moorhen 0.8.2 → 0.8.4

package/README.md

@@ -67,8 +67,16 @@ Binaries are available on the releases page. Please read the instructions there
 5. Build gsl, Boost, RDKIt, Coot, the CCP4 libraries and examples:  
 <br>In this branch, it is intended that you do the build in the source directory. 
 <br/>After first checkout you should run the following script to build:  
-`./initial_build.sh`  
+`./moorhen_build.sh`  
 This should build all dependencies and then `Moorhen`. 
+\
+\
+It is also possible to build a 64-bit version of Moorhen which (currently) can address up to 8GB memory:  
+`./moorhen_build.sh --64bit`  
+Note that you need a 64-bit WASM capable web browser to use this. Most browsers are not 64-bit capable by default. Some have
+64-bit capability available as an option or in development versions.  
+See the `MEMORY64` feature at [https://webassembly.org/features/](https://webassembly.org/features/)  
+Moorhen developers have seen success with Firefox Nightly on MacOS and Linux and Chrome Canary (with `chrome://flags/#enable-experimental-webassembly-features`) on MacOS.
 
 6. To run the Moorhen molecular graphics application:  
 `cd baby-gru`  

package/baby-gru/CootWorker.js

@@ -1 +1 @@
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I=F.get(k).point_id;a?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=A.size(),D=0;D<J;D++){var C=A.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;S.push(R[0]),S.push(R[1]),S.push(R[2])}A.delete();var P=x.instancing_data_A,E=P.size();if(E>0)for(var U=0;U<E;U++){var L=(q=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=q.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=x.instancing_data_B,V=j.size();if(V>0)for(U=0;U<V;U++){var q;if(!((B=(q=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=q.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;T.push(H[0][0]),T.push(H[0][1]),T.push(H[0][2]),T.push(H[0][3]),T.push(H[1][0]),T.push(H[1][1]),T.push(H[1][2]),T.push(H[1][3]),T.push(H[2][0]),T.push(H[2][1]),T.push(H[2][2]),T.push(H[2][3]),T.push(H[3][0]),T.push(H[3][1]),T.push(H[3][2]),T.push(H[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 K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?r?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[l,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[l,null],instance_orientations:[_,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.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),performance.now();var r=e.vertices,t=e.triangles,o=r.size(),s=t.size(),n=new Uint32Array(3*s),i=new Float32Array(3*o),c=new Float32Array(3*o),l=new 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e.delete(),a},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 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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;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}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.set_refinement_is_verbose(!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("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});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,g=m.size(),h=0;h<g;h++){var f=r,v=[],y=[],S=[],b=[],M=[],z=[],T=[],x=m.get(h);"spherical-atoms"===x.name&&(f=!0);for(var A=x.vertices,F=x.triangles,w=F.size(),k=0;k<w;k++){var I=F.get(k).point_id;a?