moorhen 0.6.8 → 0.7.1

package/README.md

@@ -15,16 +15,11 @@ The sources of CCP4, Coot, Privateer, FFTW, and GSL are not included. They are d
 the `get_sources` script, which is part of the build process of this project.
 
 The following libraries/programs are compiled to Web Assembly:
-* libccp4 (bzr)
-* clipper (bzr)
-* ssm (bzr)
-* mmdb2 (bzr)
-* ccp4srs (bzr)
+* libccp4 (8.0.0)
+* clipper (2.1)
+* ssm (1.4.0)
+* mmdb2 (2.0.22)
 * gemmi 0.5.8
-* rvapi (bzr)
-* gesamt (bzr)
-* ccp4mg (partial) (bzr)
-* privateer MKIV
 * Coot 1.0 ('gtk3' git branch)
 * fftw 2.1.5
 * gsl 2.7.1
@@ -45,7 +40,6 @@ Binaries are available on the releases page. Please read the instructions there
 **Requirements** 
 
 * A Bourne-like shell
-* bzr
 * git
 * curl
 * patch
@@ -79,7 +73,7 @@ This should build all dependencies and then `Moorhen`.
 6. To run the Moorhen molecular graphics application:  
 `cd baby-gru`  
 `npm start`  
-And then point a web browser at `http://localhost:3000/` .  
+And then point a web browser at `http://localhost:5173/` .  
 
 ## **Updating**
 
@@ -96,14 +90,9 @@ And then point a web browser at `http://localhost:3000/` .
 
 ## **What else can do with the compiled libraries?**
 
-See `example/example.cc` or `checkout/privateer-MKIV/src/privateer.cpp` to see how to create a command line (node) program. The
-latter is quite long and a patched version of the original privateer code. It might be more helpful to look at the patch file
-`patches/privateer-emscripten.patch`. This should show how to patch an existing command line program which reads files to one
-that will work within node.
-
 See `coot/moorhen-wrappers.cc` to see use of `EMSCRIPTEN_BINDINGS` to expose Coot methods to the web browser.
 
-Any program you write, which uses the *subset* of Coot, Clipper, Privateer code which this project compiles to WASM, can
+Any program you write, which uses the *subset* of Coot, Clipper, code which this project compiles to WASM, can
 itself be compiled to WASM and used within node or Web Browser. Studying the examples should show you to do I/O, which is
 different in the 2 cases. If you require more classes or methods from the libraries to be exposed to JavaScript, then changes need to be made to
 `coot/moorhen-wrappers.cc`. This should only be necessary for browser usage - in node your whole program can be written in C++.

package/baby-gru/CootWorker.js

@@ -1 +1 @@
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t.delete(),a?{prim_types:[["NORMALLINES"]],useIndices:[[!0]],idx_tri:[[s]],vert_tri:[[o]],additional_norm_tri:[[n]],norm_tri:[[n]],col_tri:[[i]]}:{prim_types:[["LINES"]],useIndices:[[!0]],idx_tri:[[s]],vert_tri:[[o]],norm_tri:[[n]],col_tri:[[i]]}},auto_open_mtz=function(e){var a=guid(),t=new Uint8Array(e);cootModule.FS_createDataFile(".","".concat(a,".mtz"),t,!0,!0);var r="./".concat(a,".mtz"),s=molecules_container.auto_read_mtz(r);return cootModule.FS_unlink(r),s},replace_map_by_mtz_from_file=function(e,a,t){var r=guid(),s="./".concat(r,".mtz"),o=new Uint8Array(a);cootModule.FS_createDataFile(".",s,o,!0,!0);var n=[e,s,t.F,t.PHI,"",!1],i=molecules_container.replace_map_by_mtz_from_file.apply(molecules_container,n);return cootModule.FS_unlink(s),i},new_positions_for_residue_atoms=function(e,a){var t=0,r=new cootModule.Vectormoved_residue_t;return a.forEach((function(e){if(e.length>0){var a=e[0].label.split("/"),t=a[3].split("."),s=t[0],o=t[1];o=o||"";var n=new 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0;switch(a){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"void":c=null;break;default:c=i}return{messageId:s,messageSendTime:Date.now(),command:t,consoleMessage:"Completed 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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),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 t=guid(),r="./".concat(t,".map");molecules_container.writeCCP4Map(e.data.molNo,r);var s=cootModule.FS.readFile(r,{encoding:"binary"});cootModule.FS_unlink(r),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:s.buffer}})}else if("delete_file_name"===e.data.message){var o=cootModule.FS_unlink(e.data.fileName);postMessage({messageId:e.data.messageId,myTimeStamp:e.data.myTimeStamp,messageTag:"result",result:o})}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&&(o=doCootCommand(e.data),postMessage(o))};
+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))};

