moorhen 0.8.3 → 0.8.5

package/README.md

@@ -67,15 +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:  
-`./initial_build.sh --64bit`  
+`./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/)
+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 @@
-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),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);var r=(performance.now(),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 Float32Array(4*o);cootModule.getPositionsFromSimpleMesh2(e,i),cootModule.getColoursFromSimpleMesh2(e,l),a?(cootModule.getReversedNormalsFromSimpleMesh2(e,c),cootModule.getPermutedTriangleIndicesFromSimpleMesh2(e,n)):(cootModule.getNormalsFromSimpleMesh2(e,c),cootModule.getTriangleIndicesFromSimpleMesh2(e,n)),performance.now();var _=i,u=l,d=c,m=n;return r.delete(),t.delete(),{prim_types:[["TRIANGLES"]],idx_tri:[[m]],vert_tri:[[_]],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,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 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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){var r=(performance.now(),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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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 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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[] = []
 
@@ -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/monomers/p/PRO.cif

@@ -7,36 +7,34 @@ _chem_comp.group
 _chem_comp.number_atoms_all
 _chem_comp.number_atoms_nh
 _chem_comp.desc_level
-PRO PRO PROLINE P-peptide 17 8 .
+PRO PRO PROLINE P-peptide 16 8 .
 
 data_comp_PRO
 loop_
 _chem_comp_atom.comp_id
 _chem_comp_atom.atom_id
-_chem_comp_atom.alt_atom_id
 _chem_comp_atom.type_symbol
 _chem_comp_atom.type_energy
 _chem_comp_atom.charge
 _chem_comp_atom.x
 _chem_comp_atom.y
 _chem_comp_atom.z
-PRO N   N   N NT2 1  39.160 37.649 83.026
-PRO CA  CA  C CH1 0  38.550 38.680 82.125
-PRO C   C   C C   0  37.155 39.077 82.602
-PRO O   O   O O   0  36.450 38.196 83.146
-PRO CB  CB  C CH2 0  38.553 38.007 80.756
-PRO CG  CG  C CH2 0  38.265 36.558 81.098
-PRO CD  CD  C CH2 0  38.934 36.298 82.416
-PRO OXT OXT O OC  -1 36.821 40.268 82.409
-PRO H   H   H H   0  40.054 37.806 83.097
-PRO H2  H2  H H   0  38.800 37.681 83.862
-PRO HA  HA  H H   0  39.125 39.473 82.102
-PRO HB3 HB3 H H   0  39.422 38.100 80.320
-PRO HB2 HB2 H H   0  37.858 38.378 80.178
-PRO HG3 HG3 H H   0  38.625 35.964 80.410
-PRO HG2 HG2 H H   0  37.302 36.406 81.169
-PRO HD3 HD3 H H   0  38.363 35.755 82.994
-PRO HD2 HD2 H H   0  39.785 35.835 82.289
+PRO N N NR15 0 39.037 37.549 83.040
+PRO CA C CH1 0 38.574 38.605 82.148
+PRO C C C 0 37.249 39.192 82.624
+PRO O O O 0 36.298 38.401 82.791
+PRO CB C CH2 0 38.459 37.920 80.773
+PRO CG C CH2 0 38.237 36.468 81.113
+PRO CD C CH2 0 39.066 36.257 82.367
+PRO OXT O OC -1 37.210 40.425 82.814
+PRO H H H 0 39.264 37.676 83.860
+PRO HA H H 0 39.261 39.316 82.107
+PRO HB3 H H 0 39.287 38.037 80.252
+PRO HB2 H H 0 37.701 38.283 80.256
+PRO HG3 H H 0 38.544 35.886 80.387
+PRO HG2 H H 0 37.289 36.288 81.286
+PRO HD3 H H 0 38.673 35.556 82.933
+PRO HD2 H H 0 39.987 36.001 82.137
 
