=performance.now();console.log("DEBUG: SIMPLE MESH TO MESH DATA C++",u-r);var d=c,m=_,p=l,h=i,g=performance.now();return console.log("DEBUG: SIMPLE MESH TO MESH DATA",g-r),t.delete(),o.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[h]],vert_tri:[[d]],norm_tri:[[p]],col_tri:[[m]]}},SuperposeResultsToJSArray=function(e){for(var a=e.aligned_pairs,r=a.size(),t=[],o=0;o<r;o++){var s=a.get(o),n=s.first,i=n.residue_spec,c=s.second,l=c.residue_spec,_={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:l.chain_id,insCode:l.ins_code,seqNum:l.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(_)}return a.delete(),{referenceSequence:e.alignment.first,movingSequence:e.alignment.second,supperposeInfo:e.superpose_info,alignedPairsData:t}},colourRulesToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=o.size(),n=[],i=0;i<s;i++){var c=o.get(i);n.push(c)}a.push(n),o.delete()}return e.delete(),a},floatArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},mapMoleculeCentreInfoToJSObject=function(e){var a=e.updated_centre,r={updated_centre:[a.x(),a.y(),a.z()],success:e.success,suggested_radius:e.suggested_radius,suggested_contour_level:e.suggested_contour_level};return a.delete(),r},fitLigandInfoArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(__assign({},o))}return e.delete(),a},intArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},stringArrayToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push(o)}return e.delete(),a},export_map_as_gltf=function(e,a,r,t,o,s){var n="".concat(guid(),".glb");molecules_container.export_map_molecule_as_gltf(e,a,r,t,o,s,n);var i=cootModule.FS.readFile(n,{encoding:"binary"});return cootModule.FS_unlink(n),i.buffer},export_molecule_as_gltf=function(e,a,r,t,o,s,n,i,c){var l="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,a,r,t,o,s,n,i,c,l);var _=cootModule.FS.readFile(l,{encoding:"binary"});return cootModule.FS_unlink(l),_.buffer},symmetryToJSData=function(e){for(var a=[],r=e.first,t=e.second,o=r.symm_trans,s=o.size(),n=0;n<s;n++){var i=o.get(n),c=i.first,l=i.second,_=t.get(n);a.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:l.us,ws:l.ws,vs:l.vs,matrix:_}),c.delete()}return o.delete(),t.delete(),a},mmrrccStatsToJSArray=function(e){var a=function(e){for(var a=[],r=e.keys(),t=r.size(),o=0;o<t;o++){var s=r.get(o),n=e.get(s);a.push({resNum:s.res_no,insCode:s.ins_code,modelNumber:s.model_number,chainId:s.chain_id,n:n.n,correlation:n.correlation()}),n.delete()}return r.delete(),a},r=e.first,t=e.second,o={"All atoms":a(r),"Side-chains":a(t)};return r.delete(),t.delete(),o},atomSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({chain_id:o.chain_id,res_no:o.res_no,ins_code:o.ins_code,atom_name:o.atom_name,alt_conf:o.alt_conf,int_user_data:o.int_user_data,float_user_data:o.float_user_data,string_user_data:o.string_user_data,model_number:o.model_number})}return e.delete(),a},residueSpecToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({resNum:o.res_no,insCode:o.ins_code,modelNumber:o.model_number,chainId:o.chain_id,intUserData:o.int_user_data})}return e.delete(),a},stringPairVectorToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({first:o.first,second:o.second})}return e.delete(),a},validationDataToJSArray=function(e,a){void 0===a&&(a=null);for(var r=[],t=e.cviv,o=t.size(),s=0;s<o;s++){var n=t.get(s);if(null!==a&&n.chain_id!==a);else{for(var i=n.rviv,c=i.size(),l=0;l<c;l++){var _=i.get(l),u=_.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:_.function_value})}i.delete()}}return t.delete(),e.delete(),r},linesBoxToJSArray=function(e){for(var a=[],r=e.line_segments,t=r.size(),o=0;o<t;o++){for(var s=[],n=r.get(o),i=n.size(),c=0;c<i;c++){var l=n.get(c),_=l.getStart(),u=l.getFinish(),d=l.amplitude(),m={x:_.x(),y:_.y(),z:_.