package/baby-gru/CootWorker.ts

@@ -114,8 +114,6 @@ const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm:
                     0.0, 0.0, 1.0, 0.0,
                     0.0, 0.0, 0.0, 1.0,
                 ])
-
-                inst_data.delete()
             }
         }
         As.delete()
@@ -164,8 +162,6 @@ const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm:
                 thisInstance_orientations.push(instDataOrientation[3][1])
                 thisInstance_orientations.push(instDataOrientation[3][2])
                 thisInstance_orientations.push(instDataOrientation[3][3])
-
-                inst_data.delete()
             }
         }
         Bs.delete()
@@ -230,38 +226,47 @@ const instancedMeshToMeshData = (instanceMesh: libcootApi.InstancedMeshT, perm:
 }
 
 const simpleMeshToMeshData = (simpleMesh: libcootApi.SimpleMeshT, perm: boolean = false): libcootApi.SimpleMeshJS => {
+
+    const print_timing = true;
+    const ts = performance.now()
+
     const vertices = simpleMesh.vertices;
     const triangles = simpleMesh.triangles;
-    let totIdxs: number[] = [];
-    let totPos: number[] = [];
-    let totNorm: number[] = [];
-    let totCol: number[] = [];
-
+    
+    const verticesSize = vertices.size();
     const trianglesSize = triangles.size()
-    for (let i = 0; i < trianglesSize; i++) {
-        const triangle = triangles.get(i)
-        const idxs = triangle.point_id;
-        if (perm)
-            totIdxs.push(...[idxs[0], idxs[2], idxs[1]]);
-        else
-            totIdxs.push(...idxs);
+
+    let totIdxs_C = new Uint32Array(trianglesSize*3)
+    let totPos_C  = new Float32Array(verticesSize*3)
+    let totNorm_C = new Float32Array(verticesSize*3)
+    let totCol_C  = new Float32Array(verticesSize*4)
+
+    cootModule.getPositionsFromSimpleMesh2(simpleMesh,totPos_C)
+    cootModule.getColoursFromSimpleMesh2(simpleMesh,totCol_C)
+
+    if (perm){
+        cootModule.getReversedNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        cootModule.getPermutedTriangleIndicesFromSimpleMesh2(simpleMesh,totIdxs_C)
+    } else {
+        cootModule.getNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+        cootModule.getTriangleIndicesFromSimpleMesh2(simpleMesh,totIdxs_C)
     }
-    triangles.delete()
 
-    const verticesSize = vertices.size()
-    for (let i = 0; i < verticesSize; i++) {
-        const vert = vertices.get(i);
-        const vertPos = vert.pos
-        const vertNormal = vert.normal
-        const vertColor = vert.color
-        totPos.push(...vertPos);
-        if (perm)
-            totNorm.push(...[-vertNormal[0], -vertNormal[1], -vertNormal[2]]);
-        else
-            totNorm.push(...vertNormal);
-        totCol.push(...vertColor);
+    const tm = performance.now()
+    if(print_timing) console.log("DEBUG: SIMPLE MESH TO MESH DATA C++",tm-ts)
+
+    let totPos =  totPos_C
+    let totCol =  totCol_C
+    let totNorm =  totNorm_C
+    let totIdxs =  totIdxs_C
+
+    if(print_timing) {
+        const te = performance.now()
+        console.log("DEBUG: SIMPLE MESH TO MESH DATA",te-ts)
     }
-    vertices.delete()
+
+    vertices.delete();
+    triangles.delete();
 
     return {
         prim_types: [["TRIANGLES"]],
@@ -373,6 +378,19 @@ const mapMoleculeCentreInfoToJSObject = (mapMoleculeCentreInfo: libcootApi.MapMo
     return returnResult;
 }
 