(v.push(I[0]),v.push(I[2]),v.push(I[1])):(v.push(I[0]),v.push(I[1]),v.push(I[2]))}F.delete();for(var J=A.size(),D=0;D<J;D++){var C=A.get(D),N=C.pos;y.push(N[0]),y.push(N[1]),y.push(N[2]);var R=C.normal;S.push(R[0]),S.push(R[1]),S.push(R[2])}A.delete();var P=x.instancing_data_A,E=P.size();if(E>0)for(var U=0;U<E;U++){var L=(q=P.get(U)).position;z.push(L[0]),z.push(L[1]),z.push(L[2]);var O=q.colour;M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var B=q.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=x.instancing_data_B,V=j.size();if(V>0)for(U=0;U<V;U++){var q;if(!((B=(q=j.get(U)).size)[2]>t)){b.push(B[0]),b.push(B[1]),b.push(B[2]),L=q.position,z.push(L[0]),z.push(L[1]),z.push(L[2]),O=q.colour,M.push(O[0]),M.push(O[1]),M.push(O[2]),M.push(O[3]);var H=q.orientation;T.push(H[0][0]),T.push(H[0][1]),T.push(H[0][2]),T.push(H[0][3]),T.push(H[1][0]),T.push(H[1][1]),T.push(H[1][2]),T.push(H[1][3]),T.push(H[2][0]),T.push(H[2][1]),T.push(H[2][2]),T.push(H[2][3]),T.push(H[3][0]),T.push(H[3][1]),T.push(H[3][2]),T.push(H[3][3])}}j.delete(),n.push(S),s.push(y),o.push(v),i.push(b),_.push(z),l.push(T),c.push(M),u.push(!0),f?d.push("PERFECT_SPHERES"):d.push("TRIANGLES")}m.delete();var K=simpleMeshToMeshData(p);return K.idx_tri.length>0&&K.idx_tri[0].length>0&&K.idx_tri[0][0].length>0?r?{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[_,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,null]}:{prim_types:[d,K.prim_types[0]],idx_tri:[o,K.idx_tri[0]],vert_tri:[s,K.vert_tri[0]],norm_tri:[n,K.norm_tri[0]],col_tri:[c,K.col_tri[0]],instance_use_colors:[u,null],instance_sizes:[i,null],instance_origins:[_,null],instance_orientations:[l,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:[_],instance_orientations:[l]}},simpleMeshToMeshData=function(e,a){void 0===a&&(a=!1),performance.now();var r=e.vertices,t=e.triangles,o=r.size(),s=t.size(),n=new Uint32Array(3*s),i=new Float32Array(3*o),c=new Float32Array(3*o),_=new Float32Array(4*o);cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getColoursFromSimpleMesh2(e,_),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,c),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,n)):(cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getTriangleIndicesFromSimpleMesh2(e,n)),performance.now();var l=i,u=_,d=c,m=n;return r.delete(),t.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[m]],vert_tri:[[l]],norm_tri:[[d]],col_tri:[[u]]}},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,_=c.residue_spec,l={reference:{chainId:i.chain_id,insCode:i.ins_code,seqNum:i.res_no,restype:"UNK",value:n.function_value,label:n.label},moving:{chainId:_.chain_id,insCode:_.ins_code,seqNum:_.res_no,restype:"UNK",value:c.function_value,label:c.label}};t.push(l)}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},textureAsFloatsToJSTextureAsFloats=function(e){var a=[],r=e.image_data.size();console.log(r);for(var t=0;t<r;t++){var o=e.image_data.get(t);a.push(o)}return e.image_data.delete(),{width:e.width,height:e.height,x_size:e.x_size,y_size:e.y_size,z_position:e.z_position,image_data:a}},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 _="".concat(guid(),".glb");molecules_container.export_model_molecule_as_gltf(e,a,r,t,o,s,n,i,c,_);var l=cootModule.FS.readFile(_,{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,_=i.second,l=t.get(n);a.push({x:c.x(),y:c.y(),z:c.z(),asString:c.symm_as_string,isym:c.isym(),us:_.us,ws:_.ws,vs:_.vs,matrix:l}),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(),_=0;_<c;_++){var l=i.get(_),u=l.residue_spec;r.push({chainId:u.chain_id,insCode:u.ins_code,seqNum:u.res_no,restype:"UNK",value:l.