From 94031fb6d6728ed1bf82cb22c8193c6d72e2f8b1 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 14 Feb 2019 17:07:10 -0800
Subject: [PATCH] pdb parser todos
---
src/mol-model-formats/structure/pdb/to-cif.ts | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index b0643d4f1..853a1b931 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -212,6 +212,8 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
if (substringStartsWith(data, s, e, 'CRYST1')) {
helperCategories.push(...parseCryst1(pdb.id || '?', data.substring(s, e)));
}
+ // TODO CONNECT records => struct_conn
+ // TODO COMPND records => entity
break;
case 'H':
if (substringStartsWith(data, s, e, 'HETATM')) {
@@ -227,6 +229,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(parseHelix(lines, i, j));
i = j - 1;
}
+ // TODO HETNAM records => chem_comp (at least partially, needs to be completed with common bases and amino acids)
break;
case 'M':
if (substringStartsWith(data, s, e, 'MODEL ')) {
@@ -243,10 +246,10 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(...parseMtrix(lines, i, j));
i = j - 1;
}
+ // TODO MODRES records => pdbx_struct_mod_residue
break;
case 'O':
- // TODO
- // ORIGX to generate _atom_sites
+ // TODO ORIGX record => cif.database_PDB_matrix.origx, cif.database_PDB_matrix.origx_vector
break;
case 'R':
if (substringStartsWith(data, s, e, 'REMARK 350')) {
@@ -271,6 +274,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
helperCategories.push(parseSheet(lines, i, j));
i = j - 1;
}
+ // TODO SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
break;
}
}
--
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