+const fitLigandInfoArrayToJSArray = (fitLigandInfoVec: emscriptem.vector<libcootApi.fitLigandInfo>): libcootApi.fitLigandInfo[] => {
+    const result: libcootApi.fitLigandInfo[] = []
+
+    const fitLigandInfoVecSize = fitLigandInfoVec.size()
+    for (let i = 0; i < fitLigandInfoVecSize; i++) {
+        const fitLigandInfo = fitLigandInfoVec.get(i)
+        result.push({ ...fitLigandInfo })
+    }
+
+    fitLigandInfoVec.delete()
+    return result
+}
+
 const intArrayToJSArray = (intArray: emscriptem.vector<number>) => {
     let returnResult: number[] = []
     const intArraySize = intArray.size()
@@ -486,7 +504,7 @@ const atomSpecToJSArray = (atomSpecs: emscriptem.vector<libcootApi.AtomSpecT>):
 }
 
 const residueSpecToJSArray = (residueSpecs: emscriptem.vector<libcootApi.ResidueSpecT>): libcootApi.ResidueSpecJS[] => {
-    let returnResult: { resNum: number; insCode: string; modelNumber: number; chainId: string; }[] = []
+    let returnResult: { resNum: number; insCode: string; modelNumber: number; chainId: string; intUserData: number; }[] = []
     const residuesSize = residueSpecs.size()
     for (let ic = 0; ic < residuesSize; ic++) {
         const residue = residueSpecs.get(ic)
@@ -494,13 +512,25 @@ const residueSpecToJSArray = (residueSpecs: emscriptem.vector<libcootApi.Residue
             resNum: residue.res_no,
             insCode: residue.ins_code,
             modelNumber: residue.model_number,
-            chainId: residue.chain_id
+            chainId: residue.chain_id,
+            intUserData: residue.int_user_data
         })
     }
     residueSpecs.delete()
     return returnResult
 }
 
+const stringPairVectorToJSArray = (stringPairsVector: emscriptem.vector<libcootApi.PairType<string, string>>) => {
+    let result: { first: string; second: string }[] = []
+    const stringPairsVectorSize = stringPairsVector.size()
+    for (let ic = 0; ic < stringPairsVectorSize; ic++) {
+        const data = stringPairsVector.get(ic)
+        result.push({first: data.first, second: data.second})
+    }
+    stringPairsVector.delete()
+    return result
+}
+
 const validationDataToJSArray = (validationData: libcootApi.ValidationInformationT, chainID: string | null = null): libcootApi.ValidationInformationJS[] => {
     let returnResult: { chainId: string; insCode: string; seqNum: number; restype: string; value: number; }[] = []
     const cviv = validationData.cviv
@@ -589,6 +619,7 @@ const vectorHBondToJSArray = (HBondData: emscriptem.vector<libcootApi.MoorhenHBo
 
 const interestingPlaceDataToJSArray = (interestingPlaceData: emscriptem.vector<libcootApi.InterestingPlaceT>): libcootApi.InterestingPlaceDataJS[] => {
     let returnResult: { 
+        intUserData: number;
         modelNumber: number;
         chainId: string;
         insCode: string;
@@ -607,6 +638,7 @@ const interestingPlaceDataToJSArray = (interestingPlaceData: emscriptem.vector<l
         const residue = interestingPlaceData.get(ir)
         const residueSpec = residue.residue_spec
         returnResult.push({
+            intUserData: residueSpec.int_user_data,
             modelNumber: residueSpec.model_number,
             chainId: residueSpec.chain_id,
             insCode: residueSpec.ins_code,
@@ -690,30 +722,59 @@ const ramachandranDataToJSArray = (ramachandraData: emscriptem.vector<libcootApi
     return returnResult
 }
 