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),_.delete(),u.delete(),l.delete()}n.delete(),a.push(s)}return r.delete(),a},vectorHBondToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({hb_hydrogen:o.hb_hydrogen,donor:o.donor,acceptor:o.acceptor,donor_neigh:o.donor_neigh,acceptor_neigh:o.acceptor_neigh,angle_1:o.angle_1,angle_2:o.angle_2,angle_3:o.angle_3,dist:o.dist,ligand_atom_is_donor:o.ligand_atom_is_donor,hydrogen_is_ligand_atom:o.hydrogen_is_ligand_atom,bond_has_hydrogen_flag:o.bond_has_hydrogen_flag})}return e.delete(),a},interestingPlaceDataToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.residue_spec;a.push({intUserData:s.int_user_data,modelNumber:s.model_number,chainId:s.chain_id,insCode:s.ins_code,resNum:s.res_no,featureType:o.feature_type,featureValue:o.feature_value,buttonLabel:o.button_label,badness:o.badness,coordX:o.x,coordY:o.y,coordZ:o.z})}return e.delete(),a},histogramInfoToJSData=function(e){var a=e.counts;return{counts:intArrayToJSArray(a),bin_width:e.bin_width,base:e.base}},autoReadMtzInfoVectToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t);a.push({idx:o.idx,F:o.F,phi:o.phi,w:o.w,weights_used:o.weights_used,Rfree:o.Rfree?o.Rfree.split("/")[3]:"",F_obs:o.F_obs?o.F_obs.split("/")[3]:"",sigF_obs:o.sigF_obs?o.sigF_obs.split("/")[3]:""})}if(e.delete(),a.some((function(e){return-1===e.idx}))){var s=a.find((function(e){return-1===e.idx}));s&&s.F_obs&&s.Rfree&&s.sigF_obs&&a.forEach((function(e){e.F_obs=s.F_obs,e.sigF_obs=s.sigF_obs,e.Rfree=s.Rfree})),a=a.filter((function(e){return-1!==e.idx}))}return a},ramachandranDataToJSArray=function(e,a){for(var r=[],t=e.size(),o=0;o<t;o++){var s=e.get(o),n=s.phi_psi;n.chain_id===a&&r.push({chainId:n.chain_id,insCode:n.ins_code,seqNum:n.residue_number,restype:s.residue_name(),isOutlier:!s.is_allowed_flag,phi:n.phi(),psi:n.psi(),is_pre_pro:"PRO"===s.residue_name()}),s.delete(),n.delete()}return e.delete(),r},vectorPairClipperCoordFloatToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s=o.second,n=o.first,i={x:n.x(),y:n.y(),z:n.z()};n.delete(),a.push({value:s,coord:i})}return e.delete(),a},simpleMeshToLineMeshData=function(e,a){performance.now();var r=e.vertices,t=e.triangles,o=t.size(),s=r.size(),n=new Uint32Array(6*o),i=new Float32Array(3*s),c=new Float32Array(3*s),l=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,l),performance.now();var _=n,u=i,d=c,m=l;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[_]],vert_tri:[[u]],norm_tri:[[d]],col_tri:[[m]]}},auto_open_mtz=function(e){var a=guid(),r=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),r,!0,!0);var t="./".concat(a,".mtz"),o=molecules_container.auto_read_mtz(t);return cootModule.FS_unlink(t),o},replace_map_by_mtz_from_file=function(e,a,r){var t=guid(),o="./".concat(t,".mtz"),s=new Uint8Array(a);cootModule.FS_createDataFile(".",o,s,!0,!0);var n=[e,o,r.F,r.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(o),i},new_positions_for_residue_atoms=function(e,a){var r=0,t=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0].label.split("/"),r=a[3].split("."),o=r[0],s=r[1];s=s||"";var n=new cootModule.moved_residue_t(a[2],parseInt(o),s);e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);n.add_atom(a),a.delete()})),t.push_back(n),n.delete()}})),r+=molecules_container.new_positions_for_atoms_in_residues(e,t),t.delete(),r},read_mtz=function(e,a,r){var t=guid(),o=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(t,".mtz"),o,!0,!0);var s="./".concat(t,".mtz"),n=[s,r.F,r.PHI,"",!1,r.isDifference],i=molecules_container.read_mtz.apply(molecules_container,n);return