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Improve connecting rotamers
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@drmeister
drmeister committed Sep 15, 2023
1 parent b3f516e commit 25e0ad9
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34 changes: 20 additions & 14 deletions src/lisp/topology/internals.lisp
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Original file line number Diff line number Diff line change
Expand Up @@ -255,12 +255,16 @@ No checking is done to make sure that the list of clusterable-context-rotamers a
())

(defclass sidechain-rotamer-shape-connections ()
((fmap :initform (make-hash-table :test 'equal)
:initarg :fmap
:accessor fmap)))
((phi-psi-map :initform (make-hash-table :test 'equal)
:initarg :phi-psi-map
:accessor phi-psi-map)))

(cando.serialize:make-class-save-load
sidechain-rotamer-shape-connections)
sidechain-rotamer-shape-connections
:print-unreadably
(lambda (obj stream)
(print-unreadable-object (obj stream :type t)
(format stream "~a" (hash-table-count (phi-psi-map obj))))))

(defun make-sidechain-rotamer-shape-connections ()
(make-instance 'sidechain-rotamer-shape-connections))
Expand All @@ -271,22 +275,28 @@ No checking is done to make sure that the list of clusterable-context-rotamers a
:accessor rotamer-indices)))

(cando.serialize:make-class-save-load
backbone-rotamer-shape-connections)
backbone-rotamer-shape-connections
:print-unreadably
(lambda (obj stream)
(print-unreadable-object (obj stream :type t)
(format stream "~a" (length (rotamer-indices obj))))))

(defun make-backbone-rotamer-shape-connections ()
(make-instance 'backbone-rotamer-shape-connections))
(defun make-backbone-rotamer-shape-connections (&optional (rotamer-indices nil rotamer-indices-p))
(if rotamer-indices-p
(make-instance 'backbone-rotamer-shape-connections :rotamer-indices rotamer-indices)
(make-instance 'backbone-rotamer-shape-connections)))

(defmethod lookup-rotamer-shape-connections ((fsc sidechain-rotamer-shape-connections) key)
(gethash key (fmap fsc)))
(gethash key (phi-psi-map fsc)))

(defmethod lookup-rotamer-shape-connections ((fsc backbone-rotamer-shape-connections) key)
(rotamer-indices fsc))

(defun append-rotamer-shape-connections (rsc key index)
(let ((allowed-rotamer-vector (gethash key (fmap rsc))))
(let ((allowed-rotamer-vector (gethash key (phi-psi-map rsc))))
(unless allowed-rotamer-vector
(setf allowed-rotamer-vector (make-array 16 :element-type 'ext:byte32 :adjustable t :fill-pointer 0))
(setf (gethash key (fmap rsc)) allowed-rotamer-vector))
(setf (gethash key (phi-psi-map rsc)) allowed-rotamer-vector))
(vector-push-extend index allowed-rotamer-vector)))

(defclass rotamer-context-connections ()
Expand All @@ -310,10 +320,6 @@ No checking is done to make sure that the list of clusterable-context-rotamers a
(defun rotamer-context-connections-count (fcc)
(hash-table-count (fmap fcc)))

(defun set-rotamer-context-connections (fcc from to value)
(check-type value rotamer-shape-connections)
(setf (gethash (cons from to) (fmap fcc)) value))

(defun lookup-rotamer-context-connections (fcc key)
(gethash key (fmap fcc)))

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6 changes: 5 additions & 1 deletion src/lisp/topology/packages.lisp
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Original file line number Diff line number Diff line change
Expand Up @@ -279,7 +279,11 @@
#:+psi-1+
#:rotamer-indices
#:make-backbone-rotamer-shape-connections
#:make-sidechain-rotamer-shape-connections))
#:make-sidechain-rotamer-shape-connections
#:assign-backbone-allowed-rotamers
#:assign-backbone-random-rotamer-indices
#:allowed-rotamer-indices
#:assign-backbone-shape-keys))