+const vectorPairClipperCoordFloatToJSArray = (vectorData: emscriptem.vector<{first: libcootApi.CootCartesian; second: number}>): libcootApi.DiffDiffMapPeaksJS => {
+    let result: {value: number; coord: { x: number; y: number; z: number }}[] = []
+    const vectorSize = vectorData.size()
+    for(let i = 0; i < vectorSize; i++) {
+        const pair = vectorData.get(i)
+        const value = pair.second
+        const clipperCoord = pair.first
+        const coord = {
+            x: clipperCoord.x(),
+            y: clipperCoord.y(),
+            z: clipperCoord.z(),
+        }
+        clipperCoord.delete()
+        result.push({value, coord})
+    }
+    vectorData.delete()
+    return result
+}
+
 const simpleMeshToLineMeshData = (simpleMesh: libcootApi.SimpleMeshT, normalLighting: boolean): libcootApi.SimpleMeshJS => {
+
+    const print_timing = false;
+    const ts = performance.now()
+
     const vertices = simpleMesh.vertices;
     const triangles = simpleMesh.triangles;
-    let totIdxs: number[] = [];
-    let totPos: number[] = [];
-    let totNorm: number[] = [];
-    let totCol: number[] = [];
-
     const trianglesSize = triangles.size()
-    for (let i = 0; i < trianglesSize; i++) {
-        const triangle = triangles.get(i)
-        const idxs = triangle.point_id;
-        totIdxs.push(...[idxs[0], idxs[1], idxs[0], idxs[2], idxs[1], idxs[2]]);
-    }
-    triangles.delete()
-
     const verticesSize = vertices.size()
-    for (let i = 0; i < verticesSize; i++) {
-        const vert = vertices.get(i);
-        totPos.push(...vert.pos);
-        totNorm.push(...vert.normal);
-        totCol.push(...vert.color);
+
+    let totIdxs_C = new Uint32Array(trianglesSize*6)
+    let totPos_C  = new Float32Array(verticesSize*3)
+    let totNorm_C = new Float32Array(verticesSize*3)
+    let totCol_C  = new Float32Array(verticesSize*4)
+    cootModule.getLineIndicesFromSimpleMesh2(simpleMesh,totIdxs_C)
+    cootModule.getPositionsFromSimpleMesh2(simpleMesh,totPos_C)
+    cootModule.getNormalsFromSimpleMesh2(simpleMesh,totNorm_C)
+    cootModule.getColoursFromSimpleMesh2(simpleMesh,totCol_C)
+
+    const tm = performance.now()
+    if(print_timing) console.log("DEBUG: SIMPLE MESH TO LINE MESH DATA C++",tm-ts)
+
+    let totIdxs = totIdxs_C
+    let totPos  = totPos_C
+    let totNorm = totNorm_C
+    let totCol  = totCol_C
+
+    if(print_timing) {
+        const te = performance.now()
+        console.log("SIMPLE MESH TO LINE MESH DATA",te-ts)
     }
-    vertices.delete()
+
+    vertices.delete();
+    triangles.delete();
 
     if (normalLighting)
         return { prim_types: [["NORMALLINES"]], useIndices: [[true]], idx_tri: [[totIdxs]], vert_tri: [[totPos]], additional_norm_tri: [[totNorm]], norm_tri: [[totNorm]], col_tri: [[totCol]] };
@@ -866,6 +927,9 @@ const doCootCommand = (messageData: {
 
