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All the "Test merge ligand" type tests seem to be OK now. 6 more fail…
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…ures left to fix.
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@stuartjamesmcnicholas
stuartjamesmcnicholas committed Oct 17, 2024
1 parent 86bc6b2 commit 8705574
Showing 1 changed file with 79 additions and 32 deletions.
111 changes: 79 additions & 32 deletions baby-gru/tests/__tests__/molecules_container.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -913,18 +913,27 @@ describe('Testing molecules_container_js', () => {

const merge_info = molecules_container.merge_molecules(coordMolNo_1, ligandMolNo.toString())
expect(merge_info.second.size()).toBe(1)
const merge_chain_id = merge_info.second.get(0).chain_id

molecules_container.write_coordinates(coordMolNo_1,"temp.cif")
const st = cootModule.read_structure_file("temp.cif",cootModule.CoorFormat.Mmcif)

const mmcifString = molecules_container.get_molecule_atoms(coordMolNo_1, 'pdb')
const st = cootModule.read_structure_from_string(mmcifString, 'test-molecule')
cootModule.gemmi_setup_entities(st)
cootModule.gemmi_add_entity_types(st, true)
const model = st.first_model()
const chains = model.chains
const chain = chains.get(2)
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)

cleanUpVariables.push(merge_info, st, model, chains, chain, ligands)
for(let ich=0;ich<chains.size();ich++){
const chain = chains.get(ich)
if(chain.name===merge_chain_id){
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)
cleanUpVariables.push(ligands)
}
cleanUpVariables.push(chain)
}

cleanUpVariables.push(merge_info, st, model, chains)
})

test("Test merge ligand.restraints dict and gemmi parse -pdb", () => {
Expand All @@ -942,18 +951,28 @@ describe('Testing molecules_container_js', () => {

const merge_info = molecules_container.merge_molecules(coordMolNo_1, ligandMolNo.toString())
expect(merge_info.second.size()).toBe(1)
const merge_chain_id = merge_info.second.get(0).chain_id

molecules_container.write_coordinates(coordMolNo_1,"temp.cif")
const st = cootModule.read_structure_file("temp.cif",cootModule.CoorFormat.Mmcif)

const mmcifString = molecules_container.get_molecule_atoms(coordMolNo_1, 'pdb')
const st = cootModule.read_structure_from_string(mmcifString, 'test-molecule')
cootModule.gemmi_setup_entities(st)
cootModule.gemmi_add_entity_types(st, true)

const model = st.first_model()
const chains = model.chains
const chain = chains.get(2)
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)

cleanUpVariables.push(merge_info, st, model, chains, chain, ligands)
for(let ich=0;ich<chains.size();ich++){
const chain = chains.get(ich)
if(chain.name===merge_chain_id){
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)
cleanUpVariables.push(ligands)
}
cleanUpVariables.push(chain)
}

cleanUpVariables.push(merge_info, st, model, chains)
})

test("Test merge ligand.restraints dict and gemmi parse -mmcif", () => {
Expand All @@ -971,18 +990,28 @@ describe('Testing molecules_container_js', () => {

const merge_info = molecules_container.merge_molecules(coordMolNo_1, ligandMolNo.toString())
expect(merge_info.second.size()).toBe(1)
const merge_chain_id = merge_info.second.get(0).chain_id

molecules_container.write_coordinates(coordMolNo_1,"temp.cif")
const st = cootModule.read_structure_file("temp.cif",cootModule.CoorFormat.Mmcif)

const mmcifString = molecules_container.get_molecule_atoms(coordMolNo_1, 'mmcif')
const st = cootModule.read_structure_from_string(mmcifString, 'test-molecule')
cootModule.gemmi_setup_entities(st)
cootModule.gemmi_add_entity_types(st, true)
const model = st.first_model()
const chains = model.chains
const chain = chains.get(2)
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)

cleanUpVariables.push(merge_info, st, model, chains, chain, ligands)
for(let ich=0;ich<chains.size();ich++){
const chain = chains.get(ich)
if(chain.name===merge_chain_id){
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)
cleanUpVariables.push(ligands)
}
cleanUpVariables.push(chain)
}


cleanUpVariables.push(merge_info, st, model, chains)
})

test("Test merge ligand and gemmi parse cross-format 1", () => {
Expand All @@ -1007,19 +1036,29 @@ describe('Testing molecules_container_js', () => {

const merge_info = molecules_container.merge_molecules(coordMolNo_1, ligandMolNo.toString())
expect(merge_info.second.size()).toBe(1)
const merge_chain_id = merge_info.second.get(0).chain_id

molecules_container.write_coordinates(coordMolNo_1,"temp.cif")
const st = cootModule.read_structure_file("temp.cif",cootModule.CoorFormat.Mmcif)

const mmcifString = molecules_container.get_molecule_atoms(coordMolNo_1, 'mmcif')
const st = cootModule.read_structure_from_string(mmcifString, 'test-molecule')
cootModule.gemmi_setup_entities(st)
cootModule.gemmi_add_entity_types(st, true)

const model = st.first_model()
const chains = model.chains
expect(chains.size()).toBe(old_chains.size() + 1)
const chain = chains.get(2)
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)

cleanUpVariables.push(merge_info, old_chains, old_model, old_st, st, model, chains, chain, ligands)
for(let ich=0;ich<chains.size();ich++){
const chain = chains.get(ich)
if(chain.name===merge_chain_id){
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)
cleanUpVariables.push(ligands)
}
cleanUpVariables.push(chain)
}


cleanUpVariables.push(merge_info, old_chains, old_model, old_st, st, model, chains)
})

test("Test merge ligand and gemmi parse cross-format 2", () => {
Expand All @@ -1044,19 +1083,27 @@ describe('Testing molecules_container_js', () => {

const merge_info = molecules_container.merge_molecules(coordMolNo_1, ligandMolNo.toString())
expect(merge_info.second.size()).toBe(1)
const merge_chain_id = merge_info.second.get(0).chain_id

molecules_container.write_coordinates(coordMolNo_1,"temp.cif")
const st = cootModule.read_structure_file("temp.cif",cootModule.CoorFormat.Mmcif)

const mmcifString = molecules_container.get_molecule_atoms(coordMolNo_1, 'pdb')
const st = cootModule.read_structure_from_string(mmcifString, 'test-molecule')
cootModule.gemmi_setup_entities(st)
cootModule.gemmi_add_entity_types(st, true)
const model = st.first_model()
const chains = model.chains
expect(chains.size()).toBe(old_chains.size() + 1)
const chain = chains.get(2)
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)

cleanUpVariables.push(merge_info, old_chains, old_model, old_st, st, model, chains, chain, ligands)
for(let ich=0;ich<chains.size();ich++){
const chain = chains.get(ich)
if(chain.name===merge_chain_id){
const ligands = chain.get_ligands_const()
expect(ligands.length()).toBe(1)
cleanUpVariables.push(ligands)
}
cleanUpVariables.push(chain)
}

cleanUpVariables.push(merge_info, old_chains, old_model, old_st, st, model, chains)
})

test.skip('Test test_the_threading --pool false', () => {
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