(defpackage #:topology.dag
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125 changes: 90 additions & 35 deletions src/lisp/topology/shape.lisp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
(monomer-context :initarg :monomer-context :accessor monomer-context)
(monomer-shape-kind :initarg :monomer-shape-kind :accessor monomer-shape-kind)
(shape-key :initarg :shape-key :accessor shape-key)
(rotamers :initarg :rotamers :accessor rotamers)
(context-rotamers :initarg :context-rotamers :accessor context-rotamers)
(allowed-rotamer-indices :initarg :allowed-rotamer-indices :accessor allowed-rotamer-indices)
(keys :initarg :keys :accessor keys)
))
Expand Down Expand Up @@ -142,7 +142,6 @@
(error "Could not find monomer-context ~s" monomer-context))
fc)
for shape-kind = (topology:shape-kind foldamer monomer oligomer)
for shape-key = (build-shape-key shape-info monomer-shape-map shape-kind monomer oligomer in-monomers out-monomers)
for couplings = (couplings monomer)
for in-monomer = (let (in-monomer)
(maphash (lambda (key coupling)
Expand All @@ -167,13 +166,13 @@
monomer
:monomer-context monomer-context
:monomer-context-key monomer-context-key
:shape-key shape-key
:monomer-shape-kind shape-kind
:context-rotamers context-rotamers)
(make-instance 'monomer-shape
:monomer monomer
:monomer-context monomer-context
:monomer-context-key monomer-context-key
:shape-key shape-key
:monomer-shape-kind shape-kind
:context-rotamers context-rotamers))
;; do (format t "monomer = ~a~%" monomer)
do (setf (gethash monomer monomer-shape-map) monomer-shape)
Expand All @@ -182,13 +181,13 @@
do (setf (aref monomer-shape-vector index) monomer-shape)
;; do (format t "monomer-context ~a~%" monomer-context)
finally (return (values monomer-shape-vector the-root-monomer in-monomers out-monomers monomer-shape-map)))
(let ((monomer-shape-build-order (sorted-build-order foldamer oligomer kind-order)))
(let ((monomer-build-order (sorted-build-order foldamer oligomer kind-order)))
(make-instance 'oligomer-shape
:oligomer oligomer
:connected-rotamers-map connected-rotamers-map
:monomer-shape-vector monomer-shape-vector
:monomer-shape-map monomer-shape-map
:monomer-shape-build-order monomer-shape-build-order
:monomer-shape-build-order (mapcar (lambda (monomer) (gethash monomer monomer-shape-map)) monomer-build-order)
:the-root-monomer the-root-monomer
:in-monomers in-monomers
:out-monomers out-monomers)))))
Expand Down Expand Up @@ -288,46 +287,102 @@
"If the monomer-shape is a shape-kind :backbone then look for the :phi,:psi,:phi-1,:psi-1 dihedrals and store them
in the shape-key slot of the monomer-shape corresponding to the sidechain"
(cond
((eq :backbone (shape-kind monomer-shape))
((eq :backbone (monomer-shape-kind monomer-shape))
(error "Do what you need for a backbone"))
((eq :sidechain (shape-kind monomer-shape))
((eq :sidechain (monomer-shape-kind monomer-shape))
(error "Do what you need for a side-chain"))
(t (error "Unknown shape-kind ~s" (shape-kind monomer-shape)))))
(t (error "Unknown shape-kind ~s" (monomer-shape-kind monomer-shape)))))


(defun incoming-and-following-monomers-for-sidechain (oligomer sidechain-monomer)
"Given a sidechain-monomer - find the monomer that is on the other side of
the in-plug (in-monomer) and also the monomer that follows the in-monomer
through its other out-plug"
(let* ((focus-monomer sidechain-monomer)
(in-coupling-plug-name (topology:in-coupling-plug-name focus-monomer))
(in-monomer (topology:monomer-on-other-side focus-monomer in-coupling-plug-name))
(in-monomer-out-plug-names (topology:out-coupling-plug-names in-monomer))
(next-monomer (loop for in-monomer-out-plug-name in in-monomer-out-plug-names
for other-monomer = (topology:monomer-on-other-side in-monomer in-monomer-out-plug-name)
when (not (eq other-monomer focus-monomer))
do (return other-monomer))))
(values in-monomer next-monomer)
))


(defun assign-backbone-rotamer-indices (oligomer-shape
&key
(monomer-shape-build-order (monomer-context-to-context-rotamers rotamers-database)))
(defun assign-backbone-allowed-rotamers (oligomer-shape
&key (monomer-shape-build-order (monomer-shape-build-order oligomer-shape)))
"For each backbone monomer-shape set the rotamer-indices."
(loop with rotamers-database = (connected-rotamers-map oligomer-shape)
for monomer-shape in monomer-shape-build-order
for monomer-context = (monomer-context monomer-shape)
for shape-kind = (shape-kind monomer-shape)
if (eq (shape-kind monomer-shape) :backbone)
do (let ((rotamer-indices (gethash monomer-context (monomer-context-to-context-rotamers rotamers-database))))
(setf (allowed-rotamer-indices monomer-shape) rotamer-indices))
else ; once we hit a sidechain we stop
do (return nil)))
(loop with rotamers-database = (connected-rotamers-map oligomer-shape)
for monomer-shape in monomer-shape-build-order
for monomer-context = (monomer-context monomer-shape)
for shape-kind = (monomer-shape-kind monomer-shape)
if (eq (monomer-shape-kind monomer-shape) :backbone)
do (let ((backbone-rotamer-shape-connections (lookup-rotamer-context-connections (rotamer-context-connections rotamers-database) monomer-context)))
(check-type backbone-rotamer-shape-connections backbone-rotamer-shape-connections)
(setf (allowed-rotamer-indices monomer-shape) (rotamer-indices backbone-rotamer-shape-connections)))
else ; once we hit a sidechain we stop
do (return nil)))