 loop_
 _chem_comp_tree.comp_id
@@ -44,40 +42,38 @@ _chem_comp_tree.atom_id
 _chem_comp_tree.atom_back
 _chem_comp_tree.atom_forward
 _chem_comp_tree.connect_type
-PRO N   n/a CA  START
-PRO CA  N   C   .
-PRO HA  CA  .   .
-PRO CB  CA  CG  .
-PRO HB3 CB  .   .
-PRO HB2 CB  .   .
-PRO CG  CB  CD  .
-PRO HG3 CG  .   .
-PRO HG2 CG  .   .
-PRO CD  CG  HD2 .
-PRO HD3 CD  .   .
-PRO HD2 CD  .   .
-PRO C   CA  .   END
-PRO O   C   .   .
-PRO OXT C   .   .
-PRO H   N   .   .
-PRO H2  N   .   .
-PRO CD  N   .   ADD
+PRO N n/a CA START
+PRO CA N C .
+PRO HA CA . .
+PRO CB CA CG .
+PRO HB3 CB . .
+PRO HB2 CB . .
+PRO CG CB CD .
+PRO HG3 CG . .
+PRO HG2 CG . .
+PRO CD CG HD2 .
+PRO HD3 CD . .
+PRO HD2 CD . .
+PRO C CA . END
+PRO O C . .
+PRO OXT C . .
+PRO H N . .
+PRO CD N . ADD
 
 loop_
 _chem_comp_acedrg.comp_id
 _chem_comp_acedrg.atom_id
 _chem_comp_acedrg.atom_type
-PRO N   N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>}
-PRO CA  C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>}
-PRO C   C(C[5]C[5]N[5]H)(O)2
-PRO O   O(CC[5]O)
-PRO CB  C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>}
-PRO CG  C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>}
-PRO CD  C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>}
+PRO N N[5](C[5]C[5]CH)(C[5]C[5]HH)(H){4|H<1>}
+PRO CA C[5](C[5]C[5]HH)(N[5]C[5]H)(COO)(H){4|H<1>}
+PRO C C(C[5]C[5]N[5]H)(O)2
+PRO O O(CC[5]O)
+PRO CB C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{3|H<1>}
+PRO CG C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,2|H<1>}
+PRO CD C[5](C[5]C[5]HH)(N[5]C[5]H)(H)2{1|C<3>,3|H<1>}
 PRO OXT O(CC[5]O)
-PRO H   H(N[5]C[5]2H)
-PRO H2  H(N[5]C[5]2H)
-PRO HA  H(C[5]C[5]N[5]C)
+PRO H H(N[5]C[5]2)
+PRO HA H(C[5]C[5]N[5]C)
 PRO HB3 H(C[5]C[5]2H)
 PRO HB2 H(C[5]C[5]2H)
 PRO HG3 H(C[5]C[5]2H)
@@ -89,29 +85,28 @@ loop_
 _chem_comp_bond.comp_id
 _chem_comp_bond.atom_id_1
 _chem_comp_bond.atom_id_2
-_chem_comp_bond.value_order
-_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
 _chem_comp_bond.value_dist_nucleus
 _chem_comp_bond.value_dist_nucleus_esd
 _chem_comp_bond.value_dist
 _chem_comp_bond.value_dist_esd
-PRO N  CA  SINGLE n 1.496 0.0142 1.496 0.0142
-PRO N  CD  SINGLE n 1.499 0.0135 1.499 0.0135
-PRO CA C   SINGLE n 1.525 0.0103 1.525 0.0103
-PRO CA CB  SINGLE n 1.526 0.0157 1.526 0.0157
-PRO C  O   DOUBLE n 1.252 0.0117 1.252 0.0117
-PRO C  OXT SINGLE n 1.252 0.0117 1.252 0.0117
-PRO CB CG  SINGLE n 1.516 0.0179 1.516 0.0179
-PRO CG CD  SINGLE n 1.497 0.0200 1.497 0.0200
-PRO N  H   SINGLE n 1.018 0.0520 0.910 0.0200
-PRO N  H2  SINGLE n 1.018 0.0520 0.910 0.0200
-PRO CA HA  SINGLE n 1.092 0.0100 0.980 0.0200
-PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145
-PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145
-PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181
-PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181
-PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199
-PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199
+PRO N CA SINGLE n 1.457 0.0100 1.457 0.0100
+PRO N CD SINGLE n 1.458 0.0200 1.458 0.0200
+PRO CA C SINGLE n 1.524 0.0159 1.524 0.0159
+PRO CA CB SINGLE n 1.534 0.0192 1.534 0.0192
+PRO C O DOUBLE n 1.248 0.0171 1.248 0.0171
+PRO C OXT SINGLE n 1.248 0.0171 1.248 0.0171
+PRO CB CG SINGLE n 1.509 0.0200 1.509 0.0200
+PRO CG CD SINGLE n 1.521 0.0187 1.521 0.0187
+PRO N H SINGLE n 1.018 0.0520 0.860 0.0100
+PRO CA HA SINGLE n 1.092 0.0100 0.990 0.0200
+PRO CB HB3 SINGLE n 1.092 0.0100 0.986 0.0200
+PRO CB HB2 SINGLE n 1.092 0.0100 0.986 0.0200
+PRO CG HG3 SINGLE n 1.092 0.0100 0.980 0.0127
+PRO CG HG2 SINGLE n 1.092 0.0100 0.980 0.0127
+PRO CD HD3 SINGLE n 1.092 0.0100 0.983 0.0176
+PRO CD HD2 SINGLE n 1.092 0.0100 0.983 0.0176
 
