From 4be903b9d5f8ca77cf018e1c39055a1d6eabb3d3 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 9 Sep 2019 17:35:16 -0700
Subject: [PATCH] added atom_site_anisotrop to mmcif schema
---
src/mol-io/reader/cif/schema/bird.ts | 2 +-
src/mol-io/reader/cif/schema/ccd.ts | 2 +-
src/mol-io/reader/cif/schema/mmcif.ts | 85 ++++++++++++++++++++++++++-
3 files changed, 86 insertions(+), 3 deletions(-)
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index ed2597930..b0b53922a 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.313, IHM 1.01, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index dc3b3f5ac..019914cf9 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.313, IHM 1.01, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 9f3e66263..e80fef22b 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.313, IHM 1.01, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.314, IHM 1.01, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -213,6 +213,89 @@ export const mmCIF_Schema = {
*/
ihm_model_id: int,
},
+ /**
+ * Data items in the ATOM_SITE_ANISOTROP category record details
+ * about anisotropic displacement parameters.
+ * If the ATOM_SITE_ANISOTROP category is used for storing these
+ * data, the corresponding ATOM_SITE data items are not used.
+ */
+ atom_site_anisotrop: {
+ /**
+ * This data item is a pointer to _atom_site.id in the ATOM_SITE
+ * category.
+ */
+ id: int,
+ /**
+ * This data item is a pointer to _atom_type.symbol in the
+ * ATOM_TYPE category.
+ */
+ type_symbol: str,
+ /**
+ * The elements of the standard anisotropic atomic
+ * displacement matrix U, which appears in the structure-factor
+ * term as:
+ *
+ * T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
+ *
+ * h = the Miller indices
+ * a* = the reciprocal space cell lengths
+ *
+ * These matrix elements may appear with atomic coordinates
+ * in the ATOM_SITE category, or they may appear in the separate
+ * ATOM_SITE_ANISOTROP category, but they may not appear in both
+ * places. Similarly, anisotropic displacements may appear as
+ * either B's or U's, but not as both.
+ *
+ * The unique elements of the real symmetric matrix are
+ * entered by row.
+ */
+ U: Matrix(3, 3),
+ /**
+ * The standard uncertainty (estimated standard deviation)
+ * of _atom_site_anisotrop.U.
+ */
+ U_esd: Matrix(3, 3),
+ /**
+ * Pointer to _atom_site.auth_seq_id
+ */
+ pdbx_auth_seq_id: str,
+ /**
+ * Pointer to _atom_site.auth_asym_id
+ */
+ pdbx_auth_asym_id: str,
+ /**
+ * Pointer to _atom_site.auth_atom_id
+ */
+ pdbx_auth_atom_id: str,
+ /**
+ * Pointer to _atom_site.auth_comp_id
+ */
+ pdbx_auth_comp_id: str,
+ /**
+ * Pointer to _atom_site.label_seq_id
+ */
+ pdbx_label_seq_id: int,
+ /**
+ * Pointer to _atom_site.label_alt_id.
+ */
+ pdbx_label_alt_id: str,
+ /**
+ * Pointer to _atom_site.label_asym_id
+ */
+ pdbx_label_asym_id: str,
+ /**
+ * Pointer to _atom_site.label_atom_id
+ */
+ pdbx_label_atom_id: str,
+ /**
+ * Pointer to _atom_site.label_comp_id
+ */
+ pdbx_label_comp_id: str,
+ /**
+ * Pointer to _atom_site.pdbx_PDB_ins_code
+ */
+ pdbx_PDB_ins_code: str,
+ },
/**
* Data items in the ATOM_SITES category record details about
* the crystallographic cell and cell transformations, which are
--
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