cootModule.FS_unlink(s),i},associate_data_mtz_file_with_map=function(e,a,r,t,o){var s=new Uint8Array(a.data);cootModule.FS_createDataFile(".","".concat(a.fileName,".mtz"),s,!0,!0);var n="./".concat(a.fileName,".mtz"),i=[e,n,r,t,o];return molecules_container.associate_data_mtz_file_with_map.apply(molecules_container,i),n},read_ccp4_map=function(e,a,r){var t=guid(),o=new Uint8Array(e),s="";a.endsWith(".map.gz")?s="map.gz":a.endsWith(".mrc.gz")&&(s="mrc.gz"),cootModule.FS_createDataFile(".","".concat(t).concat(s),o,!0,!0);var n="./".concat(t).concat(s),i=[n,r],c=molecules_container.read_ccp4_map.apply(molecules_container,i);return cootModule.FS_unlink(n),c},setUserDefinedBondColours=function(e,a,r){void 0===r&&(r=!1);var t=new cootModule.MapIntFloat3,o=new cootModule.VectorStringUInt_pair;a.forEach((function(e,a){t.set(a+51,e.rgb);var r={first:e.cid,second:a+51};o.push_back(r)})),molecules_container.set_user_defined_bond_colours(e,t),molecules_container.set_user_defined_atom_colour_by_selection(e,o,r),o.delete(),t.delete()},doCootCommand=function(e){var a=e.returnType,r=e.command,t=e.commandArgs,o=e.messageId,s=e.myTimeStamp,n=e.message;try{var i=void 0;switch(r){case"shim_new_positions_for_residue_atoms":i=new_positions_for_residue_atoms.apply(void 0,t);break;case"shim_read_mtz":i=read_mtz.apply(void 0,t);break;case"shim_auto_open_mtz":i=auto_open_mtz.apply(void 0,t);break;case"shim_read_ccp4_map":i=read_ccp4_map.apply(void 0,t);break;case"shim_associate_data_mtz_file_with_map":i=associate_data_mtz_file_with_map.apply(void 0,t);break;case"shim_replace_map_by_mtz_from_file":i=replace_map_by_mtz_from_file.apply(void 0,t);break;case"shim_set_bond_colours":i=setUserDefinedBondColours.apply(void 0,t);break;case"shim_export_map_as_gltf":i=export_map_as_gltf.apply(void 0,t);break;case"shim_export_molecule_as_gltf":i=export_molecule_as_gltf.apply(void 0,t);break;default:i=molecules_container[r].apply(molecules_container,t)}var c=void 0;switch(a){case"fit_ligand_info_array":c=fitLigandInfoArrayToJSArray(i);break;case"string_array_array":c=stringArrayArrayToJSArray(i);break;case"instanced_mesh_perm":c=instancedMeshToMeshData(i,!0);break;case"histogram_info_t":c=histogramInfoToJSData(i);break;case"symmetry":c=symmetryToJSData(i);break;case"mmrrcc_stats":c=mmrrccStatsToJSArray(i);break;case"colour_rules":c=colourRulesToJSArray(i);break;case"instanced_mesh_perfect_spheres":c=instancedMeshToMeshData(i,!1,!0);break;case"instanced_mesh":c=instancedMeshToMeshData(i,!1,!1,5);break;case"mesh_perm":c=simpleMeshToMeshData(i,!0);break;case"mesh":c=simpleMeshToMeshData(i);break;case"lit_lines_mesh":c=simpleMeshToLineMeshData(i,!0);break;case"lines_mesh":c=simpleMeshToLineMeshData(i,!1);break;case"float_array":c=floatArrayToJSArray(i);break;case"int_array":c=intArrayToJSArray(i);break;case"auto_read_mtz_info_array":c=autoReadMtzInfoVectToJSArray(i);break;case"map_molecule_centre_info_t":c=mapMoleculeCentreInfoToJSObject(i);break;case"string_array":c=stringArrayToJSArray(i);break;case"residue_specs":c=residueSpecToJSArray(i);break;case"atom_specs":c=atomSpecToJSArray(i);break;case"ramachandran_data":c=ramachandranDataToJSArray(i,e.chainID);break;case"validation_data":c=validationDataToJSArray(i,e.chainID);break;case"interesting_places_data":c=interestingPlaceDataToJSArray(i);break;case"superpose_results":c=SuperposeResultsToJSArray(i);break;case"generic_3d_lines_bonds_box":c=linesBoxToJSArray(i);break;case"vector_hbond":c=vectorHBondToJSArray(i);break;case"status_instanced_mesh_pair":c={status:i.first,mesh:instancedMeshToMeshData(i.second,!1,!1,5)};break;case"string_string_pair_vector":c=stringPairVectorToJSArray(i);break;case"void":c=null;break;case"vector_pair_clipper_coord_float":c=vectorPairClipperCoordFloatToJSArray(i);break;default:c=i}return{messageId:o,messageSendTime:Date.now(),command:r,consoleMessage:"Completed ".concat(r," in ").concat(Date.now()-s," ms"),result:{status:"Completed",result:c}}}catch(e){return console.log(e),{messageId:o,myTimeStamp:s,message:n,consoleMessage:"EXCEPTION RAISED IN ".concat(r,", ").concat(e),result:{status:"Exception"}}}};onmessage=function(e){if("CootInitialize"===e.data.message)createRSRModule({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"moorhen.js",print,printErr:print}).then((function(a){postMessage({consoleMessage:"Initialized molecules_container",message:e.data.message,messageId:e.data.messageId}),(molecules_container=new(cootModule=a).molecules_container_js(!1)).set_use_gemmi(!1),molecules_container.set_show_timings(!1),molecules_container.fill_rotamer_probability_tables(),molecules_container.set_map_sampling_rate(1.7),molecules_container.set_map_is_contoured_with_thread_pool(!0),molecules_container.set_max_number_of_threads(3),cootModule.FS.mkdir("COOT_BACKUP")})).catch((function(e){console.log(e),print(e)})),createCCP4Module({locateFile:function(e){return"./wasm/".concat(e)},onRuntimeInitialized:function(){},mainScriptUrlOrBlob:"web_example.js",print,printErr:print}).then((function(e){ccp4Module=e})).catch((function(e){console.log(e),print(e)}));else if("get_mtz_data"===e.data.message){var a=cootModule.FS.readFile(e.data.fileName,{encoding:"binary"});postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched mtz data for map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mtzData:a}})}else if("get_map"===e.data.message){var r=guid(),t="./".concat(r,".map");molecules_container.writeCCP4Map(e.data.molNo,t);var o=cootModule.FS.readFile(t,{encoding:"binary"});cootModule.FS_unlink(t),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Fetched map of map ".concat(e.data.molNo),message:e.data.message,result:{molNo:e.data.molNo,mapData:o.buffer}})}else if("delete_file_name"===e.data.message){var s=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:s})}else if("coot_command_list"===e.data.message){var n=e.data.commandList.map((function(a){return doCootCommand(__assign(__assign({},e.data),a))}));postMessage({messageId:e.data.messageId,resultList:n})}"coot_command"===e.data.message&&(s=doCootCommand(e.data),postMessage(s))};

package/baby-gru/CootWorker.ts

@@ -413,11 +413,40 @@ const stringArrayToJSArray = (stringArray: emscriptem.vector<string>) => {
     return returnResult;
 }
 
+const export_map_as_gltf = (imol: number, x: number, y: number, z: number, radius: number, contourLevel: number) => {
+    const fileName = `${guid()}.glb`
+    molecules_container.export_map_molecule_as_gltf(imol, x, y, z, radius, contourLevel, fileName)
+    const fileContents = cootModule.FS.readFile(fileName, { encoding: 'binary' }) as Uint8Array
+    cootModule.FS_unlink(fileName)
+    return fileContents.buffer
+}
+
+const export_molecule_as_gltf = (
+    imol: number, cid: string, mode: string, isDark: boolean, bondWidth: number, 
+    atomRadius: number, bondSmoothness: number, drawHydrogens: boolean, drawMissingResidues: boolean
+) => {
+    const fileName = `${guid()}.glb`
+    molecules_container.export_model_molecule_as_gltf(
+        imol,
+        cid,
+        mode,
+        isDark,
+        bondWidth,
+        atomRadius,
+        bondSmoothness,
+        drawHydrogens,
+        drawMissingResidues,
+        fileName
+    )
+    const fileContents = cootModule.FS.readFile(fileName, { encoding: 'binary' }) as Uint8Array
