validate¶

A validate task allows you to perform validation tests on the current state files (PDB/PSF/XSC) to ensure, for example, that modifications requested in previous tasks have been successfully applied.

Validation tests are performed in VMD sessions managed by the task. There are three types of validation tests available:

Attribute test: Allows you to query atom attributes in an atom selection of the current state for expected values.
Connection test: Allows you to check on existence of inter-residue connections in an atom selection of the current state.
Residue test: Allows you to check a count of atoms and a count of residues in an atom selection of the current state.

After all tests are performed, the task parses all VMD logs for results and generates a summary report. By default, if any test fails, the task raises an exception and the run is aborted.

Attribute test¶

A common use of an attribute test is to check that a mutation requested in a previous task has been successfully applied. An attribute test requires four fields to be specified, along with one optional field:

name: a descriptive name for the test – this is up to you.
selection: a string that represents VMD atomselect logic
attribute: the name of the atom attribute to query
value: the expected value of the atom attribute
value_count: the expected number of atoms in the selection with this attribute (defaults to 1)

For example, if you mutated resid 11 on chain A from threonine to cysteine, you can check that the residue name of that residue is in fact CYS:

tasks:
  - ... (prior tasks here)
  - validate:
      tests:
        - attribute_test:
            name: point mutation
            selection: protein and chain A and resid 11 and name CA
            attribute: resname
            value: CYS
  - ... (subsequent tasks here)

This test will generate and execute a VMD input script that looks like this:

(... read in psf and pdb of current state ...)
set test_selection [atomselect top "{self.selection}"]
set result [$test_selection get {self.attribute}]
set count [llength [lsearch -nocase -exact -all $result {target}]]
if {$count != 1} {
    vmdcon "FAIL resname has unexpected count $count of value CYS (expected 1) in selection protein and chain A and resid 11 and name CA"
} else {
    vmdcon "PASS resname has expected count $count of value CYS (expected 1) in selection protein and chain A and resid 11 and name CA"
}

The validate tasks manages all VMD logs it generates, so it will extract pass and fail information once all tests are run.

Connection test¶

A connection test can be used to check for the presence or absence of an inter-residue bond. This test requires three fields to be specified, along with one optional field:

name: a descriptive name for the test – this is up to you.
selection: a string that represents VMD atomselect logic
connection_type: the type of connection to check for (one of interresidue, disulfide, or glycosylation)
connection_count: the expected number of connections (defaults to 1)

There are three types of connections that can be checked:

interresidue: Checks for bonds between atoms in different residues. The selection field should be atomselect logic that selects atoms in at most two distinct residues.
disulfide: Checks for disulfide bonds between cysteine residues. The selection field should be atomselect logic that selects two residues that participate in the disulfide bond. This test will check that the bond is in fact between to CYS residues and two SG atoms.
glycosylation: Checks for glycosylation sites on asparagine residues. The selection field should be atomselect logic that selects for one asparagine residue. This test will validate that the ND2 atom of the ASN residue is bonded to the C1 atom of a glycan monomer. For example:

tasks:
  - ... (prior tasks here)
  - validate:
      tests:
     - connection_test:
         name: graft 61 chain A
         selection: protein and chain A and resid 61
         connection_type: glycosylation
         connection_count: 1
  - ... (subsequent tasks follow)

Residue test¶

This test allows you to check the number of atoms and/or residues in an atomselection. A residue test requires four fields to be specified:

name: a descriptive name for the test – this is up to you.
selection: a string that represents VMD atomselect logic
measure: the type of measurement to perform (one of atom_count or residue_count)
value: the expected value of the measurement

For example, if you excluded a residue by residue name, you might want to test that no such residues remain in the system:

tasks:
  - ... (prior tasks here)
  - validate:
      tests:
        - residue_test:
            name: no POPC residues
            selection: resname POPC
            measure: residue_count
            value: 0
  - ... (subsequent tasks here)