 loop_
 _chem_comp_angle.comp_id
@@ -120,39 +115,36 @@ _chem_comp_angle.atom_id_2
 _chem_comp_angle.atom_id_3
 _chem_comp_angle.value_angle
 _chem_comp_angle.value_angle_esd
-PRO CA  N  CD  107.978 1.50
-PRO CA  N  H   109.889 3.00
-PRO CA  N  H2  109.889 3.00
-PRO CD  N  H   110.257 3.00
-PRO CD  N  H2  110.257 3.00
-PRO H   N  H2  108.772 3.00
-PRO N   CA C   110.397 1.50
-PRO N   CA CB  103.994 1.50
-PRO N   CA HA  109.579 1.50
-PRO C   CA CB  113.159 3.00
-PRO C   CA HA  109.687 1.50
-PRO CB  CA HA  109.910 1.89
-PRO CA  C  O   116.979 3.00
-PRO CA  C  OXT 116.979 3.00
-PRO O   C  OXT 126.043 1.52
-PRO CA  CB CG  101.701 3.00
-PRO CA  CB HB3 110.865 1.50
-PRO CA  CB HB2 110.865 1.50
-PRO CG  CB HB3 110.891 1.59
-PRO CG  CB HB2 110.891 1.59
+PRO CA N CD 110.881 3.00
+PRO CA N H 124.203 1.50
+PRO CD N H 124.916 3.00
+PRO N CA C 111.610 3.00
+PRO N CA CB 102.532 3.00
+PRO N CA HA 109.054 1.85
+PRO C CA CB 112.350 1.50
+PRO C CA HA 109.862 1.50
+PRO CB CA HA 109.576 1.50
+PRO CA C O 117.170 3.00
+PRO CA C OXT 117.170 3.00
+PRO O C OXT 125.661 1.52
+PRO CA CB CG 103.478 1.50
+PRO CA CB HB3 110.876 1.50
+PRO CA CB HB2 110.876 1.50
+PRO CG CB HB3 110.891 1.59
+PRO CG CB HB2 110.891 1.59
 PRO HB3 CB HB2 108.880 2.25
-PRO CB  CG CD  105.541 3.00
-PRO CB  CG HG3 110.897 1.50
-PRO CB  CG HG2 110.897 1.50
-PRO CD  CG HG3 110.621 1.50
-PRO CD  CG HG2 110.621 1.50
+PRO CB CG CD 104.486 3.00
+PRO CB CG HG3 110.897 1.50
+PRO CB CG HG2 110.897 1.50
+PRO CD CG HG3 110.795 1.50
+PRO CD CG HG2 110.795 1.50
 PRO HG3 CG HG2 108.871 1.50
-PRO N   CD CG  104.386 2.30
-PRO N   CD HD3 110.569 1.50
-PRO N   CD HD2 110.569 1.50
-PRO CG  CD HD3 111.131 1.62
-PRO CG  CD HD2 111.131 1.62
-PRO HD3 CD HD2 109.116 1.50
+PRO N CD CG 104.878 3.00
+PRO N CD HD3 110.854 1.50
+PRO N CD HD2 110.854 1.50
+PRO CG CD HD3 110.755 1.50
+PRO CG CD HD2 110.755 1.50
+PRO HD3 CD HD2 108.734 1.82
 