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 _=n.get(c),l=_.getStart(),u=_.getFinish(),d=_.amplitude(),m={x:l.x(),y:l.y(),z:l.z()},p={x:u.x(),y:u.y(),z:u.z()};s.push({start:m,end:p,dist:d}),l.delete(),u.delete(),_.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},vectorPairStringIntToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){var o=e.get(t),s={residue:o.first,slice:o.second};a.push(s)}return e.delete(),a},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),_=new Float32Array(4*s);cootModule.getLineIndicesFromSimpleMesh2(e,n),cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getColoursFromSimpleMesh2(e,_),performance.now();var l=n,u=i,d=c,m=_;return r.delete(),t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[l]],vert_tri:[[u]],additional_norm_tri:[[d]],norm_tri:[[d]],col_tri:[[m]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[l]],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],r=new cootModule.moved_residue_t(a.chain_id,parseInt(a.res_no),"");e.forEach((function(e){var a=new cootModule.moved_atom_t(e.name,e.alt_loc,e.x,e.y,e.z,-1);r.add_atom(a),a.delete()})),t.push_back(r),r.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=-1;try{c=molecules_container.read_ccp4_map.apply(molecules_container,i)}catch(e){console.warn(e)}finally{cootModule.FS_unlink(n)}return 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()},privateerValidationToJSArray=function(e){for(var a=[],r=e.size(),t=0;t<r;t++){for(var o=e.get(t),s=[],n=o.torsions,i=n.size(),c=0;c<i;c++)s.push(n.get(c));n.delete();var _={torsions:s,svg:o.svg.replace(/: *32/g,""),id:o.id.replace(/: *32/g,""),chain:o.chain,wurcs:o.wurcs,glyconnect_id:o.glyconnect_id,glytoucan_id:o.glytoucan_id,torsion_err:o.torsion_err,anomer_err:o.anomer_err,conformation_err:o.conformation_err,puckering_err:o.puckering_err,chirality_err:o.chirality_err};a.push(_)}return e.delete(),a},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"texture_as_floats_t":c=textureAsFloatsToJSTextureAsFloats(i);break;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;case"vector_pair_string_int":c=vectorPairStringIntToJSArray(i);break;case"privateer_results":c=privateerValidationToJSArray(i);break;default:c=i}try{i.delete()}catch(e){}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.set_refinement_is_verbose(!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("close"===e.data.message)null==molecules_container||molecules_container.delete(),postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,consoleMessage:"Closed molecules container",message:e.data.message,result:{}});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

@@ -379,6 +379,29 @@ const mapMoleculeCentreInfoToJSObject = (mapMoleculeCentreInfo: libcootApi.MapMo
     return returnResult;
 }
 
+const textureAsFloatsToJSTextureAsFloats = (data:libcootApi.textureAsFloats): libcootApi.textureAsFloatsJS => {
+
+    let image_data = []
+
+    const imageDataVecSize = data.image_data.size()
+    console.log(imageDataVecSize);
+    for (let i = 0; i < imageDataVecSize; i++) {
+        const texVal = data.image_data.get(i)
+        image_data.push(texVal)
+    }
+
+    data.image_data.delete()
+
+    return {
+        width:data.width,
+        height:data.height,
+        x_size:data.x_size,