         let returnResult;
         switch (returnType) {
+            case 'fit_ligand_info_array':
+                returnResult = fitLigandInfoArrayToJSArray(cootResult)
+                break;
             case 'string_array_array':
                 returnResult = stringArrayArrayToJSArray(cootResult)
                 break;
@@ -944,13 +1008,20 @@ const doCootCommand = (messageData: {
             case 'status_instanced_mesh_pair':
                 returnResult = { status: cootResult.first, mesh: instancedMeshToMeshData(cootResult.second, false, false, 5) }
                 break;
+            case 'string_string_pair_vector':
+                returnResult = stringPairVectorToJSArray(cootResult)
+                break
             case 'void':
                 returnResult = null
                 break
+            case 'vector_pair_clipper_coord_float':
+                returnResult = vectorPairClipperCoordFloatToJSArray(cootResult)
+                break
             case 'status':
             default:
                 returnResult = cootResult
                 break;
+            //cootResult.delete()
         }
 
         return {
@@ -986,7 +1057,9 @@ onmessage = function (e) {
                 molecules_container.set_show_timings(false)
                 molecules_container.fill_rotamer_probability_tables()
                 molecules_container.set_map_sampling_rate(1.7)
-                cootModule.FS.mkdir("COOT_BACKUP");
+                molecules_container.set_map_is_contoured_with_thread_pool(true)
+                molecules_container.set_max_number_of_threads(3)
+                cootModule.FS.mkdir("COOT_BACKUP")
             })
             .catch((e) => {
                 console.log(e)

package/baby-gru/moorhen.css

@@ -64,6 +64,59 @@ div.darkly text.base {fill:#000!important;}
 div.darkly text.start-label {fill:#FFF !important;}
 div.darkly text.end-label {fill:#FFF !important;}
 
+.moorhen-hex-input-decorator {
+  display: flex;
+  align-items: "center";
+  justify-content: "center";
+  float: left;
+  border: 1px solid #ddd;
+  border-radius: 4px 0px 0px 4px;
+  background: #eee;
+  color: #98a1a4;
+  outline: none;
+  margin: 0.1rem 0 0;
+  padding: 0.1rem;
+  vertical-align: baseline;
+  text-align: center
+}
+
+.moorhen-hex-input {
+  display: block;
+  box-sizing: border-box;
+  width: 90px;
+  margin: 0.1rem 0 0;
+  padding: 0.1rem;
+  border: 1px solid #ddd;
+  border-radius: 0px 4px 4px 0px;
+  background: #f0f0f0;
+  outline: none;
+  font: inherit;
+  text-transform: uppercase;
+  text-align: center;
+  color: #000;
+}
+
+.scene-settings-panel, .scene-settings-panel-flex-between, .scene-settings-panel-flex-center {
+  width: 100%;
+  height: 100%;
+  padding: 0.5rem;
+  border-style: solid;
+  border-radius: 0.5rem;
+  border-color: #ced4da;
+  border-width: 1px;
+}
+
+.scene-settings-panel-flex-between {
+  justify-content: space-between;
+  display: flex;
+  flex-direction: column;
+}
+
+.scene-settings-panel-flex-center {
+  justify-content: center;
+  display: flex;
+}
+
 .tab-content{
   height: calc(100% - 3rem);
 }
@@ -72,11 +125,18 @@ div.darkly text.end-label {fill:#FFF !important;}
   height: 3rem;
 }
 
+.rama-validation-tool-container-row {
+  width: 100%;
+  margin: 0;
+  padding: 0;
+  height: 100%;
+}
+
 .big-validation-tool-container-row {
   width: 100%;
   margin: 0;
   padding: 0;
-  height: calc(100% - 10rem);
+  height: calc(100% - 6rem);
 }
 
 .small-validation-tool-container-row {
@@ -177,6 +237,10 @@ div.darkly text.end-label {fill:#FFF !important;}
 }
 
 .moorhen-draggable-card {
+  box-shadow: 0px 2px 2px -1px rgba(0,0,0,0.2),0px 3px 5px 0px rgba(0,0,0,0.14),0px 1px 9px 0px rgba(0,0,0,0.12);
+}
+
+.moorhen-draggable-card-focused {
   box-shadow: 0px 3px 5px -1px rgba(0,0,0,0.2),0px 6px 10px 0px rgba(0,0,0,0.14),0px 1px 18px 0px rgba(0,0,0,0.12);
 }