From 8471d337a23dd529d37c0fb51144cfcb748d4b16 Mon Sep 17 00:00:00 2001
From: JonStargaryen <sebastian.bittrich@rcsb.org>
Date: Tue, 20 Oct 2020 12:31:02 -0700
Subject: [PATCH] add protvar atoms to cca.bcif
---
src/cli/chem-comp-dict/create-table.ts | 64 +++++++++++++++++++++++---
1 file changed, 57 insertions(+), 7 deletions(-)
diff --git a/src/cli/chem-comp-dict/create-table.ts b/src/cli/chem-comp-dict/create-table.ts
index d21c22639..7221e6276 100644
--- a/src/cli/chem-comp-dict/create-table.ts
+++ b/src/cli/chem-comp-dict/create-table.ts
@@ -27,6 +27,10 @@ function ccbKey(compId: string, atomId1: string, atomId2: string) {
return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`;
}
+function ccaKey(compId: string, atomId: string) {
+ return `${compId}:${atomId}`;
+}
+
function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
for (let i = 0, il = ccb._rowCount; i < il; ++i) {
set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)));
@@ -36,7 +40,7 @@ function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
for (let i = 0, il = cca._rowCount; i < il; ++i) {
- set.add(cca.atom_id.value(i));
+ set.add(ccaKey(cca.comp_id.value(i), cca.atom_id.value(i)));
}
return set;
}
@@ -82,6 +86,27 @@ function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
}
}
+function checkAddingAtomsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
+ const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set());
+
+ for (const k in pvcd) {
+ const { chem_comp, chem_comp_atom } = pvcd[k];
+ if (chem_comp_atom._rowCount) {
+ const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+ if (parentIds.length === 0) {
+ const set = ccbSetByParent.getDefault(chem_comp.id.value(0));
+ addChemCompAtomToSet(set, chem_comp_atom);
+ } else {
+ for (let i = 0, il = parentIds.length; i < il; ++i) {
+ const parentId = parentIds[i];
+ const set = ccbSetByParent.getDefault(parentId);
+ addChemCompAtomToSet(set, chem_comp_atom);
+ }
+ }
+ }
+ }
+}
+
async function createBonds(
ccd: DatabaseCollection<CCD_Schema>,
pvcd: DatabaseCollection<CCD_Schema>,
@@ -152,10 +177,12 @@ async function createBonds(
{ chem_comp_bond: bondTable }
);
- return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd) : void 0 };
+ return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd, pvcd) : void 0 };
}
-function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
+function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollection<CCD_Schema>) {
+ const ccaSet = new Set<string>();
+
const comp_id: string[] = [];
const atom_id: string[] = [];
const charge: number[] = [];
@@ -163,10 +190,33 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
function addAtoms(compId: string, cca: CCA) {
for (let i = 0, il = cca._rowCount; i < il; ++i) {
- atom_id.push(cca.atom_id.value(i));
- comp_id.push(compId);
- charge.push(cca.charge.value(i));
- pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
+ const atomId = cca.atom_id.value(i);
+ const k = ccaKey(compId, atomId);
+ if (!ccaSet.has(k)) {
+ atom_id.push(atomId);
+ comp_id.push(compId);
+ charge.push(cca.charge.value(i));
+ pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
+ ccaSet.add(k);
+ }
+ }
+ }
+
+ // check adding atoms from PVCD
+ checkAddingAtomsFromPVCD(pvcd);
+
+ // add atoms from PVCD
+ for (const k in pvcd) {
+ const { chem_comp, chem_comp_atom } = pvcd[k];
+ if (chem_comp_atom._rowCount) {
+ const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+ if (parentIds.length === 0) {
+ addAtoms(chem_comp.id.value(0), chem_comp_atom);
+ } else {
+ for (let i = 0, il = parentIds.length; i < il; ++i) {
+ addAtoms(parentIds[i], chem_comp_atom);
+ }
+ }
}
}
--
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