+        y_size:data.y_size,
+        z_position:data.z_position,
+        image_data:image_data,
+    };
+}
+
 const fitLigandInfoArrayToJSArray = (fitLigandInfoVec: emscriptem.vector<libcootApi.fitLigandInfo>): libcootApi.fitLigandInfo[] => {
     const result: libcootApi.fitLigandInfo[] = []
 
@@ -768,7 +791,7 @@ const ramachandranDataToJSArray = (ramachandraData: emscriptem.vector<libcootApi
 const vectorPairStringIntToJSArray = (vectorData: emscriptem.vector<{first: string; second: number}>) => {
     let result: {residue: string; slice: number; }[] = []
     const vectorSize = vectorData.size()
-    for(let i = 0; i < vectorSize; i++) {
+    for (let i = 0; i < vectorSize; i++) {
         const pair = vectorData.get(i)
         const residue = pair.first
         const slice = pair.second
@@ -1040,6 +1063,9 @@ const doCootCommand = (messageData: {
 
         let returnResult;
         switch (returnType) {
+            case 'texture_as_floats_t':
+                returnResult = textureAsFloatsToJSTextureAsFloats(cootResult)
+                break;
             case 'fit_ligand_info_array':
                 returnResult = fitLigandInfoArrayToJSArray(cootResult)
                 break;

package/baby-gru/wasm/RDKit_minimal.js

@@ -0,0 +1 @@
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er.shift()})(),put_char(r,t){null===t||10===t?(y(tr(r.output,0)),r.output=[]):0!=t&&r.output.push(t)},fsync(r){r.output&&r.output.length>0&&(y(tr(r.output,0)),r.output=[])},ioctl_tcgets:r=>({c_iflag:25856,c_oflag:5,c_cflag:191,c_lflag:35387,c_cc:[3,28,127,21,4,0,1,0,17,19,26,0,18,15,23,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]}),ioctl_tcsets:(r,t,e)=>0,ioctl_tiocgwinsz:r=>[24,80]},default_tty1_ops:{put_char(r,t){null===t||10===t?(w(tr(r.output,0)),r.output=[]):0!=t&&r.output.push(t)},fsync(r){r.output&&r.output.length>0&&(w(tr(r.output,0)),r.output=[])}}},lr=r=>{x()},hr={ops_table:null,mount:r=>hr.createNode(null,"/",16895,0),createNode(r,t,e,n){if(pr.isBlkdev(e)||pr.isFIFO(e))throw new pr.ErrnoError(63);hr.ops_table||(hr.ops_table={dir:{node:{getattr:hr.node_ops.getattr,setattr:hr.node_ops.setattr,lookup:hr.node_ops.lookup,mknod:hr.node_ops.mknod,rename:hr.node_ops.rename,unlink:hr.node_ops.unlink,rmdir:hr.node_ops.rmdir,readdir:hr.node_ops.readdir,symlink:hr.node_ops.symlink},stream:{llseek:hr.stream_ops.llseek}},file:{node:{getattr:hr.node_ops.getattr,setattr:hr.node_ops.setattr},stream:{llseek:hr.stream_ops.llseek,read:hr.stream_ops.read,write:hr.stream_ops.write,allocate:hr.stream_ops.allocate,mmap:hr.stream_ops.mmap,msync:hr.stream_ops.msync}},link:{node:{getattr:hr.node_ops.getattr,setattr:hr.node_ops.setattr,readlink:hr.node_ops.readlink},stream:{}},chrdev:{node:{getattr:hr.node_ops.getattr,setattr:hr.node_ops.setattr},stream:pr.chrdev_stream_ops}});var o=pr.createNode(r,t,e,n);return pr.isDir(o.mode)?(o.node_ops=hr.ops_table.dir.node,o.stream_ops=hr.ops_table.dir.stream,o.contents={}):pr.isFile(o.mode)?(o.node_ops=hr.ops_table.file.node,o.stream_ops=hr.ops_table.file.stream,o.usedBytes=0,o.contents=null):pr.isLink(o.mode)?(o.node_ops=hr.ops_table.link.node,o.stream_ops=hr.ops_table.link.stream):pr.isChrdev(o.mode)&&(o.node_ops=hr.ops_table.chrdev.node,o.stream_ops=hr.ops_table.chrdev.stream),o.timestamp=Date.now(),r&&(r.contents[t]=o,r.timestamp=o.timestamp),o},getFileDataAsTypedArray:r=>r.contents?r.contents.subarray?r.contents.subarray(0,r.usedBytes):new Uint8Array(r.contents):new Uint8Array(0),expandFileStorage(r,t){var e=r.contents?r.contents.length:0;if(!