(defun assign-backbone-random-rotamer-indices (oligomer-shape
&key (monomer-shape-build-order (monomer-shape-build-order oligomer-shape)))
(loop with rotamers-database = (connected-rotamers-map oligomer-shape)
for monomer-shape in monomer-shape-build-order
if (eq (shape-kind monomer-shape) :backbone)
do (let ((rnd (random (length (allowed-rotamers monomer-shape)))))
(setf (fragment-conformation-index monomer-shape) (aref (allowed-rotamers monomer-shape) rnd)))
if (eq (monomer-shape-kind monomer-shape) :backbone)
do (let ((rnd (random (length (allowed-rotamer-indices monomer-shape)))))
(setf (fragment-conformation-index monomer-shape) (aref (allowed-rotamer-indices monomer-shape) rnd)))
else ; stop once we hit a sidechain
do (return nil)))

(defun assign-backbone-shape-keys (oligomer-shape &key (monomer-shape-build-order (monomer-shape-build-order oligomer-shape)))

(defun assign-sidechain-shape-keys (oligomer-shape
&key (monomer-shape-build-order (monomer-shape-build-order oligomer-shape)))
(let ((oligomer (oligomer oligomer-shape)))
(loop with rotamers-database = (connected-rotamers-map oligomer-shape)
with monomer-shape-map = (monomer-shape-map oligomer-shape)
for monomer-shape in monomer-shape-build-order
if (eq (monomer-shape-kind monomer-shape) :sidechain)
do (let* ((sidechain-monomer (monomer monomer-shape)))
(multiple-value-bind (in-monomer next-monomer)
(incoming-and-following-monomers-for-sidechain oligomer sidechain-monomer)
(let* ((in-monomer-shape (gethash in-monomer monomer-shape-map))
(in-monomer-rotamer-index (fragment-conformation-index in-monomer-shape))
(in-monomer-rotamers (context-rotamers in-monomer-shape))
(in-monomer-rotamer (aref (fragments in-monomer-rotamers) in-monomer-rotamer-index))
(in-monomer-shape-key-values (shape-key-values in-monomer-rotamer))
(next-monomer-shape (gethash next-monomer monomer-shape-map))
(next-monomer-rotamer-index (fragment-conformation-index next-monomer-shape))
(next-monomer-rotamers (context-rotamers next-monomer-shape))
(next-monomer-rotamer (aref (fragments next-monomer-rotamers) next-monomer-rotamer-index))
(next-monomer-shape-key-values (shape-key-values next-monomer-rotamer))
(phi-key-value (or (cdr (assoc :phi (shape-key-values in-monomer-rotamer)))
(cdr (assoc :phi-1 (shape-key-values next-monomer-rotamer)))
(error "Could not find :phi or :phi-1")))
(psi-key-value (or (cdr (assoc :psi (shape-key-values in-monomer-rotamer)))
(cdr (assoc :psi-1 (shape-key-values next-monomer-rotamer)))
(error "Could not find :psi or :psi-1")))
)
(setf (shape-key monomer-shape) (cons phi-key-value psi-key-value))))))))


(defun assign-sidechain-allowed-rotamers (oligomer-shape
&key (monomer-shape-build-order (monomer-shape-build-order oligomer-shape)))
"For each backbone monomer-shape set the rotamer-indices."
(format t "In fn~%")
(loop with rotamers-database = (connected-rotamers-map oligomer-shape)
for monomer-shape in monomer-shape-build-order
if (eq (shape-kind monomer-shape) :backbone)
do (let* ((topology (monomer-topology (monomer monomer-shape) (oligomer oligomer-shape)))
(constitution (topology:constitution topology))
(residue-properties (topology:residue-properties constitution))
(_ (error "At this point get the shape-key values out of the rotamer fragments and put it into the monomer-shape"))
)
(format t "monomer: ~a topology: ~a~%" monomer topology))
else
do (return nil)))

for monomer-context = (monomer-context monomer-shape)
for shape-kind = (monomer-shape-kind monomer-shape)
do (format t "monomer-shape ~a~%" monomer-shape)
if (eq (monomer-shape-kind monomer-shape) :sidechain)
do (let ((sidechain-rotamer-shape-connections (lookup-rotamer-context-connections (rotamer-context-connections rotamers-database) monomer-context)))
(check-type sidechain-rotamer-shape-connections sidechain-rotamer-shape-connections)
(format t "Setting allowed-rotamer-indices for ~a~%" monomer-shape)
(let* ((phi-psi-map (phi-psi-map sidechain-rotamer-shape-connections))
(shape-key (shape-key monomer-shape))
(rotamer-indices (gethash shape-key phi-psi-map)))
(unless rotamer-indices
(break "rotamer-indices is nil for key: ~s keys: ~s" shape-key (alexandria:hash-table-keys phi-psi-map)))
(setf (allowed-rotamer-indices monomer-shape) rotamer-indices)))
))

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