+    cootModule.FS_unlink(fileName)
+    return fileContents.buffer
+}
+
 const symmetryToJSData = (symmetryDataPair: libcootApi.PairType<libcootApi.SymmetryData, emscriptem.vector<number[][]>>) => {
     let result: { x: number; y: number; z: number; asString: string; isym: number; us: number; ws: number; vs: number; matrix: number[][]; }[]= []
     const symmetryData = symmetryDataPair.first
     const symmetryMatrices = symmetryDataPair.second
-    const cell = symmetryData.cell
     const symm_trans = symmetryData.symm_trans
     const symmetrySize = symm_trans.size()
 
@@ -441,7 +470,6 @@ const symmetryToJSData = (symmetryDataPair: libcootApi.PairType<libcootApi.Symme
         symTransT.delete()
     }
 
-    cell.delete()
     symm_trans.delete()
     symmetryMatrices.delete()
     return result
@@ -686,13 +714,27 @@ const autoReadMtzInfoVectToJSArray = (autoReadMtzInfoArray: emscriptem.vector<li
             F: autoReadMtzInfo.F,
             phi: autoReadMtzInfo.phi,
             w: autoReadMtzInfo.w,
-            Rfree: autoReadMtzInfo.Rfree,
-            F_obs: autoReadMtzInfo.F_obs,
-            sigF_obs: autoReadMtzInfo.sigF_obs,
             weights_used: autoReadMtzInfo.weights_used,
+            // This relies on the column label being of the form /crystal/dataset/label
+            Rfree: autoReadMtzInfo.Rfree ? autoReadMtzInfo.Rfree.split('/')[3] : "",
+            F_obs: autoReadMtzInfo.F_obs ? autoReadMtzInfo.F_obs.split('/')[3] : "",
+            sigF_obs: autoReadMtzInfo.sigF_obs ? autoReadMtzInfo.sigF_obs.split('/')[3] : "",
         })
     }
     autoReadMtzInfoArray.delete()
+
+    // Add the column labels for the observations to the returned maps
+    if (returnResult.some(item => item.idx === -1)) {
+        const obsColumnsData = returnResult.find(item => item.idx === -1)
+        if (obsColumnsData && obsColumnsData.F_obs && obsColumnsData.Rfree && obsColumnsData.sigF_obs) {
+            returnResult.forEach(item => {
+                item.F_obs = obsColumnsData.F_obs
+                item.sigF_obs = obsColumnsData.sigF_obs
+                item.Rfree = obsColumnsData.Rfree
+            })
+        }
+        returnResult = returnResult.filter(item => item.idx !== -1)
+    }
     
     return returnResult
 }
@@ -920,6 +962,12 @@ const doCootCommand = (messageData: {
             case 'shim_set_bond_colours':
                 cootResult = setUserDefinedBondColours(...commandArgs as [number, { cid: string; rgb: [number, number, number] }[], boolean])
                 break
+            case 'shim_export_map_as_gltf':
+                cootResult = export_map_as_gltf(...commandArgs as [number, number, number, number, number, number])
+                break
+            case 'shim_export_molecule_as_gltf':
+                cootResult = export_molecule_as_gltf(...commandArgs as [number, string, string, boolean, number, number, number, boolean, boolean])
+                break
             default:
                 cootResult = molecules_container[command](...commandArgs)
                 break
@@ -1054,6 +1102,7 @@ onmessage = function (e) {
                 postMessage({ consoleMessage: 'Initialized molecules_container', message: e.data.message, messageId: e.data.messageId })
                 cootModule = returnedModule;
                 molecules_container = new cootModule.molecules_container_js(false)
+                molecules_container.set_use_gemmi(false)
                 molecules_container.set_show_timings(false)
                 molecules_container.fill_rotamer_probability_tables()
                 molecules_container.set_map_sampling_rate(1.7)