(e>=t)){t=Math.max(t,e*(e<1048576?2:1.125)>>>0),0!=e&&(t=Math.max(t,256));var n=r.contents;r.contents=new Uint8Array(t),r.usedBytes>0&&r.contents.set(n.subarray(0,r.usedBytes),0)}},resizeFileStorage(r,t){if(r.usedBytes!=t)if(0==t)r.contents=null,r.usedBytes=0;else{var e=r.contents;r.contents=new Uint8Array(t),e&&r.contents.set(e.subarray(0,Math.min(t,r.usedBytes))),r.usedBytes=t}},node_ops:{getattr(r){var t={};return t.dev=pr.isChrdev(r.mode)?r.id:1,t.ino=r.id,t.mode=r.mode,t.nlink=1,t.uid=0,t.gid=0,t.rdev=r.rdev,pr.isDir(r.mode)?t.size=4096:pr.isFile(r.mode)?t.size=r.usedBytes:pr.isLink(r.mode)?t.size=r.link.length:t.size=0,t.atime=new Date(r.timestamp),t.mtime=new Date(r.timestamp),t.ctime=new Date(r.timestamp),t.blksize=4096,t.blocks=Math.ceil(t.size/t.blksize),t},setattr(r,t){void 0!==t.mode&&(r.mode=t.mode),void 0!==t.timestamp&&(r.timestamp=t.timestamp),void 0!==t.size&&hr.resizeFileStorage(r,t.size)},lookup(r,t){throw pr.genericErrors[44]},mknod:(r,t,e,n)=>hr.createNode(r,t,e,n),rename(r,t,e){if(pr.isDir(r.mode)){var n;try{n=pr.lookupNode(t,e)}catch(r){}if(n)for(var o in n.contents)throw new pr.ErrnoError(55)}delete r.parent.contents[r.name],r.parent.timestamp=Date.now(),r.name=e,t.contents[e]=r,t.timestamp=r.parent.timestamp,r.parent=t},unlink(r,t){delete r.contents[t],r.timestamp=Date.now()},rmdir(r,t){var e=pr.lookupNode(r,t);for(var n in e.contents)throw new pr.ErrnoError(55);delete r.contents[t],r.timestamp=Date.now()},readdir(r){var t=[".",".."];for(var e in r.contents)r.contents.hasOwnProperty(e)&&t.push(e);return t},symlink(r,t,e){var n=hr.createNode(r,t,41471,0);return n.link=e,n},readlink(r){if(!pr.isLink(r.mode))throw new pr.ErrnoError(28);return r.link}},stream_ops:{read(r,t,e,n,o){var a=r.node.contents;if(o>=r.node.usedBytes)return 0;var i=Math.min(r.node.usedBytes-o,n);if(i>8&&a.subarray)t.set(a.subarray(o,o+i),e);else for(var s=0;s<i;s++)t[e+s]=a[o+s];return i},write(r,t,e,n,o,a){if(!n)return 0;var i=r.node;if(i.timestamp=Date.now(),t.subarray&&(!i.contents||i.contents.subarray)){if(a)return i.contents=t.subarray(e,e+n),i.usedBytes=n,n;if(0===i.usedBytes&&0===o)return i.contents=t.slice(e,e+n),i.usedBytes=n,n;if(o+n<=i.usedBytes)return i.contents.set(t.subarray(e,e+n),o),n}if(hr.expandFileStorage(i,o+n),i.contents.subarray&&t.subarray)i.contents.set(t.subarray(e,e+n),o);else for(var s=0;s<n;s++)i.contents[o+s]=t[e+s];return i.usedBytes=Math.max(i.usedBytes,o+n),n},llseek(r,t,e){var n=t;if(1===e?n+=r.position:2===e&&pr.isFile(r.node.mode)&&(n+=r.node.usedBytes),n<0)throw new pr.ErrnoError(28);return n},allocate(r,t,e){hr.expandFileStorage(r.node,t+e),r.node.usedBytes=Math.max(r.node.usedBytes,t+e)},mmap(r,t,e,n,o){if(!pr.isFile(r.node.mode))throw new pr.ErrnoError(43);var a,i,s=r.node.contents;if(2&o||s.buffer!==g.buffer){if((e>0||e+t<s.length)&&(s=s.subarray?s.subarray(e,e+t):Array.prototype.slice.call(s,e,e+t)),i=!0,!(a=lr()))throw new pr.ErrnoError(48);g.set(s,a)}else i=!1,a=s.byteOffset;return{ptr:a,allocated:i}},msync:(r,t,e,n,o)=>(hr.stream_ops.write(r,t,0,n,e,!1),0)}},dr=o.preloadPlugins||[],fr=(r,t)=>{var e=0;return r&&(e|=365),t&&(e|=146),e},pr={root:null,mounts:[],devices:{},streams:[],nextInode:1,nameTable:null,currentPath:"/",initialized:!1,ignorePermissions:!0,ErrnoError:null,genericErrors:{},filesystems:null,syncFSRequests:0,lookupPath(r,t={}){if(!