 loop_
 _chem_comp_tor.comp_id
@@ -164,12 +156,12 @@ _chem_comp_tor.atom_id_4
 _chem_comp_tor.value_angle
 _chem_comp_tor.value_angle_esd
 _chem_comp_tor.period
-PRO chi1       N  CA CB CG -60.000 10.0 3
-PRO chi2       CA CB CG CD 180.000 10.0 3
-PRO sp3_sp3_1  CB CA N  CD 60.000  10.0 3
-PRO sp3_sp3_28 N  CD CG CB -60.000 10.0 3
-PRO sp3_sp3_37 CG CD N  CA 180.000 10.0 3
-PRO sp2_sp3_1  O  C  CA N  0.000   10.0 6
+PRO chi1 N CA CB CG -60.000 10.0 3
+PRO chi2 CA CB CG CD 180.000 10.0 3
+PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3
+PRO sp3_sp3_25 N CD CG CB -60.000 10.0 3
+PRO sp3_sp3_34 CG CD N CA 180.000 10.0 3
+PRO sp2_sp3_1 O C CA N 0.000 10.0 6
 
 loop_
 _chem_comp_chir.comp_id
@@ -180,16 +172,21 @@ _chem_comp_chir.atom_id_2
 _chem_comp_chir.atom_id_3
 _chem_comp_chir.volume_sign
 PRO chir_1 CA N C CB positive
+PRO chir_2 N CA CD H both
 
 loop_
 _chem_comp_plane_atom.comp_id
 _chem_comp_plane_atom.plane_id
 _chem_comp_plane_atom.atom_id
 _chem_comp_plane_atom.dist_esd
-PRO plan-1 C   0.020
-PRO plan-1 CA  0.020
-PRO plan-1 O   0.020
-PRO plan-1 OXT 0.020
+PRO plan-1 CA 0.020
+PRO plan-1 CD 0.020
+PRO plan-1 H 0.020
+PRO plan-1 N 0.020
+PRO plan-2 C 0.020
+PRO plan-2 CA 0.020
+PRO plan-2 O 0.020
+PRO plan-2 OXT 0.020
 
 loop_
 _pdbx_chem_comp_descriptor.comp_id
@@ -197,20 +194,20 @@ _pdbx_chem_comp_descriptor.type
 _pdbx_chem_comp_descriptor.program
 _pdbx_chem_comp_descriptor.program_version
 _pdbx_chem_comp_descriptor.descriptor
-PRO SMILES           ACDLabs              10.04 "O=C(O)C1NCCC1"
-PRO SMILES_CANONICAL CACTVS               3.341 "OC(=O)[C@@H]1CCCN1"
-PRO SMILES           CACTVS               3.341 "OC(=O)[CH]1CCCN1"
-PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O"
-PRO SMILES           "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O"
-PRO InChI            InChI                1.03  "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"
-PRO InChIKey         InChI                1.03  ONIBWKKTOPOVIA-BYPYZUCNSA-N
+PRO SMILES ACDLabs 10.04 O=C(O)C1NCCC1
+PRO SMILES_CANONICAL CACTVS 3.341 OC(=O)[C@@H]1CCCN1
+PRO SMILES CACTVS 3.341 OC(=O)[CH]1CCCN1
+PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@H](NC1)C(=O)O
+PRO SMILES "OpenEye OEToolkits" 1.5.0 C1CC(NC1)C(=O)O
+PRO InChI InChI 1.03 InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
+PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-N
 
 loop_
 _pdbx_chem_comp_description_generator.comp_id
 _pdbx_chem_comp_description_generator.program_name
 _pdbx_chem_comp_description_generator.program_version
 _pdbx_chem_comp_description_generator.descriptor
-PRO acedrg          281       "dictionary generator"
-PRO acedrg_database 12        "data source"
-PRO rdkit           2019.09.1 "Chemoinformatics tool"
-PRO refmac5         5.8.0419  "optimization tool"
+PRO acedrg 278 "dictionary generator"
+PRO acedrg_database 12 "data source"
+PRO rdkit 2019.09.1 "Chemoinformatics tool"
+PRO refmac5 5.8.0419 "optimization tool"

