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Add support for specifying the user-defined CCD using a file
Prompted by https://github.com/google-deepmind/alphafold3/issues/325. PiperOrigin-RevId: 734476458 Change-Id: I0fa681f6e3cb77284b3a3b4b6f429cef14e1638b
This commit is contained in:
Augustin Zidek
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Copybara-Service
Copybara-Service
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eca194325f
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2eb2a50b62
@ -113,10 +113,11 @@ The top-level structure of the input JSON is:
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{"dna": {...}},
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{"ligand": {...}}
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],
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"bondedAtomPairs": [...], # Optional
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"userCCD": "...", # Optional
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"dialect": "alphafold3", # Required
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"version": 2 # Required
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"bondedAtomPairs": [...], # Optional.
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"userCCD": "...", # Optional, mutually exclusive with userCCDPath.
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"userCCDPath": "...", # Optional, mutually exclusive with userCCD.
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"dialect": "alphafold3", # Required.
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"version": 3 # Required.
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}
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```
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@ -140,6 +141,12 @@ The fields specify the following:
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in such cases since it doesn't give the possibility of uniquely naming all
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atoms. It can also be used to provide a reference conformer for cases where
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RDKit fails to generate a conformer. See more below.
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* `userCCDPath: str`: An optional path to a file that contains the
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user-provided chemical components dictionary instead of providing it inline
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using the `userCCD` field. The path can be either absolute, or relative to
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the input JSON path. The file must be in the
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[CCD mmCIF format](https://www.wwpdb.org/data/ccd#mmcifFormat), and could be
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either plain text, or compressed using gzip, xz, or zstd.
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* `dialect: str`: The dialect of the input JSON. This must be set to
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`alphafold3`. See
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[AlphaFold Server JSON Compatibility](#alphafold-server-json-compatibility)
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@ -151,12 +158,14 @@ The fields specify the following:
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## Versions
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The top-level `version` field (for the `alphafold3` dialect) can be either `1`
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or `2`. The following features have been added in respective versions:
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The top-level `version` field (for the `alphafold3` dialect) can be either `1`,
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`2`, or `3`. The following features have been added in respective versions:
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* `1`: the initial AlphaFold 3 input format.
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* `2`: added the option of specifying external MSA and templates using newly
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added fields `unpairedMsaPath`, `pairedMsaPath`, and `mmcifPath`.
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* `3`: added the option of specifying external user-provided CCD using newly
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added field `userCCDPath`.
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## Sequences
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@ -480,7 +489,7 @@ an empty string (`""`).
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For instance, if there are two chains `DEEP` and `MIND` which we want to be
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paired on organism A and C, we can achieve it as follows:
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```text
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```txt
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> query
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DEEP
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> match 1 (organism A)
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@ -491,7 +500,7 @@ DD-P
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DD-P
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```
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```text
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```txt
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> query
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MIND
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> match 1 (organism A)
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@ -504,7 +513,7 @@ MIN-
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The resulting MSA when chains are concatenated will then be:
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```text
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```txt
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> query
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DEEPMIND
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> match 1 + match 1
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@ -717,20 +726,27 @@ increasinging the number of RDKit conformer iterations using the
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### User-provided CCD Format
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The user-provided CCD must be passed in the `userCCD` field (in the root of the
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input JSON) as a string. Note that JSON doesn't allow newlines within strings,
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so newline characters (`\n`) must be used to delimit lines. Single rather than
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double quotes should also be used around strings like the chemical formula.
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The user-provided CCD must be passed either:
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* In the `userCCD` field (in the root of the input JSON) as a string. Note
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that JSON doesn't allow newlines within strings, so newline characters
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(`\n`) must be used to delimit lines. Single rather than double quotes
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should also be used around strings like the chemical formula.
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* In the `userCCDPath` field, as a path to a file that contains the
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user-provided chemical components dictionary. The path can be either
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absolute, or relative to the input JSON path. The file must be in the
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[CCD mmCIF format](https://www.wwpdb.org/data/ccd#mmcifFormat), and could be
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either plain text, or compressed using gzip, xz, or zstd.
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The main pieces of information used are the atom names and elements, bonds, and
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also the ideal coordinates (`pdbx_model_Cartn_{x,y,z}_ideal`) which essentially
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serve as a structural template for the ligand if RDKit fails to generate
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conformers for that ligand.
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The `userCCD` can also be used to redefine standard chemical components in the
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CCD. This can be useful if you need to redefine the ideal coordinates.
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The user-provided CCD can also be used to redefine standard chemical components
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in the CCD. This can be useful if you need to redefine the ideal coordinates.
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Below is an example `userCCD` redefining component X7F, which serves to
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Below is an example user-provided CCD redefining component X7F, which serves to
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illustrate the required sections. For readability purposes, newlines have not
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been replaced by `\n`.
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@ -948,7 +964,7 @@ certain fields and the sequences are not biologically meaningful.
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],
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"userCCD": ...,
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"dialect": "alphafold3",
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"version": 2
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"version": 3
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}
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```
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