(r=Q.resolve(r)))return{path:"",node:null};if((t=Object.assign({follow_mount:!0,recurse_count:0},t)).recurse_count>8)throw new pr.ErrnoError(32);for(var e=r.split("/").filter((r=>!!r)),n=pr.root,o="/",a=0;a<e.length;a++){var i=a===e.length-1;if(i&&t.parent)break;if(n=pr.lookupNode(n,e[a]),o=J.join2(o,e[a]),pr.isMountpoint(n)&&(!i||i&&t.follow_mount)&&(n=n.mounted.root),!i||t.follow)for(var s=0;pr.isLink(n.mode);){var u=pr.readlink(o);if(o=Q.resolve(J.dirname(o),u),n=pr.lookupPath(o,{recurse_count:t.recurse_count+1}).node,s++>40)throw new pr.ErrnoError(32)}}return{path:o,node:n}},getPath(r){for(var t;;){if(pr.isRoot(r)){var e=r.mount.mountpoint;return t?"/"!==e[e.length-1]?`${e}/${t}`:e+t:e}t=t?`${r.name}/${t}`:r.name,r=r.parent}},hashName(r,t){for(var e=0,n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n)|0;return(r+e>>>0)%pr.nameTable.length},hashAddNode(r){var t=pr.hashName(r.parent.id,r.name);r.name_next=pr.nameTable[t],pr.nameTable[t]=r},hashRemoveNode(r){var t=pr.hashName(r.parent.id,r.name);if(pr.nameTable[t]===r)pr.nameTable[t]=r.name_next;else for(var e=pr.nameTable[t];e;){if(e.name_next===r){e.name_next=r.name_next;break}e=e.name_next}},lookupNode(r,t){var e=pr.mayLookup(r);if(e)throw new pr.ErrnoError(e,r);for(var n=pr.hashName(r.id,t),o=pr.nameTable[n];o;o=o.name_next){var a=o.name;if(o.parent.id===r.id&&a===t)return o}return pr.lookup(r,t)},createNode(r,t,e,n){var o=new pr.FSNode(r,t,e,n);return pr.hashAddNode(o),o},destroyNode(r){pr.hashRemoveNode(r)},isRoot:r=>r===r.parent,isMountpoint:r=>!!r.mounted,isFile:r=>32768==(61440&r),isDir:r=>16384==(61440&r),isLink:r=>40960==(61440&r),isChrdev:r=>8192==(61440&r),isBlkdev:r=>24576==(61440&r),isFIFO:r=>4096==(61440&r),isSocket:r=>49152==(49152&r),flagsToPermissionString(r){var t=["r","w","rw"][3&r];return 512&r&&(t+="w"),t},nodePermissions:(r,t)=>pr.ignorePermissions||(!t.includes("r")||292&r.mode)&&(!t.includes("w")||146&r.mode)&&(!t.includes("x")||73&r.mode)?0:2,mayLookup:r=>pr.nodePermissions(r,"x")||(r.node_ops.lookup?0:2),mayCreate(r,t){try{return pr.lookupNode(r,t),20}catch(r){}return pr.nodePermissions(r,"wx")},mayDelete(r,t,e){var n;try{n=pr.lookupNode(r,t)}catch(r){return r.errno}var o=pr.nodePermissions(r,"wx");if(o)return o;if(e){if(!pr.isDir(n.mode))return 54;if(pr.isRoot(n)||pr.getPath(n)===pr.cwd())return 10}else if(pr.isDir(n.mode))return 31;return 0},mayOpen:(r,t)=>r?pr.isLink(r.mode)?32:pr.isDir(r.mode)&&("r"!==pr.flagsToPermissionString(t)||512&t)?31:pr.nodePermissions(r,pr.flagsToPermissionString(t)):44,MAX_OPEN_FDS:4096,nextfd(){for(var r=0;r<=pr.MAX_OPEN_FDS;r++)if(!pr.streams[r])return r;throw new pr.ErrnoError(33)},getStreamChecked(r){var t=pr.getStream(r);if(!t)throw new pr.ErrnoError(8);return t},getStream:r=>pr.streams[r],createStream:(r,t=-1)=>(pr.FSStream||(pr.FSStream=function(){this.shared={}},pr.FSStream.prototype={},Object.defineProperties(pr.FSStream.prototype,{object:{get(){return this.node},set(r){this.node=r}},isRead:{get(){return 1!=(2097155&this.flags)}},isWrite:{get(){return 0!