package/baby-gru/monomers/t/TYR.cif

@@ -19,30 +19,30 @@ _chem_comp_atom.charge
 _chem_comp_atom.x
 _chem_comp_atom.y
 _chem_comp_atom.z
-TYR N N NT3 1 5.311 5.160 15.589
-TYR CA C CH1 0 5.358 6.374 16.456
-TYR C C C 0 4.823 7.578 15.662
-TYR O O O 0 3.988 8.305 16.245
-TYR CB C CH2 0 6.763 6.679 16.994
-TYR CG C CR6 0 7.348 5.630 17.938
-TYR CD1 C CR16 0 7.096 5.672 19.314
-TYR CD2 C CR16 0 8.161 4.597 17.458
-TYR CE1 C CR16 0 7.628 4.720 20.176
-TYR CE2 C CR16 0 8.697 3.641 18.313
-TYR CZ C CR6 0 8.431 3.702 19.674
-TYR OH O OH1 0 8.982 2.738 20.476
-TYR OXT O OC -1 5.248 7.759 14.496
-TYR H H H 0 5.552 4.421 16.046
-TYR H2 H H 0 5.856 5.257 14.876
-TYR H3 H H 0 4.470 5.038 15.288
-TYR HA H H 0 4.756 6.220 17.232
-TYR HB3 H H 0 6.733 7.543 17.464
-TYR HB2 H H 0 7.369 6.788 16.227
-TYR HD1 H H 0 6.552 6.358 19.667
-TYR HD2 H H 0 8.350 4.543 16.534
-TYR HE1 H H 0 7.444 4.765 21.099
-TYR HE2 H H 0 9.240 2.953 17.971
-TYR HH H H 0 8.782 2.828 21.308
+TYR N N NT3 1 5.363 5.148 15.619
+TYR CA C CH1 0 5.352 6.374 16.467
+TYR C C C 0 4.808 7.551 15.649
+TYR O O O 0 4.011 8.328 16.222
+TYR CB C CH2 0 6.754 6.687 17.001
+TYR CG C CR6 0 7.337 5.635 17.936
+TYR CD1 C CR16 0 7.089 5.671 19.307
+TYR CD2 C CR16 0 8.139 4.603 17.449
+TYR CE1 C CR16 0 7.618 4.714 20.164
+TYR CE2 C CR16 0 8.674 3.642 18.296
+TYR CZ C CR6 0 8.413 3.697 19.657
+TYR OH O OH1 0 8.936 2.754 20.494
+TYR OXT O OC -1 5.198 7.654 14.465
+TYR H H H 0 6.035 5.195 15.019
+TYR H2 H H 0 4.582 5.061 15.177
+TYR H3 H H 0 5.479 4.415 16.133
+TYR HA H H 0 4.747 6.216 17.240
+TYR HB3 H H 0 6.719 7.546 17.478
+TYR HB2 H H 0 7.360 6.798 16.235
+TYR HD1 H H 0 6.549 6.359 19.662
+TYR HD2 H H 0 8.323 4.557 16.524
+TYR HE1 H H 0 7.439 4.755 21.088
+TYR HE2 H H 0 9.213 2.952 17.948
+TYR HH H H 0 9.793 2.799 20.487
 
 loop_
 _chem_comp_tree.comp_id
@@ -205,7 +205,7 @@ TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
 TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
 TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
 TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
-TYR hh1 CE1 CZ OH HH 0.000 5.0 2
+TYR hh1 CE1 CZ OH HH 90.000 5.0 2
 TYR sp3_sp3_1 C CA N H 180.000 10.0 3
 TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1
 TYR sp2_sp3_1 O C CA N 0.000 10.0 6
@@ -265,4 +265,3 @@ TYR acedrg 278 "dictionary generator"
 TYR acedrg_database 12 "data source"
 TYR rdkit 2019.09.1 "Chemoinformatics tool"
 TYR refmac5 5.8.0419 "optimization tool"
-TYR servalcat 0.4.57 'optimization tool'