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Commit 5eaf2069 authored by Bienchen's avatar Bienchen
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Start counting entities at 1 in the mmCIF writer

parent 053de38b
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......@@ -864,7 +864,7 @@ namespace {
const std::vector<ost::io::MMCifWriterEntity>& entity_info) {
std::vector<ost::io::StarWriterValue> ent_data(2);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
ent_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
ent_data[0] = ost::io::StarWriterValue::FromInt(entity_idx+1);
ent_data[1] = ost::io::StarWriterValue::FromString(entity_info[entity_idx].type);
entity_ptr->AddData(ent_data);
}
......@@ -876,7 +876,7 @@ namespace {
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
for(auto asym_id : entity_info[entity_idx].asym_ids) {
asym_data[0] = ost::io::StarWriterValue::FromString(asym_id);
asym_data[1] = ost::io::StarWriterValue::FromInt(entity_idx);
asym_data[1] = ost::io::StarWriterValue::FromInt(entity_idx+1);
struct_asym_ptr->AddData(asym_data);
}
}
......@@ -889,7 +889,7 @@ namespace {
if(entity_info[entity_idx].is_poly) {
const std::vector<String>& mon_ids = entity_info[entity_idx].mon_ids;
for(size_t mon_idx = 0; mon_idx < mon_ids.size(); ++mon_idx) {
entity_poly_seq_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
entity_poly_seq_data[0] = ost::io::StarWriterValue::FromInt(entity_idx+1);
entity_poly_seq_data[1] = ost::io::StarWriterValue::FromString(mon_ids[mon_idx]);
entity_poly_seq_data[2] = ost::io::StarWriterValue::FromInt(mon_idx+1);
entity_poly_seq_ptr->AddData(entity_poly_seq_data);
......@@ -903,7 +903,7 @@ namespace {
std::vector<ost::io::StarWriterValue> entity_poly_data(4);
for(size_t entity_idx = 0; entity_idx < entity_info.size(); ++entity_idx) {
if(entity_info[entity_idx].is_poly) {
entity_poly_data[0] = ost::io::StarWriterValue::FromInt(entity_idx);
entity_poly_data[0] = ost::io::StarWriterValue::FromInt(entity_idx+1);
entity_poly_data[1] = ost::io::StarWriterValue::FromString(entity_info[entity_idx].poly_type);
std::stringstream seq;
std::stringstream seq_can;
......@@ -956,7 +956,7 @@ namespace {
std::vector<ost::io::StarWriterValue> branch_data(2);
for(size_t i = 0; i < entity_infos.size(); ++i) {
if(entity_infos[i].type == "branched") {
branch_data[0] = ost::io::StarWriterValue::FromInt(i);
branch_data[0] = ost::io::StarWriterValue::FromInt(i+1);
branch_data[1] = ost::io::StarWriterValue::FromString(entity_infos[i].branch_type);
pdbx_entity_branch_ptr->AddData(branch_data);
}
......@@ -1066,7 +1066,7 @@ namespace {
tmp,
false,
entity_info);
Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
tmp);
} else {
// this should not happen...
......@@ -1100,14 +1100,14 @@ namespace {
*poly_chains[i],
false,
entity_info);
Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
*poly_chains[i]);
// still check whether we're dealing with poly here, we could have a
// lonely amino acid that ends up as non-poly and doesn't need
// pdbx_poly_seq_scheme
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
entity_id, entity_info[entity_id], *poly_chains[i]);
entity_id+1, entity_info[entity_id], *poly_chains[i]);
}
}
}
......@@ -1125,7 +1125,7 @@ namespace {
W_chain,
false,
entity_info);
Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
W_chain);
}
// process sugar chain
......@@ -1147,7 +1147,7 @@ namespace {
Z_chain,
false,
entity_info);
Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
Z_chain);
}
}
......@@ -1200,11 +1200,11 @@ namespace {
res_list,
true,
entity_info);
Feed_atom_site(atom_site, chain_name, entity_id, entity_info[entity_id],
Feed_atom_site(atom_site, chain_name, entity_id+1, entity_info[entity_id],
res_list);
if(entity_info[entity_id].is_poly) {
Feed_pdbx_poly_seq_scheme(pdbx_poly_seq_scheme, chain_name,
entity_id, entity_info[entity_id], res_list);
entity_id+1, entity_info[entity_id], res_list);
}
}
} else {
......
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