=(2097155&this.flags)}},isAppend:{get(){return 1024&this.flags}},flags:{get(){return this.shared.flags},set(r){this.shared.flags=r}},position:{get(){return this.shared.position},set(r){this.shared.position=r}}})),r=Object.assign(new pr.FSStream,r),-1==t&&(t=pr.nextfd()),r.fd=t,pr.streams[t]=r,r),closeStream(r){pr.streams[r]=null},chrdev_stream_ops:{open(r){var t=pr.getDevice(r.node.rdev);r.stream_ops=t.stream_ops,r.stream_ops.open&&r.stream_ops.open(r)},llseek(){throw new pr.ErrnoError(70)}},major:r=>r>>8,minor:r=>255&r,makedev:(r,t)=>r<<8|t,registerDevice(r,t){pr.devices[r]={stream_ops:t}},getDevice:r=>pr.devices[r],getMounts(r){for(var t=[],e=[r];e.length;){var n=e.pop();t.push(n),e.push.apply(e,n.mounts)}return t},syncfs(r,t){"function"==typeof r&&(t=r,r=!1),pr.syncFSRequests++,pr.syncFSRequests>1&&w(`warning: ${pr.syncFSRequests} FS.syncfs operations in flight at once, probably just doing extra work`);var e=pr.getMounts(pr.root.mount),n=0;function o(r){return pr.syncFSRequests--,t(r)}function a(r){if(r)return a.errored?void 0:(a.errored=!0,o(r));++n>=e.length&&o(null)}e.forEach((t=>{if(!t.type.syncfs)return a(null);t.type.syncfs(t,r,a)}))},mount(r,t,e){var n,o="/"===e,a=!e;if(o&&pr.root)throw new pr.ErrnoError(10);if(!o&&!a){var i=pr.lookupPath(e,{follow_mount:!1});if(e=i.path,n=i.node,pr.isMountpoint(n))throw new pr.ErrnoError(10);if(!pr.isDir(n.mode))throw new pr.ErrnoError(54)}var s={type:r,opts:t,mountpoint:e,mounts:[]},u=r.mount(s);return u.mount=s,s.root=u,o?pr.root=u:n&&(n.mounted=s,n.mount&&n.mount.mounts.push(s)),u},unmount(r){var t=pr.lookupPath(r,{follow_mount:!1});if(!pr.isMountpoint(t.node))throw new pr.ErrnoError(28);var e=t.node,n=e.mounted,o=pr.getMounts(n);Object.keys(pr.nameTable).forEach((r=>{for(var t=pr.nameTable[r];t;){var e=t.name_next;o.includes(t.mount)&&pr.destroyNode(t),t=e}})),e.mounted=null;var a=e.mount.mounts.indexOf(n);e.mount.mounts.splice(a,1)},lookup:(r,t)=>r.node_ops.lookup(r,t),mknod(r,t,e){var n=pr.lookupPath(r,{parent:!0}).node,o=J.basename(r);if(!o||"."===o||".."===o)throw new pr.ErrnoError(28);var a=pr.mayCreate(n,o);if(a)throw new pr.ErrnoError(a);if(!n.node_ops.mknod)throw new pr.ErrnoError(63);return n.node_ops.mknod(n,o,t,e)},create:(r,t)=>(t=void 0!==t?t:438,t&=4095,t|=32768,pr.mknod(r,t,0)),mkdir:(r,t)=>(t=void 0!==t?t:511,t&=1023,t|=16384,pr.mknod(r,t,0)),mkdirTree(r,t){for(var e=r.split("/"),n="",o=0;o<e.length;++o)if(e[o]){n+="/"+e[o];try{pr.mkdir(n,t)}catch(r){if(20!=r.errno)throw r}}},mkdev:(r,t,e)=>(void 0===e&&(e=t,t=438),t|=8192,pr.mknod(r,t,e)),symlink(r,t){if(!Q.resolve(r))throw new pr.ErrnoError(44);var e=pr.lookupPath(t,{parent:!0}).node;if(!e)throw new pr.ErrnoError(44);var n=J.basename(t),o=pr.mayCreate(e,n);if(o)throw new pr.ErrnoError(o);if(!e.node_ops.symlink)throw new pr.ErrnoError(63);return e.node_ops.symlink(e,n,r)},rename(r,t){var e,n,o=J.dirname(r),a=J.dirname(t),i=J.basename(r),s=J.basename(t);if(e=pr.lookupPath(r,{parent:!0}).node,n=pr.lookupPath(t,{parent:!0}).node,!e||!n)throw new pr.ErrnoError(44);if(e.mount!==n.mount)throw new pr.ErrnoError(75);var u,c=pr.lookupNode(e,i),l=Q.relative(r,a);if("."!==l.charAt(0))throw new pr.ErrnoError(28);if("."!==(l=Q.relative(t,o)).charAt(0))throw new pr.ErrnoError(55);try{u=pr.lookupNode(n,s)}catch(r){}if(c!==u){var h=pr.isDir(c.mode),d=pr.mayDelete(e,i,h);if(d)throw new pr.ErrnoError(d);if(d=u?pr.mayDelete(n,s,h):pr.mayCreate(n,s))throw new pr.ErrnoError(d);if(!e.node_ops.rename)throw new pr.ErrnoError(63);if(pr.isMountpoint(c)||u&&pr.isMountpoint(u))throw new pr.ErrnoError(10);if(n!