Hack to fix AF3 mmCIF _citation.title breaking gemmi

steineggerlab · May 9, 2024 · f5b9588 · f5b9588
1 parent 9ef6d18
commit f5b9588
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Showing 2 changed files with 45 additions and 2 deletions.
diff --git a/src/strucclustutils/GemmiWrapper.cpp b/src/strucclustutils/GemmiWrapper.cpp
@@ -10,6 +10,8 @@
 #include "foldcomp.h"
 #include "cif.hpp"
 
+#include <algorithm>
+
 GemmiWrapper::GemmiWrapper(){
     threeAA2oneAA = {{"ALA",'A'},  {"ARG",'R'},  {"ASN",'N'}, {"ASP",'D'},
                      {"CYS",'C'},  {"GLN",'Q'},  {"GLU",'E'}, {"GLY",'G'},
@@ -33,6 +35,7 @@ GemmiWrapper::GemmiWrapper(){
                      {"CSD",'C'}, {"SEC",'C'},
                      // unknown
                      {"UNK",'X'}};
+    fixupBuffer = NULL;
 }
 
 std::unordered_map<std::string, int> getEntityTaxIDMapping(gemmi::cif::Document& doc) {
@@ -99,7 +102,20 @@ bool GemmiWrapper::load(const std::string& filename, Format format) {
         std::unordered_map<std::string, int> entity_to_tax_id;
         switch (format) {
             case Format::Mmcif: {
-                gemmi::cif::Document doc = gemmi::cif::read(infile);
+                gemmi::CharArray mem = read_into_buffer(infile);
+                char* data = mem.data();
+                size_t dataSize = mem.size();
+
+                // hack to fix broken _citation.title in AF3
+                const char* target = "_citation.title";
+                size_t target_len = strlen(target);
+                char* it = std::search(data, data + dataSize, target, target + target_len);
+                if (it != data + dataSize) {
+                    it[0] = '#';
+                    it[1] = ' ';
+                }
+
+                gemmi::cif::Document doc = gemmi::cif::read_memory(mem.data(), mem.size(), infile.path().c_str());
                 entity_to_tax_id = getEntityTaxIDMapping(doc);
                 st = gemmi::make_structure(doc);
                 break;
@@ -161,7 +177,25 @@ bool GemmiWrapper::loadFromBuffer(const char * buffer, size_t bufferSize, const
                 st = gemmi::pdb_impl::read_pdb_from_stream(gemmi::MemoryStream(buffer, bufferSize), name, gemmi::PdbReadOptions());
                 break;
             case Format::Mmcif: {
-                gemmi::cif::Document doc = gemmi::cif::read_memory(buffer, bufferSize, name.c_str());
+                const char* targetBuffer = buffer;
+                // hack to fix broken _citation.title in AF3
+                const char* target = "_citation.title";
+                size_t target_len = strlen(target);
+                const char* it = std::search(targetBuffer, targetBuffer + bufferSize, target, target + target_len);
+                if (it != targetBuffer + bufferSize) {
+                    if (fixupBuffer == NULL) {
+                        fixupBufferSize = bufferSize;
+                        fixupBuffer = (char*)malloc(fixupBufferSize);
+                    } else if (bufferSize > fixupBufferSize) {
+                        fixupBufferSize = bufferSize * 1.5;
+                        fixupBuffer = (char*)realloc(fixupBuffer, fixupBufferSize);
+                    }
+                    memcpy(fixupBuffer, targetBuffer, bufferSize);
+                    *(fixupBuffer + (it - targetBuffer)) = '#';
+                    *(fixupBuffer + (it - targetBuffer) + 1) = ' ';
+                    targetBuffer = fixupBuffer;
+                }
+                gemmi::cif::Document doc = gemmi::cif::read_memory(targetBuffer, bufferSize, name.c_str());
                 entity_to_tax_id = getEntityTaxIDMapping(doc);
                 st = gemmi::make_structure(doc);
                 break;

diff --git a/src/strucclustutils/GemmiWrapper.h b/src/strucclustutils/GemmiWrapper.h
@@ -22,6 +22,11 @@ class GemmiWrapper {
     };
 
     GemmiWrapper();
+    ~GemmiWrapper() {
+        if (fixupBuffer) {
+            delete fixupBuffer;
+        }
+    }
 
     bool loadFromBuffer(const char * buffer, size_t bufferSize, const std::string& name, Format format = Format::Detect);
 
@@ -42,6 +47,10 @@ class GemmiWrapper {
     std::vector<std::pair<size_t ,size_t>> chain;
     std::vector<int> taxIds;
     std::string title;
+
+    char* fixupBuffer;
+    size_t fixupBufferSize;
+
 private:
     std::unordered_map<std::string,char> threeAA2oneAA;
     int modelIt;