==e&&(d=pr.nodePermissions(e,"w")))throw new pr.ErrnoError(d);pr.hashRemoveNode(c);try{e.node_ops.rename(c,n,s)}catch(r){throw r}finally{pr.hashAddNode(c)}}},rmdir(r){var t=pr.lookupPath(r,{parent:!0}).node,e=J.basename(r),n=pr.lookupNode(t,e),o=pr.mayDelete(t,e,!0);if(o)throw new pr.ErrnoError(o);if(!t.node_ops.rmdir)throw new pr.ErrnoError(63);if(pr.isMountpoint(n))throw new pr.ErrnoError(10);t.node_ops.rmdir(t,e),pr.destroyNode(n)},readdir(r){var t=pr.lookupPath(r,{follow:!0}).node;if(!t.node_ops.readdir)throw new pr.ErrnoError(54);return t.node_ops.readdir(t)},unlink(r){var t=pr.lookupPath(r,{parent:!0}).node;if(!t)throw new pr.ErrnoError(44);var e=J.basename(r),n=pr.lookupNode(t,e),o=pr.mayDelete(t,e,!1);if(o)throw new pr.ErrnoError(o);if(!t.node_ops.unlink)throw new pr.ErrnoError(63);if(pr.isMountpoint(n))throw new pr.ErrnoError(10);t.node_ops.unlink(t,e),pr.destroyNode(n)},readlink(r){var t=pr.lookupPath(r).node;if(!t)throw new pr.ErrnoError(44);if(!t.node_ops.readlink)throw new pr.ErrnoError(28);return Q.resolve(pr.getPath(t.parent),t.node_ops.readlink(t))},stat(r,t){var e=pr.lookupPath(r,{follow:!t}).node;if(!e)throw new pr.ErrnoError(44);if(!e.node_ops.getattr)throw new pr.ErrnoError(63);return e.node_ops.getattr(e)},lstat:r=>pr.stat(r,!0),chmod(r,t,e){var n;if(!(n="string"==typeof r?pr.lookupPath(r,{follow:!e}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);n.node_ops.setattr(n,{mode:4095&t|-4096&n.mode,timestamp:Date.now()})},lchmod(r,t){pr.chmod(r,t,!0)},fchmod(r,t){var e=pr.getStreamChecked(r);pr.chmod(e.node,t)},chown(r,t,e,n){var o;if(!(o="string"==typeof r?pr.lookupPath(r,{follow:!n}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);o.node_ops.setattr(o,{timestamp:Date.now()})},lchown(r,t,e){pr.chown(r,t,e,!0)},fchown(r,t,e){var n=pr.getStreamChecked(r);pr.chown(n.node,t,e)},truncate(r,t){if(t<0)throw new pr.ErrnoError(28);var e;if(!(e="string"==typeof r?pr.lookupPath(r,{follow:!0}).node:r).node_ops.setattr)throw new pr.ErrnoError(63);if(pr.isDir(e.mode))throw new pr.ErrnoError(31);if(!pr.isFile(e.mode))throw new pr.ErrnoError(28);var n=pr.nodePermissions(e,"w");if(n)throw new pr.ErrnoError(n);e.node_ops.setattr(e,{size:t,timestamp:Date.now()})},ftruncate(r,t){var e=pr.getStreamChecked(r);if(0==(2097155&e.flags))throw new pr.ErrnoError(28);pr.truncate(e.node,t)},utime(r,t,e){var n=pr.lookupPath(r,{follow:!0}).node;n.node_ops.setattr(n,{timestamp:Math.max(t,e)})},open(r,t,e){if(""===r)throw new pr.ErrnoError(44);var n;if(e=void 0===e?438:e,e=64&(t="string"==typeof t?(r=>{var t={r:0,"r+":2,w:577,"w+":578,a:1089,"a+":1090}[r];if(void 0===t)throw new Error(`Unknown file open mode: ${r}`);return t})(t):t)?4095&e|32768:0,"object"==typeof r)n=r;else{r=J.normalize(r);try{n=pr.lookupPath(r,{follow:!(131072&t)}).node}catch(r){}}var a=!1;if(64&t)if(n){if(128&t)throw new pr.ErrnoError(20)}else n=pr.mknod(r,e,0),a=!0;if(!n)throw new pr.ErrnoError(44);if(pr.isChrdev(n.mode)&&(t&=-513),65536&t&&!pr.isDir(n.mode))throw new pr.ErrnoError(54);if(!a){var i=pr.mayOpen(n,t);if(i)throw new pr.ErrnoError(i)}512&t&&!a&&pr.truncate(n,0),t&=-131713;var s=pr.createStream({node:n,path:pr.getPath(n),flags:t,seekable:!0,position:0,stream_ops:n.stream_ops,ungotten:[],error:!1});return s.stream_ops.open&&s.stream_ops.open(s),!o.logReadFiles||1&t||(pr.readFiles||(pr.readFiles={}),r in pr.readFiles||(pr.readFiles[r]=1)),s},close(r){if(pr.isClosed(r))throw new pr.ErrnoError(8);r.getdents&&(r.getdents=null);try{r.stream_ops.close&&r.stream_ops.close(r)}catch(r){throw 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